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Habib KA, Islam MJ, Sakib MN, Brishti PS, Neogi AK. DNA barcoding of reef-associated fishes of Saint Martin's Island, Northern Bay of Bengal, Bangladesh. Ecol Evol 2023; 13:e10641. [PMID: 37877103 PMCID: PMC10590961 DOI: 10.1002/ece3.10641] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 10/09/2023] [Accepted: 10/10/2023] [Indexed: 10/26/2023] Open
Abstract
This study employs the DNA barcoding approach to make a molecular taxonomic catalog of reef fishes of Saint Martin's Island (SMI), an ecologically critical area (ECA), and Marine Protected Area (MPA) in Bangladesh. DNA barcoding, along with morphological analysis, confirmed 84 reef-associated fish species in SMI belonging to 16 orders, 39 families, and 67 genera. A total of 184 sequences were obtained in this study where 151 sequences (534-604 bp) of 81 species were identified from the COI barcode gene and 33 sequences (609 bp) of 19 species from the 16S rRNA gene region which were submitted to the GenBank and Barcode of Life Data System (BOLD). Among these sequences, 70 sequences of the COI gene and 16 sequences of 16S rRNA gene region from 41 species were submitted for the first time into the GenBank from Bangladesh. For molecular characterization analysis, another 37 sequences of 15 reef fish species of SMI were added from previous studies, making a total of 221 DNA sequences which comprised 179 sequences of 96 species for the COI gene and 42 sequences of 26 species for the 16S rRNA gene region. The COI sequences contain 145 haplotypes with 337 polymorphic sites, and the mean genetic distances within species, genera, and families were calculated as 0.34%, 12.26%, and 19.03%, respectively. On the contrary, 16S rRNA sequences comprised 31 haplotypes with 241 polymorphic sites, and the mean genetic divergences within species, genera, and families were 0.94%, 4.72%, and 12.43%, respectively. This study is a significant contribution to the marine biodiversity of Bangladesh which would facilitate the assessment of species diversity for strategizing management action. It is also an important input to the DNA barcode library of reef fishes of the northern Bay of Bengal.
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Affiliation(s)
- Kazi Ahsan Habib
- Department of Fisheries Biology and Genetics, Faculty of Fisheries, Aquaculture and Marine ScienceSher‐e‐Bangla Agricultural UniversityDhakaBangladesh
- Aquatic Bioresource Research Lab, Department of Fisheries Biology and GeneticsSher‐e‐Bangla Agricultural UniversityDhakaBangladesh
| | - Md. Jayedul Islam
- Aquatic Bioresource Research Lab, Department of Fisheries Biology and GeneticsSher‐e‐Bangla Agricultural UniversityDhakaBangladesh
| | - Md. Nazmus Sakib
- Department of Fisheries Biology and Genetics, Faculty of Fisheries, Aquaculture and Marine ScienceSher‐e‐Bangla Agricultural UniversityDhakaBangladesh
- Aquatic Bioresource Research Lab, Department of Fisheries Biology and GeneticsSher‐e‐Bangla Agricultural UniversityDhakaBangladesh
| | - Parsha Shanjana Brishti
- Aquatic Bioresource Research Lab, Department of Fisheries Biology and GeneticsSher‐e‐Bangla Agricultural UniversityDhakaBangladesh
| | - Amit Kumer Neogi
- Aquatic Bioresource Research Lab, Department of Fisheries Biology and GeneticsSher‐e‐Bangla Agricultural UniversityDhakaBangladesh
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Kagoshima H, Maslen R, Kito K, Imura S, Niki H, Convey P. Integrated taxonomy combining morphological and molecular biological analyses of soil nematodes from maritime Antarctica. Polar Biol 2019. [DOI: 10.1007/s00300-019-02482-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Gasparrini S, Alborali GL, Pitozzi A, Guarneri F, Giacomini E, Baldo V, Scali F, Lazzaro M, Boniotti MB. Characterization of Brachyspira hyodysenteriae isolates from Italy by multilocus sequence typing and multiple locus variable number tandem repeat analysis. J Appl Microbiol 2017; 123:340-351. [PMID: 28510989 DOI: 10.1111/jam.13492] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 03/02/2017] [Accepted: 04/07/2017] [Indexed: 10/19/2022]
Abstract
AIMS To evaluate and compare the capabilities of multilocus sequence typing (MLST) and multiple locus variable number tandem repeat analysis (MLVA) techniques to characterize Brachyspira hyodysenteriae isolates and to investigate the relationship between pleuromutilin resistance and genetic variability. METHODS AND RESULTS MLST genotyping was performed on 180 B. hyodysenteriae isolates, and the results were evaluated considering profiles from 108 other strains previously reported in the database. In total, 37 sequence types were obtained. The MLVA approach completely characterized 172 strains and grouped the isolates into 22 different profiles. The combination of MLST and MLVA showed a slight increase in the discriminatory power, identifying 33 joint profiles. An antibiotic resistance analysis showed a reduction in the susceptibility to pleuromutilins over time, and a weak association between susceptibility to valnemulin and inclusion in clonal complex 4. CONCLUSION MLST and MLVA are reliable methods for characterizing B. hyodysenteriae strains and they have comparable discriminatory power. SIGNIFICANCE AND IMPACT OF THE STUDY The genotyping of B. hyodysenteriae isolates and a database of all the genetic profiles collected during the diagnostic activities could support traditional epidemiological investigations in identifying infection sources and routes of transmission among herds, and in developing more effective control measures.
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Affiliation(s)
- S Gasparrini
- Istituto Zooprofilattico Sperimentale della Lombardia ed Emilia Romagna "Bruno Ubertini", Brescia, Italy
| | - G L Alborali
- Istituto Zooprofilattico Sperimentale della Lombardia ed Emilia Romagna "Bruno Ubertini", Brescia, Italy
| | - A Pitozzi
- Istituto Zooprofilattico Sperimentale della Lombardia ed Emilia Romagna "Bruno Ubertini", Brescia, Italy
| | - F Guarneri
- Istituto Zooprofilattico Sperimentale della Lombardia ed Emilia Romagna "Bruno Ubertini", Brescia, Italy
| | - E Giacomini
- Istituto Zooprofilattico Sperimentale della Lombardia ed Emilia Romagna "Bruno Ubertini", Brescia, Italy
| | - V Baldo
- Istituto Zooprofilattico Sperimentale della Lombardia ed Emilia Romagna "Bruno Ubertini", Brescia, Italy
| | - F Scali
- Istituto Zooprofilattico Sperimentale della Lombardia ed Emilia Romagna "Bruno Ubertini", Brescia, Italy
| | - M Lazzaro
- Istituto Zooprofilattico Sperimentale della Lombardia ed Emilia Romagna "Bruno Ubertini", Brescia, Italy
| | - M B Boniotti
- Istituto Zooprofilattico Sperimentale della Lombardia ed Emilia Romagna "Bruno Ubertini", Brescia, Italy
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Bayegan AH, Garcia-Martin JA, Clote P. New tools to analyze overlapping coding regions. BMC Bioinformatics 2016; 17:530. [PMID: 27964762 PMCID: PMC5155393 DOI: 10.1186/s12859-016-1389-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2016] [Accepted: 11/26/2016] [Indexed: 11/10/2022] Open
Abstract
Background Retroviruses transcribe messenger RNA for the overlapping Gag and Gag-Pol polyproteins, by using a programmed -1 ribosomal frameshift which requires a slippery sequence and an immediate downstream stem-loop secondary structure, together called frameshift stimulating signal (FSS). It follows that the molecular evolution of this genomic region of HIV-1 is highly constrained, since the retroviral genome must contain a slippery sequence (sequence constraint), code appropriate peptides in reading frames 0 and 1 (coding requirements), and form a thermodynamically stable stem-loop secondary structure (structure requirement). Results We describe a unique computational tool, RNAsampleCDS, designed to compute the number of RNA sequences that code two (or more) peptides p,q in overlapping reading frames, that are identical (or have BLOSUM/PAM similarity that exceeds a user-specified value) to the input peptides p,q. RNAsampleCDS then samples a user-specified number of messenger RNAs that code such peptides; alternatively, RNAsampleCDS can exactly compute the position-specific scoring matrix and codon usage bias for all such RNA sequences. Our software allows the user to stipulate overlapping coding requirements for all 6 possible reading frames simultaneously, even allowing IUPAC constraints on RNA sequences and fixing GC-content. We generalize the notion of codon preference index (CPI) to overlapping reading frames, and use RNAsampleCDS to generate control sequences required in the computation of CPI. Moreover, by applying RNAsampleCDS, we are able to quantify the extent to which the overlapping coding requirement in HIV-1 [resp. HCV] contribute to the formation of the stem-loop [resp. double stem-loop] secondary structure known as the frameshift stimulating signal. Using our software, we confirm that certain experimentally determined deleterious HCV mutations occur in positions for which our software RNAsampleCDS and RNAiFold both indicate a single possible nucleotide. We generalize the notion of codon preference index (CPI) to overlapping coding regions, and use RNAsampleCDS to generate control sequences required in the computation of CPI for the Gag-Pol overlapping coding region of HIV-1. These applications show that RNAsampleCDS constitutes a unique tool in the software arsenal now available to evolutionary biologists. Conclusion Source code for the programs and additional data are available at http://bioinformatics.bc.edu/clotelab/RNAsampleCDS/. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-1389-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Amir H Bayegan
- Biology Department, Boston College, 140 Commonwealth Avenue, Chestnut Hill MA, 02467, USA
| | | | - Peter Clote
- Biology Department, Boston College, 140 Commonwealth Avenue, Chestnut Hill MA, 02467, USA.
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Ito K, Yotsuyanagi H, Sugiyama M, Yatsuhashi H, Karino Y, Takikawa Y, Saito T, Arase Y, Imazeki F, Kurosaki M, Umemura T, Ichida T, Toyoda H, Yoneda M, Tanaka Y, Mita E, Yamamoto K, Michitaka K, Maeshiro T, Tanuma J, Korenaga M, Murata K, Masaki N, Koike K, Mizokami M. Geographic distribution and characteristics of genotype A hepatitis B virus infection in acute and chronic hepatitis B patients in Japan. J Gastroenterol Hepatol 2016; 31:180-189. [PMID: 26110395 DOI: 10.1111/jgh.13030] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2015] [Revised: 06/01/2015] [Accepted: 06/02/2015] [Indexed: 12/13/2022]
Abstract
BACKGROUND AND AIMS The prevalence of sexually transmitted acute infections of the genotype A hepatitis B virus (HBV) has been increasing in Japan. Genotype A HBV is associated with an increased risk of HBV progression to chronic infection after acute hepatitis B (AHB) in adults. A nationwide survey was conducted to evaluate the geographic distribution, clinical, and virologic characteristics of genotype A AHB and chronic hepatitis B (CHB) in Japan. METHODS Five hundred seventy AHB patients were recruited between 2005 and 2010, and 3682 CHB patients were recruited between 2010 and 2011. HBV genotypes were determined for 552 and 3619 AHB and CHB patients, respectively. Clinical characteristics were compared among different genotypes in AHB and CHB patients. Genomic characteristics of HBV genotype A were examined by molecular evolutionary analysis. RESULTS Hepatitis B virus genotype A was the predominant genotype for AHB between 2005 and 2010. Phylogenetic analysis showed that all strains in the AHB patients with genotype A were classified into subtype Ae. Among CHB patients, the occurrence of genotype A was 4.1%, and genotype A was spreading in young adults. In genotype A CHB patients, early stage liver diseases were predominant, although liver diseases progressed to cirrhosis or hepatocellular carcinoma in some patients. CONCLUSIONS The distribution of HBV genotypes is quite different between AHB and CHB in Japanese patients. Genotype A infection is spreading in young adults of Japanese CHB patients. Sequences derived from Japanese AHB patients were identical to or closely resembled the sequences derived from other Japanese AHB patients.
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Affiliation(s)
- Kiyoaki Ito
- The Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, Ichikawa
- Department of Gastroenterology, Aichi Medical University School of Medicine, Nagakute
| | - Hiroshi Yotsuyanagi
- Department of Internal Medicine, Graduate School of Medicine, The University of Tokyo
| | - Masaya Sugiyama
- The Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, Ichikawa
| | | | - Yoshiyasu Karino
- Department of Gastroenterology, Sapporo Kosei General Hospital, Sapporo
| | - Yasuhiro Takikawa
- Division of Hepatology, Department of Internal Medicine, Iwate Medical University, Morioka
| | - Takafumi Saito
- Department of Gastroenterology, Yamagata University School, Yamagata
| | | | - Fumio Imazeki
- Department of Medicine and Clinical Oncology, Graduate School of Medicine, Chiba University, Chiba
| | - Masayuki Kurosaki
- Division of Gastroenterology and Hepatology, Musashino Red Cross Hospital, Tokyo
| | - Takeji Umemura
- Department of Medicine, Shinshu University School of Medicine, Matsumoto
| | - Takafumi Ichida
- Department of Gastroenterology and Hepatology, Juntendo University Shizuoka Hospital, Shizuoka
| | - Hidenori Toyoda
- Department of Gastroenterology, Ogaki Municipal Hospital, Ogaki
| | - Masashi Yoneda
- Department of Gastroenterology, Aichi Medical University School of Medicine, Nagakute
| | - Yasuhito Tanaka
- Nagoya City University Graduate School of Medical Sciences, Nagoya
| | - Eiji Mita
- National Hospital Organization Osaka National Hospital, Osaka
| | - Kazuhide Yamamoto
- Department of Gastroenterology and Hepatology, Okayama University Graduate School of Medicine, Okayama
| | - Kojiro Michitaka
- Department of Gastroenterology, Ehime University Graduate School of Medicine, Toon
| | - Tatsuji Maeshiro
- First Department of Internal Medicine, University Hospital, Faculty of Medicine, University of the Ryukyu, Okinawa, Japan
| | - Junko Tanuma
- AIDS Clinical Center, National Center for Global Health and Medicine, Tokyo
| | - Masaaki Korenaga
- The Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, Ichikawa
| | - Kazumoto Murata
- The Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, Ichikawa
| | - Naohiko Masaki
- The Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, Ichikawa
| | - Kazuhiko Koike
- Department of Internal Medicine, Graduate School of Medicine, The University of Tokyo
| | - Masashi Mizokami
- The Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, Ichikawa
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Yamada H, Takahashi K, Lim O, Svay S, Chuon C, Hok S, Do SH, Fujimoto M, Akita T, Goto N, Katayama K, Arai M, Tanaka J. Hepatitis E Virus in Cambodia: Prevalence among the General Population and Complete Genome Sequence of Genotype 4. PLoS One 2015; 10:e0136903. [PMID: 26317620 PMCID: PMC4552640 DOI: 10.1371/journal.pone.0136903] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 08/09/2015] [Indexed: 12/25/2022] Open
Abstract
Hepatitis E virus (HEV) is a growing public health problem in many countries. In this study, we investigated HEV seroprevalence among the general population in the Siem Reap province, Cambodia, and performed HEV genetic analysis with the aim to develop an HEV prevention strategy. This seroepidemiological cross-sectional study conducted from 2010 to 2014 included 868 participants from four different locations in Siem Reap province, Cambodia. They answered questionnaires and provided blood samples for the analysis of hepatitis virus infections. Among the participants (360 men and 508 women; age range, 7-90 years), the prevalence of anti-HEV IgG was 18.4% (95% confidence interval: 15.9-21.0); HEV RNA was detected in two participants (0.23%) and was classified as genotype 3 and 4. Full-length genome of the genotype 4 isolate, CVS-Sie10, was sequenced; it contained 7,222 nucleotides and three ORFs and demonstrated high sequence identity with the swine China isolates swGX40 (95.57%), SS19 (94.37%), and swDQ (91.94%). Multivariate logistic regression analysis revealed that men, elderly people, and house workers were risk groups significantly associated with the positivity for anti-HEV IgG. This is the first report on the detection of HEV genotype 4 in humans in Cambodia and on the complete genome sequence of HEV genotype 4 from this country. Our study demonstrates that new HEV infection cases occur frequently among the general population in Cambodia, and effective preventive measures are required.
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Affiliation(s)
- Hiroko Yamada
- Department of Epidemiology, Infectious Disease Control and Prevention, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Kazuaki Takahashi
- Department of Medical Sciences, Toshiba General Hospital, Tokyo, Japan
| | - Olline Lim
- Ministry of Health, Phnom Penh, Cambodia
| | | | - Channarena Chuon
- Department of Epidemiology, Infectious Disease Control and Prevention, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Sirany Hok
- Ministry of Health, Phnom Penh, Cambodia
| | - Son Huy Do
- Department of Epidemiology, Infectious Disease Control and Prevention, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
- Binh Thuan Medical College, Phan Thiet City, Binh Thuan Province, Vietnam
| | - Mayumi Fujimoto
- Department of Epidemiology, Infectious Disease Control and Prevention, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Tomoyuki Akita
- Department of Epidemiology, Infectious Disease Control and Prevention, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Noboru Goto
- Department of Management Studies, Graduate School of Social Sciences, Hiroshima University, Hiroshima, Japan
| | - Keiko Katayama
- Department of Epidemiology, Infectious Disease Control and Prevention, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Masahiro Arai
- Department of Medical Sciences, Toshiba General Hospital, Tokyo, Japan
| | - Junko Tanaka
- Department of Epidemiology, Infectious Disease Control and Prevention, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
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Barusrux S, Sengthong C, Urwijitaroon Y. Epidemiology of hepatitis C virus genotypes in northeastern Thai blood samples. Asian Pac J Cancer Prev 2015; 15:8837-42. [PMID: 25374216 DOI: 10.7314/apjcp.2014.15.20.8837] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Hepatitis C virus (HCV) infection is an important cause of liver cancer in Thailand. The highest prevalence of anti-HCV positive among Thai blood donors is found in the northeastern region. The present analysis of the genotype distribution among anti-HCV positive northeastern-Thai blood donors was conducted to provide a base for the epidemiological pattern of HCV infection in this region. MATERIALS AND METHODS A total of 112 HCV seropositive healthy blood donors were randomly selected and tested for the presence of HCV-RNA by RT-PCR. HCV-RNA positive samples were genotyped by direct sequencing at core region genomes and confirmed by phylogenetic analysis. RESULTS HCV viremia was found in 94.6% (106/112) of HCV seropositive blood donors. There were 3 major genotypes distributed among this population. HCV genotype 3a was the most prevalent (71.7%) followed by genotypes 1a (7.5%), 1b (7.5%), 6i (3.8%), 6f (2.8%) and 6n (1.9%). CONCLUSIONS HCV genotype 3a in asymptomatic infections in northeastern Thailand is significantly higher than other previous reports. Subgenotype 6 prevalence is less than in neighboring countries and distribution patterns differ. The findings are relevant as predictors for using interferon therapy in this population.
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Affiliation(s)
- Sahapat Barusrux
- Centre for Research and Development of Medical Diagnostic Laboratories, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand E-mail :
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Molecular Epidemiology of Novel Pathogen "Brachyspira hampsonii" Reveals Relationships between Diverse Genetic Groups, Regions, Host Species, and Other Pathogenic and Commensal Brachyspira Species. J Clin Microbiol 2015; 53:2908-18. [PMID: 26135863 DOI: 10.1128/jcm.01236-15] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 06/22/2015] [Indexed: 11/20/2022] Open
Abstract
Outbreaks of bloody diarrhea in swine herds in the late 2000s signaled the reemergence of an economically significant disease, swine dysentery, in the United States. Investigations confirmed the emergence of a novel spirochete in swine, provisionally designated "Brachyspira hampsonii," with two genetically distinct clades. Although it has since been detected in swine and migratory birds in Europe and North America, little is known about its genetic diversity or its relationships with other Brachyspira species. This study characterizes B. hampsonii using a newly developed multilocus sequence typing (MLST) approach and elucidates the diversity, distribution, population structure, and genetic relationships of this pathogen from diverse epidemiological sources globally. Genetic characterization of 81 B. hampsonii isolates, originating from six countries, with our newly established MLST scheme identified a total of 20 sequence types (STs) belonging to three clonal complexes (CCs). B. hampsonii showed a heterogeneous population structure with evidence of microevolution locally in swine production systems, while its clustering patterns showed associations with its epidemiological origins (country, swine production system, and host species). The close genetic relatedness of B. hampsonii isolates from different countries and host species highlights the importance of strict biosecurity control measures. A comparative analysis of 430 isolates representing seven Brachyspira species (pathogens and commensals) from 19 countries and 10 host species depicted clustering by microbial species. It revealed the close genetic relatedness of B. hampsonii with commensal Brachyspira species and also provided support for the two clades of B. hampsonii to be considered a single species.
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Bamaniya DC, Pavan-Kumar A, Gireesh-Babu P, Sharma N, Reang D, Krishna G, Lakra WS. DNA barcoding of marine ornamental fishes from India. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:3093-7. [DOI: 10.3109/19401736.2014.1003923] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Dhaval C. Bamaniya
- ICAR – Central Institute of Fisheries Education (CIFE), Mumbai, Maharashtra, India
| | - A. Pavan-Kumar
- ICAR – Central Institute of Fisheries Education (CIFE), Mumbai, Maharashtra, India
| | - P. Gireesh-Babu
- ICAR – Central Institute of Fisheries Education (CIFE), Mumbai, Maharashtra, India
| | - Niti Sharma
- ICAR – Central Institute of Fisheries Education (CIFE), Mumbai, Maharashtra, India
| | - Dhalongsaih Reang
- ICAR – Central Institute of Fisheries Education (CIFE), Mumbai, Maharashtra, India
| | - Gopal Krishna
- ICAR – Central Institute of Fisheries Education (CIFE), Mumbai, Maharashtra, India
| | - W. S. Lakra
- ICAR – Central Institute of Fisheries Education (CIFE), Mumbai, Maharashtra, India
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Tsai CC, Chiang YC, Weng IS, Lin YS, Chou CH. Evidence of purifying selection and co-evolution at the fold-back arm of the novel precursor microRNA159 gene in Phalaenopsis Species (Orchidaceae). PLoS One 2014; 9:e114493. [PMID: 25470008 PMCID: PMC4254996 DOI: 10.1371/journal.pone.0114493] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Accepted: 11/07/2014] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND MicroRNAs (miRNAs) are small, endogenously transcribed, non-protein-coding RNAs that play important roles in regulation of gene expression in animals and plants. Here, selective constraints on the novel precursor microRNA159 (pre-miR159) gene were investigated in 42 Phalaenopsis species (Orchidaceae). METHODS/RESULTS A novel precursor microRNA159 gene was isolated from 42 Phalaenopsis species using a new microRNA-PCR (miR-PCR) approach. Sequencing of pre-miR159 genes revealed differences from the canonical pre-miR159 gene in Phalaenopsis species and other plants. Results demonstrated that the 5' and 3' fold-back arms and the terminal loop of the novel pre-miR159 gene have undergone purifying selection and selective constraint for stabilizing the secondary hairpin structure. Two conserved motifs within the 5' fold-back arm had the highest purifying selective pressure within the novel pre-miR159 gene. Evidence of sequence co-evolution between the 5' and 3' fold-back regions was observed. CONCLUSIONS Functional selective pressure might arise from the constraint of forming a hairpin structure and demonstrate co-evolution of sequences between the 5' and 3' fold-back regions of the novel pre-miR159 gene in Phalaenopsis species.
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Affiliation(s)
- Chi-Chu Tsai
- Kaohsiung District Agricultural Research and Extension Station, Pingtung, 908, Taiwan
- Department of Biological Science and Technology, National Pingtung University of Science and Technology, Pingtung, 912, Taiwan
| | - Yu-Chung Chiang
- Department of Biological Sciences, National Sun Yat-sen University, Kaohsiung, 804, Taiwan
- * E-mail: (YCC); (CHC)
| | - I-Szu Weng
- Kaohsiung District Agricultural Research and Extension Station, Pingtung, 908, Taiwan
| | - Yu-Shium Lin
- Kaohsiung District Agricultural Research and Extension Station, Pingtung, 908, Taiwan
| | - Chang-Hung Chou
- Research Center for Biodiversity, China Medical University, Taichung, 404, Taiwan
- * E-mail: (YCC); (CHC)
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Carmel A, Musa-Lempel N, Tsur D, Ziv-Ukelson M. The worst case complexity of maximum parsimony. J Comput Biol 2014; 21:799-808. [PMID: 25302568 DOI: 10.1089/cmb.2014.0128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
One of the core classical problems in computational biology is that of constructing the most parsimonious phylogenetic tree interpreting an input set of sequences from the genomes of evolutionarily related organisms. We reexamine the classical maximum parsimony (MP) optimization problem for the general (asymmetric) scoring matrix case, where rooted phylogenies are implied, and analyze the worst case bounds of three approaches to MP: The approach of Cavalli-Sforza and Edwards, the approach of Hendy and Penny, and a new agglomerative, "bottom-up" approach we present in this article. We show that the second and third approaches are faster than the first one by a factor of Θ(√n) and Θ(n), respectively, where n is the number of species.
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Affiliation(s)
- Amir Carmel
- Department of Computer Science, Ben-Gurion University of the Negev , Beer Sheva, Israel
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Mirajkar NS, Gebhart CJ. Understanding the molecular epidemiology and global relationships of Brachyspira hyodysenteriae from swine herds in the United States: a multi-locus sequence typing approach. PLoS One 2014; 9:e107176. [PMID: 25192199 PMCID: PMC4156428 DOI: 10.1371/journal.pone.0107176] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Accepted: 08/14/2014] [Indexed: 11/19/2022] Open
Abstract
Outbreaks of mucohemorrhagic diarrhea in pigs caused by Brachyspira hyodysenteriae in the late 2000s indicated the re-emergence of Swine Dysentery (SD) in the U.S. Although the clinical disease was absent in the U.S. since the early 1990s, it continued to cause significant economic losses to other swine rearing countries worldwide. This study aims to fill the gap in knowledge pertaining to the re-emergence and epidemiology of B. hyodysenteriae in the U.S. and its global relationships using a multi-locus sequence typing (MLST) approach. Fifty-nine post re-emergent isolates originating from a variety of sources in the U.S. were characterized by MLST, analyzed for epidemiological relationships (within and between multiple sites of swine systems), and were compared with pre re-emergent isolates from the U.S. Information for an additional 272 global isolates from the MLST database was utilized for international comparisons. Thirteen nucleotide sequence types (STs) including a predominant genotype (ST93) were identified in the post re-emergent U.S. isolates; some of which showed genetic similarity to the pre re-emergent STs thereby suggesting its likely role in the re-emergence of SD. In the U.S., in general, no more than one ST was found on a site; multiple sites of a common system shared a ST; and STs found in the U.S. were distinct from those identified globally. Of the 110 STs characterized from ten countries, only two were found in more than one country. The U.S. and global populations, identified as clonal and heterogeneous based on STs, showed close relatedness based on amino acid types (AATs). One predicted founder type (AAT9) and multiple predicted subgroup founder types identified for both the U.S. and the global population indicate the potential microevolution of this pathogen. This study elucidates the strain diversity and microevolution of B. hyodysenteriae, and highlights the utility of MLST for epidemiological and surveillance studies.
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Affiliation(s)
- Nandita S. Mirajkar
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, United States of America
- * E-mail:
| | - Connie J. Gebhart
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, United States of America
- Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, United States of America
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13
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Wolf M, Koetschan C, Müller T. ITS2, 18S, 16S or any other RNA - simply aligning sequences and their individual secondary structures simultaneously by an automatic approach. Gene 2014; 546:145-9. [PMID: 24881812 DOI: 10.1016/j.gene.2014.05.065] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Revised: 05/28/2014] [Accepted: 05/29/2014] [Indexed: 11/29/2022]
Abstract
Secondary structures of RNA sequences are increasingly being used as additional information in reconstructing phylogenies and/or in distinguishing species by compensatory base change (CBC) analyses. However, in most cases just one secondary structure is used in manually correcting an automatically generated multiple sequence alignment and/or just one secondary structure is used in guiding a sequence alignment still completely generated by hand. With the advent of databases and tools offering individual RNA secondary structures, here we re-introduce a twelve letter code already implemented in 4SALE - a tool for synchronous sequence and secondary structure alignment and editing - that enables one to align RNA sequences and their individual secondary structures synchronously and fully automatic, while dramatically increasing the phylogenetic information content. We further introduce a scaled down non-GUI version of 4SALE particularly designed for big data analysis, and available at: http://4sale.bioapps.biozentrum.uni-wuerzburg.de.
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Affiliation(s)
- Matthias Wolf
- Department of Bioinformatics, Biocenter, University of Würzburg, 97074 Würzburg, Germany.
| | - Christian Koetschan
- Department of Bioinformatics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Tobias Müller
- Department of Bioinformatics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
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14
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Yotsuyanagi H, Ito K, Yamada N, Takahashi H, Okuse C, Yasuda K, Suzuki M, Moriya K, Mizokami M, Miyakawa Y, Koike K. High Levels of Hepatitis B Virus After the Onset of Disease Lead to Chronic Infection in Patients With Acute Hepatitis B. Clin Infect Dis 2013; 57:935-42. [DOI: 10.1093/cid/cit348] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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15
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Wang Y, Li C, Chen Z, Xu B, Li G, Liu G. Complete genome comparison of duck hepatitis virus type 1 parental and attenuated strains. Virus Genes 2012; 45:398-401. [PMID: 22723199 PMCID: PMC7088869 DOI: 10.1007/s11262-012-0767-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2012] [Accepted: 05/28/2012] [Indexed: 12/02/2022]
Abstract
Two complete duck hepatitis virus type 1 (DHV-1) genomes, strain SY5 and its chicken embryos passage descendent vaccine strain ZJ-A, were compared and analyzed in order to identify possible sites of attenuation. Of the 205 nucleotide changes, 22 resulted in sense mutations, 174 produced nonsense mutations. Besides, there are 7 consistent nucleotides substitutions in 5′UTR and 2 in 3′UTR. Three of these 22 sense mutations resided in VP0, 6 exists in VP1, one exists in VP3, 3 exists in 2A2, 3 exists in 2C, one was detected in 3B and 5 was in 3D. These results suggested that VP0, VP1, 3D, and 5′/3′UTR may contribute to the attenuation of DHV-1 in chicken/duck/embryos. The results provide a genetic basis for future manipulation of a DHV-1 infectious clone.
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Affiliation(s)
- Yong Wang
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
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16
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Context-Dependent Evolutionary Models for Non-Coding Sequences: An Overview of Several Decades of Research and an Analysis of Laurasiatheria and Primate Evolution. Evol Biol 2011. [DOI: 10.1007/s11692-011-9139-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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17
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Sugiyama M, Inui A, Shin-I T, Komatsu H, Mukaide M, Masaki N, Murata K, Ito K, Nakanishi M, Fujisawa T, Mizokami M. Easy-to-use phylogenetic analysis system for hepatitis B virus infection. Hepatol Res 2011; 41:936-945. [PMID: 21883742 DOI: 10.1111/j.1872-034x.2011.00859.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
AIM The molecular phylogenetic analysis has been broadly applied to clinical and virological study. However, the appropriate settings and application of calculation parameters are difficult for non-specialists of molecular genetics. In the present study, the phylogenetic analysis tool was developed for the easy determination of genotypes and transmission route. METHODS A total of 23 patients of 10 families infected with hepatitis B virus (HBV) were enrolled and expected to undergo intrafamilial transmission. The extracted HBV DNA were amplified and sequenced in a region of the S gene. RESULTS The software to automatically classify query sequence was constructed and installed on the Hepatitis Virus Database (HVDB). Reference sequences were retrieved from HVDB, which contained major genotypes from A to H. Multiple-alignments using CLUSTAL W were performed before the genetic distance matrix was calculated with the six-parameter method. The phylogenetic tree was output by the neighbor-joining method. User interface using WWW-browser was also developed for intuitive control. This system was named as the easy-to-use phylogenetic analysis system (E-PAS). Twenty-three sera of 10 families were analyzed to evaluate E-PAS. The queries obtained from nine families were genotype C and were located in one cluster per family. However, one patient of a family was classified into the cluster different from her family, suggesting that E-PAS detected the sample distinct from that of her family on the transmission route. CONCLUSIONS The E-PAS to output phylogenetic tree was developed since requisite material was sequence data only. E-PAS could expand to determine HBV genotypes as well as transmission routes.
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Affiliation(s)
- Masaya Sugiyama
- The Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, Ichikawa Department of Biochemistry and Cell Biology, Nagoya City University Graduate School of Medical Sciences, Nagoya Department of Pediatrics, Eastern Yokohama Hospital, Yokohama SRL, Inc. Tokyo, Japan
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18
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Abstract
BACKGROUND Phylogenetic analyses reveal probable patterns of divergence of present day organisms from common ancestors. The points of divergence of lineages can be dated if a corresponding historical or fossil record exists. For many species, in particular viruses, such records are rare. Recently, Bayesian phylogenetic analysis using sequences from closely related organisms isolated at different times have been used to calibrate divergences. Phylogenetic analyses depend on the assumption that the average substitution rates that can be calculated from the data apply throughout the course of evolution. RESULTS The present study tests this crucial assumption by charting the kinds of substitutions observed between pairs of sequences with different levels of total substitutions. Datasets of aligned sequences, both viral and non-viral, were assembled. For each pair of sequences in an aligned set, the distribution of nucleotide interchanges and the total number of changes were calculated. Data were binned according to total numbers of changes and plotted. The accumulation of the six possible interchange types in retroelements as a function of distance followed closely the expected hyperbolic relationship. For other datasets, however, significant deviations from this relationship were noted. A rapid initial accumulation of transition interchanges was frequent among the datasets and anomalous changes occurred at specific divergence levels. CONCLUSIONS The accumulation profiles suggested that substantial changes in frequencies of types of substitutions occur over the course of evolution and that such changes should be considered in evaluating and dating viral phylogenies.
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Affiliation(s)
- Ulrich Melcher
- Department of Biochemistry & Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA.
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19
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Baele G, Van de Peer Y, Vansteelandt S. Using non-reversible context-dependent evolutionary models to study substitution patterns in primate non-coding sequences. J Mol Evol 2010; 71:34-50. [PMID: 20623275 DOI: 10.1007/s00239-010-9362-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2009] [Accepted: 05/26/2010] [Indexed: 11/28/2022]
Abstract
We discuss the importance of non-reversible evolutionary models when analyzing context-dependence. Given the inherent non-reversible nature of the well-known CpG-methylation-deamination process in mammalian evolution, non-reversible context-dependent evolutionary models may be well able to accurately model such a process. In particular, the lack of constraints on non-reversible substitution models might allow for more accurate estimation of context-dependent substitution parameters. To demonstrate this, we have developed different time-homogeneous context-dependent evolutionary models to analyze a large genomic dataset of primate ancestral repeats based on existing independent evolutionary models. We have calculated the difference in model fit for each of these models using Bayes Factors obtained via thermodynamic integration. We find that non-reversible context-dependent models can drastically increase model fit when compared to independent models and this on two primate non-coding datasets. Further, we show that further improvements are possible by clustering similar parameters across contexts.
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Affiliation(s)
- Guy Baele
- Department of Plant Systems Biology, VIB, Ghent University, Technologiepark 927, 9052, Ghent, Belgium.
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20
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Qi YJ, Qiu WY. Symmetry Analysis of an X-palindrome in Human and Chimpanzee. CHINESE J CHEM PHYS 2009. [DOI: 10.1088/1674-0068/22/04/401-405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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21
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Mayden RL, Chen WJ, Bart HL, Doosey MH, Simons AM, Tang KL, Wood RM, Agnew MK, Yang L, Hirt MV, Clements MD, Saitoh K, Sado T, Miya M, Nishida M. Reconstructing the phylogenetic relationships of the earth’s most diverse clade of freshwater fishes—order Cypriniformes (Actinopterygii: Ostariophysi): A case study using multiple nuclear loci and the mitochondrial genome. Mol Phylogenet Evol 2009; 51:500-14. [DOI: 10.1016/j.ympev.2008.12.015] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2008] [Revised: 12/14/2008] [Accepted: 12/15/2008] [Indexed: 11/28/2022]
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22
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THORPE JOHNP. Possible effects of interprotein variation in mean rate of amino acid substitution on the relationship of genetic distance with time since evolutionary divergence. Biol J Linn Soc Lond 2009. [DOI: 10.1111/j.1095-8312.1989.tb01909.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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23
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Matsuura K, Tanaka Y, Hige S, Yamada G, Murawaki Y, Komatsu M, Kuramitsu T, Kawata S, Tanaka E, Izumi N, Okuse C, Kakumu S, Okanoue T, Hino K, Hiasa Y, Sata M, Maeshiro T, Sugauchi F, Nojiri S, Joh T, Miyakawa Y, Mizokami M. Distribution of hepatitis B virus genotypes among patients with chronic infection in Japan shifting toward an increase of genotype A. J Clin Microbiol 2009; 47:1476-1483. [PMID: 19297602 PMCID: PMC2681832 DOI: 10.1128/jcm.02081-08] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2008] [Revised: 12/17/2008] [Accepted: 03/02/2009] [Indexed: 02/06/2023] Open
Abstract
Acute hepatitis B virus (HBV) infection has been increasing through promiscuous sexual contacts, and HBV genotype A (HBV/A) is frequent in patients with acute hepatitis B (AHB) in Japan. To compare the geographic distribution of HBV genotypes in patients with chronic hepatitis B (CHB) in Japan between 2005 and 2006 and between 2000 and 2001, with special attention to changes in the proportion of HBV/A, a cohort study was performed to survey changes in genotypes of CHB patients at 16 hospitals throughout Japan. Furthermore, we investigated the clinical characteristics of each genotype and examined the genomic characteristics of HBV/A isolates by molecular evolutionary analyses. Of the 1,271 patients, 3.5%, 14.1%, and 82.3% were infected with HBV/A, -B, and -C, respectively. In comparison with our previous survey during 2000 and 2001, HBV/A was twice as frequent (3.5% versus 1.7%; P = 0.02). The mean age was lower in the patients with HBV/A than in those with HBV/B or -C. Based on phylogenetic analyses of 11 full-length genomes and 29 pre-S2/S region sequences from patients, HBV/A isolates were imported from Europe and the United States, as well as the Philippines and India. They clustered with HBV/A from AHB patients and have spread throughout Japan. HBV/A has been increasing in CHB patients in Japan as a consequence of AHB spreading in the younger generation through promiscuous sexual contacts, aided by a tendency of HBV/A to induce chronic hepatitis. The spread of HBV/A infection in Japan should be prevented by universal vaccination programs.
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Affiliation(s)
- Kentaro Matsuura
- Department of Clinical Molecular Informative Medicine, Nagoya City University Graduate School of Medical Sciences, Kawasumi, Mizuho, Nagoya, Japan
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24
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McPeek M. The Ecological Dynamics of Clade Diversification and Community Assembly. Am Nat 2008; 172:E270-84. [DOI: 10.1086/593137] [Citation(s) in RCA: 250] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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25
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Balbi KJ, Rocha EPC, Feil EJ. The temporal dynamics of slightly deleterious mutations in Escherichia coli and Shigella spp. Mol Biol Evol 2008; 26:345-55. [PMID: 18984902 DOI: 10.1093/molbev/msn252] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The Shigella are recently emerged clones of Escherichia coli, which have independently adopted an intracellular pathogenic lifestyle. We examined the molecular evolutionary consequences of this niche specialization by comparing the normalized, directional frequency profiles of unique polymorphisms within 2,098 orthologues representing the intersection of five E. coli and four Shigella genomes. We note a surfeit of AT-enriching changes (GC-->AT), transversions, and nonsynonymous changes in the Shigella genomes. By examining these differences within a temporal framework, we conclude that our results are consistent with relaxed or inefficient selection in Shigella owing to a reduced effective population size. Alternative interpretations, and the interesting exception of Shigella sonnei, are discussed. Finally, this analysis lends support to the view that nucleotide composition typically does not lie at mutational equilibrium but that selection plays a role in maintaining a higher GC content than would result solely from mutation bias. This argument sheds light on the enrichment of adenine and thymine in the genomes of bacterial endosymbionts where purifying selection is very weak.
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Affiliation(s)
- Kevin J Balbi
- Department of Biology and Biochemistry, University of Bath, Claverton Down, United Kingdom
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26
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Kimura T, Imamura M, Hiraga N, Hatakeyama T, Miki D, Noguchi C, Mori N, Tsuge M, Takahashi S, Fujimoto Y, Iwao E, Ochi H, Abe H, Maekawa T, Arataki K, Tateno C, Yoshizato K, Wakita T, Okamoto T, Matsuura Y, Chayama K. Establishment of an infectious genotype 1b hepatitis C virus clone in human hepatocyte chimeric mice. J Gen Virol 2008; 89:2108-2113. [DOI: 10.1099/vir.0.83658-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The establishment of clonal infection of hepatitis C virus (HCV) in a small-animal model is important for the analysis of HCV virology. A previous study developed models of molecularly cloned genotype 1a and 2a HCV infection using human hepatocyte-transplanted chimeric mice. This study developed a new model of molecularly cloned genotype 1b HCV infection. A full-length genotype 1b HCV genome, HCV-KT9, was cloned from a serum sample from a patient with severe acute hepatitis. The chimeric mice were inoculated intrahepatically with in vitro-transcribed HCV-KT9 RNA. Inoculated mice developed viraemia at 2 weeks post-infection, and this persisted for more than 6 weeks. Passage experiments indicated that the sera of these mice contained infectious HCV. Interestingly, a similar clone, HCV-KT1, in which the poly(U/UC) tract was 29 nt shorter than in HCV-KT9, showed poorer in vivo infectivity and replication ability. An in vitro study showed that no virus was produced in the culture medium from HCV-KT9-transfected cells. In conclusion, this study developed a genetically engineered genotype 1b HCV-infected mouse. This mouse model will be useful for the study of HCV virology, particularly the mechanism underlying the variable resistance of HCV genotypes to interferon therapy.
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Affiliation(s)
- Takashi Kimura
- Liver Research Project Center, Hiroshima University, Hiroshima, Japan
- Department of Medicine and Molecular Science, Division of Frontier Medical Science, Programs for Biomedical Research, Graduate School of Biomedical Sciences, Hiroshima University, Hiroshima, Japan
| | - Michio Imamura
- Liver Research Project Center, Hiroshima University, Hiroshima, Japan
- Department of Medicine and Molecular Science, Division of Frontier Medical Science, Programs for Biomedical Research, Graduate School of Biomedical Sciences, Hiroshima University, Hiroshima, Japan
| | - Nobuhiko Hiraga
- Liver Research Project Center, Hiroshima University, Hiroshima, Japan
- Department of Medicine and Molecular Science, Division of Frontier Medical Science, Programs for Biomedical Research, Graduate School of Biomedical Sciences, Hiroshima University, Hiroshima, Japan
| | - Tsuyoshi Hatakeyama
- Liver Research Project Center, Hiroshima University, Hiroshima, Japan
- Department of Medicine and Molecular Science, Division of Frontier Medical Science, Programs for Biomedical Research, Graduate School of Biomedical Sciences, Hiroshima University, Hiroshima, Japan
| | - Daiki Miki
- Liver Research Project Center, Hiroshima University, Hiroshima, Japan
- Department of Medicine and Molecular Science, Division of Frontier Medical Science, Programs for Biomedical Research, Graduate School of Biomedical Sciences, Hiroshima University, Hiroshima, Japan
| | - Chiemi Noguchi
- Liver Research Project Center, Hiroshima University, Hiroshima, Japan
- Department of Medicine and Molecular Science, Division of Frontier Medical Science, Programs for Biomedical Research, Graduate School of Biomedical Sciences, Hiroshima University, Hiroshima, Japan
| | - Nami Mori
- Liver Research Project Center, Hiroshima University, Hiroshima, Japan
- Department of Medicine and Molecular Science, Division of Frontier Medical Science, Programs for Biomedical Research, Graduate School of Biomedical Sciences, Hiroshima University, Hiroshima, Japan
| | - Masataka Tsuge
- Liver Research Project Center, Hiroshima University, Hiroshima, Japan
- Department of Medicine and Molecular Science, Division of Frontier Medical Science, Programs for Biomedical Research, Graduate School of Biomedical Sciences, Hiroshima University, Hiroshima, Japan
| | - Shoichi Takahashi
- Liver Research Project Center, Hiroshima University, Hiroshima, Japan
- Department of Medicine and Molecular Science, Division of Frontier Medical Science, Programs for Biomedical Research, Graduate School of Biomedical Sciences, Hiroshima University, Hiroshima, Japan
| | - Yoshifumi Fujimoto
- Liver Research Project Center, Hiroshima University, Hiroshima, Japan
- Department of Medicine and Molecular Science, Division of Frontier Medical Science, Programs for Biomedical Research, Graduate School of Biomedical Sciences, Hiroshima University, Hiroshima, Japan
| | - Eiji Iwao
- Research Division, Mitsubishi Tanabe Pharma Corporation, Osaka, Japan
| | - Hidenori Ochi
- Laboratory for Liver Disease, SNP Research Center, Institute of Physical and Chemical Research (RIKEN), Yokohama, Japan
- Liver Research Project Center, Hiroshima University, Hiroshima, Japan
| | - Hiromi Abe
- Laboratory for Liver Disease, SNP Research Center, Institute of Physical and Chemical Research (RIKEN), Yokohama, Japan
- Liver Research Project Center, Hiroshima University, Hiroshima, Japan
- Department of Medicine and Molecular Science, Division of Frontier Medical Science, Programs for Biomedical Research, Graduate School of Biomedical Sciences, Hiroshima University, Hiroshima, Japan
| | - Toshiro Maekawa
- Laboratory for Liver Disease, SNP Research Center, Institute of Physical and Chemical Research (RIKEN), Yokohama, Japan
| | - Keiko Arataki
- Hirosimakinen-Hospital, Internal Medicine, Hiroshima, Japan
| | - Chise Tateno
- Developmental Biology Laboratory, Department of Biological Science, Graduate School of Science, Hiroshima University, Higashihiroshima, Japan
- Liver Research Project Center, Hiroshima University, Hiroshima, Japan
| | - Katsutoshi Yoshizato
- Developmental Biology Laboratory, Department of Biological Science, Graduate School of Science, Hiroshima University, Higashihiroshima, Japan
- Liver Research Project Center, Hiroshima University, Hiroshima, Japan
| | - Takaji Wakita
- Department of Virology II, National Institute of Infectious Diseases, Shinjuku-ku, Japan
| | - Toru Okamoto
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Yoshiharu Matsuura
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Kazuaki Chayama
- Laboratory for Liver Disease, SNP Research Center, Institute of Physical and Chemical Research (RIKEN), Yokohama, Japan
- Liver Research Project Center, Hiroshima University, Hiroshima, Japan
- Department of Medicine and Molecular Science, Division of Frontier Medical Science, Programs for Biomedical Research, Graduate School of Biomedical Sciences, Hiroshima University, Hiroshima, Japan
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Tanaka Y, Sanchez LV, Sugiyama M, Sakamoto T, Kurbanov F, Tatematsu K, Roman S, Takahashi S, Shirai T, Panduro A, Mizokami M. Characteristics of hepatitis B virus genotype G coinfected with genotype H in chimeric mice carrying human hepatocytes. Virology 2008; 376:408-415. [PMID: 18474388 DOI: 10.1016/j.virol.2008.04.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2008] [Revised: 03/18/2008] [Accepted: 04/01/2008] [Indexed: 12/17/2022]
Abstract
Accumulated evidence indicated that hepatitis B virus genotype G (HBV/G) is present exclusively in coinfection with other HBV genotypes. In Mexico, HBV/G from 6 men who had sex with men were coinfected with HBV/H. Phylogenetically complete genomes of the 6 Mexican HBV/G strains were closely related to previous ones from the US/Europe. Using uPA/SCID mice with human hepatocytes, monoinfection with HBV/G did not result in detectable HBV DNA in serum, whereas superinfection with HBV/G at week 10 inoculated HBV/H when HBV/H DNA was elevated to >10(7) copies/mL has enhanced the replication of HBV/G. The HBV/G was enhanced in another 3 inoculated with a serum passage containing HBV/G with a trace of HBV/H. Coinfection of mice with HBV/G and H induced fibrosis in the liver. In conclusion, the replication of HBV/G can be enhanced remarkably when it is coinfected with HBV/H. Coinfection with HBV/G may be directly cytopathic in immunosuppressive conditions.
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Affiliation(s)
- Yasuhito Tanaka
- Department of Clinical Molecular Informative Medicine, Nagoya City University Graduate School of Medical Sciences, Nagoya, 467-8601 Japan
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28
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Prediction of sites under adaptive evolution in cytochrome P450 sequences and their relationship to substrate recognition sites. Pharmacogenet Genomics 2008; 18:467-76. [DOI: 10.1097/fpc.0b013e3282f9b68e] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Shin-I T, Tanaka Y, Tateno Y, Mizokami M. Development and public release of a comprehensive hepatitis virus database. Hepatol Res 2008; 38:234-243. [PMID: 17877727 DOI: 10.1111/j.1872-034x.2007.00262.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
AIM Currently, approximately 44 000 hepatitis C virus (HCV), 11 000 hepatitis B virus (HBV), and 1600 hepatitis E virus (HEV) sequences are available at the International Nucleotide Sequence Database Collaboration (INSDC, previously known as DDBJ/EMBL/GenBank), and the number of these virus sequences is growing rapidly. However, since INDSC is not specialized to hepatitis viruses, it is difficult to retrieve information of virological or clinical interests from it. Thus, it is quite worthwhile to construct a specialized database for the hepatitis virus sequences and to make it accessible to researchers worldwide. METHODS We developed a WWW-based database hepatitis virus database (HVDB), which contains all the HCV, HBV, and HEV sequences available at INSDC. In the HVDB, all piece sequences obtained from INSDC are arranged to the genomesequence of each virus. Also given in the database are the phylogenetic relationships of each locus on the genome among variants for each virus. RESULTS Users of the database can easily retrieve entries (sequences with annotations) of the specific genotype by referring to the phylogenetic relationships or those of specific loci by referring to the genome map information. HVDB provides users with a tool for phylogenetic analysis that can be used in combination with the data retrieval tools. CONCLUSION The latest release is publicly accessible at the HVDB website: http://s2as02.genes.nig.ac.jp.
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Affiliation(s)
- Tadasu Shin-I
- Department of Clinical Molecular Informative Medicine, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
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Elkady A, Tanaka Y, Kurbanov F, Oynsuren T, Mizokami M. Virological and clinical implication of core promoter C1752/V1753 and T1764/G1766 mutations in hepatitis B virus genotype D infection in Mongolia. J Gastroenterol Hepatol 2008; 23:474-481. [PMID: 18318825 DOI: 10.1111/j.1440-1746.2008.05321.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND AND AIM The aim of the present study was to reveal virological and clinical features of hepatitis B virus (HBV) genotype D infection. METHODS One hundred and twenty-two Mongolian chronic liver disease (CLD) patients infected with HBV were subjected for serological HBV-markers screening and HBV-enzyme immunoassay (EIA) genotyping. Nucleotide sequences were analyzed for 48 HBV/D strains (23 isolated from hepatocellular carcinoma (HCC) and 25 from CLD patients). RESULTS Prevalence of hepatitis B e antigen (HBeAg) positivity was low (25.9%) in young patients (< or =30 years old) indicating early HBeAg seroclearance in HBV/D carriers. The T1764/G1766 double mutation was the most common basal core promoter (BCP) mutation (29.2%) and was frequent in HBeAg-negative patients (39.3%). Patients harboring T1764/G1766 mutants exhibited lower HBV-DNA and HBV core antigen (HBcAg) levels than those with wild-type BCP strains (P = 0.024, 0.049, respectively). C1752 and/or V (not T) 1753 mutation was significantly prevalent in HCC patients (HCC vs CLD; 52.2% vs 20%, P = 0.033). T1762/A1764 mutation was detected in 75.0% of HCC patients with high viral load (> or =5 log copies/mL). Precore stop codon mutation A1896 was detected in (70.8%) of HBV/D-infected patients. CONCLUSIONS In Mongolians infected with HBV/D, C1752 and/or V1753 mutation was associated with HCC.
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MESH Headings
- Adult
- Carcinoma, Hepatocellular/virology
- Codon, Terminator
- DNA, Viral/blood
- Female
- Genotype
- Hepatitis B Core Antigens/blood
- Hepatitis B e Antigens/blood
- Hepatitis B virus/genetics
- Hepatitis B virus/immunology
- Hepatitis B, Chronic/complications
- Hepatitis B, Chronic/etiology
- Hepatitis B, Chronic/genetics
- Hepatitis B, Chronic/immunology
- Hepatitis C, Chronic/complications
- Hepatitis C, Chronic/etiology
- Hepatitis C, Chronic/genetics
- Hepatitis D, Chronic/complications
- Hepatitis D, Chronic/etiology
- Hepatitis D, Chronic/genetics
- Humans
- Liver Neoplasms/virology
- Male
- Middle Aged
- Molecular Sequence Data
- Mongolia
- Mutation
- Phenotype
- Phylogeny
- Promoter Regions, Genetic
- Viral Core Proteins/genetics
- Viral Load
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Affiliation(s)
- Abeer Elkady
- Department of Clinical Molecular Informative Medicine, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
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Elkady A, Tanaka Y, Kurbanov F, Hirashima N, Sugiyama M, Khan A, Kato H, Okumura A, Mizokami M. Evaluation of anti-hepatitis E virus (HEV) immunoglobulin A in a serological screening for HEV infection. J Gastroenterol 2007; 42:911-917. [PMID: 18008036 DOI: 10.1007/s00535-007-2109-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2007] [Accepted: 08/20/2007] [Indexed: 02/04/2023]
Abstract
BACKGROUND Several formulations of serological diagnostic kits were developed recently in Japan for detecting hepatitis E virus (HEV) infection. The present study was conducted to evaluate a novel anti-HEV serological kit based on detection of class A immunoglobulin antibody (anti-HEV IgA). METHODS Serum samples from 81 acute hepatitis (AH) and 112 chronic hepatitis (CH) patients were tested for anti-HEV IgG, anti-HEV IgM, and anti-HEV IgA by enzyme immunoassay, and HEV RNA was detected by reverse transcription-polymerase chain reaction. RESULTS Eight of 81 (9.9%) AH patients were positive for anti-HEV IgG; 6/81 (7.4%) were positive for anti-HEV IgM; and 3/81 (3.7%) were positive for anti-HEV IgA. HEV RNA was detected only in two patients, and both were positive for anti-HEV IgA and negative for hepatitis A, B, and C virus markers. Of 112 CH patients, reactivity to anti-HEV IgM and anti-HEV IgG was found in two and four patients, respectively. None of these six patients was positive for anti-HEV IgA or HEV RNA. For these six CH patients, serial serum samples stored during the clinical follow-up (1994-2003) were further subjected to anti-HEV IgG, IgM, IgA, and HEV RNA examinations. None of the examined stored samples was reactive for anti-HEV IgA or HEV RNA despite reactivity to anti-HEV IgM and IgG. CONCLUSIONS Serological examination for anti-HEV IgA together with IgM and IgG allows sensitive and specific determination of acute or past infection with HEV. Although its prevalence is low, HEV infection must be investigated in acute hepatitis patients even in nonendemic HEV countries.
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Affiliation(s)
- Abeer Elkady
- Department of Clinical Molecular Informative Medicine, Nagoya City University Graduate School of Medical Sciences, 1 Kawasumi, Mizuho-ku, Nagoya 467-8601, Japan
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32
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Tajiri H, Tanaka Y, Kagimoto S, Murakami J, Tokuhara D, Mizokami M. Molecular evidence of father-to-child transmission of hepatitis B virus. J Med Virol 2007; 79:922-926. [PMID: 17516534 DOI: 10.1002/jmv.20916] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
At present in Japan, only high-risk infants born to chronic hepatitis B virus (HBV)-infected mothers are given HBV vaccine. However, children can contract the virus from other HBV-infected family members, including fathers. The aim of this study is to present substantial and unequivocal evidence of father-to-child transmission of HBV infection using techniques including homology analysis and phylogenetic analysis. Thirteen chronic HBV-infected members of five families that included eight children and their respective fathers were enrolled in this study. Homology analysis and phylogenetic analyses of 2 coding region, the S gene and X gene, from the HBV genome were performed comparing the 13 nucleotide sequences from the 13 subjects. The nucleotide homology among the five sets of fathers and children was quite high (99.3-100%). A phylogenetic tree constructed on the 13 nucleotide sequences showed that all 5 sets of fathers and children were grouped into the same cluster with high bootstrap values. These results strongly indicate that father-to-child transmission is an important route of HBV infection in Japan and it is recommend that universal vaccination against HBV infection be instituted immediately in Japan for all children, in accordance with the WHO recommendation of 1997.
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Zheng D, Frankish A, Baertsch R, Kapranov P, Reymond A, Choo SW, Lu Y, Denoeud F, Antonarakis SE, Snyder M, Ruan Y, Wei CL, Gingeras TR, Guigó R, Harrow J, Gerstein MB. Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution. Genome Res 2007; 17:839-51. [PMID: 17568002 PMCID: PMC1891343 DOI: 10.1101/gr.5586307] [Citation(s) in RCA: 156] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2006] [Accepted: 10/03/2006] [Indexed: 10/23/2022]
Abstract
Arising from either retrotransposition or genomic duplication of functional genes, pseudogenes are "genomic fossils" valuable for exploring the dynamics and evolution of genes and genomes. Pseudogene identification is an important problem in computational genomics, and is also critical for obtaining an accurate picture of a genome's structure and function. However, no consensus computational scheme for defining and detecting pseudogenes has been developed thus far. As part of the ENCyclopedia Of DNA Elements (ENCODE) project, we have compared several distinct pseudogene annotation strategies and found that different approaches and parameters often resulted in rather distinct sets of pseudogenes. We subsequently developed a consensus approach for annotating pseudogenes (derived from protein coding genes) in the ENCODE regions, resulting in 201 pseudogenes, two-thirds of which originated from retrotransposition. A survey of orthologs for these pseudogenes in 28 vertebrate genomes showed that a significant fraction ( approximately 80%) of the processed pseudogenes are primate-specific sequences, highlighting the increasing retrotransposition activity in primates. Analysis of sequence conservation and variation also demonstrated that most pseudogenes evolve neutrally, and processed pseudogenes appear to have lost their coding potential immediately or soon after their emergence. In order to explore the functional implication of pseudogene prevalence, we have extensively examined the transcriptional activity of the ENCODE pseudogenes. We performed systematic series of pseudogene-specific RACE analyses. These, together with complementary evidence derived from tiling microarrays and high throughput sequencing, demonstrated that at least a fifth of the 201 pseudogenes are transcribed in one or more cell lines or tissues.
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Affiliation(s)
- Deyou Zheng
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Adam Frankish
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1HH, United Kingdom
| | - Robert Baertsch
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, California 95064, USA
| | | | - Alexandre Reymond
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
- Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland
| | - Siew Woh Choo
- Genome Institute of Singapore, Singapore 138672, Singapore
| | - Yontao Lu
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, California 95064, USA
| | - France Denoeud
- Grup de Recerca en Informática Biomèdica, Institut Municipal d’Investigació Mèdica/Universitat Pompeu Fabra, Passeig Marítim de la Barceloneta, 37-49, 08003, Barcelona, Catalonia, Spain
| | - Stylianos E. Antonarakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland
| | - Michael Snyder
- Molecular, Cellular & Developmental Biology Department, Yale University, New Haven, Connecticut 06520, USA
| | - Yijun Ruan
- Genome Institute of Singapore, Singapore 138672, Singapore
| | - Chia-Lin Wei
- Genome Institute of Singapore, Singapore 138672, Singapore
| | | | - Roderic Guigó
- Grup de Recerca en Informática Biomèdica, Institut Municipal d’Investigació Mèdica/Universitat Pompeu Fabra, Passeig Marítim de la Barceloneta, 37-49, 08003, Barcelona, Catalonia, Spain
- Center for Genomic Regulation, Passeig Marítim de la Barceloneta, 37-49, 08003, Barcelona, Catalonia, Spain
| | - Jennifer Harrow
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1HH, United Kingdom
| | - Mark B. Gerstein
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
- Department of Computer Science, Yale University, New Haven, Connecticut 06520, USA
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06520, USA
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34
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Kato H, Maeno Y, Seko-Nakamura Y, Monma-Ohtaki J, Sugiura S, Takahashi K, Zhe LX, Matsumoto T, Kurvanov F, Mizokami M, Nagao M. Identification and phylogenetic analysis of hepatitis C virus in forensic blood samples obtained from injecting drug users. Forensic Sci Int 2007; 168:27-33. [PMID: 16829004 DOI: 10.1016/j.forsciint.2006.06.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2006] [Revised: 06/05/2006] [Accepted: 06/06/2006] [Indexed: 01/11/2023]
Abstract
Injecting drug users (IDUs) are a high-risk group for contracting hepatitis B virus (HBV), hepatitis C virus (HCV), and human immunodeficiency virus (HIV) infections. In Japan, data on the prevalence of those blood-borne viruses among IDUs are very limited. Blood samples were obtained from 12 cadavers of IDUs sent to Nagoya City University for the purpose of judicious autopsy and two alive IDUs with hepatitis C referred to a local hospital at the same period. The viruses were detected by polymerase chain reaction and phylogenetic analysis was performed. Two (16.6%) of the 12 autopsy cases were positive for HCV, but no case was positive for either HBV or HIV. Phylogenetic analysis of the two HCV isolates revealed that one was classified into genotype 1b and another was genotype 2b. Furthermore, nucleotide sequences of two isolates recovered from IDUs with hepatitis C were identical, that indicated the transmission of HCV between them, and those HCV were phylogenetically classified into genotype 2a. The prevalence of HCV infection among IDUs in Japan, despite the case of judicious autopsy, seems to be high, but HIV infection seems to be rare. The transmission of HCV between IDUs was demonstrated, and this indicates that phylogenetic analysis would applicable to also forensic analysis. HCV isolates identified in this study did not phylogenetically segregate, thus multiple transmission route of HCV among IDUs seems be exist in Japan.
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Affiliation(s)
- H Kato
- Department of Forensic Medical Science, Nagoya City University Graduate School of Medical Sciences, Kawasumi 1, Mizuho-cho, Mizuho-ku, Nagoya 467-8601, Japan.
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35
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Tamura A, Shimizu YK, Tanaka T, Kuroda K, Arakawa Y, Takahashi K, Mishiro S, Shimizu K, Moriyama M. Persistent infection of hepatitis E virus transmitted by blood transfusion in a patient with T-cell lymphoma. Hepatol Res 2007; 37:113-20. [PMID: 17300706 DOI: 10.1111/j.1872-034x.2007.00024.x] [Citation(s) in RCA: 156] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
AIM With advent of reverse-transcription (RT)/polymerase chain reaction (PCR) for detection of the hepatitis E viral genome, we carried out retrospective examinations. METHODS Serum samples collected from 68 patients diagnosed as viral hepatitis with unknown etiology were tested for viral markers of hepatitis virus. RESULTS Two of them were found positive for hepatitis E viral RNA. While the clinical course of one patient (patient 1) was typical as acute hepatitis E, another patient (patient 2) was persistently infected with HEV. Patient 2 was infected with the virus via blood transfusion during chemotherapy against T-cell lymphoma. The entire viral genome from the donor was identical with that from the serum of patient 2 obtained on day 170 after the transfusion of the implicated red blood cell (RBC) product, confirming the transmission of HEV by transfusion. The patient remained negative for anti-HEV antibodies for the follow-up period of six months, probably due to immune suppression by lymphoma and chemotherapy. CONCLUSION We report here an unusual case of long-term HEV infection in a patient with T-cell lymphoma. Persistent infection with HEV was probably due to the absence of anti-HEV antibodies, which was caused by lymphoma and chemotherapy.
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Affiliation(s)
- Akinori Tamura
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Nihon University School of Medicine, Itabashi-ku, Tokyo, Japan
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36
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Koike M, Takahashi K, Mishiro S, Matsui A, Inao M, Nagoshi S, Ohno A, Mochida S, Fujiwara K. Full-Length Sequences of Two Hepatitis E Virus Isolates Representing an Eastern China-Indigenous Subgroup of Genotype 4. Intervirology 2007; 50:181-9. [PMID: 17259737 DOI: 10.1159/000098961] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2006] [Accepted: 09/27/2006] [Indexed: 11/19/2022] Open
Abstract
Although the majority of hepatitis E virus (HEV) infections in Japan are 'domestic' due to the presence of indigenous strains, there are still 'imported' cases as well. Among 83 patients with non-A, non-B and non-C acute liver diseases admitted to Saitama Medical University Hospital, 7 (8.4%) were positive for serum HEV-RNA, of whom 2 had a recent history of traveling to China, one to Xian and another to Shanghai. We determined the full-genome sequences of HEV from these 2 patients (isolate names are JKO-ChiSai98c and JYI-ChiSai01c, genotype 4 in both) for phylogenetic analyses. Initially, when compared only to the 13 full-genome sequences of genotype 4 so far reported, our 2 isolates were thought to be novel strains because they showed a significant genetic difference from the sequences known to date. However, when we included a set of short sequences (150 nt) recently reported from China in the comparison, we found that our 2 isolates represent a subgroup of genotype 4, which seems to be restricted to eastern China. In conclusion, the 2 HEV isolates reported here could serve as full-genome prototypes for an eastern China-indigenous subgroup of the genotype 4 HEV.
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Affiliation(s)
- Masami Koike
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Saitama Medical University, Saitama, Japan
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37
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Som A. A new approach for estimating the efficiencies of the nucleotide substitution models. Theory Biosci 2007; 125:133-45. [PMID: 17412292 DOI: 10.1016/j.thbio.2006.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2006] [Revised: 11/16/2006] [Accepted: 11/21/2006] [Indexed: 11/20/2022]
Abstract
In this article, a new approach is presented for estimating the efficiencies of the nucleotide substitution models in a four-taxon case and then this approach is used to estimate the relative efficiencies of six substitution models under a wide variety of conditions. In this approach, efficiencies of the models are estimated by using a simple probability distribution theory. To assess the accuracy of the new approach, efficiencies of the models are also estimated by using the direct estimation method. Simulation results from the direct estimation method confirmed that the new approach is highly accurate. The success of the new approach opens a unique opportunity to develop analytical methods for estimating the relative efficiencies of the substitution models in a straightforward way.
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Affiliation(s)
- Anup Som
- Center for Evolutionary Functional Genomics, The Biodesign Institute, Arizona State University, Tempe, AZ 85287-5301, USA.
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38
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Sánchez LV, Tanaka Y, Maldonado M, Mizokami M, Panduro A. Difference of hepatitis B virus genotype distribution in two groups of mexican patients with different risk factors. High prevalence of genotype H and G. Intervirology 2006; 50:9-15. [PMID: 17164552 DOI: 10.1159/000096307] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2005] [Accepted: 10/26/2005] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Hepatitis B virus (HBV) has been classified in eight genotypes, from A to H (HBV/A to HBV/H). HBV genotypes were determined in two groups with different risk factors. METHODS Group I consisted of 42 patients with chronic and acute hepatitis and group II with 25 men who have sex with men (MSM). HBV genotypes were determined by DNA sequencing of the S-gene. RESULTS Both groups differed with respect to genotype distribution (p < 0.001). In group I, there were 31 (74%), 9 (21%) and 2 patients (5%) with HBV/H, HBV/D and HBV/A; respectively. In group II, HBV/H, HBV/A, and HBV/G were found in 13 (52%), 8 (32%) and 4 (16%) cases, respectively. By using an HBV/G-specific PCR, 3 more cases of HBV/G were identified in group II, rising to a total 28%. All HBV/G strains were present in coinfection with other HBV genotypes, 86% with HBV/H, and 14% with HBV/A. CONCLUSIONS HBV/H predominated in both groups. A high frequency of HBV/G was found in MSM, which was always coinfected with HBV/H or HBV/A. Significant differences in HBV genotype distribution were also found, since HBV/D was present only in patients with liver disease, whereas HBV/G was present only in MSM.
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Affiliation(s)
- L V Sánchez
- Department of Molecular Biology in Medicine, Civil Hospital of Guadalajara, Health Sciences Center, University of Guadalajara, Guadalajara, Mexico
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39
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Banerjee A, Kurbanov F, Datta S, Chandra PK, Tanaka Y, Mizokami M, Chakravarty R. Phylogenetic relatedness and genetic diversity of hepatitis B virus isolates in Eastern India. J Med Virol 2006; 78:1164-1174. [PMID: 16847957 DOI: 10.1002/jmv.20677] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Hepatitis B virus (HBV) has been classified into eight genotypes, and several subgenotypes, distinctly distributed geographically. The genotypes A and D were previously reported to be predominant in India. Recent studies indicated evidence of circulation of genotype C in Eastern part of India. With the aim to confirm the phylogenetic relation and molecular genetic characteristics of the HBV circulating in Kolkata, the most populous city in Eastern India, 11 strains were isolated and the complete genome sequences were analyzed. Phylogenetic analysis determined; three genotype C (adr-serotype) isolates closely related with C1 (Cs) subgenotype references from South East Asia, and three genotype A (adw2-serotype) isolates, related to Asia-variant references of subgenotype A1 (Aa). Whereas, five genotype D (ayw2, ayw3 serotype) isolates were highly divergent; one was related to subgenotype D1, two to subgenotype D3, and the remaining two clustered with a single genotype D isolate from Japan belonging to an unclassified subgenotype. Together, these two isolates differed from HBV D1-D4 subgenotypes by nucleotide differences ranging from 5.0 to 5.49%, probably indicating a new subgenotype, which we designate as D5. All serotype ayw3 of genotype D isolates had specific amino acid substitution Threonine at codon 118 and Methionine at codon 125 in antigenic determinant of surface gene that has not been reported previously in isolates from other parts of India. In conclusion; using the complete genome analyses this study has confirmed circulation of the genotype C in Eastern part of India and demonstrated considerable genotypic heterogeneity of the Indian genotype D.
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Affiliation(s)
- Arup Banerjee
- ICMR Virus Unit, ID & BG Hospital Campus, Kolkata, West Bengal, India
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40
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Theoretical foundation to estimate the relative efficiencies of the Jukes-Cantor+gamma model and the Jukes-Cantor model in obtaining the correct phylogenetic tree. Gene 2006; 385:103-10. [PMID: 16979305 DOI: 10.1016/j.gene.2006.03.027] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2005] [Revised: 01/25/2006] [Accepted: 03/08/2006] [Indexed: 11/26/2022]
Abstract
This paper deals with the theoretical foundation to estimate the relative efficiency (probability of inferring the true tree) of different nucleotide substitution models. A novel theoretical approach has been developed to estimate the relative efficiency of nucleotide substitution models based on the neighbor-relation method. The theory was developed directly by using the four-point condition. Initially theoretical formulas for the Jukes-Cantor+gamma (JC+Gamma) model and the Jukes-Cantor (JC) model were developed to estimate their relative efficiencies. Theoretical formulas were used on several model topologies for both models to obtain a true tree. Extensive simulations were performed on the same set of trees to test the strength of the theoretical approach. Simulation results demonstrated a good agreement with results obtained by the theoretical estimation. Overall the theoretical foundation for estimating model efficiencies is very accurate.
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41
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Hasegawa I, Tanaka Y, Kurbanov F, Yoshihara N, El-Gohary A, Lyamuya E, Matee M, Magessa P, Fujiwara K, Ozasa A, Sugauchi F, Orito E, Ueda R, Mizokami M. Molecular epidemiology of hepatitis B virus in the United Republic of Tanzania. J Med Virol 2006; 78:1035-1042. [PMID: 16789015 DOI: 10.1002/jmv.20659] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In the United Republic of Tanzania, 457 voluntary blood donors were enrolled in hepatitis B virus (HBV) serological screening; 4.8% (22/457) carried HBsAg, 13.6% (3/22) of whom were HBeAg-positive. The mean age among HBeAg-negative carriers was 31 years. HBV DNA was detectable in 81.8% (18/22), the mean level was 3.67 (+/-1.77) log copies/ml. Genotype A was determined in 90.9% (20/22) and 18/20 were classified into subgenotype Aa (Asia/Africa). The basal core promoter, precore and partial core nucleotide sequences were analyzed in the 18 strains; T1809/T1812 ("Kozak" sequence) and A/T1888 (encapsidation signal) variants were identified in 100% and 78%, respectively. The complete genome sequencing for one of the Tanzanian strains revealed no recombination. In conclusion, HBV seroprevalence is high among general population in Tanzania, and the HBV/Aa-infection is predominant. The indicated tendency to early HBeAg seroconversion and declining of the viral load should be confirmed further in case-control studies.
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Affiliation(s)
- Izumi Hasegawa
- Department of Clinical Molecular Informative Medicine, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
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42
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Sakamoto T, Tanaka Y, Orito E, Co J, Clavio J, Sugauchi F, Ito K, Ozasa A, Quino A, Ueda R, Sollano J, Mizokami M. Novel subtypes (subgenotypes) of hepatitis B virus genotypes B and C among chronic liver disease patients in the Philippines. J Gen Virol 2006; 87:1873-1882. [PMID: 16760389 DOI: 10.1099/vir.0.81714-0] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Several hepatitis B virus (HBV) subtypes (subgenotypes), HBV/Aa (A1 : Asia/Africa), Ae (A2 : Europe), Bj (B1 : Japan) and Ba (B2 : Asia), have been reported with respect to clinical differences between patients infected with these subtypes (subgenotypes). HBV genotype distribution among patients with chronic liver diseases was investigated in the Philippines, where such studies have not been carried out previously. One hundred sera were obtained from such patients, consisting of 32 chronic hepatitis (CH), 37 cirrhosis and 31 hepatocellular carcinoma (HCC) patients. Nine complete genomes and 100 core promoter/precore genes of HBV were sequenced directly. Phylogenetic analyses revealed 51 HBV/A (Aa/A1), 22 HBV/B and 27 HBV/C strains. Interestingly, most HBV/C strains in the Philippines formed a specific cluster distinct from previous HBV/C strains (C1-4), indicating a novel subtype (subgenotype), HBV/C5. Moreover, most HBV/B strains fell within the specific cluster of the HBV/B subtype (subgenotype) B5, with viral characteristics of HBV/Ba (B2) carrying a recombination with HBV/C over the precore and core genes. Of the three genotypes, HBV/B and HBV/C were significantly more prevalent than HBV/A in cirrhosis and HCC patients (P<0.02). The prevalence of the core promoter mutations T1762/A1764 was higher in HCC patients with HBV/B and HBV/C. Multivariate analysis indicated that age [odds ratio (OR) 3.43; 95 % confidence interval (CI) 1.04-11.36; P=0.044] and the core promoter mutation (OR 14.08; 95% CI 3.62-4.74; P<0.001) were significant factors for HCC development. In conclusion, novel HBV subtypes (subgenotypes) C5 and B5 are prevalent in the Philippines, as well as HBV/Aa (A1).
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Affiliation(s)
- Tomoyuki Sakamoto
- Department of Internal Medicine and Molecular Science, Nagoya City University Graduate School of Medical Sciences, Kawasumi, Mizuho, Nagoya 467-8601, Japan
- Department of Clinical Molecular Informative Medicine, Nagoya City University Graduate School of Medical Sciences, Kawasumi, Mizuho, Nagoya 467-8601, Japan
| | - Yasuhito Tanaka
- Department of Clinical Molecular Informative Medicine, Nagoya City University Graduate School of Medical Sciences, Kawasumi, Mizuho, Nagoya 467-8601, Japan
| | - Etsuro Orito
- Department of Internal Medicine and Molecular Science, Nagoya City University Graduate School of Medical Sciences, Kawasumi, Mizuho, Nagoya 467-8601, Japan
| | - Jonard Co
- Section of Gastroenterology, University of Santo Tomas, Manila, Philippines
| | - Joseph Clavio
- Section of Gastroenterology, University of Santo Tomas, Manila, Philippines
| | - Fuminaka Sugauchi
- Department of Internal Medicine and Molecular Science, Nagoya City University Graduate School of Medical Sciences, Kawasumi, Mizuho, Nagoya 467-8601, Japan
| | - Kiyoaki Ito
- Department of Internal Medicine and Molecular Science, Nagoya City University Graduate School of Medical Sciences, Kawasumi, Mizuho, Nagoya 467-8601, Japan
| | - Atsushi Ozasa
- Department of Internal Medicine and Molecular Science, Nagoya City University Graduate School of Medical Sciences, Kawasumi, Mizuho, Nagoya 467-8601, Japan
| | - Alvin Quino
- Section of Gastroenterology, University of Santo Tomas, Manila, Philippines
| | - Ryuzo Ueda
- Department of Internal Medicine and Molecular Science, Nagoya City University Graduate School of Medical Sciences, Kawasumi, Mizuho, Nagoya 467-8601, Japan
| | - Jose Sollano
- Section of Gastroenterology, University of Santo Tomas, Manila, Philippines
| | - Masashi Mizokami
- Department of Clinical Molecular Informative Medicine, Nagoya City University Graduate School of Medical Sciences, Kawasumi, Mizuho, Nagoya 467-8601, Japan
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43
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Liu CH, Chen BF, Chen SC, Lai MY, Kao JH, Chen DS. Selective transmission of hepatitis C virus quasi species through a needlestick accident in acute resolving hepatitis. Clin Infect Dis 2006; 42:1254-1259. [PMID: 16586384 DOI: 10.1086/503040] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2005] [Accepted: 12/23/2005] [Indexed: 11/03/2022] Open
Abstract
BACKGROUND Little is known about the transmission of variant hepatitis C virus (HCV) genome through needlestick injuries. METHODS To demonstrate how HCV quasi species are transmitted and adapt to the new host in acute resolving infection, we analyzed the nucleotide and deduced amino acid sequences of the hypervariable region 1 (HVR-1) in the E2 domain of HCV in both the source of the virus ("donor") and the person who received the virus through a needlestick accident ("recipient"). In addition, we also performed phylogenetic analysis of HCV quasi species in these patients to document the viral transmission. RESULTS We obtained a total of 33 clones at different time points by using polymerase chain reaction amplification and cloning and sequencing of HVR-1. A predominant HVR-1 variant (in 4 of 10 isolates) in the donor was not present in the recipient 6 and 14 weeks after the accident. In contrast, a minor variant (in 1 of 10 isolates) in the donor became the predominant strain in the recipient 6 weeks (in 10 of 12 isolates) and 14 weeks (in 6 of 11 isolates) after the accident. Additional phylogenetic analysis showed high homology of nucleotide sequences between isolates obtained from the donor and isolates obtained from the recipient. In addition, the variants in the recipient's virus showed substantial genetic preservation in the course of acute resolving hepatitis. CONCLUSIONS These data suggested that a minor HCV variant from a donor was transmitted to the recipient through a needlestick injury and that it prevailed as the dominant species. The preserved genetic homogeneity of the transmitted viral variants in patients with acute HCV infection may account for their clinical outcomes of resolving hepatitis.
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Affiliation(s)
- Chen-Hua Liu
- Department of Internal Medicine, National Taiwan University Hospital, Yun-Lin Branch, Taiwan
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Bohl E, Lancaster P. Implementation of a Markov model for phylogenetic trees. J Theor Biol 2006; 239:324-33. [PMID: 16171829 DOI: 10.1016/j.jtbi.2005.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2004] [Revised: 07/04/2005] [Accepted: 08/01/2005] [Indexed: 11/27/2022]
Abstract
A recently developed mathematical model for the analysis of phylogenetic trees is applied to comparative data for 48 species. The model represents a return to fundamentals and makes no hypothesis with respect to the reversibility of the process. The species have been analysed in all subsets of three, and a measure of reliability of the results is provided. The numerical results of the computations on 17,296 triples of species are made available on the Internet. These results are discussed and the development of reliable tree structures for several species is illustrated. It is shown that, indeed, the Markov model is capable of considerably more interesting predictions than has been recognized to date.
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Affiliation(s)
- Erich Bohl
- Fakultät für Mathematik, Universität Konstanz, Postfach D 194, 78457 Konstanz, Germany.
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45
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Shi X, Wang X, Li Z, Zhu Q, Tang W, Ge S, Luo J. Nucleotide substitution pattern in rice paralogues: implication for negative correlation between the synonymous substitution rate and codon usage bias. Gene 2006; 376:199-206. [PMID: 16644142 DOI: 10.1016/j.gene.2006.03.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2005] [Revised: 03/02/2006] [Accepted: 03/10/2006] [Indexed: 10/24/2022]
Abstract
Understanding the correlation between synonymous substitution rate and GC content is essential to decipher the gene evolution. However, it has been controversial on their relationship. We analyzed the GC content and synonymous substitution rate in 1092 paralogues produced by two large-scale duplication events in the rice genome. According to the GC content at the third codon sites (GC3), the paralogues were classified into GC3-rich and GC3-poor genes. By referring to their outgroup sequences, we inferred the last common ancestor of sister paralogues and, consequently, calculated the average synonymous substitution rate for two gene classes. The results suggest that average synonymous substitution rate is lower in GC3-rich genes than that in GC3-poor genes, indicating that the synonymous substitution rate is negatively correlated with GC content in the rice genome. Through characterizing the synonymous nucleotide substitution pattern, we found a strong synonymous nucleotide substitution frequency bias from AT to GC in GC3-rich genes. This indicates possible limitations of commonly used methods developed to estimate the synonymous substitution rate. Their estimates might produce misleading results on correlation between the synonymous substitution rate and GC content.
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Affiliation(s)
- Xiaoli Shi
- College of Life Sciences, National Laboratory of Plant Genetic Engineering and Protein Engineering, Center of Bioinformatics, Peking University, Beijing 100871, China
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46
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Revell LJ, Harmon LJ, Glor RE. Underparameterized model of sequence evolution leads to bias in the estimation of diversification rates from molecular phylogenies. Syst Biol 2006; 54:973-83. [PMID: 16385778 DOI: 10.1080/10635150500354647] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Affiliation(s)
- Liam J Revell
- Department of Biology, Campus Box 1229, Washington University, St. Louis, Missouri 63130, USA.
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47
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Kato H, Fujiwara K, Gish RG, Sakugawa H, Yoshizawa H, Sugauchi F, Orito E, Ueda R, Tanaka Y, Kato T, Miyakawa Y, Mizokami M. Classifying genotype F of hepatitis B virus into F1 and F2 subtypes. World J Gastroenterol 2005; 11:6295-6304. [PMID: 16419158 PMCID: PMC4320333 DOI: 10.3748/wjg.v11.i40.6295] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2004] [Revised: 12/21/2004] [Accepted: 12/23/2004] [Indexed: 02/06/2023] Open
Abstract
AIM To explore the propriety of providing hepatitis B virus (HBV) genotypes F and H with two distinct genotypes. METHODS Eleven HBV isolates of genotype F (HBV/F) were recovered from patients living in San Francisco, Japan, Panama, and Venezuela, and their full-length sequences were determined. Phylogenetic analysis was carried out among them along with HBV isolates previously reported. RESULTS Seven of them clustered with reported HBV/F isolates in the phylogenetic tree constructed on the entire genomic sequence. The remaining four flocked on another branch along with three HBV isolates formerly reported as genotype H. These seven HBV isolates, including the four in this study and the three reported, had a sequence divergence of 7.3-9.5% from the other HBV/F isolates, and differed by > 13.7% from HBV isolates of the other six genotypes (A-E and G). Based on a marked genomic divergence, falling just short of > 8% separating the seven genotypes, these seven HBV/F isolates were classified into F2 subtype and the former seven into F1 subtype provisionally. In a pairwise comparison of the S-gene sequences among the 7 HBV/F2 isolates and against 47 HBV/F1 isolates as well as 136 representing the other six genotypes (A-E and G), two clusters separated by distinct genetic distances emerged. CONCLUSION Based on these analyses, classifying HBV/F isolates into two subtypes (F1 and F2) would be more appropriate than providing them with two distinct genotypes (F and H).
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Affiliation(s)
- Hideaki Kato
- Department of Internal Medicine and Molecular Science, Nagoya City University Graduate School of Medical Sciences, Nagoya 467-8601, Japan
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Kurbanov F, Tanaka Y, Fujiwara K, Sugauchi F, Mbanya D, Zekeng L, Ndembi N, Ngansop C, Kaptue L, Miura T, Ido E, Hayami M, Ichimura H, Mizokami M. A new subtype (subgenotype) Ac (A3) of hepatitis B virus and recombination between genotypes A and E in Cameroon. J Gen Virol 2005; 86:2047-2056. [PMID: 15958684 DOI: 10.1099/vir.0.80922-0] [Citation(s) in RCA: 136] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Blood samples (n=544) from two different populations (Pygmies and Bantus) in Cameroon, West Africa, were analysed. Serological tests indicated that the anti-hepatitis C virus (HCV) prevalence in Bantus (20.3 %) was higher than that in Pygmies (2.3 %, P<0.0001), whereas the distribution of hepatitis B virus (HBV) serological markers was equally high in both populations: in total, 9.4, 17.3 and 86.8 % for HBsAg, anti-HBs and anti-HBc, respectively. HBV genotype A (HBV/A) and HBV/E were predominant (43.5 % each) in both populations, and HBV/D was found in a minority (13 %). The preS/S region was sequenced in nine cases (five HBV/A and four HBV/E) and the complete genome in six cases (four HBV/A and two HBV/E). Subsequent phylogenetic analysis revealed that the HBV/A strains were distinct from the subtypes (subgenotypes) described previously, Ae (A2) and Aa (A1), and in the preS/S region they clustered with previously reported sequences from Cameroon. Based on the nucleotide difference from Aa (A1) and Ae (A2), more than 4 % in the complete genome, the Cameroonian strains were suggested to represent a new subtype (subgenotype), designated HBV/Ac (A3). A high (3.9 %) nucleotide divergence in HBV/Ac (A3) strains suggested that the subtype (subgenotype) has a long natural history in the population of Cameroon. One of the HBV/Ac (A3) strains was found to be a recombinant with an HBV/E-specific sequence in the polymerase reverse transcriptase domain. Further cohort studies will be required to assess detailed epidemiological, virological and clinical characteristics of HBV/Ac (A3), as well as its recombinant form.
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Affiliation(s)
- Fuat Kurbanov
- Department of Clinical Molecular Informative Medicine, Nagoya City University Graduate School of Medical Sciences, Kawasumi, Mizuho, Nagoya 467-8601, Japan
| | - Yasuhito Tanaka
- Department of Clinical Molecular Informative Medicine, Nagoya City University Graduate School of Medical Sciences, Kawasumi, Mizuho, Nagoya 467-8601, Japan
| | - Kei Fujiwara
- Department of Internal Medicine and Molecular Science, Nagoya City University Graduate School of Medical Sciences, Kawasumi, Mizuho, Nagoya 467-8601, Japan
| | - Fuminaka Sugauchi
- Department of Internal Medicine and Molecular Science, Nagoya City University Graduate School of Medical Sciences, Kawasumi, Mizuho, Nagoya 467-8601, Japan
| | - Dora Mbanya
- Department of Hematology, Faculty of Medicine and Biomedical Sciences, University of Yaounde, Yaounde BP1937, Cameroon
| | - Leopold Zekeng
- Department of Hematology, Faculty of Medicine and Biomedical Sciences, University of Yaounde, Yaounde BP1937, Cameroon
| | - Nicaise Ndembi
- Department of Hematology, Faculty of Medicine and Biomedical Sciences, University of Yaounde, Yaounde BP1937, Cameroon
| | - Charlotte Ngansop
- Department of Hematology, Faculty of Medicine and Biomedical Sciences, University of Yaounde, Yaounde BP1937, Cameroon
| | - Lazare Kaptue
- Department of Hematology, Faculty of Medicine and Biomedical Sciences, University of Yaounde, Yaounde BP1937, Cameroon
| | - Tomoyuki Miura
- Laboratory of Primate Mode, Institute for Virus Research, Kyoto University, Kyoto 606-8507, Japan
| | - Eiji Ido
- Laboratory of Viral Pathogenesis, Institute for Virus Research, Kyoto University, Kyoto 606-8507, Japan
| | - Masanori Hayami
- Laboratory of Viral Pathogenesis, Institute for Virus Research, Kyoto University, Kyoto 606-8507, Japan
| | - Hiroshi Ichimura
- Department of Viral Infection and International Health, Graduate School of Medical Science, Kanazawa University, Kanazawa, Ishikawa 920-8640, Japan
| | - Masashi Mizokami
- Department of Clinical Molecular Informative Medicine, Nagoya City University Graduate School of Medical Sciences, Kawasumi, Mizuho, Nagoya 467-8601, Japan
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Kobayashi M, Suzuki F, Akuta N, Tsubota A, Ikeda K, Arase Y, Suzuki Y, Saitoh S, Kobayashi M, Hosaka T, Someya T, Matsuda M, Sato J, Miyakawa Y, Kumada H. Virological differences between patients infected with subtypes Ba and Bj of hepatitis B virus genotype B. J Gastroenterol Hepatol 2005; 20:570-6. [PMID: 15836705 DOI: 10.1111/j.1440-1746.2005.03798.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
BACKGROUND Hepatitis B virus (HBV) genotype B is classified into subtype Ba with the recombination with genotype C in the precore region plus core gene and subtype Bj without recombination. Virological and clinical differences between infections with subtypes Ba and Bj, however, are yet to be determined. METHODS During 1976 through 2001, 224 patients visited Toranomon Hospital in Tokyo, Japan who were infected with HBV genotype B. Subtypes of genotype B were determined by sequencing HBV-DNA recovered from sera for detecting recombination with genotype C. RESULTS Subtype Ba was detected in 53 patients (24%) and Bj in 167 (75%); subtypes were not able to be determined in the remaining four (1%). The only virological difference was that detection of hepatitis B e antigen at the presentation was more frequent in the patients infected with subtype Ba than those with Bj (63% vs 33%, P = 0.016). There were no differences in the distribution of liver disease of various forms between the patients infected with subtypes Ba and Bj at presentation. No differences were noted, either, in the development of liver cirrhosis or hepatocellular carcinoma, or the loss of hepatitis B surface antigen from serum, between the patients infected with subtypes Ba and Bj during follow up of up to 26 years. CONCLUSIONS Although there were some virological differences between the patients infected with subtypes Ba and Bj of HBV genotype B, they do not seem to influence the long-term clinical outcome.
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Affiliation(s)
- Mariko Kobayashi
- Research Institute for Hepatology, Toranomon Hospital, Tokyo, Japan.
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Mukaide M, Tanaka Y, Kakuda H, Fujiwara K, Kurbanov F, Orito E, Yoshioka K, Fujise K, Harada S, Kozaki T, Takemura K, Hikiji K, Mizokami M. New combination test for hepatitis C virus genotype and viral load determination using Amplicor GT HCV MONITOR test v2.0. World J Gastroenterol 2005; 11:469-475. [PMID: 15641128 PMCID: PMC4250793 DOI: 10.3748/wjg.v11.i4.469] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2004] [Revised: 03/31/2004] [Accepted: 06/25/2004] [Indexed: 02/06/2023] Open
Abstract
AIM To develop a new sensitive and inexpensive hepatitis C virus (HCV) combination test (HCV Guideline test) that enables the determination of HCV genotypes 1, 2 and 3, and simultaneous determination of HCV viral load using commercial Amplicor GT HCV MONITOR test v2.0 (microwell version). METHODS The HCV Guideline test used the PCR product generated in commercial Amplicor GT HCV Monitor test v2.0 for viral load measurement using microwell plate version of Amplicor HCV Monitor and also captured on separate plates containing capture probes and competitive oligonucleotide probes specific for HCV genotypes 1, 2 and 3, The HCV genotype was subsequently determined using the biotin-labeled PCR product and five biotin-labeled HCV-specific probes. RESULTS The sensitivity of the HCV Guideline test was 0.5 KIU/mL. Specificity of the HCV Guideline test was confirmed by direct sequencing of HCV core region and molecular evolutionary analyses based on a panel of 31 samples. The comparison of the HCV Guideline test and an in-house HCV core genotyping assay using 252 samples from chronic hepatitis C patients indicated concordant results for 97.2% of samples (59.5% genotype 1, 33.7% genotype 2, 6.0% genotype 3, and 0.8% mixed genotypes). Similarly, the HCV Guideline test showed concordance with a serological test, and the serological test failed to assign any serotype in 12.7% of the samples, indicating a better sensitivity of the HCV Guideline test. CONCLUSION Clinically, both viral load and genotypes (1, 2 and 3) have been found to be major predictors of antiviral therapy outcome regarding chronic hepatitis C based on guidelines and they are, in normal circumstances, performed as separate stand-alone assays. The HCV Guideline test is a useful method for screening large cohorts in a routine clinical setting for determining the treatment regimen and for predicting the outcome of antiviral therapy of chronic hepatitis C.
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Affiliation(s)
- Motokazu Mukaide
- Department of Clinical Molecular Informative Medicine, Nagoya City University Graduate School of Medical Science, Kawasumi, Mizuho, Nagoya 467-8601, Japan
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