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Smith MR, Trofimova M, Weber A, Duport Y, Kühnert D, von Kleist M. Rapid incidence estimation from SARS-CoV-2 genomes reveals decreased case detection in Europe during summer 2020. Nat Commun 2021; 12:6009. [PMID: 34650062 PMCID: PMC8517019 DOI: 10.1038/s41467-021-26267-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 09/24/2021] [Indexed: 12/24/2022] Open
Abstract
By October 2021, 230 million SARS-CoV-2 diagnoses have been reported. Yet, a considerable proportion of cases remains undetected. Here, we propose GInPipe, a method that rapidly reconstructs SARS-CoV-2 incidence profiles solely from publicly available, time-stamped viral genomes. We validate GInPipe against simulated outbreaks and elaborate phylodynamic analyses. Using available sequence data, we reconstruct incidence histories for Denmark, Scotland, Switzerland, and Victoria (Australia) and demonstrate, how to use the method to investigate the effects of changing testing policies on case ascertainment. Specifically, we find that under-reporting was highest during summer 2020 in Europe, coinciding with more liberal testing policies at times of low testing capacities. Due to the increased use of real-time sequencing, it is envisaged that GInPipe can complement established surveillance tools to monitor the SARS-CoV-2 pandemic. In post-pandemic times, when diagnostic efforts are decreasing, GInPipe may facilitate the detection of hidden infection dynamics.
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Affiliation(s)
- Maureen Rebecca Smith
- Systems Medicine of Infectious Disease (P5), Robert Koch Institute, Berlin, Germany.
- Bioinformatics (MF1), Robert Koch Institute, Berlin, Germany.
| | - Maria Trofimova
- Systems Medicine of Infectious Disease (P5), Robert Koch Institute, Berlin, Germany
- Bioinformatics (MF1), Robert Koch Institute, Berlin, Germany
| | - Ariane Weber
- Transmission, Infection, Diversification and Evolution Group, Max-Planck Institute for the Science of Human History, Jena, Germany
| | - Yannick Duport
- Systems Medicine of Infectious Disease (P5), Robert Koch Institute, Berlin, Germany
- Bioinformatics (MF1), Robert Koch Institute, Berlin, Germany
| | - Denise Kühnert
- Transmission, Infection, Diversification and Evolution Group, Max-Planck Institute for the Science of Human History, Jena, Germany
- German COVID Omics Initiative (deCOI), Bonn, Germany
| | - Max von Kleist
- Systems Medicine of Infectious Disease (P5), Robert Koch Institute, Berlin, Germany.
- Bioinformatics (MF1), Robert Koch Institute, Berlin, Germany.
- German COVID Omics Initiative (deCOI), Bonn, Germany.
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2
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Cremer J, Hofstraat SHI, van Heiningen F, Veldhuijzen IK, van Benthem BHB, Benschop KSM. Genetic variation of hepatitis B surface antigen among acute and chronic hepatitis B virus infections in The Netherlands. J Med Virol 2018; 90:1576-1585. [PMID: 29797607 PMCID: PMC6120544 DOI: 10.1002/jmv.25232] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 05/14/2018] [Indexed: 12/18/2022]
Abstract
Genetic variation within hepatitis B surface antigen (HBsAg), in particular within the major hydrophobic region (MHR), is related to immune/vaccine and test failures and can have a significant impact on the vaccination and diagnosis of acute infection. This study shows, for the first time, variation among acute cases and compares the amino acid variation within the HBsAg between acute and chronic infections. We analyzed the virus isolated from 1231 acute and 585 chronic cases reported to an anonymized public health surveillance database between 2004 and 2014 in The Netherlands. HBsAg analysis revealed the circulation of 6 genotypes (Gt); GtA was the dominant genotype followed by GtD among both acute (68.2% and 17.4%, respectively) and chronic (34.9% and 34.2%, respectively) cases. Variation was the highest among chronic strains compared to that among acute strains. Both acute and chronic GtD showed the highest variation compared to that of other genotypes (P < .01). Substitutions within the MHR were found in 8.5% of the acute strains and 18.6% of the chronic strains. Specific MHR substitutions described to have an impact on vaccine/immune escape and/or HBsAg test failure were found among 4.1% of the acute strains and 7.0% of the chronic strains. In conclusion, we show a high variation of HBsAg among acute and chronic hepatitis B virus–infected cases in The Netherlands, in particular among those infected with GtD, and compare, for the first time, variation in frequencies between acute and chronic cases. Additional studies on the impact of these variations on vaccination and test failure need to be conducted, as well as whether HBsAg false–negative variants have been missed.
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Affiliation(s)
- Jeroen Cremer
- Laboratory for Infectious Diseases and Screening, Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Sanne H I Hofstraat
- Laboratory for Infectious Diseases and Screening, Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Francoise van Heiningen
- Laboratory for Infectious Diseases and Screening, Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Irene K Veldhuijzen
- Laboratory for Infectious Diseases and Screening, Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Birgit H B van Benthem
- Laboratory for Infectious Diseases and Screening, Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Kimberley S M Benschop
- Laboratory for Infectious Diseases and Screening, Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
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3
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Rietbergen C, Debray TPA, Klugkist I, Janssen KJM, Moons KGM. Reporting of Bayesian analysis in epidemiologic research should become more transparent. J Clin Epidemiol 2017; 86:51-58.e2. [PMID: 28428139 DOI: 10.1016/j.jclinepi.2017.04.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Revised: 02/13/2017] [Accepted: 04/07/2017] [Indexed: 12/12/2022]
Abstract
OBJECTIVES The objective of this systematic review is to investigate the use of Bayesian data analysis in epidemiology in the past decade and particularly to evaluate the quality of research papers reporting the results of these analyses. STUDY DESIGN AND SETTING Complete volumes of five major epidemiological journals in the period 2005-2015 were searched via PubMed. In addition, we performed an extensive within-manuscript search using a specialized Java application. Details of reporting on Bayesian statistics were examined in the original research papers with primary Bayesian data analyses. RESULTS The number of studies in which Bayesian techniques were used for primary data analysis remains constant over the years. Though many authors presented thorough descriptions of the analyses they performed and the results they obtained, several reports presented incomplete method sections and even some incomplete result sections. Especially, information on the process of prior elicitation, specification, and evaluation was often lacking. CONCLUSION Though available guidance papers concerned with reporting of Bayesian analyses emphasize the importance of transparent prior specification, the results obtained in this systematic review show that these guidance papers are often not used. Additional efforts should be made to increase the awareness of the existence and importance of these checklists to overcome the controversy with respect to the use of Bayesian techniques. The reporting quality in epidemiological literature could be improved by updating existing guidelines on the reporting of frequentist analyses to address issues that are important for Bayesian data analyses.
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Affiliation(s)
- Charlotte Rietbergen
- Department of Methodology and Statistics, Utrecht University, Padualaan 14, Utrecht 3584 CH, The Netherlands.
| | - Thomas P A Debray
- Department of Epidemiology, Julius Center for Health Sciences and Primary Care, UMC Utrecht, Huispost Str. 6.131, PO Box 85500, Utrecht 3508 GA, The Netherlands; Cochrane Netherlands, Julius Center for Health Sciences and Primary Care, UMC Utrecht, Huispost Str. 6.131, PO Box 85500, Utrecht 3508 GA, The Netherlands
| | - Irene Klugkist
- Department of Methodology and Statistics, Utrecht University, Padualaan 14, Utrecht 3584 CH, The Netherlands; Section of Research Methodology, Measurement and Data Analysis, Department of Behavioural, Management and Social Sciences, Twente University, P.O. Box 217, Enschede 7500 AE, The Netherlands
| | - Kristel J M Janssen
- Department of Epidemiology, Julius Center for Health Sciences and Primary Care, UMC Utrecht, Huispost Str. 6.131, PO Box 85500, Utrecht 3508 GA, The Netherlands
| | - Karel G M Moons
- Department of Epidemiology, Julius Center for Health Sciences and Primary Care, UMC Utrecht, Huispost Str. 6.131, PO Box 85500, Utrecht 3508 GA, The Netherlands
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Streck AF, Canal CW, Truyen U. Molecular epidemiology and evolution of porcine parvoviruses. INFECTION GENETICS AND EVOLUTION 2015; 36:300-306. [DOI: 10.1016/j.meegid.2015.10.007] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Revised: 10/03/2015] [Accepted: 10/06/2015] [Indexed: 11/16/2022]
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Grad YH, Lipsitch M. Epidemiologic data and pathogen genome sequences: a powerful synergy for public health. Genome Biol 2014; 15:538. [PMID: 25418119 PMCID: PMC4282151 DOI: 10.1186/s13059-014-0538-4] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Epidemiologists aim to inform the design of public health interventions with evidence on the evolution, emergence and spread of infectious diseases. Sequencing of pathogen genomes, together with date, location, clinical manifestation and other relevant data about sample origins, can contribute to describing nearly every aspect of transmission dynamics, including local transmission and global spread. The analyses of these data have implications for all levels of clinical and public health practice, from institutional infection control to policies for surveillance, prevention and treatment. This review highlights the range of epidemiological questions that can be addressed from the combination of genome sequence and traditional ‘line lists’ (tables of epidemiological data where each line includes demographic and clinical features of infected individuals). We identify opportunities for these data to inform interventions that reduce disease incidence and prevalence. By considering current limitations of, and challenges to, interpreting these data, we aim to outline a research agenda to accelerate the genomics-driven transformation in public health microbiology.
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Zehender G, Ebranati E, Gabanelli E, Sorrentino C, Lo Presti A, Tanzi E, Ciccozzi M, Galli M. Enigmatic origin of hepatitis B virus: An ancient travelling companion or a recent encounter? World J Gastroenterol 2014; 20:7622-7634. [PMID: 24976700 PMCID: PMC4069291 DOI: 10.3748/wjg.v20.i24.7622] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 01/08/2014] [Accepted: 03/13/2014] [Indexed: 02/06/2023] Open
Abstract
Hepatitis B virus (HBV) is the leading cause of liver disease and infects an estimated 240 million people worldwide. It is characterised by a high degree of genetic heterogeneity because of the use of a reverse transcriptase during viral replication. The ten genotypes (A-J) that have been described so far further segregate into a number of subgenotypes which have distinct ethno-geographic distribution. Genotypes A and D are ubiquitous and the most prevalent genotypes in Europe (mainly represented by subgenotypes D1-3 and A2); genotypes B and C are restricted to eastern Asia and Oceania; genotype E to central and western Africa; and genotypes H and F (classified into 4 subgenotypes) to Latin America and Alaska. This review summarises the data obtained by studying the global phylodynamics and phylogeography of HBV genotypes, particularly those concerning the origin and dispersion histories of genotypes A, D, E and F and their subgenotypes. The lack of any consensus concerning the HBV substitution rate and the conflicting data obtained using different calibration approaches make the time of origin and divergence of the various genotypes and subgenotypes largely uncertain. It is hypothesised that HBV evolutionary rates are time dependent, and that the changes depend on the main transmission routes of the genotypes and the dynamics of the infected populations.
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Streck AF, Homeier T, Foerster T, Truyen U. Population dynamics and in vitro antibody pressure of porcine parvovirus indicate a decrease in variability. J Gen Virol 2013; 94:2050-2055. [DOI: 10.1099/vir.0.052555-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
To estimate the impact of porcine parvovirus (PPV) vaccines on the emergence of new phenotypes, the population dynamic history of the virus was calculated using the Bayesian Markov chain Monte Carlo method with a Bayesian skyline coalescent model. Additionally, an in vitro model was performed with consecutive passages of the ‘Challenge’ strain (a virulent field strain) and NADL2 strain (a vaccine strain) in a PK-15 cell line supplemented with polyclonal antibodies raised against the vaccine strain. A decrease in genetic diversity was observed in the presence of antibodies in vitro or after vaccination (as estimated by the in silico model). We hypothesized that the antibodies induced a selective pressure that may reduce the incidence of neutral selection, which should play a major role in the emergence of new mutations. In this scenario, vaccine failures and non-vaccinated populations (e.g. wild boars) may have an important impact in the emergence of new phenotypes.
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Affiliation(s)
- André Felipe Streck
- CAPES Foundation, Ministry of Education of Brazil, Setor Bancário Norte, Quadra 2, Bloco L, Lote 06, 70040-020, Brasília, Brazil
- Institute of Animal Hygiene and Veterinary Public Health, Faculty of Veterinary Medicine, University of Leipzig, An den Tierkliniken 1, 04103, Leipzig, Germany
| | - Timo Homeier
- Institute of Animal Hygiene and Veterinary Public Health, Faculty of Veterinary Medicine, University of Leipzig, An den Tierkliniken 1, 04103, Leipzig, Germany
| | - Tessa Foerster
- Institute of Animal Hygiene and Veterinary Public Health, Faculty of Veterinary Medicine, University of Leipzig, An den Tierkliniken 1, 04103, Leipzig, Germany
| | - Uwe Truyen
- Institute of Animal Hygiene and Veterinary Public Health, Faculty of Veterinary Medicine, University of Leipzig, An den Tierkliniken 1, 04103, Leipzig, Germany
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Hahné S, van Houdt R, Koedijk F, van Ballegooijen M, Cremer J, Bruisten S, Coutinho R, Boot H. Selective hepatitis B virus vaccination has reduced hepatitis B virus transmission in the Netherlands. PLoS One 2013; 8:e67866. [PMID: 23922651 PMCID: PMC3726692 DOI: 10.1371/journal.pone.0067866] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Accepted: 05/22/2013] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND & AIMS In the Netherlands, a selective hepatitis B virus (HBV) vaccination programme started in 2002 for men having sex with men, drug users, commercial sex workers and heterosexuals with frequent partner changes. We assessed the programme's effectiveness to guide policy on HBV prevention. METHODS We analysed reports of acute HBV infection in the Netherlands between 2004 and 2010 requesting serum from patients for HBV-genome S- and C-region sequencing. We used coalescence analyses to assess genetic diversity of nonimported genotype-A cases over time. RESULTS 1687 patients with acute HBV infection were reported between 2004 and 2010. The incidence of reported acute HBV infection decreased from 1.8 to 1.2 per 100,000 inhabitants, mostly due to a reduction in the number of cases in men who have sex with men. Men were overrepresented among cases with an unknown route of transmission, especially among genotype A2 cases mainly associated with transmission through male homosexual contact. The genetic diversity of nonimported genotype-A strains obtained from men who have sex with men decreased from 2006 onwards, suggesting HBV incidence in this group decreased. CONCLUSIONS The selective HBV-vaccination programme for behavioural high-risk groups very likely reduced the incidence of HBV infection in the Netherlands mainly by preventing HBV infections in men who have sex with men. A considerable proportion of cases in men who did not report risk behaviour was probably acquired through homosexual contact. Our findings support continuation of the programme, and adopting similar approaches in other countries where HBV transmission is focused in high-risk adults.
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Affiliation(s)
- Susan Hahné
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands.
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Ypma RJF, Donker T, van Ballegooijen WM, Wallinga J. Finding evidence for local transmission of contagious disease in molecular epidemiological datasets. PLoS One 2013; 8:e69875. [PMID: 23922835 PMCID: PMC3724731 DOI: 10.1371/journal.pone.0069875] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Accepted: 06/14/2013] [Indexed: 11/19/2022] Open
Abstract
Surveillance systems of contagious diseases record information on cases to monitor incidence of disease and to evaluate effectiveness of interventions. These systems focus on a well-defined population; a key question is whether observed cases are infected through local transmission within the population or whether cases are the result of importation of infection into the population. Local spread of infection calls for different intervention measures than importation of infection. Besides standardized information on time of symptom onset and location of cases, pathogen genotyping or sequencing offers essential information to address this question. Here we introduce a method that takes full advantage of both the genetic and epidemiological data to distinguish local transmission from importation of infection, by comparing inter-case distances in temporal, spatial and genetic data. Cases that are part of a local transmission chain will have shorter distances between their geographical locations, shorter durations between their times of symptom onset and shorter genetic distances between their pathogen sequences as compared to cases that are due to importation. In contrast to generic clustering algorithms, the proposed method explicitly accounts for the fact that during local transmission of a contagious disease the cases are caused by other cases. No pathogen-specific assumptions are needed due to the use of ordinal distances, which allow for direct comparison between the disparate data types. Using simulations, we test the performance of the method in identifying local transmission of disease in large datasets, and assess how sensitivity and specificity change with varying size of local transmission chains and varying overall disease incidence.
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Affiliation(s)
- Rolf J F Ypma
- Center for Infectious Disease Control, National Institute of Public Health and the Environment, Bilthoven, The Netherlands.
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10
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Xiridou M, van Houdt R, Hahné S, Coutinho R, van Steenbergen J, Kretzschmar M. Hepatitis B vaccination of men who have sex with men in the Netherlands: should we vaccinate more men, younger men or high-risk men? Sex Transm Infect 2013; 89:666-71. [PMID: 23812794 DOI: 10.1136/sextrans-2012-050900] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
OBJECTIVES The selective vaccination programme against hepatitis B virus (HBV) was introduced in the Netherlands in 2002 targeting high-risk groups, including men who have sex with men (MSM). Despite the high average age of vaccination in MSM, the number of notifications of acute HBV recently declined. We investigate whether this can be attributed to the selective vaccination programme. We examine how vaccination strategies could be improved and the impact of universal infant vaccination introduced in 2011. METHODS We use a mathematical model for HBV transmission among MSM. The incidence of HBV was calculated from the model and from notification data of acute HBV. RESULTS A decline was observed in the incidence of HBV since 2006, as calculated from the model; this decline was smaller than that observed in data if all MSM were equally likely to be vaccinated. Assuming that high-risk MSM were more likely to be vaccinated than low-risk MSM resulted in a steeper decline in modelled incidence and better agreement with observed incidence. Vaccinating MSM at a younger age or doubling the vaccination rate would increase the impact of selective vaccination, but is less effective than vaccinating high-risk MSM. CONCLUSIONS Selective HBV vaccination of MSM in the Netherlands has had a substantial impact in reducing HBV incidence. The reduction suggests that vaccination rates among high-risk MSM were higher than those among low-risk MSM. Countries that have not yet reached 35-year cohorts with universal childhood vaccination should actively implement or continue selective high-risk MSM vaccination.
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Affiliation(s)
- Maria Xiridou
- Centre for Infectious Disease Control, National Institute of Public Health and the Environment, , Bilthoven, The Netherlands
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11
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Abstract
Viral phylodynamics is defined as the study of how epidemiological, immunological, and evolutionary processes act and potentially interact to shape viralphylogenies. Since the coining of the term in 2004, research on viral phylodynamics has focused on transmission dynamics in an effort to shed light on how these dynamics impact viral genetic variation. Transmission dynamics can be considered at the level of cells within an infected host, individual hosts within a population, or entire populations of hosts. Many viruses, especially RNA viruses, rapidly accumulate genetic variation because of short generation times and high mutation rates. Patterns of viral genetic variation are therefore heavily influenced by how quickly transmission occurs and by which entities transmit to one another. Patterns of viral genetic variation will also be affected by selection acting on viral phenotypes. Although viruses can differ with respect to many phenotypes, phylodynamic studies have to date tended to focus on a limited number of viral phenotypes. These include virulence phenotypes, phenotypes associated with viral transmissibility, cell or tissue tropism phenotypes, and antigenic phenotypes that can facilitate escape from host immunity. Due to the impact that transmission dynamics and selection can have on viral genetic variation, viral phylogenies can therefore be used to investigate important epidemiological, immunological, and evolutionary processes, such as epidemic spread[2], spatio-temporal dynamics including metapopulation dynamics[3], zoonotic transmission, tissue tropism[4], and antigenic drift[5]. The quantitative investigation of these processes through the consideration of viral phylogenies is the central aim of viral phylodynamics.
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Affiliation(s)
- Erik M Volz
- Department of Epidemiology, University of Michigan, Ann Arbor, Michigan, United States of America.
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12
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Tom JA, Sinsheimer JS, Suchard MA. Does history repeat itself? Wavelets and the phylodynamics of influenza A. Mol Biol Evol 2011; 29:1367-77. [PMID: 22160768 DOI: 10.1093/molbev/msr305] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Unprecedented global surveillance of viruses will result in massive sequence data sets that require new statistical methods. These data sets press the limits of Bayesian phylogenetics as the high-dimensional parameters that comprise a phylogenetic tree increase the already sizable computational burden of these techniques. This burden often results in partitioning the data set, for example, by gene, and inferring the evolutionary dynamics of each partition independently, a compromise that results in stratified analyses that depend only on data within a given partition. However, parameter estimates inferred from these stratified models are likely strongly correlated, considering they rely on data from a single data set. To overcome this shortfall, we exploit the existing Monte Carlo realizations from stratified Bayesian analyses to efficiently estimate a nonparametric hierarchical wavelet-based model and learn about the time-varying parameters of effective population size that reflect levels of genetic diversity across all partitions simultaneously. Our methods are applied to complete genome influenza A sequences that span 13 years. We find that broad peaks and trends, as opposed to seasonal spikes, in the effective population size history distinguish individual segments from the complete genome. We also address hypotheses regarding intersegment dynamics within a formal statistical framework that accounts for correlation between segment-specific parameters.
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Affiliation(s)
- Jennifer A Tom
- Department of Biostatistics, School of Public Health, University of California, Los Angeles, CA, USA.
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13
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Prevalence of hepatitis B virus infection in The Netherlands in 1996 and 2007. Epidemiol Infect 2011; 140:1469-80. [PMID: 22078095 DOI: 10.1017/s095026881100224x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
We aimed to assess differences in the prevalence of hepatitis B virus (HBV) infection in The Netherlands between 1996 and 2007, and to identify risk factors for HBV infection in 2007. Representative samples of the Dutch population in 1996 and 2007 were tested for antibodies to hepatitis B core antigen (anti-HBc), hepatitis B surface antigen (HBsAg) and HBV-DNA. In 2007, the weighted anti-HBc prevalence was 3·5% (95% CI 2·2-5·5) and the HBsAg prevalence was 0·2% (95% CI 0·1-0·4). In indigenous Dutch participants, the anti-HBc prevalence was lower in 2007 than in 1996 (P=0·06). First-generation migrants (FGMs) had a 13-fold greater risk of being HBsAg- and/or HBV-DNA-positive than indigenous Dutch participants. In indigenous Dutch participants, risk factors for anti-HBc positivity were older age and having received a blood product before 1990. In FGMs, being of Asian origin was a risk factor. In second-generation migrants, having a foreign-born partner and injecting drug use were risk factors. FGMs are the main target group for secondary HBV prevention in The Netherlands.
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14
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Abstract
Estimates of the coalescent effective population size N(e) can be poorly correlated with the true population size. The relationship between N(e) and the population size is sensitive to the way in which birth and death rates vary over time. The problem of inference is exacerbated when the mechanisms underlying population dynamics are complex and depend on many parameters. In instances where nonparametric estimators of N(e) such as the skyline struggle to reproduce the correct demographic history, model-based estimators that can draw on prior information about population size and growth rates may be more efficient. A coalescent model is developed for a large class of populations such that the demographic history is described by a deterministic nonlinear dynamical system of arbitrary dimension. This class of demographic model differs from those typically used in population genetics. Birth and death rates are not fixed, and no assumptions are made regarding the fraction of the population sampled. Furthermore, the population may be structured in such a way that gene copies reproduce both within and across demes. For this large class of models, it is shown how to derive the rate of coalescence, as well as the likelihood of a gene genealogy with heterochronous sampling and labeled taxa, and how to simulate a coalescent tree conditional on a complex demographic history. This theoretical framework encapsulates many of the models used by ecologists and epidemiologists and should facilitate the integration of population genetics with the study of mathematical population dynamics.
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15
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Houweling H, Wittevrongel CFW, Verweij M, Ruitenberg EJ. Public vaccination programmes against hepatitis B in The Netherlands: assessing whether a targeted or a universal approach is appropriate. Vaccine 2010; 28:7723-30. [PMID: 20933042 DOI: 10.1016/j.vaccine.2010.09.068] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2010] [Revised: 09/15/2010] [Accepted: 09/21/2010] [Indexed: 10/19/2022]
Abstract
To date, the policy to control hepatitis B in the Netherlands is to vaccinate specific risk groups, rather than all children. Low incidence of the disease has fueled debate whether such a targeted vaccination strategy or rather a universal strategy, as recommended by the World Health Organization, is appropriate. The standard framework for assessing whether a particular vaccination should be included in a public programme, as recently proposed by the Health Council of the Netherlands (HCN), was applied to the various options for hepatitis B vaccination. This framework includes seven selection criteria, grouped under five thematic headings: seriousness and extent of the disease burden, effectiveness and safety of the vaccination, acceptability of the vaccination, efficiency of the vaccination, and priority of the vaccination. From about 1990 the disease burden has stayed more or less the same over time and careful assessment has made it clear that the targeted approach has failed to reach a significant part of the risk groups. Models suggest that the public health benefits obtained through targeted programmes could be augmented considerably by universal vaccination. Based on the assessment that universal vaccination means better protection for high-risk groups as well as the whole population, the HCN calls for universal immunisation, even though hepatitis B to a large extent is limited to specific high-risk groups. Should the Netherlands adopt universal vaccination, several immunisation programmes targeted to high-risk groups will, however, remain of crucial importance for years to come.
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Affiliation(s)
- Hans Houweling
- Health Council of the Netherlands, The Hague, The Netherlands.
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16
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Frost SDW, Volz EM. Viral phylodynamics and the search for an 'effective number of infections'. Philos Trans R Soc Lond B Biol Sci 2010; 365:1879-90. [PMID: 20478883 PMCID: PMC2880113 DOI: 10.1098/rstb.2010.0060] [Citation(s) in RCA: 109] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Information on the dynamics of the effective population size over time can be obtained from the analysis of phylogenies, through the application of time-varying coalescent models. This approach has been used to study the dynamics of many different viruses, and has demonstrated a wide variety of patterns, which have been interpreted in the context of changes over time in the ‘effective number of infections’, a quantity proportional to the number of infected individuals. However, for infectious diseases, the rate of coalescence is driven primarily by new transmissions i.e. the incidence, and only indirectly by the number of infected individuals through sampling effects. Using commonly used epidemiological models, we show that the coalescence rate may indeed reflect the number of infected individuals during the initial phase of exponential growth when time is scaled by infectivity, but in general, a single change in time scale cannot be used to estimate the number of infected individuals. This has important implications when integrating phylogenetic data in the context of other epidemiological data.
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Affiliation(s)
- Simon D W Frost
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, Cambridgeshire CB3 0ES, UK.
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Halloran ME, Holmes EC. Invited commentary: Evaluating vaccination programs using genetic sequence data. Am J Epidemiol 2009; 170:1464-6; discussion 1467-8. [PMID: 19910381 DOI: 10.1093/aje/kwp366] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Genomic data will become an increasingly important component of epidemiologic studies in coming years. The authors of the accompanying Journal article, van Ballegooijen et al. (Am J Epidemiol. 2009;170(12):1455-1463), are to be commended for attempting to use the coalescent analysis of viral sequence data to evaluate a hepatitis B vaccination program. Coalescent theory attempts to link the phylogenetic history of populations with rates of population growth and decline. In particular, under certain assumptions, a reduction in genetic diversity can be interpreted as a reduction in disease incidence. However, the authors of this commentary contend that van Ballegooijen et al.'s interpretation of changes in viral genetic diversity as a measure of hepatitis B vaccine effectiveness has major limitations. Because of the potential use of these methods in future vaccination studies, the authors discuss the utility of these methods and the data requirements needed for them to be convincing. First, data sets should be large enough to provide sufficient epidemiologic-scale resolution. Second, data need to reflect sufficiently fine-grained temporal sampling. Third, other processes that can potentially influence genetic diversity and confuse demographic inferences should be considered.
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van Ballegooijen WM, van Houdt R, Bruisten SM, Boot HJ, Coutinho RA, Wallinga J. Van Ballegooijen et al. Respond to "Evaluating Vaccination Programs Using Genetic Sequence Data". Am J Epidemiol 2009. [DOI: 10.1093/aje/kwp368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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