Since the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) initiated a global pandemic resulting in an estimated 775 million infections with over 7 million deaths, it has become evident that COVID-19 is not solely a pulmonary disease. Emerging evidence has shown that, in a subset of patients, certain symptoms - including chest pain, stroke, anosmia, dysgeusia, diarrhea and abdominal pain - all indicate a role of vascular, neurological and gastrointestinal (GI) pathology in the disease process. Many of these disease processes persist long after the acute disease has been resolved, resulting in 'long COVID' or post-acute sequelae of COVID-19 (PASC). The molecular mechanisms underlying the acute and systemic conditions associated with COVID-19 remain incompletely defined. Appropriate animal models provide a method of understanding underlying disease mechanisms at the system level through the study of disease progression, tissue pathology, immune system response to the pathogen and behavioral responses. However, very few studies have addressed PASC and whether existing models hold promise for studying this challenging problem. Here, we review the current literature on cardiovascular, neurological and GI pathobiology caused by COVID-19 in patients, along with established animal models of the acute disease manifestations and their prospects for use in PASC studies. Our aim is to provide guidance for the selection of appropriate models in order to recapitulate certain aspects of the disease to enhance the translatability of mechanistic studies.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was originally described as a respiratory illness; however, it is now known that the infection can spread to the gastrointestinal tract, leading to shedding in feces potentially being a source of infection through wastewater. We aimed to assess the prevalence and persistence of SARS-CoV-2 in fecal and saliva samples for up to 7 weeks post-detection in a cohort of 98 participants from Norfolk, United Kingdom using RT-qPCR. Secondary goals included sequencing the viral isolates present in fecal samples and comparing the genetic sequence with isolates in the saliva of the same participant. Furthermore, we sought to identify factors associated with the presence of detectable virus in feces or saliva after a positive SARS-CoV-2 test. Saliva remained SARS-CoV-2-positive for longer periods compared to fecal samples, with all positive fecal samples occurring within 4 weeks of the initial positive test. Detectable virus in fecal samples was positively associated with the number of symptoms experienced by the individuals. Based on the genome sequencing and taxonomic classification of the virus, one donor had a distinct strain in feces compared to saliva on the same collection date, which suggests that different isolates could dominate different tissues. Our results underscore the importance of considering multiple biological samples, such as feces, in the detection and characterization of SARS-CoV-2, particularly in clinical procedures involving patient fecal material transplant. Such insights could contribute to enhancing the safety protocols surrounding the handling of patient samples and aid in devising effective strategies for mitigating the spread of coronavirus disease.

This study provides critical insights into the dynamics of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) shedding in fecal and saliva samples, demonstrating that while viral RNA is detectable shortly after diagnosis, its prevalence declines rapidly over the course of infection. Detection was more common among individuals with more concurrent symptoms, emphasizing the potential influence of symptom burden on viral persistence. By analyzing a United Kingdom-based cohort, this study fills a significant gap in the literature, which has largely focused on Asian and North American populations, offering a geographically unique perspective on viral shedding dynamics. Our findings contribute to a globally relevant understanding of SARS-CoV-2 shedding by revealing differences in shedding durations compared to studies from other regions. These differences highlight the need for geographically diverse research to account for variations in genetic background, immune response, and healthcare practices.

Wastewater-based epidemiology (WBE) has been employed for monitoring the presence of SARS-CoV-2 infected population. Herein, the study aims to apply the WBE for surveillance and monitoring SARS-CoV-2 in Bangkok, where the highest official covid-19 cases reported in Thailand, during the fully opening for international tourists in early 2023. A total of 200 wastewater samples (100 influent and 100 effluent samples) were collected from 10 wastewater treatment plants (WWTPs) during January-May 2023. SARS-CoV-2 RNA was detected by real time qRT-PCR with accounting for 51% (102/200). Of these, 88% (88/100) and 14% (14/100) were detected in influent and effluent samples, respectively. The SARS-CoV-2 RNA concentration was detected in ranged of 4.76 × 102-1.48 × 105 copies/L. The amount of SARS-CoV-2 RNA has increased approximately 4 times from the lag phase (January-March) to the log phase (April-May). Spearman's correlation coefficient revealed that correlation between estimated infected population and weekly reported cases was statistically significant (p-value = 0.017). SARS-CoV-2 RNA in influent had a statistically significant relationship with weekly reported cases (r = 0.481, p-value < 0.001). Lag time analysis revealed early warning 1-3 weeks before rising covid-19 cases observed. GIS was applied for spatial-temporal analysis at the province level, suggesting real time dashboard should be further developed.

Many wastewater-based epidemiology (WBE) programs are being implemented worldwide due to their usefulness in monitoring residents' health. Modeling wastewater dynamics in outbreak scenarios can provide important data for designing wastewater surveillance plans. For outbreak modeling to be effective, researchers must coordinate with public health authorities and laboratory services, using frameworks to ensure that their modeling and output data are relevant for informed decision-making. However, theoretical and institutional frameworks typically omit modeling, and the connection between theoretical frameworks and models is often unrecognized. A framework that surpasses theoretical conceptualization for promoting collaboration between actors by integrating modeling can achieve the required synchrony toward sustainable wastewater surveillance plans. First, we build on an existing theoretical framework to create a collaborative framework that integrates modeling and suggests stakeholder activities for designing WBE programs. Then, we demonstrate our framework for developing a WBE plan via a COVID-19 case study where we answer when, how often, and where to sample wastewater to detect and monitor an outbreak. We evaluate the results in space and time for three outbreak phases (early detection, peak, and tail). The modeling outputs indicate the need for different sampling strategies for these outbreak phases. Our results also quantify the differences in the likelihood of capturing viral events in wastewater between the sampling hours at different disease phases for COVID-19 and various spatial locations in the sewer network. This framework lays the foundation for sustainable WBE to improve the detection efficiency of wastewater surveillance plans.

This study aims to assess the feasibility of evaluating the COVID-19 epidemic trend through monitoring the positive percentage of SARS-CoV-19 RNA in wastewater.

The study collected data from January to August 2023, including the number of reported cases, the positive ratio of nucleic acid samples in sentinel hospitals, the incidence rate of influenza-like symptoms in students, and the positive ratio of wastewater samples in different counties and districts in Shangrao City. Wastewater samples were obtained through grabbing and laboratory testing was completed within 24 h. The data were then normalized using Z-score normalization and analyzed for lag time and correlation using the xcorr function and Spearman correlation coefficient.

A total of 2797 wastewater samples were collected. The wastewater monitoring study, based on sampling point distribution, was divided into two phases. Wuyuan County consistently showed high levels of positive ratio in wastewater samples in both phases, reaching peak values of 91.67% and 100% respectively. The lag time analysis results indicated that the peak positive ratio in all wastewater samples in Shangrao City appeared around 2 weeks later compared to the other three indicators. The correlation analysis revealed a strong linear correlation across all four types of data, with Spearman correlation coefficients ranging from 0.783 to 0.977, all of which were statistically significant.

The positive ratio of all wastewater samples in Shangrao City accurately reflected the COVID-19 epidemic trend from January to August 2023. This study confirmed the lag effect of wastewater percent positive and its strong correlation with the reported incidence rate and the positive ratio of nucleic acid samples in sentinel hospitals, supporting the use of wastewater percent positive monitoring as a supplementary tool for infectious disease surveillance in the regions with limited resources.

The persistence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) on substrates, and the impact of fomites on Coronavirus Disease 19 (COVID-19) transmission, is until now, widely discussed. Consequently, further investigations are required for a correct risk assessment in high-risk facilities such as hospitals, healthcare facilities (HCFs), and long-term care facilities (LTCFs). Therefore, appropriate surveillance and disinfection programs represent the best approach to guarantee the safety of these communities. This study proposes an environmental SARS-CoV-2 surfaces routine monitoring approach in HCF and communities' settings, to provide rapid and effective evaluation of surface hygienic conditions and the effectiveness of applied sanitization measures. Surfaces samples (n = 118) were collected using the SRK® kit (Copan Italia) from 2020 to 2023. Three molecular techniques were compared: Reverse Transcription Loop mediated isothermal AMPlification (RT-LAMP, Enbiotech), Reverse-Transcription quantitative polymerase chain reaction (RT-qPCR) (RT-qPCR, Seegene) and droplet digital PCR (ddPCR, Bio-Rad). For ddPCR, two RNA extraction methods were compared: TRIzol LS (Invitrogen) versus QIAmp Viral Mini kit (QIAGEN), showing how the latter is more suitable for surfaces. Regarding the quantitative ddPCR results, the ROC analysis allowed to reduce the manufacturer cut-off for droplets number (from 3 to 1) for the positive samples. Moreover, a new cut-off for the viral RNA copies' number/μL for each target (N1 and N2) on environmental monitoring was fixed at 2,82. The results obtained using the QIAmp kit, suggested that the N2 target is more stable in the environment and could be most suitable for the virus environmental detection. The percentage of positive samples was similar among the techniques (26% for RT-LAMP, 36% for ddPCR and 23% for RT-qPCR). Using RT-qPCR as reference method, a sensitivity (SE) of 30% for RT-LAMP and 41% for ddPCR was observed. By contrast, specificity (SP) was higher for RT-LAMP (75%) respect to ddPCR (66%). Comparing the faster RT-LAMP with the sensitive ddPCR the 26% and 74% of SE and SP for RT-LAMP, were reported. The low sensitivity for RT-LAMP and ddPCR could be explained with the use of clinical rather than environmental kits, other than the changing in the virus prevalence during the sampling campaign. Although the RT-LAMP requires improvements in term of SE and SP, this research presents an innovative environmental monitoring and prevention method for SARS-CoV-2, that could be extended to other pathogens that are under environmental surveillance.

The COVID-19 pandemic highlighted the critical role of viral genomic surveillance, prompting numerous countries to enhance their monitoring systems for acute respiratory infections (ARIs), especially influenza-like illnesses (ILIs). Given the significance of asymptomatic cases in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission, cases often undetected by the ILI surveillance, a more comprehensive approach was essential to track the circulation of SARS-CoV-2 variants in the population. In response, many countries swiftly adopted wastewater surveillance, which allowed the early detection of SARS-CoV-2 variants before they were identified through molecular characterization from confirmed clinical cases. In this report, we detail the implementation of SARS-CoV-2 wastewater genomic surveillance in Panama during the first half of 2024. Wastewater samples were collected monthly in duplicate at two collection points from three districts of Panama city metropolitan area for testing by SARS-CoV-2 RT-qPCR, and positive samples were analyzed by next-generation sequencing to identify sublineages. A total of 36 wastewater samples and 822 samples obtained through the clinical surveillance were analyzed for molecular detection and sequencing. Sublineages detected by wastewater surveillance were compared to those detected by clinical surveillance for the same period of time. Wastewater surveillance allowed the identification of the Omicron sublineage JN.1.16.1 in the capital city and its surroundings, which was not detected by the clinical surveillance in the country, despite its global circulation. This highlights the critical need to sustain both genomic surveillance programs beyond the pandemic in countries like Panama that serve as pivotal exchange hubs.

During the COVID-19 pandemic schools closed due to concerns over disease spread resulting in lost learning opportunities. One approach for documenting disease spread includes wastewater (WW) surveillance of the virus that causes COVID-19 (Severe Acute Respiratory Syndrome Coronavirus 2, SARS-CoV-2) and other infectious pathogens. The objective of this study was to evaluate whether wastewater can be used to track children's health at grade schools in an underserved community, which was vulnerable due to limited health-based data and difficulties in implementing mitigation measures. The 18-month study was initiated during January 2022 at 9 grade schools (3 high, 2 middle, and 4 elementary schools) characterized as low income. Children's health was evaluated through absenteeism due to difficulties in attaining representative clinical diagnoses through school-based clinics. Wastewater measurements of SARS-CoV-2 were available weekly through grab sample collection and RNA extraction followed by quantification using qPCR. The average absenteeism rate was 7.1%, ranging from 4.6% to 12.5% per school. Fraction of WW samples positive for SARS-CoV-2 was 38% with SARS-Cov-2 levels ranging from detection limits (100 gc/L) to a maximum of 10.2 million gc/L. When data were aggregated across all schools, a statistically significant association was observed between weekly absenteeism rates and WW SARS-CoV-2 with a one percent increase in the loge WW SARS-CoV-2 associated with a 1.4% increase in student absence (p < 0.05). When evaluating the data by individual school, this association was strongest at schools with enclosed architecture characterized by limited natural ventilation. For schools with limited resources for clinical diagnosis of illnesses, school absenteeism coupled with wastewater-based monitoring should be utilized for assessing overall health of student populations. Strategies to maintain schools open during pandemics should include consideration of school architecture along with appropriate messaging of WW monitoring results to inform administrators and families.

Donor-derived fecal microbiota treatments are efficacious in preventing recurrent Clostridioides difficile infection (rCDI), but they have inherently variable quality attributes, are difficult to scale and harbor the risk of pathogen transfer. In contrast, VE303 is a defined consortium of eight purified, clonal bacterial strains developed for prevention of rCDI. In the phase 2 CONSORTIUM study, high-dose VE303 was well tolerated and reduced the odds of rCDI by more than 80% compared to placebo. VE303 organisms robustly colonized the gut in the high-dose group and were among the top taxa associated with non-recurrence. Multi-omic modeling identified antibiotic history, baseline stool metabolites and serum cytokines as predictors of both on-study CDI recurrence and VE303 colonization. VE303 potentiated early recovery of the host microbiome and metabolites with increases in short-chain fatty acids, secondary bile acids and bile salt hydrolase genes after antibiotic treatment for CDI, which is considered important to prevent CDI recurrences. These results support the idea that VE303 promotes efficacy in rCDI through multiple mechanisms.

COVID-19-associated gastrointestinal (GI) symptoms are often self-limiting; however, gastrointestinal bleeding (GIB) is a critical complication in patients with COVID-19. The present study investigates the etiology, risk factors, esophagogastroduodenoscopy (EGD) findings, and outcomes associated with upper gastrointestinal bleeding (UGIB) in hospital inpatients with COVID-19.

In this retrospective case-control study, 127 patients with COVID-19 in Kerman, Iran, were diagnosed using reverse transcription polymerase chain reaction (RT-PCR) and subsequently divided into case and control groups from January 2022 to July 2022.

This study evaluated 64 patients with COVID-19 with UGIB and 63 patients without. The case group reported previous history of GIB and cirrhosis at 17.2% and 12.5%, respectively (P=0.001 and P=0.01). Melena (37.5%) and peptic ulcer (21.87%) were the most common UGIB symptom and EGD findings, respectively. In the comparison of the case group with the control group, the duration of the patient's stay in the intensive care unit (ICU) (11.58±1.13 vs. 8.29±1.06 days), the need for invasive mechanical ventilation (IMV) (17.2% vs. 8.1%), and the mortality rate (26.6% vs. 18.9%) were recorded (P=0.03, 0.124, and 0.07, respectively).

Patients with COVID-19 and UGIB have a more prevalent ICU stay compared with those without. Melena and peptic ulcer were the most common presentations and EGD findings in these patients. Additionally, liver cirrhosis and a history of previous GIB increased the risk of GIB in patients with COVID-19.

Despite significant effort, a clear understanding of host tissue-specific responses and their implications for immunopathogenicity against the severe acute respiratory syndrome coronavirus2 (SARS-CoV-2) variant infection has remained poorly defined. To shed light on the interaction between tissues and SARS-CoV-2 variants, we sought to characterize the complex relationship among acute multisystem manifestations, dysbiosis of the gut microbiota, and the resulting implications for SARS-CoV-2 variant-specific immunopathogenesis in the Golden Syrian Hamster (GSH) model using multi-omics approaches. Our investigation revealed the presence of increased SARS-CoV-2 genomic RNA in diverse tissues of delta-infected GSH compared to the omicron variant. Multi-omics analyses uncovered distinctive metabolic responses between the delta and omicron variants, with the former demonstrating dysregulation in synaptic transmission proteins associated with neurocognitive disorders. Additionally, delta-infected GSH exhibited an altered fecal microbiota composition, marked by increased inflammation-associated taxa and reduced commensal bacteria compared to the omicron variant. These findings underscore the SARS-CoV-2-mediated tissue insult, characterized by modified host metabolites, neurological protein dysregulation, and gut dysbiosis, highlighting the compromised gut-lung-brain axis during acute infection.

COVID-19 symptoms are often perceived as respiratory only. However, recent findings have shown that gastrointestinal symptoms are being reported in a significant number of patients, ranging from 17% to more than 50%, with some studies speculating that the figure may be even higher, but that it is under-reported and overlooked. Therefore, a hypothesis was put forward that gastrointestinal symptoms related to COVID-19 may make pouch or stoma function deteriorate or even mimic pouchitis symptoms in ileoanal pouches and gastroenteritis in stoma patients; the intention was to investigate this further and to test the hypothesis. A retrospective analysis of patients with a stoma or ileoanal pouch was conducted, including those who reported having gastrointestinal symptoms following a positive COVID-19 test in the preceding 4 years (2020-2024). It was anticipated that gaining insight into this topic can help improve care for this patient group.

The administration of proton pump inhibitors (PPIs) is anticipated to elevate an individual's susceptibility to enteric infections as a result of altering the gut flora. The influence of PPIs on the clinical manifestation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is still uncertain. This study aims to investigate the impact of PPI usage on the clinical manifestation of COVID-19, namely its gastrointestinal symptoms.

This is a cross-sectional cohort study involving COVID-19 patients. Patients were interviewed using a predesigned questionnaire that asked about their demographics, clinical manifestations of COVID-19 infection, and the extent and type of PPIs in use. PPI usage was confirmed by reviewing patients' electronic medical records. The primary outcome was to establish any association between the use of PPI and the symptoms and clinical presentation of COVID-19.

Out of a total of 254 participants, 69 (27.2%) were considered PPI users. Patients who were on PPI medications reported a significantly lower rate of myalgia (27.5% vs 51.9%; p = 0.0006) and heartburn (5.7% vs 15.6%; p = 0.03) but had a significantly higher rate of abdominal pain (27.5% vs 13.5%; p = 0.001) and diarrhoea (28.9% vs 14.5%, p = 0.02) when compared to those who were not using PPIs. Patients on PPIs were also shown to have significantly higher odds of developing diarrhoea (OR 2.0, 95% CI: 1.08 to 3.93, p = 0.02) and abdominal pain (OR 2.0, 95% CI: 1.22 to 3.93, p = 0.03), but a lower risk of developing myalgia (OR 0.5, 95% CI: 0.3 to 0.9, p = 0.02) when compared to non-PPI users.

This study shows that the use of PPIs could impact COVID-19 clinical presentation toward more gastrointestinal manifestations. Further studies investigating the link between other acid suppression medications and COVID-19 manifestations and severity should be carried out.

The bourgeoning field of wastewater-based epidemiology (WBE) for the surveillance of several respiratory viruses which includes Influenza A, H1N1pdm09, H3N2, respiratory syncytial viruses (RSV), and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is of interest for public health concerns. However, there are few long-term monitoring studies globally. In this study, respiratory viruses were detected and quantified from 11 sewer sheds by utilizing reverse transcription-quantitative polymerase chain reaction analysis in Pune city, India, from Jan 2022 to Dec 2023. The RNA fragments of respiratory viruses were detected in sewage samples before clinical cases were reported, underscoring the potential of WBE for early detection and monitoring within the population. The Spearman correlation of wastewater viral copies was positively and significantly correlated with the clinically positive case of H1N1pdm09 (ρ = 0.55, p = 1.4 × 10-9), H3N2 (ρ = 0.25, p = 9.9 × 10-3), and SARS-CoV-2 (ρ = 0.43, p = 4.1 × 10-6). The impact of public health interventions on the circulation of infectious respiratory diseases showed a significant difference in the viral load during the period when many preventing measures were carried out against the COVID-19 pandemic (restriction phase), compared to the period when no such preventive measures are followed (no-restriction phase) for Influenza A, H1N1pdm09, H3N2, and RSV with p-value < 0.05, which indicates the influence of health policy implementation in controlling disease spread. The present study provides an effective approach to detecting multiple respiratory viruses from wastewater and provides insights into the epidemiology of respiratory illnesses. The WBE aids in providing information on the spread of pathogens (viruses) in the community, offering a proactive strategy for public health management, allowing for timely interventions and implementing targeted measures to mitigate the spread of these viruses under one health approach.

Wastewater-based epidemiological surveillance has proven to be a useful and cost-effective tool for detecting COVID-19 outbreaks. Here, our objective was to evaluate its potential as an early warning system in Venezuela by detecting SARS-CoV-2 RNA in wastewater and its correlation with reported cases of COVID-19. Viral RNA was concentrated from wastewater collected at various sites in Caracas (northern Venezuela), from September 2021 to July 2023, using the polyethylene glycol (PEG) precipitation method. Viral quantification was performed by RT-qPCR targeting the N1 and ORF1ab genes. A significant association (p < 0.05) was found between viral load in wastewater and reported cases of COVID-19 up to six days after sampling. During the whole study, two populated areas of the city were persistent hotspots of viral infection. The L452R mutation, suggestive of the presence of the Delta variant, was identified in the only sample where a complete genomic sequence could be obtained. Significant differences (p < 0.05) between the physicochemical conditions of the wastewater samples positive and negative for the virus were found. Our results support proof of concept that wastewater surveillance can serve as an early warning system for SARS-CoV-2 outbreaks, complementing public health surveillance in those regions where COVID-19 is currently underreported.

Objectives. To describe 4 unique models of operationalizing wastewater-based surveillance (WBS) for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in jails of graduated sizes and different architectural designs. Methods. We summarize how jails of Cook County, Illinois (average daily population [ADP] 6000); Fulton County, Georgia (ADP 3000); Middlesex County, Massachusetts (ADP 875); and Washington, DC (ADP 1600) initiated WBS between 2020 and 2023. Results. Positive signals for SARS-CoV-2 via WBS can herald a new onset of infections in previously uninfected jail housing units. Challenges implementing WBS included political will and realized value, funding, understanding the building architecture, and the need for details in the findings. Conclusions. WBS has been effective for detecting outbreaks of SARS-CoV-2 in different sized jails, those with both dorm- and cell-based architectural design. Public Health Implications. Given its effectiveness in monitoring SARS-CoV-2, WBS provides a model for population-based surveillance in carceral facilities for future infectious disease outbreaks. (Am J Public Health. 2024;114(11):1232-1241. https://doi.org/10.2105/AJPH.2024.307785).

This study investigated the efficiency of the treatment processes of wastewater treatment plants (WWTPs) to remove severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and pepper mild mottle virus (PMMoV) from the wastewater and sewage sludge, as well as the influence of the mode of operation on the quality of the treated wastewater. SARS-CoV-2 and PMMoV were detected and quantified at different stages of the wastewater and sludge treatment process of three major WWTPs in Stockholm, Sweden. The results showed that primary, biological, and advanced membrane treatment processes are effective in removing SARS-CoV-2 from the wastewater with removal efficiencies of 99-100 % for all WWTPs, while the virus was accumulated in the primary and waste-activated sludges due to higher affinity to biosolids. Operation strategies such as bypass reintroduced the virus into the treated wastewater. The WWTPs achieved relatively low PMMoV removal efficiencies (63-87 %) most probably due to the robust capsid structure of the virus. Anaerobic digestion could not completely remove SARS-CoV-2 and PMMoV from the sludge leading to increased levels of SARS-CoV-2 and PMMoV in dewatered sludge. The study gives an overview of WWTPs' role in tackling pathogen spread in society in the event of a pandemic and disease breakout.

Coinfection of pathogenic bacteria and viruses is associated with multiple diseases. During the COVID-19 pandemic, the co-infection of other pathogens with SARS-CoV-2 was one of the important determinants of the severity. Although primarily a respiratory virus gastric manifestation of the SARS-CoV-2 infection was widely reported. This study highlights the possible consequences of SARS-CoV-2 -Helicobacter pylori coinfection in the gastrointestinal cells. We utilized the transfection and infection model for SARS-CoV-2 spike Delta (δ) and H. pylori respectively in colon carcinoma cell line HT-29 to develop the coinfection model to study inflammation, mitochondrial function, and cell death. The results demonstrate increased transcript levels of inflammatory markers like TLR2 (p < 0.01), IL10 (p < 0.05), TNFα (p < 0.05) and CXCL1 (p < 0.05) in pre-H. pylori infected cells as compared to the control. The protein levels of the β-Catenin (p < 0.01) and c-Myc (p < 0.01) were also significantly elevated in pre-H. pylori infected group in case of co-infection. Further investigation of apoptotic and necrotic markers (Caspase-3, Caspase-8, and RIP-1) reveals a necroptotic cell death in the coinfected cells. The infection and coinfection also damage the mitochondria in HT-29 cells, further implicating mitochondrial dysfunction in the necrotic cell death process. Our study also highlights the detrimental effect of pre-H. pylori exposure in the coinfection model compared to post-exposure and lone infection of H. pylori and SARS-CoV-2. This knowledge could aid in developing targeted interventions and therapeutic strategies to mitigate the severity of COVID-19 and improve patient outcomes.

Human enteric and some respiratory viruses are identified to be involved with acute gastroenteritis that can be shed in feces of infected persons into the environment. Understanding the abundance of these viruses in wastewater is significant when assessing the public health impacts associated with discharge of wastewater into the environment. This study aimed to investigate the prevalence and seasonal variation of human enteric adenovirus (HAdV), Aichi virus (AiV-1), bocavirus (HBoV), and respiratory syndrome coronavirus 2 virus (SARS-CoV-2) in wastewater as well as their prevalence among hospitalized children with acute gastroenteritis. The viruses were detected and quantified with real-time PCR. HAdV was the most detected virus in raw sewage (88.5%), treated sewage (28%), and stool gastroenteritis (74%), followed by HBoV (45.8% for raw sewage, 14.6% for treated sewage, and 55.3% for stool samples). The detection rate of AiV-1 was 59.4%, 19.8%, and 62.6% in raw sewage, treated sewage, and stool samples, respectively. The rate of SARS-CoV-2 detection in raw sewage, treated sewage, and stool samples was 33.3%, 7.3%, and 20.6%, respectively. The viral concentrations ranged between 4.50 × 101 and 8.75 × 107 GC/ml in raw sewage samples, 1.20 × 101 and 5.43 × 106 GC/ml in treated sewage samples, and 4.80 × 101 and 9.88 × 108 GC/gram in stool samples. The overall log means of virus reduction during the wastewater treatment process ranged from 1.68 log10 (HAdV) to 3.31 log10 (AiV-1). The peak prevalence of the four viruses in raw sewage samples occurred during the winter season. This study showed the high detection rates of the four targeted viruses in wastewater and demonstrated that virological surveillance of wastewater in local wastewater treatment plants is a suitable model for epidemiological monitoring of diarrheal and respiratory diseases in middle- and low-resource countries.

Wastewater treatment plants (WWTPs) are the final stage of the anthropogenic water cycle where a wide range of chemical and biological markers of human activity can be found. In COVID-19 disease contexts, wastewater surveillance has been used to infer community trends based on viral abundance and SARS-CoV-2 RNA variant composition, which has served to anticipate and establish appropriate protocols to prevent potential viral outbreaks. Numerous studies worldwide have provided reliable and robust tools to detect and quantify SARS-CoV-2 RNA in wastewater, although due to the high dilution and degradation rate of the viral RNA in such samples, the detection limit of the pathogen has been a bottleneck for the proposed protocols so far. The current work provides a comprehensive and systematic study of the different parameters that may affect the detection of SARS-CoV-2 RNA in wastewater and hinder its quantification. The results obtained using synthetic viral RNA as a template allow us to consider that 10 genome copies per µL is the minimum RNA concentration that provides reliable and consistent values for the quantification of SARS-CoV-2 RNA. RT-qPCR analysis of wastewater samples collected at the WWTP in Salamanca (western Spain) and at six pumping stations in the city showed that below this threshold, positive results must be confirmed by sequencing to identify the specific viral sequence. This allowed us to find correlations between the SARS-CoV-2 RNA levels found in wastewater and the COVID-19 clinical data reported by health authorities. The close match between environmental and clinical data from the Salamanca case study has been confirmed by similar experimental approaches in four other cities in the same region. The present methodological approach reinforces the usefulness of wastewater-based epidemiology (WBE) studies in the face of future pandemic outbreaks.

Wastewater-based epidemiology (WBE) surveillance has been proposed as an early warning system (EWS) for community SARS-CoV-2 transmission. However, there is limited data from low-and middle-income countries (LMICs). This study aimed to assess the ability of WBE surveillance to detect SARS-CoV-2 in formal and informal environments in Indonesia using different methods of sample collection, to compare WBE data with patterns of clinical cases of COVID-19 within the relevant communities, and to assess the WBE potential to be used as an EWS for SARS-CoV-2 outbreaks within a community.

We conducted WBE surveillance in three districts in Yogyakarta province, Indonesia, over eleven months (27 July 2021 to 7 January 2022 [Delta wave]; 18 January to 3 June 2022 [Omicron wave]). Water samples using grab, and/or passive sampling methods and soil samples were collected either weekly or fortnightly. RNA was extracted from membrane filters from processed water samples and directly from soil. Reverse-transcription quantitative real-time polymerase chain reaction (RT-qPCR) was performed to detect the SARS-CoV-2 N and ORF1ab genes.

A total of 1,582 samples were collected. Detection rates of SARS-CoV-2 in wastewater reflected the incidence of community cases, with rates of 85% at the peak to 2% at the end of the Delta wave and from 94% to 11% during the Omicron wave. A 2-week lag time was observed between the detection of SARS-CoV-2 in wastewater and increasing cases in the corresponding community.

WBE surveillance for SARS-CoV-2 in Indonesia was effective in monitoring patterns of cases of COVID-19 and served as an early warning system, predicting the increasing incidence of COVID-19 cases in the community.

This study aimed to assess the use of cross-assembled phage (crAssphage) as an endogenous control employing a multivariate normalization analysis and its application as a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) data normalizer.

A total of 188 twelve-hour composite raw sewage samples were obtained from eight wastewater treatment plants (WWTP) during a 1-year monitoring period. Employing the N1 and N2 target regions, SARS-CoV-2 RNA was detected in 94% (177) and 90% (170) of the samples, respectively, with a global median of 5 log10 genomic copies per liter (GC l-1). CrAssphage was detected in 100% of the samples, ranging from 8.29 to 10.43 log10 GC l-1, with a median of 9.46 ± 0.40 log10 GC l-1, presenting both spatial and temporal variabilities.

Although SARS-CoV-2 data normalization employing crAssphage revealed a correlation with clinical cases occurring during the study period, crAssphage normalization by the flow per capita per day of each WWTP increased this correlation, corroborating the importance of normalizing wastewater surveillance data in disease trend monitoring.

The COVID-19 pandemic caused by SARS-CoV-2 has led to a wide range of clinical presentations, with respiratory symptoms being common. However, emerging evidence suggests that the gastrointestinal (GI) tract is also affected, with angiotensin-converting enzyme 2, a key receptor for SARS-CoV-2, abundantly expressed in the ileum and colon. The virus has been detected in GI tissues and fecal samples, even in cases with negative results of the reverse transcription polymerase chain reaction in the respiratory tract. GI symptoms have been associated with an increased risk of ICU admission and mortality. The gut microbiome, a complex ecosystem of around 40 trillion bacteria, plays a crucial role in immunological and metabolic pathways. Dysbiosis of the gut microbiota, characterized by a loss of beneficial microbes and decreased microbial diversity, has been observed in COVID-19 patients, potentially contributing to disease severity. We conducted a comprehensive gut microbiome study in 204 hospitalized COVID-19 patients using both shallow and deep shotgun sequencing methods. We aimed to track microbiota composition changes induced by hospitalization, link these alterations to clinical procedures (antibiotics administration) and outcomes (ICU referral, survival), and assess the predictive potential of the gut microbiome for COVID-19 prognosis. Shallow shotgun sequencing was evaluated as a cost-effective diagnostic alternative for clinical settings. Our study demonstrated the diverse effects of various combinations of clinical parameters, microbiome profiles, and patient metadata on the precision of outcome prognostication in patients. It indicates that microbiological data possesses greater reliability in forecasting patient outcomes when contrasted with clinical data or metadata. Furthermore, we established that shallow shotgun sequencing presents a viable and cost-effective diagnostic alternative to deep sequencing within clinical environments.

In the United States, the growing number of people experiencing homelessness has become a socioeconomic crisis with public health ramifications, recently exacerbated by the COVID-19 pandemic. We hypothesized that the environmental surveillance of flood control infrastructure may be an effective approach to understand the prevalence of infectious disease. From December 2021 through July 2022, we tested for SARS-CoV-2 RNA from two flood control channels known to be impacted by unsheltered individuals residing in upstream tunnels. Using qPCR, we detected SARS-CoV-2 RNA in these environmental water samples when significant COVID-19 outbreaks were occurring in the surrounding community. We also performed whole genome sequencing to identify SARS-CoV-2 lineages. Variant compositions were consistent with those of geographically and temporally matched municipal wastewater samples and clinical specimens. However, we also detected 10 of 22 mutations specific to the Alpha variant in the environmental water samples collected during January 2022-one year after the Alpha infection peak. We also identified mutations in the spike gene that have never been identified in published reports. Our findings demonstrate that environmental surveillance of flood control infrastructure may be an effective tool to understand public health conditions among unsheltered individuals-a vulnerable population that is underrepresented in clinical surveillance data.

In this study, we sought to determine whether faecal shedding occurs among SARS-COV-2 positive Ghanaians, as reported elsewhere. Hence we assayed for SARS-COV-2 in the stools of 48 SARS-COV-2 confirmed patients at the Ho Municipal Hospital in Ghana.

Of the 48 COVID-19 patients, 45 (93.8%) had positive tests for SARS-CoV-2 faecal shedding. About 60% reported no respiratory symptoms, while only 2% (1 patient) reported gastrointestinal (GI) symptoms in the form of nausea. Other symptoms reported included headache (57.9%), weakness (57.9%), cough (52.6%), blocked/runny nose (47.4%), fever (31.6%), sore throat (31.6%), and shortness of breath (21.1%). One person complained of nausea (5.3%) Semi-quantitative comparison of the SARS COV-2 viral loads in matched respiratory and faecal samples using the cycle threshold (CT) values revealed no statistical differences. Furthermore, the duration between collection of respiratory and faecal samples did not have any direct influence on the differences in the CT values. This suggests that treatment and use of sewage for environmental surveillance of SARS COV-2 could be a potential public health countermeasure.

Previous literature has demonstrated that COronaVIrus Disease of 2019 (COVID-19) impacts an individual gastrointestinal tract (GIT), causing symptoms like nausea, diarrhea, and loss of appetite. Severe acute respiratory syndrome coronavirus RNA has been discovered in the stool of infected individuals in earlier research. It was discovered that severe acute respiratory syndrome coronavirus was significantly expressed in the GIT, indicating that the virus can also infect the digestive system. Angiotensin-converting enzyme 2 functions as the viral receptor. The chronic illness known as gastroesophageal reflux disease (GERD) is typified by frequent reflux of stomach acid into the esophagus. By triggering the sensitized esophageal-bronchial neuronal circuit or aspirating into the airways (microaspiration), GER exacerbates respiratory diseases. Aspiration is a well-known risk to be considered when treating patients in intensive care units. Strong genetic correlations have been identified between COVID-19 infection and GERD susceptibility, suggesting a shared genetic basis for both conditions. Nonetheless, even though GERD, extraesophageal reflex, and COVID-19 have a number of significant risk factors and exhibit similar symptoms, the relationship between these illnesses has not yet been examined in depth. This review is the first of its kind to critically examine the association between the COVID-19 epidemic and GER and its associated diseases. The key objective of this work is to promote the creation of prevention plans, treatment plans, and guidelines while also enhancing and optimizing our understanding of the relationship between COVID-19 and GERs.

Wastewater surveillance represents an alternative approach to regulating contamination and the early detection of infectious agents and outbreaks of diseases of public health importance. This study evaluated domestic wastewater effects on recreational waters in estuarine and seawater bodies in Guayas and Santa Elena provinces in Ecuador, South America. Fecal indicator bacteria (thermotolerant coliforms) served as key indicators for evaluation. Physical, chemical, and microbiological quality markers following the Ecuadorian environmental quality standard and the discharge of effluents to the water resource were analyzed. Samples were collected from 44 coastal sites and 2 oxidation lagoons during the dry and rainy seasons of 2020 and 2021, respectively. SARS-CoV-2 RNA was detected in samples with higher E. coli concentrations using reverse transcription quantitative PCR to detect the genes N and ORF1ab. All samples analyzed for SARS-CoV-2 showed Ct ˂ 40 for at least one gene. Four samples showed at least 20 genome copies of gene N per reaction. These were at an artisanal fishing port, an estuarine area (Palmar), a recreational bay, and an oxidation lagoon. A moderate correlation was found between SARS-CoV-2 RNA, thermotolerant coliform and E. coli (p-value ≤ 0.0037), and a strong and positive correlation between thermotolerant coliform and E. coli. (p-value ≤ 0.00001), highlighting the utility of these established parameters as a proxy of the virus. Significant differences were found in the concentrations of thermotolerant coliforms between seasons (p-value = 0.016) and sites (p-value = 0.005). The highest levels of coliforms were found in the dry season (63000 MPN/100 mL) in Anconcito and during the rainy season (14000 MPN/100 mL) at Esterillo in Playas County. It is recommended that the decentralized autonomous governments of the surveyed provinces in Ecuador implement urgent corrective actions and establish medium-term mechanisms to minimize a potential contamination route. Additional parameters must be included in the monitoring, such as Enterococcus and intestinal parasites, due to their public health implications. In the oxidation lagoons, maintenance actions must be carried out, including the dissolution of sediments, an increase in water retention times, and in situ treatment of the sludge, to improve the system's performance.

Wastewater-based surveillance (WBS) is an important epidemiological and public health tool for tracking pathogens across the scale of a building, neighbourhood, city, or region. WBS gained widespread adoption globally during the SARS-CoV-2 pandemic for estimating community infection levels by qPCR. Sequencing pathogen genes or genomes from wastewater adds information about pathogen genetic diversity, which can be used to identify viral lineages (including variants of concern) that are circulating in a local population. Capturing the genetic diversity by WBS sequencing is not trivial, as wastewater samples often contain a diverse mixture of viral lineages with real mutations and sequencing errors, which must be deconvoluted computationally from short sequencing reads. In this study we assess nine different computational tools that have recently been developed to address this challenge. We simulated 100 wastewater sequence samples consisting of SARS-CoV-2 BA.1, BA.2, and Delta lineages, in various mixtures, as well as a Delta-Omicron recombinant and a synthetic 'novel' lineage. Most tools performed well in identifying the true lineages present and estimating their relative abundances and were generally robust to variation in sequencing depth and read length. While many tools identified lineages present down to 1 % frequency, results were more reliable above a 5 % threshold. The presence of an unknown synthetic lineage, which represents an unclassified SARS-CoV-2 lineage, increases the error in relative abundance estimates of other lineages, but the magnitude of this effect was small for most tools. The tools also varied in how they labelled novel synthetic lineages and recombinants. While our simulated dataset represents just one of many possible use cases for these methods, we hope it helps users understand potential sources of error or bias in wastewater sequencing analysis and to appreciate the commonalities and differences across methods.

Wastewater-based surveillance (WBS) has undergone dramatic advancement in the context of the coronavirus disease 2019 (COVID-19) pandemic. The power and potential of this platform technology were rapidly realized when it became evident that not only did WBS-measured SARS-CoV-2 RNA correlate strongly with COVID-19 clinical disease within monitored populations but also, in fact, it functioned as a leading indicator. Teams from across the globe rapidly innovated novel approaches by which wastewater could be collected from diverse sewersheds ranging from wastewater treatment plants (enabling community-level surveillance) to more granular locations including individual neighborhoods and high-risk buildings such as long-term care facilities (LTCF). Efficient processes enabled SARS-CoV-2 RNA extraction and concentration from the highly dilute wastewater matrix. Molecular and genomic tools to identify, quantify, and characterize SARS-CoV-2 and its various variants were adapted from clinical programs and applied to these mixed environmental systems. Novel data-sharing tools allowed this information to be mobilized and made immediately available to public health and government decision-makers and even the public, enabling evidence-informed decision-making based on local disease dynamics. WBS has since been recognized as a tool of transformative potential, providing near-real-time cost-effective, objective, comprehensive, and inclusive data on the changing prevalence of measured analytes across space and time in populations. However, as a consequence of rapid innovation from hundreds of teams simultaneously, tremendous heterogeneity currently exists in the SARS-CoV-2 WBS literature. This manuscript provides a state-of-the-art review of WBS as established with SARS-CoV-2 and details the current work underway expanding its scope to other infectious disease targets.

Persons living in long-term care facilities (LTCFs) were disproportionately affected by COVID-19. We used wastewater surveillance to detect SARS-CoV-2 infection in this setting by collecting and testing 24-hour composite wastewater samples 2-4 times weekly at 6 LTCFs in Kentucky, USA, during March 2021-February 2022. The LTCFs routinely tested staff and symptomatic and exposed residents for SARS-CoV-2 using rapid antigen tests. Of 780 wastewater samples analyzed, 22% (n = 173) had detectable SARS-CoV-2 RNA. The LTCFs reported 161 positive (of 16,905) SARS-CoV-2 clinical tests. The wastewater SARS-CoV-2 signal showed variable correlation with clinical test data; we observed the strongest correlations in the LTCFs with the most positive clinical tests (n = 45 and n = 58). Wastewater surveillance was 48% sensitive and 80% specific in identifying SARS-CoV-2 infections found on clinical testing, which was limited by frequency, coverage, and rapid antigen test performance.

This review presents comparative information corresponding to the progress in knowledge of some aspects of infection by the porcine epidemic diarrhea virus (PEDV) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) coronaviruses. PEDV is an alphacoronavirus of great economic importance due to the million-dollar losses it generates in the pig industry. PEDV has many similarities to the SARS-CoV-2 betacoronavirus that causes COVID-19 disease. This review presents possible scenarios for SARS-CoV-2 based on the collected literature on PEDV and the tools or strategies currently developed for SARS-CoV-2 that would be useful in PEDV research. The speed of the study of SARS-CoV-2 and the generation of strategies to control the pandemic was possible due to the knowledge derived from infections caused by other human coronaviruses such as severe acute respiratory syndrome (SARS) and middle east respiratory syndrome (MERS). Therefore, from the information obtained from several coronaviruses, the current and future behavior of SARS-CoV-2 could be inferred and, with the large amount of information on the virus that causes COVID-19, the study of PEDV could be improved and probably that of new emerging and re-emerging coronaviruses.