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Wastewater-based epidemiology (WBE) emerged during the coronavirus disease 2019 (COVID-19) pandemic as a scalable and broadly applicable method for community-level monitoring of infectious disease burden. The lack of high-resolution fecal shedding data for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) limits our ability to link WBE measurements to disease burden. In this study, we present longitudinal, quantitative fecal shedding data for SARS-CoV-2 RNA, as well as for the commonly used fecal indicators pepper mild mottle virus (PMMoV) RNA and crAss-like phage (crAssphage) DNA. The shedding trajectories from 48 SARS-CoV-2-infected individuals suggest a highly individualized, dynamic course of SARS-CoV-2 RNA fecal shedding. Of the individuals that provided at least three stool samples spanning more than 14 days, 77% had one or more samples that tested positive for SARS-CoV-2 RNA. We detected PMMoV RNA in at least one sample from all individuals and in 96% (352/367) of samples overall. CrAssphage DNA was detected in at least one sample from 80% (38/48) of individuals and was detected in 48% (179/371) of all samples. The geometric mean concentrations of PMMoV and crAssphage in stool across all individuals were 8.7 × 10 4 and 1.4 × 10 4 gene copies/milligram-dry weight, respectively, and crAssphage shedding was more consistent for individuals than PMMoV shedding. These results provide us with a missing link needed to connect laboratory WBE results with mechanistic models, and this will aid in more accurate estimates of COVID-19 burden in sewersheds. Additionally, the PMMoV and crAssphage data are critical for evaluating their utility as fecal strength normalizing measures and for source-tracking applications. This research represents a critical step in the advancement of wastewater monitoring for public health. To date, mechanistic materials balance modeling of wastewater-based epidemiology has relied on SARS-CoV-2 fecal shedding estimates from small-scale clinical reports or meta-analyses of research using a wide range of analytical methodologies. Additionally, previous SARS-CoV-2 fecal shedding data have not contained sufficient methodological information for building accurate materials balance models. Like SARS-CoV-2, fecal shedding of PMMoV and crAssphage has been understudied to date. The data presented here provide externally valid and longitudinal fecal shedding data for SARS-CoV-2, PMMoV, and crAssphage which can be directly applied to WBE models and ultimately increase the utility of WBE.

•Fecal Rotarix vaccine virus shedding and HBGAphenotype frequency were investigated.•Virus shedding was higher (23.6%) after the first dose than the second dose (4.7%).•Most of vaccine virus-shedding infants were secretor HBGA positive while none of the non-fecal vaccine virus shedding infants were secretor HBGA positive. Most of the virus-shedders were secretor+ compared to none of the non-virus shedders.•Low vaccine virus shedding was significantly associated with non-secretor phenotype. Histo-blood group antigens are recognized by rotaviruses in a P- genotype dependent manner and their frequency in a population can influence fecal virus shedding. This study investigated the rate of fecal shedding of Rotarix vaccine and its association with HBGA phenotype distribution in South Africa. Stool and saliva specimens were collected from 150 infants attending immunization on the day of both first and second doses and 7 days later. Virus shedding was detected by real-time qPCR while HBGA phenotypes in saliva were determined by enzyme linked immunosorbent assay. Vaccine virus shedding was higher (23.6%) after the first dose than the second dose (4.7%). About 77% of virus-shedding infants were secretors (OR = 129; 95% CI, 6.088 – 2733), compared with none of non-virus shedding infants. Non-secretor status was significantly associated with low vaccine virus shedding while the likelihood of shedding was significantly higher in secretors.

SARS-CoV-2 RNA loads can be detected in the excreta of individuals with COVID-19 and have demonstrated positive correlations with clinical infection trends. Consequently, wastewater-based epidemiology (WBE) approaches have been implemented globally as a public health surveillance tool to monitor community-level prevalence of infections. The majority of wastewater specimens are gathered as either composite samples via automatic samplers (autosamplers) or grab samples. However, autosamplers are expensive and can be challenging to maintain in cold weather, while grab samples are particularly susceptible to temporal variation when sampling sewage directly from complex matrices outside residential buildings. Passive sampling can provide an affordable, practical, and scalable sampling system while maintaining a reproducible SARS-CoV-2 signal. In this regard, we deployed tampons as passive samplers outside of a COVID-19 isolation unit (a segregated residence hall) at a university campus from 1 February 2021–21 May 2021. Samples (n = 64) were collected 3–5 times weekly and remained within the sewer for a median duration of 24 h. SARS-CoV-2 RNA was quantified using reverse-transcription quantitative polymerase chain reaction (RT-qPCR) targeting the N1 and N2 gene fragments. We quantified the mean viral load captured per individual and the association between the daily viral load and total persons, adjusting for covariates using multivariable models to provide a baseline estimate of viral shedding. Samples were processed through two distinct laboratory pipelines on campus, yielding highly correlated N2 concentrations. Data obtained here highlight the success of passive sampling utilizing tampons to capture SARS-CoV-2 in wastewater coming from a COVID-19 isolation residence, indicating that this method can help inform building-level public health responses.

Twenty-four solid-organ-transplant recipients with chronic hepatitis E virus (HEV) infections were given ribavirin therapy for 3 months. All the patients with protracted fecal HEV shedding during treatment suffered a relapse. Monitoring HEV fecal excretion could be used to determine the optimal duration of ribavirin therapy.

Inactivated polio virus (IPV) vaccinations are a mainstay of immunization schedules in developed countries, while oral polio vaccine (OPV) is administered in developing countries and is the main vaccine in outbreaks. Due to circulating wild poliovirus (WPV1) detection in Israel (2013), oral bivalent polio vaccination (bOPV) was administered to IPV primed children and incorporated into the vaccination regimen. We aimed to determine the extent and timeframe of fecal and salivary polio vaccine virus (Sabin strains) shedding following bOPV vaccination among IPV primed children. Fecal samples were collected from a convenience sample of infants and toddlers attending 11 Israeli daycare centers. Salivary samples were collected from infants and toddlers following bOPV vaccination. 398 fecal samples were collected from 251 children (ages: 6–32 months), 168 received bOPV vaccination 4–55 days prior to sample collection. Fecal excretion continued among 80 %, 50 %, and 20 %, 2, 3, and 7 weeks following vaccination. There were no significant differences in the rate and duration of positive samples among children immunized with 3 or 4 IPV doses. Boys were 2.3-fold more likely to excrete the virus (p = 0.006). Salivary shedding of Sabin strains occurred in 1/47 (2 %) and 1/49 (2 %) samples 4, and 6 days following vaccination respectively. Fecal detection of Sabin strains among IPV-primed children continues for 7 weeks; additional doses of IPV do not augment intestinal immunity; limited salivary shedding occurs for up to a week. This data can enhance understanding of intestinal immunity achieved by different vaccination schedules and guide recommendations for contact precautions of children following bOPV vaccination.

Worldwide, acute gastroenteritis (AGE) is a major cause of morbidity and mortality in children under 5 years of age. Viruses, including norovirus, rotavirus, and enteric adenovirus, are the leading causes of pediatric AGE. In this prospective cohort study, we investigated the viral load and duration of shedding of norovirus, rotavirus, and adenovirus in stool samples collected from 173 children (median age: 15 months) with AGE who presented to emergency departments (EDs) across Canada on Day 0 (day of enrollment), and 5 and 28 days after enrollment. Quantitative RT-qPCR was performed to assess the viral load. On Day 0, norovirus viral load was significantly lower compared to that of rotavirus and adenovirus (p < 0.001). However, on Days 5 and 28, the viral load of norovirus was higher than that of adenovirus and rotavirus (p < 0.05). On Day 28, norovirus was detected in 70% (35/50) of children who submitted stool specimens, while rotavirus and adenovirus were detected in 52.4% (11/24) and 13.6% (3/22) of children (p < 0.001), respectively. Overall, in stool samples of children with AGE who presented to EDs, rotavirus and adenovirus had higher viral loads at presentation compared to norovirus; however, norovirus was shed in stool for the longest duration.

Background/Objectives: Lawsonia intracellularis is a bacterium that causes Proliferative Enteropathy, an enteric infection characterized mainly by diarrhea and growth retardation, leading to important economic losses. Acute and chronic infections are easily diagnosed, and their control by vaccination has been proven efficacious. However, subclinical infections, despite being very prevalent, often remain underdiagnosed and uncontrolled in practice. Scarce research is available on the control of subclinical infections by vaccination, and the benefit in these scenarios remains to be elucidated. Two field trials were carried out to (1) determine the association between the growth and fecal shedding of L. intracellularis in unvaccinated and intramuscularly vaccinated pigs in a farm with subclinical infection and (2) assess the impact of intradermal vaccination against L. intracellularis on clinical performance and carcass quality in a herd with subclinical infection. Methods: A pig herd with subclinical infection was selected. Pigs were vaccinated intramuscularly (study 1) or intradermally (study 2) at weaning. Fecal shedding, performance, clinical parameters, and carcass quality were investigated. Results: Growth was negatively associated with the fecal load of L. intracellularis in non-vaccinated pigs, whereas in vaccinated pigs, growth performance was not impacted by fecal load (study 1). Vaccinated pigs presented a significantly lower fecal load, lower prevalence of tail biting (31.7%) compared with controls (54.2%), less back fat, and a greater Lean Meat percentage (study 2). Conclusions: Vaccination against L. intracellularis in a herd with subclinical infection and low fecal bacterial shedding led to a reduction in fecal shedding, a lower prevalence of tail biting, and an improvement in carcass quality.

Background Group A Rotavirus (RVA), despite being an important pathogen in hospitalized children, is less studied in pediatric outpatients, and even rarely investigated in adults. This study aims to understand the genetic diversity of RVA in outpatients across all age groups in Shanghai, and thus providing a molecular basis for vaccine implementation and evaluation. Methods Stool samples were first screened by Real-time Reverse Transcription Polymerase Chain Reaction (rRT-PCR). RVA genotyping was performed through the amplification of partial VP7 and VP4 gene. Strains of interest were further sequenced and analyzed using MEGA 6.0. Results Four thousand nine hundred one samples were collected, from which 7.61% (373 cases) were screened positive for RVA. RVA prevalence was higher in children (9.30%) than in adults (7.21%) (χ 2  = 4.72, P  < 0.05). 9.38% RVA positive cases had taken antibiotics before hospital visit while 49.60% had been prescribed antibiotics afterwards. RVA displayed a strong seasonality in both adults and children with a shared commonality in genotype repertoire, where G9P[8] was the most prevalent strain (67.96%) followed by G3P[8] (15.49%) and G1P[8] (12.32%). Meanwhile the first local case of fecal shedding of the G10P[15] vaccine strain was also discovered. Conclusions While the prevalence of rotavirus is highest during cold seasons, it is revealed for the first time that G9P[8] is the predominant genotype in both adults and pediatric outpatients. Clinically, higher occurrence of nausea or vomiting was observed in RVA positive cases. Antibiotic overuse was implicated in both non-clinical and clinical settings. The finding emphasizes the importance of RVA genotyping in surveillance as it provides the basis for new vaccine application as well as a baseline for future vaccine efficacy evaluation.

A correlate of protection for rotavirus (RV) has not been consistently identified. Shedding of RV following an oral rotavirus vaccine (ORV) challenge has been investigated as a potential model to assess protection of parenteral RV vaccines. We previously showed that shedding of a challenge ORV dose was significantly reduced among recipients of a parenteral monovalent RV subunit vaccine (P2-VP8-P[8]) compared to placebo recipients. This secondary data analysis assessed the association between fecal shedding of RV, as determined by ELISA one week after receipt of a Rotarix challenge dose at 18 weeks of age, and serum RV-specific antibody responses, one and six months after vaccination with the third dose of the P2-VP8-P[8] vaccine or placebo. We did not find any association between serum RV-specific immune responses measured one month post-P2-VP8-P[8] vaccination and fecal shedding of RV post-challenge. At nine months of age, six months after the third P2-VP8-P[8] or placebo injection and having received three doses of Rotarix, infants shedding RV demonstrated higher immune responses than non-shedders, showing that RV shedding is reflective of vaccine response following ORV. Further evaluation is needed in a larger sample before fecal shedding of an ORV challenge can be used as a measure of field efficacy in RV vaccine trials.

Since the coronavirus disease 2019 (COVID-19) pandemic, wastewater-based epidemiology (WBE) has been widely applied in many countries and regions for monitoring COVID-19 transmission in the population through testing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in wastewater. However, the amount of virus shed by individuals over time based on the stage of infection and accurate number of infections in the community creates challenges in predicting COVID-19 prevalence in the population and interpreting WBE results. In this study, we measured SARS-CoV-2, pepper mild mottle virus (PMMoV), and human mitochondrial DNA (mtDNA) in longitudinal fecal samples collected from 42 COVID-19 patients for up to 42 days after diagnosis. SARS-CoV-2 RNA was detected in 73.1% (19/26) of inpatient study participants in at least one of the collected fecal specimens during the sampling period. Most participants shed the virus within 3 weeks after diagnosis, but five inpatient participants still shed the virus between 20 and 60 days after diagnosis. The median concentration of SARS-CoV-2 in positive fecal samples was 1.08 × 10 5 genome copies (GC)/gram dry fecal material. PMMoV and mtDNA were detected in 99.4% (154/155) and 100% (155/155) of all fecal samples, respectively. The median concentrations of PMMoV RNA and mtDNA in fecal samples were 1.73 × 10 7 and 2.49 × 10 8 GC/dry gram, respectively. These results provide important information about the dynamics of fecal shedding of SARS-CoV-2 and two human fecal indicators in COVID-19 patients. mtDNA showed higher positive rates, higher concentrations, and less variability between and within individuals than PMMoV, suggesting that mtDNA could be a better normalization factor for WBE results than PMMoV.