Longitudinal and quantitative fecal shedding dynamics of SARS-CoV-2, pepper mild mottle virus, and crAssphage

Arts, Peter J.; Kelly, John D.; Midgley, Claire M; Anglin, Khamal; Lu, Scott; Abedi, Glen R.; Andino, Raul; Bakker, Kevin; Banman, Bryon; Boehm, Alexandria B.; Briggs-Hagen, Melissa; Brouwer, Andrew F.; Davidson, Michelle; Eisenberg, Marisa C.; Garcia-Knight, Miguel; Knight, Sterling; Peluso, Michael J.; Pineda-Ramirez, Jesus; Sanchez, Ruth Diaz; Saydah, Sharon; Tassetto, Michel; Martin, Jeffrey N.; Wigginton, Krista

doi:10.1128/msphere.00132-23

Cited by 33 publications

(20 citation statements)

References 43 publications

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“…In this study, PMMoV was detected in 99.4% fecal samples, with a median concentration of 1.73×10 7 GC/dry gram. The PMMoV concentrations measured in this study are similar to those reported in one recent publication that also quantified PMMoV in human stool samples using digital PCR and reported dry mass concentrations (27). In concordance with their results, we observed significant variations of PMMoV concentrations between and within individuals throughout the sampling period.…”

Section: Discussionsupporting

confidence: 88%

“…Another study reported the fecal shedding results from 48 SARS-CoV-2 infected individuals and observed that approximately 80% of the fecal samples collected within the first 5 days were positive for SARS-CoV-2, and this positivity rate dropped to 10% at 28 days after symptom onset. A median concentration of three orders GC of magnitude/mg dry weight was reported in positive fecal samples (27), which is one order GC of magnitude higher compared to this study.…”

Section: Discussioncontrasting

confidence: 71%

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Longitudinal Fecal Shedding of SARS-CoV-2, Pepper Mild Mottle Virus, and Human Mitochondrial DNA in COVID-19 Patients

Liu,

Sablon,

Wang

et al. 2024

Preprint

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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 lack of dynamic level of viral shedding in the wastewater 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 three 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 1.08x105 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 1.73x107 and 2.49x108 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.

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Section: Discussionsupporting

confidence: 88%

Section: Discussioncontrasting

confidence: 71%

Longitudinal Fecal Shedding of SARS-CoV-2, Pepper Mild Mottle Virus, and Human Mitochondrial DNA in COVID-19 Patients

Liu,

Sablon,

Wang

et al. 2024

Preprint

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“…There is no quantitative data on longitudinal RSV shedding in human excretions, and it is possible prolonged shedding in convalescing or recovered individuals occurs . Shedding magnitude and duration, while unknown, are key drivers of wastewater RSV concentrations . The positivity rate is not a measure of disease incidence or prevalence but is often used as a proxy for disease occurrence.…”

Section: Discussionmentioning

confidence: 99%

Observations of Respiratory Syncytial Virus (RSV) Nucleic Acids in Wastewater Solids Across the United States in the 2022–2023 Season: Relationships with RSV Infection Positivity and Hospitalization Rates

Zulli,

Varkila,

Parsonnet

et al. 2024

ACS EST Water

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Respiratory syncytial virus (RSV) is a leading cause of respiratory illness and hospitalization, but clinical surveillance detects only a minority of cases. Wastewater surveillance could determine the onset and extent of RSV circulation in the absence of sensitive case detection, but to date, studies of RSV in wastewater are few. We measured RSV RNA concentrations in wastewater solids from 176 sites during the 2022−2023 RSV season and compared those to publicly available RSV infection positivity and hospitalization rates. Concentrations ranged from undetectable to 10 7 copies per gram. RSV RNA concentration aggregated at state and national levels correlated with infection positivity and hospitalization rates. RSV season onset was determined using both wastewater and clinical positivity rates using independent algorithms for 14 states where both data were available at the start of the RSV season. In 4 of 14 states, wastewater and clinical surveillance identified RSV season onset during the same week; in 3 states, wastewater onset preceded clinical onset, and in 7 states, wastewater onset occurred after clinical onset. Wastewater concentrations generally peaked in the same week as hospitalization rates but after case positivity rates peaked. Differences in onset and peaks in wastewater versus clinical data may reflect inherent differences in the surveillance approaches.

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“…While our serosurvey only captured adults, wastewater testing included minors. COVID-19 infected individuals can, in rare instances, shed fecal SARS-CoV-2 up to 7 months post diagnosis; 27 viral shedding of SARS-CoV-2 can vary in relation to vaccination status and variant 28,29 and thus was not included in our model. One of the major advances of this paper is the presentation of a relatively simple and flexible analytical model capable of using wastewater concentration to predict the effect of vaccination and new variants on prevalence and hospitalization rates.…”

Section: Discussionmentioning

confidence: 99%

Wastewater and seroprevalence for pandemic preparedness: variant analysis, vaccination effect, and hospitalization forecasting for SARS-CoV-2, in Jefferson County, Kentucky

Holm

Rempała

Choi

et al. 2023

Preprint

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Background Since early in the COVID-19 pandemic, SARS-CoV-2 wastewater concentration has been measured as a surrogate for community prevalence. However, our knowledge remains limited regarding wastewater concentration and effects of the COVID-19 vaccination on overall disease burden as measured by hospitalization rates. Methods We used weekly SARS-CoV-2 wastewater concentration with a stratified random sampling of seroprevalence, and spatially linked vaccination and hospitalization data, from April to August 2021. Our susceptible (S), vaccinated (V), variant-specific infected (I1 and I2), recovered (R), and seropositive (T) model (SVI2RT) tracked prevalence longitudinally. This was related to wastewater concentration for a spatial analysis of strain mutation, vaccination effect, and overall hospitalization burden. Findings We found strong linear association between wastewater concentration and estimated community prevalence (r=0.916). Based on the corresponding regression model, the 64% county vaccination rate translated into about 57% decrease in SARS-CoV-2 incidence. During the study period, the estimated effect of SARS-CoV-2 Delta variant emergence was seen as an over 7-fold increase of infection counts, which corresponded to over 12-fold increase in wastewater concentration. Hospitalization burden and wastewater concentration had the strongest correlation (r=0.963) at 1 week lag time. We estimated the community vaccination campaign resulted in about 63% reduction in the number of daily admissions over the study period. This protective effect was counteracted by the emergence of SARS-CoV-2 Delta strain mutation. Interpretation Wastewater samples can be used to estimate the effects of vaccination and hospitalization burden. Our study underscores the importance of continued environmental surveillance post-vaccine and provides a proof of concept for environmental epidemiology monitoring.

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Longitudinal and quantitative fecal shedding dynamics of SARS-CoV-2, pepper mild mottle virus, and crAssphage

Cited by 33 publications

References 43 publications

Longitudinal Fecal Shedding of SARS-CoV-2, Pepper Mild Mottle Virus, and Human Mitochondrial DNA in COVID-19 Patients

Longitudinal Fecal Shedding of SARS-CoV-2, Pepper Mild Mottle Virus, and Human Mitochondrial DNA in COVID-19 Patients

Observations of Respiratory Syncytial Virus (RSV) Nucleic Acids in Wastewater Solids Across the United States in the 2022–2023 Season: Relationships with RSV Infection Positivity and Hospitalization Rates

Wastewater and seroprevalence for pandemic preparedness: variant analysis, vaccination effect, and hospitalization forecasting for SARS-CoV-2, in Jefferson County, Kentucky

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