The role of time-varying viral shedding in modelling environmental surveillance for public health: revisiting the 2013 poliovirus outbreak in Israel

Brouwer, Andrew F.; Eisenberg, Marisa C.; Shulman, Lester M.; Koopman, James S.; Kroiss, Steve J.; Hindiyeh, Musa; Manor, Yossi; Grotto, Itamar; Eisenberg, Joseph N.S.

doi:10.1098/rsif.2022.0006

Cited by 11 publications

(9 citation statements)

References 74 publications

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“…The idiosyncrasies of the shedding trajectories highlight the potential complications of using models to directly predict epidemiological parameters such as community prevalence. Such attempts have often relied on static distributions rather than trajectories; however, recent work with polio and SARS-CoV-2 has demonstrated methods for incorporating time-varying shedding into mechanistic WBE models ( 10 , 31 ). Using a static distribution for fecal shedding assumes a uniform likelihood of being at any stage in the shedding period.…”

Section: Discussionmentioning

confidence: 99%

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

Arts

Kelly

Midgley

et al. 2023

mSphere

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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. IMPORTANCE 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.

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Section: Discussionmentioning

confidence: 99%

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

Arts

Kelly

Midgley

et al. 2023

mSphere

Self Cite

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show abstract

“…Such attempts have often relied on static distributions rather than trajectories, however recent work with polio and SARS-CoV-2 have demonstrated methods for incorporating time varying shedding into mechanistic WBE models. 10,30 Using a static distribution for fecal shedding assumes a uniform likelihood of being at any stage in the shedding period. However, early in an outbreak the majority of individuals are likely in the early stages of infection; while late in an outbreak, it is more likely a mix of early and late stage of infection.…”

Section: Crass-like Phage (Crassphage)mentioning

confidence: 99%

Longitudinal and Quantitative Fecal Shedding Dynamics of SARS-CoV-2, Pepper Mild Mottle Virus and CrAssphage

Arts

Kelly

Midgley³

et al. 2023

Preprint

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Wastewater-based epidemiology (WBE) emerged during the COVID-19 pandemic as a scalable and broadly applicable method for community-level monitoring of infectious disease burden, though the lack of high-quality, longitudinal fecal shedding data of SARS-CoV-2 and other viruses limits the interpretation and applicability of wastewater measurements. In this study, we present longitudinal, quantitative fecal shedding data for SARS-CoV-2 RNA, as well as 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, with individual measurements varying from below limit of detection to 2.79x10^6 gene copies/mg - dry mass of stool (gc/mg-dw). Of individuals that contributed at least 3 samples covering a range of at least 15 of the first 30 days after initial acute symptom onset, 77.4% had at least one positive SARS-CoV-2 RNA stool sample measurement. We detected PMMoV RNA in at least one sample from all individuals and in 96% (352/367) of samples overall; and measured crAssphage DNA above detection limits in 80% (38/48) of individuals and 48% (179/371) of samples. Median shedding values for PMMoV and crAssphage nucleic acids were 1x10^5 gc/mg-dw and 1.86x10^3 gc/mg-dw, respectively. These results can be used to inform and build mechanistic models to significantly broaden the potential of WBE modeling and to provide more accurate insight into SARS-CoV-2 prevalence estimates.

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“…It could also be used to monitor at-risk farms as an alternative to pre-emptive culling, thereby reducing the number of animals culled. Because of the ability to infer the disease status of a population without testing many individuals, environmental surveillance has also been utilized for other pathogens that cause animal diseases such as Johne's disease ( 9 ) and avian influenza ( 10 ), as well as human diseases including COVID-19 ( 11 , 12 ) and polio ( 13 – 15 ).…”

Section: Introductionmentioning

confidence: 99%

Assessing the effectiveness of environmental sampling for surveillance of foot-and-mouth disease virus in a cattle herd

Ellis

Brown²,

Colenutt³

et al. 2023

Front. Vet. Sci.

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The survival of foot-and-mouth disease virus (FMDV) in the environment provides an opportunity for indirect transmission, both within and between farms. However it also presents the possibility of surveillance and detection via environmental sampling. This study assesses the effectiveness of environmental sampling strategies in the event of an outbreak, using a previous model for transmission of FMDV in a cattle herd that had been parameterized using data from transmission experiments and outbreaks. We show that environmental sampling can be an effective means of detecting FMDV in a herd, but it requires multiple samples to be taken on multiple occasions. In addition, environmental sampling can potentially detect FMDV in a herd more quickly than clinical inspection. For example, taking 10 samples every 3 days results in a mean time to detection of 6 days, which is lower than the mean time to detection estimated for the 2001 UK epidemic (8 days). We also show how environmental sampling could be used in a herd considered to be at risk as an alternative to pre-emptive culling. However, because of the time taken for virus to accumulate at the start of an outbreak, a reasonable level of confidence (> 99%) that an at-risk herd is indeed free from infection is unlikely to be achieved in less than 1 week.

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The role of time-varying viral shedding in modelling environmental surveillance for public health: revisiting the 2013 poliovirus outbreak in Israel

Cited by 11 publications

References 74 publications

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

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

Longitudinal and Quantitative Fecal Shedding Dynamics of SARS-CoV-2, Pepper Mild Mottle Virus and CrAssphage

Assessing the effectiveness of environmental sampling for surveillance of foot-and-mouth disease virus in a cattle herd

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