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

The study, “Longitudinal and Quantitative Fecal Shedding Dynamics of SARS-CoV-2, Pepper Mild Mottle Virus, and CrAssphage” provides critical insights into the fecal shedding patterns of these viruses, with a focus on SARS-CoV-2.

Here’s a detailed summary:

Study Overview

  • This research, part of the wastewater-based epidemiology (WBE), aimed to understand fecal shedding dynamics of SARS-CoV-2, along with Pepper Mild Mottle Virus (PMMoV) and CrAssphage, two commonly used fecal indicators.
  • The study analyzed shedding patterns from 48 individuals infected with SARS-CoV-2, revealing highly individualized shedding trajectories. It is significant in linking WBE measurements to actual disease burden in communities​​.

Cohort and Methodology

  • Participants were from the San Francisco Bay Area, part of the CDC-funded FIND COVID project. They were not hospitalized but lived with at least one other person. Stool samples were collected periodically over approximately 30 days after symptom onset​​.
  • The cohort comprised a diverse demographic, including individuals who were symptomatic and asymptomatic, as well as vaccinated individuals​​.

Key Findings

  1. SARS-CoV-2 Shedding:
    • About 51% of the samples showed SARS-CoV-2 RNA above the detection limit, and 73% of participants contributed at least one positive sample. Interestingly, three out of four vaccinated individuals had detectable SARS-CoV-2 RNA at some point​​.
    • The study noted a high variability in shedding patterns among individuals. For instance, peak shedding varied from as early as 2 days after symptom onset (ASO) to 27 days. Notably, shedding was detected in some individuals up to 288 days ASO​​.
  2. PMMoV and CrAssphage Shedding:
    • PMMoV RNA was detected in all participants, with 96% of samples testing positive. However, measurements varied significantly between individuals​​.
    • CrAssphage DNA was less frequently detected than PMMoV, found in 48% of all samples and 79% of individuals. Notably, CrAssphage shedding was more consistent over time than PMMoV shedding​​.

Significance and Implications

  • The data collected fills important gaps in understanding the dynamics of viral nucleic acid shedding in feces, crucial for WBE.
  • The study’s high-resolution data offer a detailed depiction of fecal shedding prevalence over the first 30 days ASO. Approximately 80% of samples collected within the first 5 days were positive for SARS-CoV-2, dropping to 10% at 28 days ASO.
  • These findings are vital for improving WBE methods, particularly in accurately estimating the COVID-19 burden in communities.
  • The study also underlines the importance of PMMoV and CrAssphage as fecal strength normalizing measures and their utility in source-tracking applications.

Limitations and Future Directions

  • The study’s scope was limited to a specific geographic area and timeframe (September 2020 – April 2021), excluding the impact of later SARS-CoV-2 variants like Delta or Omicron.
  • Future research should extend to include healthy individuals and explore how fecal shedding dynamics are influenced by different variants, demographic factors, and vaccination status​​.

This research represents a significant advancement in understanding the complexities of viral shedding and its implications for public health monitoring and disease burden estimation using wastewater-based epidemiology.

Read More: https://journals.asm.org/doi/epub/10.1128/msphere.00132-23

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