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Interpretation of temporal and spatial trends of SARS-CoV-2 RNA in San Francisco Bay Area wastewater [article]

Hannah D. Greenwald, Lauren C. Kennedy, Adrian Hinkle, Oscar N. Whitney, Vinson B. Fan, Alexander Crits-Christoph, Sasha Harris-Lovett, Avi I. Flamholz, Basem Al-Shayeb, Lauren D. Liao, Matt Beyers, Daniel Brown (+9 others)
2021 medRxiv   pre-print

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https://web.archive.org/web/20210717053140/https://www.medrxiv.org/content/medrxiv/early/2021/05/07/2021.05.04.21256418.full.pdf

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Wastewater surveillance for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA can be integrated with COVID-19 case data to inform timely pandemic response. However, more research is needed to apply and develop systematic methods to interpret the true SARS-CoV-2 signal from noise introduced in wastewater samples (e.g., from sewer conditions, sampling and extraction methods, etc.). In this study, raw wastewater was collected weekly from five sewersheds and one residential facility,
more » ... and wastewater SARS-CoV-2 concentrations were compared to geocoded COVID-19 clinical testing data. SARS-CoV-2 was reliably detected (95% positivity) in frozen wastewater samples when reported daily new COVID-19 cases were 2.4 or more per 100,000 people. To adjust for variation in sample fecal content, crAssphage, pepper mild mottle virus, Bacteroides ribosomal RNA (rRNA), and human 18S rRNA were evaluated as normalization biomarkers, and crAssphage displayed the least spatial and temporal variability. Both unnormalized SARS-CoV-2 RNA signal and signal normalized to crAssphage had positive and significant correlation with clinical testing data (Kendall's Tau-b=0.43 and 0.38, respectively). Locational dependencies and the date associated with testing data impacted the lead time of wastewater for clinical trends, and no lead time was observed when the sample collection date (versus the result date) was used for both wastewater and clinical testing data. This study supports that trends in wastewater surveillance data reflect trends in COVID-19 disease occurrence and presents approaches that could be applied to make wastewater signal more interpretable and comparable across studies.
doi:10.1101/2021.05.04.21256418 fatcat:bwe32xrw3fcfbnmgq57joxxw4u
Citation

Hannah D. Greenwald, Lauren C. Kennedy, Adrian Hinkle, Oscar N. Whitney, Vinson B. Fan, Alexander Crits-Christoph, Sasha Harris-Lovett, Avi I. Flamholz, Basem Al-Shayeb, Lauren D. Liao, Matt Beyers, Daniel Brown, Alicia R. Chakrabarti, Jason Dow, Dan Frost, Mark Koekemoer, Chris Lynch, Payal Sarkar, Eileen White, Rose Kantor, Kara L. Nelson. "Interpretation of temporal and spatial trends of SARS-CoV-2 RNA in San Francisco Bay Area wastewater." medRxiv (2021)