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Kim, Sooyeol; Kennedy, Lauren C.; Wolfe, Marlene K.; Criddle, Craig S.; Duong, Dorothea H.; Topol, Aaron; White, Bradley J.; Kantor, Rose S.; Nelson, Kara L.; Steele, Joshua A.; et al(
, Environmental Science: Water Research & Technology)
Wastewater-based epidemiology has gained attention throughout the world for detection of SARS-CoV-2 RNA in wastewater to supplement clinical testing. Raw wastewater consists of small particles, or solids, suspended in liquid. Methods have been developed to measure SARS-CoV-2 RNA in the liquid and the solid fraction of wastewater, with some studies reporting higher concentrations in the solid fraction. To investigate this relationship further, six laboratories collaborated to conduct a study across five publicly owned treatment works (POTWs) where both primary settled solids obtained from primary clarifiers and raw wastewater influent samples were collected and quantified for SARS-CoV-2 RNA. Settled solids andmore »influent samples were processed by participating laboratories using their respective methods and retrospectively paired based on date of collection. SARS-CoV-2 RNA concentrations, on a mass equivalent basis, were higher in settled solids than in influent by approximately three orders of magnitude. Concentrations in matched settled solids and influent were positively and significantly correlated at all five POTWs. RNA concentrations in both settled solids and influent were correlated to COVID-19 incidence rates in the sewersheds and thus representative of disease occurrence; the settled solids methods appeared to produce a comparable relationship between SARS-CoV-2 RNA concentration measurements and incidence rates across all POTWs. Settled solids and influent methods showed comparable sensitivity, N gene detection frequency, and calculated empirical incidence rate lower limits. Analysis of settled solids for SARS-CoV-2 RNA has the advantage of using less sample volume to achieve similar sensitivity to influent methods.« less
Free, publicly-accessible full text available February 15, 2023
Crits-Christoph, Alexander; Kantor, Rose S.; Olm, Matthew R.; Whitney, Oscar N.; Al-Shayeb, Basem; Lou, Yue Clare; Flamholz, Avi; Kennedy, Lauren C.; Greenwald, Hannah; Hinkle, Adrian; et al(
, mBio)
Pettigrew, Melinda M.
(Ed.)
ABSTRACT Viral genome sequencing has guided our understanding of the spread and extent of genetic diversity of SARS-CoV-2 during the COVID-19 pandemic. SARS-CoV-2 viral genomes are usually sequenced from nasopharyngeal swabs of individual patients to track viral spread. Recently, RT-qPCR of municipal wastewater has been used to quantify the abundance of SARS-CoV-2 in several regions globally. However, metatranscriptomic sequencing of wastewater can be used to profile the viral genetic diversity across infected communities. Here, we sequenced RNA directly from sewage collected by municipal utility districts in the San Francisco Bay Area to generate complete and nearly complete SARS-CoV-2 genomes. Themore »major consensus SARS-CoV-2 genotypes detected in the sewage were identical to clinical genomes from the region. Using a pipeline for single nucleotide variant calling in a metagenomic context, we characterized minor SARS-CoV-2 alleles in the wastewater and detected viral genotypes which were also found within clinical genomes throughout California. Observed wastewater variants were more similar to local California patient-derived genotypes than they were to those from other regions within the United States or globally. Additional variants detected in wastewater have only been identified in genomes from patients sampled outside California, indicating that wastewater sequencing can provide evidence for recent introductions of viral lineages before they are detected by local clinical sequencing. These results demonstrate that epidemiological surveillance through wastewater sequencing can aid in tracking exact viral strains in an epidemic context.« less
McClary-Gutierrez, Jill S.; Aanderud, Zachary T.; Al-faliti, Mitham; Duvallet, Claire; Gonzalez, Raul; Guzman, Joe; Holm, Rochelle H.; Jahne, Michael A.; Kantor, Rose S.; Katsivelis, Panagis; et al(
, Environmental Science: Water Research & Technology)
SARS-CoV-2 RNA detection in wastewater is being rapidly developed and adopted as a public health monitoring tool worldwide. With wastewater surveillance programs being implemented across many different scales and by many different stakeholders, it is critical that data collected and shared are accompanied by an appropriate minimal amount of meta-information to enable meaningful interpretation and use of this new information source and intercomparison across datasets. While some databases are being developed for specific surveillance programs locally, regionally, nationally, and internationally, common globally-adopted data standards have not yet been established within the research community. Establishing such standards will require national andmore »international consensus on what meta-information should accompany SARS-CoV-2 wastewater measurements. To establish a recommendation on minimum information to accompany reporting of SARS-CoV-2 occurrence in wastewater for the research community, the United States National Science Foundation (NSF) Research Coordination Network on Wastewater Surveillance for SARS-CoV-2 hosted a workshop in February 2021 with participants from academia, government agencies, private companies, wastewater utilities, public health laboratories, and research institutes. This report presents the primary two outcomes of the workshop: (i) a recommendation on the set of minimum meta-information that is needed to confidently interpret wastewater SARS-CoV-2 data, and (ii) insights from workshop discussions on how to improve standardization of data reporting.« less
White, S.; Irwin, R.; Warwick, J. R.; Gribakin, G. F.; Sarri, G.; Keenan, F. P.; Riley, D.; Rose, S. J.; Hill, E. G.; Ferland, G. J.; et al(
, Physical Review E)
Liddick, S. N.; Larsen, A. C.; Guttormsen, M.; Spyrou, A.; Crider, B. P.; Naqvi, F.; Midtbø, J. E.; Bello Garrote, F. L.; Bleuel, D. L.; Crespo Campo, L.; et al(
, Physical Review C)
Tveten, G. M.; Spyrou, A.; Schwengner, R.; Naqvi, F.; Larsen, A. C.; Eriksen, T. K.; Bello Garrote, F. L.; Bernstein, L. A.; Bleuel, D. L.; Crespo Campo, L.; et al(
, Physical Review C)
