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High-throughput sequencing of SARS-CoV-2 in wastewater provides insights into circulating variants

2021; Elsevier BV; Volume: 205; Linguagem: Inglês

10.1016/j.watres.2021.117710

1879-2448

Rafaela S. Fontenele, Simona Kraberger, James Hadfield, Erin M. Driver, Devin A. Bowes, LaRinda A. Holland, Temitope O. C. Faleye, Sangeet Adhikari, Rahul Kumar, Rosa Inchausti, Wydale Holmes, Stephanie Deitrick, Philip N. Brown, Darrell Duty, Ted Smith, Aruni Bhatnagar, Ray Yeager, Rochelle H. Holm, Natalia Hoogesteijn von Reitzenstein, Elliott Wheeler, Kevin Dixon, Tim Constantine, Melissa A. Wilson, Efrem S. Lim, Xiaofang Jiang, Rolf U. Halden, Matthew Scotch, Arvind Varsani,

Biosensors and Analytical Detection

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) likely emerged from a zoonotic spill-over event and has led to a global pandemic. The public health response has been predominantly informed by surveillance of symptomatic individuals and contact tracing, with quarantine, and other preventive measures have then been applied to mitigate further spread. Non-traditional methods of surveillance such as genomic epidemiology and wastewater-based epidemiology (WBE) have also been leveraged during this pandemic. Genomic epidemiology uses high-throughput sequencing of SARS-CoV-2 genomes to inform local and international transmission events, as well as the diversity of circulating variants. WBE uses wastewater to analyse community spread, as it is known that SARS-CoV-2 is shed through bodily excretions. Since both symptomatic and asymptomatic individuals contribute to wastewater inputs, we hypothesized that the resultant pooled sample of population-wide excreta can provide a more comprehensive picture of SARS-CoV-2 genomic diversity circulating in a community than clinical testing and sequencing alone. In this study, we analysed 91 wastewater samples from 11 states in the USA, where the majority of samples represent Maricopa County, Arizona (USA). With the objective of assessing the viral diversity at a population scale, we undertook a single-nucleotide variant (SNV) analysis on data from 52 samples with >90% SARS-CoV-2 genome coverage of sequence reads, and compared these SNVs with those detected in genomes sequenced from clinical patients. We identified 7973 SNVs, of which 548 were "novel" SNVs that had not yet been identified in the global clinical-derived data as of 17