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

Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) 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 5680 were “novel” SNVs that had not yet been identified in the global clinical-derived data as of 17th June 2020 (the day after our last wastewater sampling date). However, between 17th of June 2020 and 20th November 2020, almost half of the SNVs have since been detected in clinical-derived data. Using the combination of SNVs present in each sample, we identified the more probable lineages present in that sample and compared them to lineages observed in North America prior to our sampling dates. The wastewater-derived SARS-CoV-2 sequence data indicates there were more lineages circulating across the sampled communities than represented in the clinical-derived data. Principal coordinate analyses identified patterns in population structure based on genetic variation within the sequenced samples, with clear trends associated with increased diversity likely due to a higher number of infected individuals relative to the sampling dates. We demonstrate that genetic correlation analysis combined with SNVs analysis using wastewater sampling can provide a comprehensive snapshot of the SARS-CoV-2 genetic population structure circulating within a community, which might not be observed if relying solely on clinical cases.

Rapid Increase of SARS-CoV-2 Variant B.1.1.7 Detected in Sewage Samples from England between October 2020 and January 2021

“…Variant D614G was first described in late February 2020 in Italy, rapidly expanding and becoming the dominant SARS-CoV-2 variant globally a few months later ( 23 ). Similar work by other groups has described the detection of cocirculating SARS-CoV-2 variants in sewage samples from different locations, including a recent report describing the identification of B.1.1.7 lineage in sewage samples from Switzerland ( 24 – 28 ).…”

RNA viromics of Southern California wastewater and detection of SARS-CoV-2 single nucleotide variants

“…Likewise, as we detected over 1000 SARS-CoV-2 SNVs across our samples, we found many SNVs of putatively unknown function that have been detected in patient samples, such as 6285C>T and 9891C>T (found in, but does not solely define, variants B.1.525 and B.1.1.318 respectively), 28854C>T and 28887C>T (40,59,60). We also detected many SNVs also found in wastewater samples from Northern California (46) and SNVs that to the best of our knowledge, have yet to be sequenced (41,46,48). As our sequencing data are not quantitative, our study suggests that sequencing wastewater is useful for SNV detection across wide catchment areas, but not the true prevalence of SNVs (46).…”

SARS-CoV-2 detection and genomic sequencing from hospital surface samples collected at UC Davis

“…(33)). Furthemore, environmental samples in particular may have been degraded or diluted, affecting the genomic RNA available for reverse transcription, as observed in multiple studies of environmental samples ((34–36).…”