ABSTRACT
The sequencing of human virus genomes from wastewater samples is an efficient method for tracking viral transmission and evolution at the community level. However, this requires the recovery of viral nucleic acids of high quality. We developed a reusable tangential-flow filtration system to concentrate and purify viruses from wastewater for whole-genome sequencing. A pilot study was conducted with 94 wastewater samples from four local sewersheds, from which viral nucleic acids were extracted, and the whole genome of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was sequenced using the ARTIC V4.0 primers. Our method yielded a high probability (0.9) of recovering complete or near-complete SARS-CoV-2 genomes (>90% coverage at 10x depth) from wastewater when the COVID-19 incidence rate exceeded 33 cases per 100 000 people. The relative abundances of sequenced SARS-CoV-2 variants followed the trends observed from patient-derived samples. We also identified SARS-CoV-2 lineages in wastewater that were underrepresented or not present in the clinical whole-genome sequencing data. The developed tangential-flow filtration system can be easily adopted for the sequencing of other viruses in wastewater, particularly those at low concentrations. SYNOPSISThe tangential-flow filtration method extracts viral nucleic acids of high enough quality from wastewater for robust and successful whole-genome sequencing. GRAPHIC FOR TABLE OF CONTENTS (TOC) O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=112 SRC="FIGDIR/small/22279692v2_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@566377org.highwire.dtl.DTLVardef@19c3ba7org.highwire.dtl.DTLVardef@106c70org.highwire.dtl.DTLVardef@3f3f8f_HPS_FORMAT_FIGEXP M_FIG C_FIG
ABSTRACT
Early in the SAR-CoV-2 pandemic, we established a whole genome sequencing pipeline to assess lineages circulating in Western New York. Initial sequences revealed entry into the region via Europe, similar to observations in New York City. However, as the pandemic progressed and variants of concern emerged, we observed distinct patterns in lineages relative to NYC. Notably, B.1.427 became dominant in Western New York, before it was displaced by B.1.1.7. Our hierarchical cluster analysis of B.1.1.7 lineages, which by May 2021 made up [~] 80% of all cases, indicated both multiple introductions and community spread. Our work highlights the importance of widespread, regional surveillance of SARS-CoV-2 across the United States.
