Abstract and Introduction
Genomic surveillance has emerged as a critical monitoring tool during the SARS-CoV-2 pandemic. Wastewater surveillance has the potential to identify and track SARS-CoV-2 variants in the community, including emerging variants. We demonstrate the novel use of multilocus sequence typing to identify SARS-CoV-2 variants in wastewater. Using this technique, we observed the emergence of the B.1.351 (Beta) variant in Linn County, Oregon, USA, in wastewater 12 days before this variant was identified in individual clinical specimens. During the study period, we identified 42 B.1.351 clinical specimens that clustered into 3 phylogenetic clades. Eighteen of the 19 clinical specimens and all wastewater B.1.351 specimens from Linn County clustered into clade 1. Our results provide further evidence of the reliability of wastewater surveillance to report localized SARS-CoV-2 sequence information.
Since its emergence in late 2019, more than 481 million COVID-19 cases have been confirmed worldwide and >79 million cases reported in the United States. Numerous variants of the causative virus, SARS-CoV-2, have emerged; variants of concern have demonstrated characteristics of public health concern, including increased transmissibility or clinical severity, reduced vaccine or therapeutic effectiveness, or diagnostic escape. SARS-CoV-2 genomic surveillance has quickly become an essential tool for tracking transmission and coordinating response.[4,5] Individual-level genomic surveillance relies on the testing of infected persons, which, in turn, requires testing access and acceptance. In the United States, testing access has improved dramatically over the course of the pandemic but remains limited, particularly in disproportionately affected communities, and testing acceptance remains an obstacle to effective disease mitigation.
SARS-CoV-2 is shed in feces, and wastewater surveillance has emerged as complementary cost-effective community-level surveillance independent of testing access and acceptance or symptomatic infection.[8–10] Using wastewater testing for SARS-CoV-2 genomic surveillance avoids the testing and symptomatic biases inherent to the sequencing of individual specimens; however, interpreting sequence data from complex mixtures of viruses at a population-level remains challenging. Multilocus sequence typing (MLST) is a method traditionally used to identify species or variants in environmental samples, including rivers, urban streams, hospital sewage, and wastewater treatment plant influents and effluents.[12,13] MLST is well-suited for the analysis of wastewater RNA because it detects a set of mutations unique to a variant and does not require these mutations to be present on a single molecule of RNA.[12–18]
During the COVID-19 pandemic, Oregon has been among the US states with the lowest cumulative case rates and among those with the highest proportion of cumulative molecular specimens sequenced in the United States. As of March 31, 2021, a total of 159,455 confirmed cases of COVID-19 had been identified in Oregon, and specimens from 5,674 (3.6%) of the cases had been sequenced and published in the GISAID database (https://www.gisaid.org). At that time, the dominant SARS-CoV-2 variant circulating in Oregon was B.1.427/B.1.429 (Epsilon), followed by B.1.2 and B.1.1.7 (Alpha); only 25 B.1.351 (Beta) and 8 P.1 (Gamma) variants had been identified.
On April 19, 2021, Oregon mandated reporting of all SARS-CoV-2 variants of concern to public health authorities; before this, genomic surveillance relied largely on deidentified data submitted to GISAID. Statewide sequencing partners have been asked to submit all individual specimen sequencing results to the State of Oregon phylodynamics resource in GISAID (https://www.gisaid.org/phylodynamics/oregon-usa).
In September 2020, the Oregon Health Authority launched wastewater surveillance in collaboration with the Oregon State University (OSU) Team-Based Rapid Assessment of Community-Level Coronavirus Epidemics (TRACE) project; >40 communities comprising ≈60% of Oregon's population currently participate. Through this program, wastewater samples from the influent of all wastewater treatment facilities are collected at least weekly and sent to OSU for SARS-CoV-2 viral RNA quantification and sequencing of all positive samples with sufficient viral loads. Through this statewide SARS-CoV-2 wastewater surveillance platform, we demonstrate the use of MLST to detect the emergence of the SARS-CoV-2 B.1.351 (Beta) variant in rural Oregon in late March 2021, before its detection in reported cases, illustrating the ability of wastewater-based epidemiology to detect emerging variants of concern.
Emerging Infectious Diseases. 2022;28(6):1101-1109. © 2022 Centers for Disease Control and Prevention (CDC)