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Wastewater surveillance of SARS-CoV-2 and quantitative analysis of the Alpha variant in Ohio
Citation:
Hart, C. AND N. Brinkman. Wastewater surveillance of SARS-CoV-2 and quantitative analysis of the Alpha variant in Ohio. Water Environment Foundation - Public Health and Water Conference & Wastewater Disease Surveillance Summit, Cincinnati, OH, March 21 - 24, 2022.
Impact/Purpose:
Wastewater monitoring of SARS-CoV-2 presents a means of tracking COVID-19 community infection dynamics on a broader geographic scale. However, accounting for environmental and sample-processing losses may be necessary for wastewater measurements to readily inform our understanding of infection prevalence. Here, we present measurements of N1 and N2 gene targets from weekly wastewater samples at three sites in Hamilton County, Ohio. N1 and N2 RT-PCR assay-based SARS-CoV-2 RNA concentrations in wastewater measured over the course of six months correlated with case data at two wastewater treatment plants, but not at a sub-sewershed-level sampling site. The utility of a spiked matrix recovery control (OC43), flownormalization, and assessment of fecal loading using endogenous fecal markers (HF183, PMMoV, crAssphage) in improving correlations of SARSCoV-2concentrations with case data were investigated. We found that adjusting for recovery, flow, and fecal indicators improved estimates of samples from a larger sewershed with greater industrial and stormwater inputs, but raw concentrations corresponded better with case data at a smaller, residential oriented sewershed.
Description:
Background: Wastewater-based surveillance is an effective tool to monitor spatial and temporal trends of COVID-19 in communities. This type of surveillance can supplement individual testing and could provide a more comprehensive analysis of COVID-19 prevalence in a community since a large proportion of cases may be asymptomatic or self-limiting and remain unrepresented in clinical data. Emergence of variants of concern (VOCs), SARS-CoV-2 lineages associated with increased transmissibility, virulence, and/or antibody escape either from prior infection or vaccination, has led to an increased need to identify and quantify these variants circulating in the community. The VOC lineage B.1.1.7 (Alpha), first recognized in the UK, emerged near the end of 2020 and evidence indicated it was more efficiently transmitted than other variants. The variant displayed a number of mutations throughout the genome, including in the spike region of the genome corresponding to a deletion of two adjacent amino acids, H69-V70, and amino acid replacement N501Y. While N501Y occurs in other VOCs, such as the B.1.351 (Beta) and P.1 (Gamma) variants, Alpha is the only VOC or variant of interest circulating in the US harboring the ΔH69/V70. In this presentation, I will summarize our efforts to monitor SARS-CoV-2 concentrations and trends in wastewater samples, the detection and quantification of N501Y and ΔH69/V70, and the prevalence of Alpha across our Ohio sampling sites. Methods: In collaboration with the Ohio Department of Health, the Ohio Water Resources Center, the Ohio EPA, and various university labs, we are actively monitoring wastewater from utilities in Ohio as part of a statewide wastewater surveillance plan to aid in determining public health responses. Concentrations of SARS-CoV-2 are determined by reverse-transcriptase droplet digital PCR (RT-ddPCR). Between the end of March 2021 to early May 2021, we also performed duplexed RT-ddPCR to quantify RNA sequences with and without the mutations corresponding to N501Y and ΔH69/V70 on a temporal and spatial scale. Furthermore, we sequenced SARS-CoV-2 RNA in wastewater using a tiled amplicon approach and a NextSeq550 to assess genetic diversity in contributing populations and verify the results of the RT-ddPCR assays. Results: Over the course of our sampling, between March - May 2021, there was a large shift in the proportion of SARS-CoV-2 RNA sequences containing the mutations that correspond to the N501Y and ΔH69/V70 amino acid changes (Figure 1). From October through November 2020, 100% of the SARS-CoV-2 RNA sequences detected were non-Alpha, as no sequences associated with the ΔH69/70 deletion detected. Between March - May 2021, the proportion of sequences associated with ΔH69/70 increases to nearly 90%, indicating Alpha was likely the dominant variant in the sampling area. Impact: We saw a large shift in the B lineage towards Alpha in all sampling sites, with Alpha becoming the dominant variant of SARS-CoV-2 by mid-late April. With the emergence and spread of new variants, such as Delta, along with increasing case counts across Ohio, continued surveillance for specific mutations in communities will be important for tracking the spread of VOCs and informing public health responses.