A rapid assessment of wastewater for genomic surveillance of SARS-CoV-2 variants at sewershed scale in Louisville, KY

Abstract

The successful viral detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in wastewater at various pooled scales (1-4) and discovery in the USA of B.1.1.7 , B.1.351 and P.1 variants (5), has led to an interest in developing reliable population-level wastewater viral genomic surveillance. The diversity of SARS-CoV-2 sequences reported to be circulating in the USA, have been determined by sequencing clinical samples; however, these variants can also be surveilled by sequencing wastewater samples (6-9). As of March 2021, the variants of concern - B.1.1.7, B.1.351, and P.1 have been widely detected in clinical samples from 47 states in the USA. In Kentucky, only five clinical cases have been linked to the presence of these variants (5),which could indicate incomplete surveillance. Broadening the application of genomic surveillance using wastewater in the community could enhance SARS-CoV-2 variant population monitoring. In this communication, we report on the genomic surveillance of SARS-CoV-2 using wastewater samples in Jefferson County, KY. Samples were collected from manholes and treatment facilities, covering populations of 8,000 to 350,000 people (Table 1). RNA isolated from wastewater samples was used to quantify SARS-CoV-2 and analyze the genetic variation through high-throughput sequencing (See Supplementary Methods). Bioinformatics approaches were used to rapidly identify single nucleotide genetic alterations, which were compared with known variants of interest and concern. In February 2021, we analyzed seven wastewater samples for SARS-CoV-2 genomic surveillance (Figure 1). We did not detect genetic variations indicative of any current variant of concern, beyond the widespread D614G spike protein mutation (Supplementary Methods Tables 2-5). In all samples, we identified at least four of ten mutations consistent with the presence of the variant of interest B.1.429, and one sample contained seven of ten mutations (Table 2). The B.1.429 variant was confirmed in patient samples in Kentucky in January 2021 (10), and a single patient in the study area was reported to be positive for B.1.1.7 on February 9, 2021 (11). With our current metrics we flagged sites 833, 891, and Treatment plant #2 for potential presence of variant B.1.429 (3/7 sites). Differences in the scale of sample pooling in the community revealed unanticipated inconsistencies in variant representation. Specifically, variants observed in smaller catchment areas, such as neighborhood manhole locations, were not observed in downstream treatment plants, suggesting catchment size or population could impact the ability to detect diversity. Given the highly variable viral genome sequence coverage recovered from wastewater samples, there is an urgent need to develop a set of consistent thresholds constituting positive/negative presence of a variant. Monitoring SARS-CoV-2 variants in wastewater may warn of an emerging variant of concern and identify variant dominance occurring when a new variant is introduced in a community. Wastewater genetic monitoring may be particularly useful in the context of limited clinical sample sequencing capacity because a broad perspective on the genetic diversity can be obtained from a few samples. To develop comprehensive epidemiological frameworks required to guide policy, population-level wastewater surveillance of viral genetic diversity should be complemented by clinical sample testing.

A Direct Capture Method for Purification and Detection of Viral Nucleic Acid Enables Epidemiological Surveillance of SARS-CoV-2

“…To determine if our direct capture purification method yielded nucleic acid compatible with next-generation sequencing, we prepared sequencing libraries with a subset of wastewater samples using a commercially available SARS-CoV-2 amplicon panel and associated library preparation kit 46,47 .…”

Quantitative SARS-CoV-2 tracking of variants Delta, Delta plus, Kappa and Beta in wastewater by allele-specific RT-qPCR

“…Current mainstream methods for variant tracking in wastewater rely on enriching and sequencing of the environmental SARS-CoV-2 genome (Napit et al, 2021, Crits-Christoph et al, 2021Fontenele et al, 2021). This method, constrained by the same bottlenecks of cost and infrastructure requirement as clinical sequencing, is further hampered by challenges in detection of low-frequency variants and is poorly quantitative due to the lack of robust modelling to quantify variant titers (Fuqua et al, 2021;Van Poelvoorde et al, 2021) . RT-qPCR-based methods have been developed for variant identification in clinical samples (Clark et al, 2021;Vogels et al, 2021;Wang et al, 2021) Yaniv et al, 2021aYaniv et al, , 2021bWurtzer et al, 2021 ).…”

Monitoring the Circulation of SARS-CoV-2 Variants by Genomic Analysis of Wastewater in Marseille, South-East France

“…Recent studies have begun to identify known genotypes of SARS-CoV-2, as well as the variants recovered from sewers, but these studies remain scarce [ 38 , 39 , 40 , 41 , 42 , 43 ]. In this context, genotyping by sequencing SARS-CoV-2 from wastewater in the city of Marseille was undertaken using different methods, and the results correlated with the results of sequencing in patients.…”

“…Previous studies have shown that the shotgun sequencing of wastewater can provide information on several viruses simultaneously [ 32 , 33 , 34 ] and enables resolved genomic [ 35 ] and phylogenetic analyses [ 36 , 37 ]. Only a few recent studies have identified known genotypes of SARS-CoV-2, in addition to as-yet-unobserved variants from RNA recovered from the sewers [ 38 , 39 , 40 , 41 , 42 , 43 ], but these studies remain very marginal. Performing the detection of the variants using genome sequencing in multiple sewage water samples is also probably unaffordable in many regions, which are poorly equipped with a sequencing capacity.…”