Tracking cryptic SARS-CoV-2 lineages detected in NYC wastewater

Abstract

Tracking SARS-CoV-2 genetic diversity is strongly indicated because diversifying selection may lead to the emergence of novel variants resistant to naturally acquired or vaccine-induced immunity. To monitor New York City (NYC) for the presence of novel variants, we deep sequence most of the receptor binding domain coding sequence of the S protein of SARS-CoV-2 isolated from the New York City wastewater. Here we report detecting increasing frequencies of novel cryptic SARS-CoV-2 lineages not recognized in GISAID’s EpiCoV database. These lineages contain mutations that had been rarely observed in clinical samples, including Q493K, Q498Y, E484A, and T572N and share many mutations with the Omicron variant of concern. Some of these mutations expand the tropism of SARS-CoV-2 pseudoviruses by allowing infection of cells expressing the human, mouse, or rat ACE2 receptor. Finally, pseudoviruses containing the spike amino acid sequence of these lineages were resistant to different classes of receptor binding domain neutralizing monoclonal antibodies. We offer several hypotheses for the anomalous presence of these lineages, including the possibility that these lineages are derived from unsampled human COVID-19 infections or that they indicate the presence of a non-human animal reservoir.

Making waves: Wastewater surveillance of SARS-CoV-2 in an endemic future

“…We anticipate that technologies that have been developed for variant monitoring in wastewater will continue to play an important role for monitoring the evolution of SARS-CoV-2 in the endemic phase, when clinical testing and sequencing will probably decrease. WBS, coupled with genomic sequencing, would play a prominent role in maintaining a watchful eye on the evolution and emergence of SARS-CoV-2 variants circulating in the community as has previously been demonstrated ( Crits-Christoph et al, 2021 ; Rothman et al, 2021 ; Smyth et al, 2022 ). Quantitative, VOC-specific PCR-based assays ( Lee et al, 2022 , 2021b , 2021a ), RT-ddPCR ( Gering et al, 2021 ; Heijnen et al, 2021 ) and nested RT-PCR ( La Rosa et al, 2021 ) will continue to provide a cost-effective means for identifying and quantifying the distribution of VOCs in populations.…”

Phylogenetic and phylodynamic approaches to understanding and combating the early SARS-CoV-2 pandemic

“…Genetic detection of viruses in wastewater has the potential to augment genome sampling before first-case detection and to estimate the impact of NPIs on local and regional prevalence 106 . Recently, SARS-CoV-2 sequences from wastewater samples have indicated genomes with novel constellations of mutations not seen in any known circulating lineage or VOC, including ‘cryptic lineages’ with multiple immune escape mutations 107 , with some studies using phylogenetics to place cryptic wastewater lineages in relation to known lineages 108 .…”

Monitoring of SARS-CoV-2 variant dynamics in wastewater by digital RT-PCR : from Alpha to Omicron BA.2 VOC

“…These approaches have been developed and applied to the emergence of Alpha and Delta VOC. To our knowledge, few data are available regarding the emergence and the dynamics of the Omicron BA.1 and BA.2 VOC (Agrawal et al, 2022b;Ahmed et al, 2022;Chassalevris et al, 2022;Kirby et al, 2022;Smyth et al, 2022) .…”

“…Wastewater-based epidemiology allows tracking the overall dynamics of the SARS-CoV-2 epidemic (Medema et al, 2020b;Randazzo et al, 2020;Wurtzer et al, 2022Wurtzer et al, , 2020. Variant identification results from sequencing, but such approach faces limitations for application in wastewater with respect to RNA quality and quantity (Lou et al, 2022), but also mathematical tools to deconvolute isolated mutations to reconstruct the original genomes in a mixture of variants (Agrawal et al, 2022b;Jahn et al, 2021;Smyth et al, 2022). Different studies have shown that it is also possible to monitor specific mutations suggestive of VOC to identify the emergence of VOC in a territory and to explain the predominance of certain VOC in epidemic waves (Caduff et al, 2022;Carcereny et al, 2022;Erster et al, 2022;Wurtzer et al, 2022).…”