In:
PLOS Pathogens, Public Library of Science (PLoS), Vol. 18, No. 10 ( 2022-10-14), p. e1010636-
Abstract:
Wastewater-based epidemiology (WBE) is an effective way of tracking the appearance and spread of SARS-COV-2 lineages through communities. Beginning in early 2021, we implemented a targeted approach to amplify and sequence the receptor binding domain (RBD) of SARS-COV-2 to characterize viral lineages present in sewersheds. Over the course of 2021, we reproducibly detected multiple SARS-COV-2 RBD lineages that have never been observed in patient samples in 9 sewersheds located in 3 states in the USA. These cryptic lineages contained between 4 to 24 amino acid substitutions in the RBD and were observed intermittently in the sewersheds in which they were found for as long as 14 months. Many of the amino acid substitutions in these lineages occurred at residues also mutated in the Omicron variant of concern (VOC), often with the same substitutions. One of the sewersheds contained a lineage that appeared to be derived from the Alpha VOC, but the majority of the lineages appeared to be derived from pre-VOC SARS-COV-2 lineages. Specifically, several of the cryptic lineages from New York City appeared to be derived from a common ancestor that most likely diverged in early 2020. While the source of these cryptic lineages has not been resolved, it seems increasingly likely that they were derived from long-term patient infections or animal reservoirs. Our findings demonstrate that SARS-COV-2 genetic diversity is greater than what is commonly observed through routine SARS-CoV-2 surveillance. Wastewater sampling may more fully capture SARS-CoV-2 genetic diversity than patient sampling and could reveal new VOCs before they emerge in the wider human population.
Type of Medium:
Online Resource
ISSN:
1553-7374
DOI:
10.1371/journal.ppat.1010636
DOI:
10.1371/journal.ppat.1010636.g001
DOI:
10.1371/journal.ppat.1010636.g002
DOI:
10.1371/journal.ppat.1010636.g003
DOI:
10.1371/journal.ppat.1010636.g004
DOI:
10.1371/journal.ppat.1010636.g005
DOI:
10.1371/journal.ppat.1010636.g006
DOI:
10.1371/journal.ppat.1010636.g007
DOI:
10.1371/journal.ppat.1010636.g008
DOI:
10.1371/journal.ppat.1010636.t001
DOI:
10.1371/journal.ppat.1010636.t002
DOI:
10.1371/journal.ppat.1010636.s001
DOI:
10.1371/journal.ppat.1010636.s002
DOI:
10.1371/journal.ppat.1010636.s003
DOI:
10.1371/journal.ppat.1010636.s004
DOI:
10.1371/journal.ppat.1010636.s005
DOI:
10.1371/journal.ppat.1010636.s006
DOI:
10.1371/journal.ppat.1010636.s007
DOI:
10.1371/journal.ppat.1010636.s008
DOI:
10.1371/journal.ppat.1010636.s009
DOI:
10.1371/journal.ppat.1010636.s010
DOI:
10.1371/journal.ppat.1010636.s011
DOI:
10.1371/journal.ppat.1010636.s012
DOI:
10.1371/journal.ppat.1010636.s013
DOI:
10.1371/journal.ppat.1010636.r001
DOI:
10.1371/journal.ppat.1010636.r002
DOI:
10.1371/journal.ppat.1010636.r003
DOI:
10.1371/journal.ppat.1010636.r004
Language:
English
Publisher:
Public Library of Science (PLoS)
Publication Date:
2022
detail.hit.zdb_id:
2205412-1
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