ArticlePLoS pathogens2022
Genetic diversity and evolutionary convergence of cryptic SARS- CoV-2 lineages detected via wastewater sequencing.
Article in PLoS pathogens, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 papers.
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49 citing papers in PubMed.
- Monoclonal antibodies from COVID-19 convalescent patients target cryptic epitopes for broad SARS-CoV-2 neutralization.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- WEPP: Phylogenetic placement achieves near-haplotype resolution in wastewater-based epidemiology.PLoS computational biology · 2026Article
- SARS-CoV-2 wastewater genomic surveillance: approaches, challenges, and opportunities.Genome biology · 2026Review
- Describing a Persistent SARS-CoV-2 Infection Outcomes and Mutations Associated With B-Cell Deficiency: A Case Report.Case reports in infectious diseases · 2026Article
- Article
- Review
- A highly divergent cryptic SARS-CoV-2 lineage exhibits strong receptor binding and immune evasion.medRxiv : the preprint server for health sciences · 2025Article
- Comprehensive wastewater genomic surveillance in the Netherlands: insights into country-wide SARS-CoV-2 lineage dynamics and implications for future surveillance.BMC public health · 2025Article
- Optimization of the Primary Sludge Processing Method for Wastewater Genomic Surveillance of SARS-CoV‑2.ACS ES&T water · 2025Article
- Real-time, multi-pathogen wastewater genomic surveillance with Freyja 2.medRxiv : the preprint server for health sciences · 2025Article
- Hospital wastewater surveillance for SARS-CoV-2 identifies intra-hospital dynamics of viral transmission and evolution.Applied and environmental microbiology · 2025Article
- Mycophenolic acid treatment drives the emergence of novel SARS-CoV-2 variants.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Detecting SARS-CoV-2 cryptic lineages using publicly available whole genome wastewater sequencing data.PLoS pathogens · 2025Article
- The consequences of SARS-CoV-2 within-host persistence.Nature reviews. Microbiology · 2025Review
- Diagnostic performance of allele-specific RT-qPCR and genomic sequencing in wastewater-based surveillance of SARS-CoV-2.Eco-Environment & Health · 2025Article
- A highly divergent sample from a nearly extinct SARS-CoV-2 lineage in a patient with long-term COVID-19.Frontiers in cellular and infection microbiology · 2025Article
- Emergence of the BA.2.87.1 lineage of SARS-CoV-2 in South Africa, a highly diverged BA.2-related lineage.Virus evolution · 2025Article
- Translating insights into therapies for Long Covid.Science translational medicine · 2024Review
- Revealing patterns of SARS-CoV-2 variant emergence and evolution using RBD amplicon sequencing of wastewater.The Journal of infection · 2024Article
- Delineating the functional activity of antibodies with cross-reactivity to SARS-CoV-2, SARS-CoV-1 and related sarbecoviruses.PLoS pathogens · 2024Article
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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.
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