ArticleNature communications2022
Tracking cryptic SARS-CoV-2 lineages detected in NYC wastewater.
Article in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 129 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
129 citing papers in PubMed, 216 citations in OpenAlex.
- Breadth of ACE2 receptor usage predicts host range and antigenic relatedness across bat sarbecoviruses.PLoS biology · 2026Article
- Using issues of water to CURE your teaching: STEM education is civic education.Journal of microbiology & biology education · 2026Article
- Large-scale genomic surveillance reveals immunosuppression drives mutation dynamics in persistent SARS-CoV-2 infections.Nature communications · 2026Article
- Statewide multi-year wastewater sequencing reveals dual origins of HIV-1 signal.Nature communications · 2026Article
- Cost-Effective Sampling Strategies for Wastewater Surveillance: A Large-Scale Longitudinal Study in Hong Kong and Shenzhen.Environmental science & technology · 2026Article
- Beyond the Mutation Abyss: Revisiting SARS-CoV-2 Receptor-Binding Domain Evolution from ACE2 Binding Optimization to Immune Epitope Remodeling.Pathogens (Basel, Switzerland) · 2026Article
- WEPP: Phylogenetic placement achieves near-haplotype resolution in wastewater-based epidemiology.PLoS computational biology · 2026Article
- Will animal reservoirs give us the next SARS-CoV-2 variant?PLoS pathogens · 2026Article
- Optimization of a Semi-nested PCR Protocol for Amplifying the Entire Spike Protein Region to Identify SARS-CoV-2 Variants in Wastewater.Food and environmental virology · 2026Article
- SARS-CoV-2 wastewater genomic surveillance: approaches, challenges, and opportunities.Genome biology · 2026Review
- Clinical metagenomics for diagnosis and surveillance of viral pathogens.Nature reviews. Microbiology · 2026Review
- Article
- Review
- Unsupervised detection and fitness estimation of emerging SARS-CoV-2 variants: Application to wastewater samples (ANRS0160).PLoS computational biology · 2025Article
- A highly divergent cryptic SARS-CoV-2 lineage exhibits strong receptor binding and immune evasion.medRxiv : the preprint server for health sciences · 2025Article
- CLAE: A High-Fidelity Nanopore Sequencing Strategy for Read-Level Viral Variant Detection and Environmental RNA Virus Discovery.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Optimization of the Primary Sludge Processing Method for Wastewater Genomic Surveillance of SARS-CoV‑2.ACS ES&T water · 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
69 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
22 authors at 5 institutions in 1 country.
Funding
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.