The DOI matches its Crossref record; 12 of the 12 references it cites were found in a registry or an index.
Tracking cryptic SARS-CoV-2 lineages detected in NYC wastewater
Open accessAbstract
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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Cites
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Cited by
Shrestha, L. B., Foster, C., Rawlinson, W., Tedla, N., & Bull, R. A. (2022) · Reviews in Medical Virology · doi:10.1002/rmv.2381 · Cited by 474
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Hale, V. L., Dennis, P. M., McBride, D. S., Nolting, J. M., Madden, C., Huey, D., Ehrlich, M., Grieser, J., Winston, J., Lombardi, D., et al. (2022) · Nature · doi:10.1038/s41586-021-04353-x · Cited by 403
Infectious potential and circulation of SARS-CoV-2 in wild rats
(2025) · doi:10.1371/journal.pone.0316882 · Cited by 4
Metadata
- Authors
- Smyth, D. S., Trujillo, M., Gregory, D. A., Cheung, K., Gao, A., Graham, M., Guan, Y., Guldenpfennig, C., Hoxie, I., Kannoly, S., Kubota, N., Lyddon, T. D., Markman, M., Rushford, C., San, K. M., Sompanya, G., Spagnolo, F., Suarez, R., Teixeiro, E., Daniels, M., Johnson, M. C., & Dennehy, J. J.
- Venue
- Nature Communications
- Published
- 2022-02-03
- Volume
- 13
- Issue
- 1
- Pages
- 635-635
- ISSN
- 2041-1723 (ISSN-L)
- OpenAlex
- W4225517141
- Cited by
- 210
- References
- 12
- FWCI
- 21.66
- Type
- journal article
- Language
- en
- Open access
- gold
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- Smyth, D. S., Trujillo, M., Gregory, D. A., Cheung, K., Gao, A., Graham, M., Guan, Y., Guldenpfennig, C., Hoxie, I., Kannoly, S., Kubota, N., Lyddon, T. D., Markman, M., Rushford, C., San, K. M., Sompanya, G., Spagnolo, F., Suarez, R., Teixeiro, E., . . . Dennehy, J. J. (2022). Tracking cryptic SARS-CoV-2 lineages detected in NYC wastewater. Nature Communications. https://doi.org/10.1038/s41467-022-28246-3
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
