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Low Viral Diversity Limits the Effectiveness of Sequence-Based Transmission Inference for SARS-CoV-2
Tracking the spread of infection amongst individuals within and between communities has been a major challenge during viral outbreaks. With the unprecedented scale of viral sequence data collection during the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, the possibility of u...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
American Society for Microbiology
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9942562/ https://www.ncbi.nlm.nih.gov/pubmed/36695609 http://dx.doi.org/10.1128/msphere.00544-22 |
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author | Farjo, Mireille Brooke, Christopher B. |
author_facet | Farjo, Mireille Brooke, Christopher B. |
author_sort | Farjo, Mireille |
collection | PubMed |
description | Tracking the spread of infection amongst individuals within and between communities has been a major challenge during viral outbreaks. With the unprecedented scale of viral sequence data collection during the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, the possibility of using phylogenetics to reconstruct past transmission events has been explored as a more rigorous alternative to traditional contact tracing; however, the reliability of sequence-based inference of transmission networks has yet to be directly evaluated. E. E. Bendall, G. Paz-Bailey, G. A. Santiago, C. A. Porucznik, et al. (mSphere 7:e00400-22, 2022, https://doi.org/10.1128/mSphere.00400-22) evaluate the potential of this technique by applying best practices sequence comparison methods to three geographically distinct cohorts that include known transmission pairs and demonstrate that linked pairs are often indistinguishable from unrelated samples. This study clearly establishes how low viral diversity limits the utility of genomic methods of epidemiological inference for SARS-CoV-2. |
format | Online Article Text |
id | pubmed-9942562 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | American Society for Microbiology |
record_format | MEDLINE/PubMed |
spelling | pubmed-99425622023-02-22 Low Viral Diversity Limits the Effectiveness of Sequence-Based Transmission Inference for SARS-CoV-2 Farjo, Mireille Brooke, Christopher B. mSphere Commentary Tracking the spread of infection amongst individuals within and between communities has been a major challenge during viral outbreaks. With the unprecedented scale of viral sequence data collection during the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, the possibility of using phylogenetics to reconstruct past transmission events has been explored as a more rigorous alternative to traditional contact tracing; however, the reliability of sequence-based inference of transmission networks has yet to be directly evaluated. E. E. Bendall, G. Paz-Bailey, G. A. Santiago, C. A. Porucznik, et al. (mSphere 7:e00400-22, 2022, https://doi.org/10.1128/mSphere.00400-22) evaluate the potential of this technique by applying best practices sequence comparison methods to three geographically distinct cohorts that include known transmission pairs and demonstrate that linked pairs are often indistinguishable from unrelated samples. This study clearly establishes how low viral diversity limits the utility of genomic methods of epidemiological inference for SARS-CoV-2. American Society for Microbiology 2023-01-25 /pmc/articles/PMC9942562/ /pubmed/36695609 http://dx.doi.org/10.1128/msphere.00544-22 Text en Copyright © 2023 Farjo and Brooke. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license (https://creativecommons.org/licenses/by/4.0/) . |
spellingShingle | Commentary Farjo, Mireille Brooke, Christopher B. Low Viral Diversity Limits the Effectiveness of Sequence-Based Transmission Inference for SARS-CoV-2 |
title | Low Viral Diversity Limits the Effectiveness of Sequence-Based Transmission Inference for SARS-CoV-2 |
title_full | Low Viral Diversity Limits the Effectiveness of Sequence-Based Transmission Inference for SARS-CoV-2 |
title_fullStr | Low Viral Diversity Limits the Effectiveness of Sequence-Based Transmission Inference for SARS-CoV-2 |
title_full_unstemmed | Low Viral Diversity Limits the Effectiveness of Sequence-Based Transmission Inference for SARS-CoV-2 |
title_short | Low Viral Diversity Limits the Effectiveness of Sequence-Based Transmission Inference for SARS-CoV-2 |
title_sort | low viral diversity limits the effectiveness of sequence-based transmission inference for sars-cov-2 |
topic | Commentary |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9942562/ https://www.ncbi.nlm.nih.gov/pubmed/36695609 http://dx.doi.org/10.1128/msphere.00544-22 |
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