Low Viral Diversity Limits the Effectiveness of Sequence-Based Transmission Inference for SARS-CoV-2
ABSTRACT 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 possibi...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
| Published: |
American Society for Microbiology
2023-02-01
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| Series: | mSphere |
| Subjects: | |
| Online Access: | https://journals.asm.org/doi/10.1128/msphere.00544-22 |
| _version_ | 1797901415574667264 |
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| author | Mireille Farjo Christopher B. Brooke |
| author_facet | Mireille Farjo Christopher B. Brooke |
| author_sort | Mireille Farjo |
| collection | DOAJ |
| description | ABSTRACT 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. |
| first_indexed | 2024-04-10T09:01:43Z |
| format | Article |
| id | doaj.art-f7abfe2836ee46699a637ba2e08887eb |
| institution | Directory Open Access Journal |
| issn | 2379-5042 |
| language | English |
| last_indexed | 2024-04-10T09:01:43Z |
| publishDate | 2023-02-01 |
| publisher | American Society for Microbiology |
| record_format | Article |
| series | mSphere |
| spelling | doaj.art-f7abfe2836ee46699a637ba2e08887eb2023-02-21T14:03:57ZengAmerican Society for MicrobiologymSphere2379-50422023-02-018110.1128/msphere.00544-22Low Viral Diversity Limits the Effectiveness of Sequence-Based Transmission Inference for SARS-CoV-2Mireille Farjo0Christopher B. Brooke1Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USADepartment of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USAABSTRACT 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.https://journals.asm.org/doi/10.1128/msphere.00544-22SARS-CoV-2genomic epidemiologytransmission networks |
| spellingShingle | Mireille Farjo Christopher B. Brooke Low Viral Diversity Limits the Effectiveness of Sequence-Based Transmission Inference for SARS-CoV-2 mSphere SARS-CoV-2 genomic epidemiology transmission networks |
| 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 | SARS-CoV-2 genomic epidemiology transmission networks |
| url | https://journals.asm.org/doi/10.1128/msphere.00544-22 |
| work_keys_str_mv | AT mireillefarjo lowviraldiversitylimitstheeffectivenessofsequencebasedtransmissioninferenceforsarscov2 AT christopherbbrooke lowviraldiversitylimitstheeffectivenessofsequencebasedtransmissioninferenceforsarscov2 |