Genomic surveillance of SARS-CoV-2 during the first year of the pandemic in the Bronx enabled clinical and epidemiological inference
The Bronx was an early epicenter of the COVID-19 pandemic in the USA. We conducted temporal genomic surveillance of 104 SARS-CoV-2 genomes across the Bronx from March October 2020. Although the local structure of SARS-CoV-2 lineages mirrored those of New York City and New York State, temporal sampli...
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| Veröffentlicht in: | Cold Spring Harbor molecular case studies 2022-08, Vol.8 (5), p.a006211 |
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| creator | Fels, J Maximilian Khan, Saad Forster, Ryan Skalina, Karin A Sirichand, Surksha Fox, Amy S Bergman, Aviv Mitchell, William B Wolgast, Lucia R Szymczak, Wendy A Bortz, 3rd, Robert H Dieterle, M Eugenia Florez, Catalina Haslwanter, Denise Jangra, Rohit K Laudermilch, Ethan Wirchnianski, Ariel S Barnhill, Jason Goldman, David L Khine, Hnin Goldstein, D Yitzchak Daily, Johanna P Chandran, Kartik Kelly, Libusha |
| description | The Bronx was an early epicenter of the COVID-19 pandemic in the USA. We conducted temporal genomic surveillance of 104 SARS-CoV-2 genomes across the Bronx from March October 2020. Although the local structure of SARS-CoV-2 lineages mirrored those of New York City and New York State, temporal sampling revealed a dynamic and changing landscape of SARS-CoV-2 genomic diversity. Mapping the trajectories of mutations, we found that while some became 'endemic' to the Bronx, other, novel mutations rose in prevalence in the late summer/early fall. Geographically resolved genomes enabled us to distinguish between cases of reinfection and persistent infection in two pediatric patients. We propose that limited, targeted, temporal genomic surveillance has clinical and epidemiological utility in managing the ongoing COVID pandemic. |
| doi_str_mv | 10.1101/mcs.a006211 |
| format | Article |
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We conducted temporal genomic surveillance of 104 SARS-CoV-2 genomes across the Bronx from March October 2020. Although the local structure of SARS-CoV-2 lineages mirrored those of New York City and New York State, temporal sampling revealed a dynamic and changing landscape of SARS-CoV-2 genomic diversity. Mapping the trajectories of mutations, we found that while some became 'endemic' to the Bronx, other, novel mutations rose in prevalence in the late summer/early fall. Geographically resolved genomes enabled us to distinguish between cases of reinfection and persistent infection in two pediatric patients. 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We conducted temporal genomic surveillance of 104 SARS-CoV-2 genomes across the Bronx from March October 2020. Although the local structure of SARS-CoV-2 lineages mirrored those of New York City and New York State, temporal sampling revealed a dynamic and changing landscape of SARS-CoV-2 genomic diversity. Mapping the trajectories of mutations, we found that while some became 'endemic' to the Bronx, other, novel mutations rose in prevalence in the late summer/early fall. Geographically resolved genomes enabled us to distinguish between cases of reinfection and persistent infection in two pediatric patients. 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| subjects | COVID-19 Epidemiology Gene mapping Genomes Genomics Mutation Pandemics Pediatrics Severe acute respiratory syndrome Severe acute respiratory syndrome coronavirus 2 Surveillance Viral diseases |
| title | Genomic surveillance of SARS-CoV-2 during the first year of the pandemic in the Bronx enabled clinical and epidemiological inference |
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