Ryder, R.; Smith, E.; Borthwick, D.; Elder, J.; Panditrao, M.; Morales, C.; Wadford, D.A. Emergence of Recombinant SARS-CoV-2 Variants in California from 2020 to 2022. Viruses2024, 16, 1209.
Ryder, R.; Smith, E.; Borthwick, D.; Elder, J.; Panditrao, M.; Morales, C.; Wadford, D.A. Emergence of Recombinant SARS-CoV-2 Variants in California from 2020 to 2022. Viruses 2024, 16, 1209.
Ryder, R.; Smith, E.; Borthwick, D.; Elder, J.; Panditrao, M.; Morales, C.; Wadford, D.A. Emergence of Recombinant SARS-CoV-2 Variants in California from 2020 to 2022. Viruses2024, 16, 1209.
Ryder, R.; Smith, E.; Borthwick, D.; Elder, J.; Panditrao, M.; Morales, C.; Wadford, D.A. Emergence of Recombinant SARS-CoV-2 Variants in California from 2020 to 2022. Viruses 2024, 16, 1209.
Abstract
The detection, characterization, and monitoring of SARS-CoV-2 recombinant variants is a challenge to public health authorities worldwide. Recombinant variants, composed of two or more SARS-CoV-2 lineages, often have unknown impacts on transmission, immune escape, and virulence in the early stages of emergence. We examined 4,213 SARS-CoV-2 recombinant SARS-CoV-2 genomes collected between 2020 and 2022 from California to describe regional and statewide trends in prevalence. Many of these recombinant genomes, such as those belonging to the XZ lineage, or novel recombinant lineages, likely originated within the state of California. We discuss the challenges and limitations surrounding Pango lineage assignments, the use of publicly available sequence data, and adequate sample sizes for epidemiologic analyses. Although these challenges will continue as SARS-CoV-2 sequencing volumes decrease globally, this study enhances our understanding of SARS-CoV-2 recombinant genomes to date while providing a foundation for future insights into emerging recombinant lineages.
Keywords
SARS-CoV-2; genomic epidemiology; genomic surveillance; recombination; whole-genome sequencing; California COVIDNet
Subject
Public Health and Healthcare, Other
Copyright:
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
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