Emergence of Recombinant SARS-CoV-2 Variants in California from 2020 to 2022
Author:
Ryder Rahil1ORCID, Smith Emily2ORCID, Borthwick Deva3, Elder Jesse1, Panditrao Mayuri3, Morales Christina1, Wadford Debra A.1ORCID
Affiliation:
1. Viral and Rickettsial Disease Laboratory, California Department of Public Health, Richmond, CA 94804, USA 2. Theiagen Genomics, Highlands Ranch, CO 80129, USA 3. COVID Control Branch, Division of Communicable Disease Control, CDPH, Richmond, CA 94804, USA
Abstract
The detection, characterization, and monitoring of SARS-CoV-2 recombinant variants constitute a challenge for 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 4213 SARS-CoV-2 recombinant SARS-CoV-2 genomes collected between 2020 and 2022 in 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.
Funder
US Centers for Disease Control and Prevention, Epidemiology and Laboratory Capacity
Reference25 articles.
1. Evidence for SARS-CoV-2 Delta and Omicron co-infections and recombination;Bolze;Med,2022 2. Pangilinan, E.A.R., Egana, J.M.C., Mantaring, R.J.Q., Telles, A.J.E., Tablizo, F.A., Lapid, C.M., Yangzon, M.S.L., Endozo, J.J.S., Padilla, K.S.A.R., and Nipales, J.E. (bioRxiv, 2023). Analysis of SARS-CoV-2 Recombinant Lineages XBC and XBC. 1 in the Philippines and Evidence for Delta-Omicron Co-infection as a Potential Origin, bioRxiv. 3. Perez-Florido, J., Casimiro-Soriguer, C.S., Ortuño, F., Fernandez-Rueda, J.L., Aguado, A., Lara, M., Riazzo, C., Rodriguez-Iglesias, M.A., Camacho-Martinez, P., and Merino-Diaz, L. (2023). Detection of High Level of Co-Infection and the Emergence of Novel SARS CoV-2 Delta-Omicron and Omicron-Omicron Recombinants in the Epidemiological Surveillance of Andalusia. Int. J. Mol. Sci., 24. 4. Roemer, C.H., Hisner, R., Frohberg, N., Sakaguchi, H., Gueli, F., and Peacock, T. (2022). SARS-CoV-2 evolution, post-Omicron. Virological.org, 564, Available online: https://virological.org/t/sars-cov-2-evolution-post-omicron/911. 5. The evolution of epidemic influenza;Nelson;Nat. Rev. Genet.,2007
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