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. 2024 Jul 27;16(8):1209.
doi: 10.3390/v16081209.

Emergence of Recombinant SARS-CoV-2 Variants in California from 2020 to 2022

Rahil Ryder  1 , Emily Smith  2 , Deva Borthwick  3 , Jesse Elder  1 , Mayuri Panditrao  3 , Christina Morales  1 , Debra A Wadford  1
Affiliations

Emergence of Recombinant SARS-CoV-2 Variants in California from 2020 to 2022

Rahil Ryder et al. Viruses. .

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.

Keywords: California COVIDNet; SARS-CoV-2; genomic epidemiology; genomic surveillance; recombination; whole-genome sequencing.

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Conflict of interest statement

The authors declare no conflicts of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript; or in the decision to publish the results.

Figures

Figure 1
Figure 1
Prevalence of SARS-CoV-2 recombinants relative to SARS-CoV-2 variants from March 2021 to December 2022. (A) The number of genomes belonging to major recombinant lineages (n ≥ 30) in California. (B) The prevalence of WHO variants and Pango lineage groupings in California data available from the California COVIDNet sequence database in Terra (left y-axis). The white line represents the percentage of COVID-19 cases sequenced in California over time (right y-axis).
Figure 2
Figure 2
Recombinant lineages in California from 2020 to 2022 classified by Public Health Officer Region (PHO). Total sequence count (n) is split via a pie chart according to major recombinant lineages, and the “Other” category includes lineages with counts less than 30. PHO regions are colored according to 2023 population size. There are 558 sequences with unknown county information; these are not depicted on this map.
Figure 3
Figure 3
Schematic of the SARS-CoV-2 genome showing approximate breakpoint locations of novel and major recombinant lineages found in California. The horizontal location of the black dots represents the approximate region of the genome where recombination occurred for the corresponding recombinant lineages. Different colors represent different regions of the SARS-CoV-2 genome. The parental lineages of the recombinants are as follows: XE (BA.1 × BA.2), XZ (BA.2 × BA.1), XAS (BA.5 × BA.2), XBB (BA.2 × BA.2), Novel #1 (BA.5 × XBC.1), Novel #2 (BA.1 × BA.2), Novel #3 (BA.1 × BA.2), and Novel #4 (BA.1 × AY.44).
Figure 4
Figure 4
Phylogeny of XZ recombinant genomes. (A) Global UShER tree of XZ genomes from GISAID. Genomes are colored according to geographical location: in California (blue), outside of California but within the US (teal), or outside the US (orange). (B) Phylogenetic tree of XZ genomes within California from Terra and GISAID. Genomes are colored according to regional location: the Association of Bay Area Health Officers (blue), Greater Sacramento (green), San Joaquin Valley Consortium (light orange), South California Health Officers (teal), or Rural Association of Northern California Health Officers (dark orange). Genomes for which regional location information was not available are shown in gray.
Figure 5
Figure 5
Phylogeny of XAS recombinant genomes. (A) Global UShER tree of XAS genomes from GISAID. Genomes are colored according to geographical location: California (orange), outside of California but within the US (blue), or outside the US (teal). (B) Phylogenetic tree of XAS genomes within California from GISAID. Genomes are colored according to regional location: the Association of Bay Area Health Officers (teal), Greater Sacramento (orange), San Joaquin Valley Consortium (green), or South California Health Officers (blue).
Figure 6
Figure 6
Global UShER tree of BA.5 × XBC.1 recombinant genomes from GISAID. Genomes from specimens originating in the Southern California Health Officers Region are shown in blue, and those for which regional location information was not available are shown in gray.
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References

    1. Bolze A., Basler T., White S., Dei Rossi A., Wyman D., Dai H., Roychoudhury P., Greninger A.L., Hayashibara K., Beatty M., et al. Evidence for SARS-CoV-2 Delta and Omicron co-infections and recombination. Med. 2022;3:848–859. doi: 10.1016/j.medj.2022.10.002. - DOI - PMC - PubMed
    1. 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., Nipales J.E., et al. 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. 2023. p. 2023-04.
    1. 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., Merino-Diaz L., et al. 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. 2023;24:2419. doi: 10.3390/ijms24032419. - DOI - PMC - PubMed
    1. Roemer C.H., Hisner R., Frohberg N., Sakaguchi H., Gueli F., Peacock T. SARS-CoV-2 evolution, post-Omicron. [(accessed on 4 March 2024)];Virological.org. 2022 564 Available online: https://virological.org/t/sars-cov-2-evolution-post-omicron/911.
    1. Nelson M., Holmes E. The evolution of epidemic influenza. Nat. Rev. Genet. 2007;8:196–205. doi: 10.1038/nrg2053. - DOI - PubMed

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