Dynamics of competing SARS-CoV-2 variants during the Omicron epidemic in England

Eales, O; de Oliveira Martins, L; Page, AJ; Wang, H; Bodinier, B; Tang, D; Haw, D; Jonnerby, J; Atchison, C; Ashby, D; Barclay, W; Taylor, G; Cooke, G; Ward, H; Darzi, A; Riley, S; Elliott, P; Donnelly, CA; Chadeau-Hyam, M

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Journal article

Dynamics of competing SARS-CoV-2 variants during the Omicron epidemic in England

Abstract:: Background: Surveillance of SARS-CoV-2 variants of concern (VOCs) and lineages is crucial for decision-making. Our objective was to study the SARS-CoV-2 clade dynamics across epidemiological waves and evaluate the reliability of SNPsig® SARS-CoV-2 EscapePLEX CE in detecting VOCs in Cameroon. Material and methods: A laboratory-based study was conducted on SARS-CoV-2 positive nasopharyngeal specimens cycle threshold (Ct)≤30 at the Chantal BIYA International Reference Centre in Yaoundé-Cameroon, between April-2020 to August-2022. Samples were analyzed in parallel with Sanger sequencing and (SNPsig® SARS-CoV-2 EscapePLEX CE), and performance characteristics were evaluated by Cohen's coefficient and McNemar test. Results: Of the 130 sequences generated, SARS-CoV-2 clades during wave-1 (April–November 2020) showed 97 % (30/31) wild-type lineages and 3 % (1/31) Gamma-variant; wave-2 (December-2020 to May-2021), 25 % (4/16) Alpha-variant, 25 % (4/16) Beta-variant, 44 % (7/16) wild-type and 6 % (1/16) mu; wave-3 (June–October 2021), 94 % (27/29) Delta-variant, 3 % (1/29) Alpha-variant, 3 % (1/29) wild-type; wave-4 (November-2021 to August-2022), 98 % (53/54) Omicron-variant and 2 % (1/54) Delta-variant. Omicron sub-variants were BA.1 (47 %), BA.5 (34 %), BA.2 (13 %) and BA.4 (6 %). Globally, the two genotyping methods accurately identified the SARS-CoV-2 VOCs (P = 0.17, McNemar test; Ka = 0.67). Conclusion: Genomic surveillance reveals a rapid dynamic in SARS-CoV-2 strains between epidemiological waves in Cameroon. For wide-spread variant surveillance in resource-limited settings, SNPsig® SARS-CoV-2 EscapePLEX CEkit represents a suitable tool, pending upgrading for distinguishing Omicron sub-lineages

Publication status:: Published

Peer review status:: Peer reviewed

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APA Style

Eales, O., de Oliveira Martins, L., Page, A. J., Wang, H., Bodinier, B., Tang, D., Haw, D., Jonnerby, J., Atchison, C., Ashby, D., Barclay, W., Taylor, G., Cooke, G., Ward, H., Darzi, A., Riley, S., Elliott, P., Donnelly, C. A., & Chadeau-Hyam, M. (2022). Dynamics of competing SARS-CoV-2 variants during the Omicron epidemic in England. Nature Communications, 13(1), 4375–4375.

MLA Style

Eales, O, et al. “Dynamics of Competing SARS-CoV-2 Variants during the Omicron Epidemic in England.” Nature Communications, vol. 13, no. 1, 2022, pp. 4375–75.

Chicago Style

Eales, O, L de Oliveira Martins, AJ Page, et al. 2022. “Dynamics of Competing SARS-CoV-2 Variants during the Omicron Epidemic in England.” Nature Communications 13 (1): 4375–75.
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