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

Domaine:

healthcare

Type de record:

paper

Créateur:

Ealde PagWan

Éditeur:

Nat

Hôte:

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

Visit

ora.ox.ac.uk

Similaires

Determination of SARS-CoV-2 Variants and Seroprevalence in Accra, Ghana during the Delta-Omicron WavesRapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern AfricaDynamics of Variants of Concern (VOC) of SARS-CoV-2 during the Different Waves of COVID-19 in SenegalThe Impact of SARS-CoV-2 Lineages (Variants) on the COVID-19 Epidemic in South AfricaRapid Replacement of SARS-CoV-2 Variants by Delta and Subsequent Arrival of Omicron, Uganda, 2021Comparison of SARS-Cov-2 omicron variant with the previously identified SARS-Cov-2 variants in Egypt, 2020–2022: insight into SARS-Cov-2 genome evolution and its impact on epidemiology, clinical picture, disease severity, and mortality

Determination of SARS-CoV-2 Variants and Seroprevalence in Accra, Ghana during the Delta-Omicron Waves

A significant proportion of SARS-CoV-2 infections in Africa are identified as asymptomatic, facilita

Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epidemic in southern Africa has bee

Dynamics of Variants of Concern (VOC) of SARS-CoV-2 during the Different Waves of COVID-19 in Senegal

Background: In Senegal, the incidence of SARS-CoV-2 evolved with four successive epidemic waves. The

The Impact of SARS-CoV-2 Lineages (Variants) on the COVID-19 Epidemic in South Africa

Abstract Emerging SARS-CoV-2 variants have been attributed to the occurrence of se

Rapid Replacement of SARS-CoV-2 Variants by Delta and Subsequent Arrival of Omicron, Uganda, 2021

Comparison of SARS-Cov-2 omicron variant with the previously identified SARS-Cov-2 variants in Egypt, 2020–2022: insight into SARS-Cov-2 genome evolution and its impact on epidemiology, clinical picture, disease severity, and mortality

Abstract Background The o severe acute respiratory coronavirus 2 (SARS-CoV-2) pandemic has killed mi