Dataset Information

Coding-Complete Genome Sequences of an Omicron Subvariant (BA.5.2.20) of SARS-CoV-2.

ABSTRACT: Here, we present the complete coding sequences of two severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains that were recovered from a nasopharyngeal swab from a female patient and the second viral passage in cell culture. After testing, both strains were identified as BA.5.2.20, a subvariant of Omicron.

SUBMITTER: Rhazzar Z

PROVIDER: S-EPMC10281103 | biostudies-literature | 2023 Jun

REPOSITORIES: biostudies-literature

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Coding-Complete Genome Sequences of an Omicron Subvariant (BA.5.2.20) of SARS-CoV-2.

Rhazzar Zineb Z Hemlali Mouhssine M Melloul Marouane M Ouarab Maha M Nyabi Omar O Elouennass Mostafa M El Fahime Elmostafa E Touil Nadia N Gala Jean-Luc JL Ennibi Khalid K

Microbiology resource announcements 20230524 6

Here, we present the complete coding sequences of two severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains that were recovered from a nasopharyngeal swab from a female patient and the second viral passage in cell culture. After testing, both strains were identified as BA.5.2.20, a subvariant of Omicron. ...[more]

PMID: 37222607

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Project description:ImportanceThe SARS-CoV-2 Omicron subvariant, BA.2, may be less severe than previous variants; however, confounding factors make interpreting the intrinsic severity challenging.ObjectiveTo compare the adjusted risks of mortality, hospitalization, intensive care unit admission, and invasive ventilation between the BA.2 subvariant and the Omicron and Delta variants, after accounting for multiple confounders.Design, setting, and participantsThis was a retrospective cohort study that applied an entropy balancing approach. Patients in a multicenter inpatient and outpatient system in New England with COVID-19 between March 3, 2020, and June 20, 2022, were identified.ExposuresCases were assigned as being exposed to the Delta (B.1.617.2) variant, the Omicron (B.1.1.529) variant, or the Omicron BA.2 lineage subvariants.Main outcomes and measuresThe primary study outcome planned before analysis was risk of 30-day mortality. Secondary outcomes included the risks of hospitalization, invasive ventilation, and intensive care unit admissions.ResultsOf 102 315 confirmed COVID-19 cases (mean [SD] age, 44.2 [21.6] years; 63 482 women [62.0%]), 20 770 were labeled as Delta variants, 52 605 were labeled as the Omicron B.1.1.529 variant, and 28 940 were labeled as Omicron BA.2 subvariants. Patient cases were excluded if they occurred outside the prespecified temporal windows associated with the variants or had minimal longitudinal data in the Mass General Brigham system before COVID-19. Mortality rates were 0.7% for Delta (B.1.617.2), 0.4% for Omicron (B.1.1.529), and 0.3% for Omicron (BA.2). The adjusted odds ratio of mortality from the Delta variant compared with the Omicron BA.2 subvariants was 2.07 (95% CI, 1.04-4.10) and that of the original Omicron variant compared with the Omicron BA.2 subvariant was 2.20 (95% CI, 1.56-3.11). For all outcomes, the Omicron BA.2 subvariants were significantly less severe than that of the Omicron and Delta variants.Conclusions and relevanceIn this cohort study, after having accounted for a variety of confounding factors associated with SARS-CoV-2 outcomes, the Omicron BA.2 subvariant was found to be intrinsically less severe than both the Delta and Omicron variants. With respect to these variants, the severity profile of SARS-CoV-2 appears to be diminishing after taking into account various factors including therapeutics, vaccinations, and prior infections.

Dataset Information

Coding-Complete Genome Sequences of an Omicron Subvariant (BA.5.2.20) of SARS-CoV-2.

Publications

Coding-Complete Genome Sequences of an Omicron Subvariant (BA.5.2.20) of SARS-CoV-2.

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