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. 2023 Feb 21;15(2):e35261.
doi: 10.7759/cureus.35261. eCollection 2023 Feb.

Clinical Characteristics and Outcomes of Laboratory-Confirmed SARS-CoV-2 Cases Infected With Omicron Subvariants and the XBB Recombinant Variant

Rajesh P Karyakarte  1   2 , Rashmita Das  1   2 , Sonali Dudhate  1 , Jeanne Agarasen  1 , Praveena Pillai  1 , Priyanka M Chandankhede  1 , Rutika S Labhshetwar  1 , Yogita Gadiyal  1 , Mansi V Rajmane  1 , Preeti P Kulkarni  1 , Safanah Nizarudeen  1 , Suvarna Joshi  1 , Varsha Potdar  3   4 , Krishanpal Karmodiya  5
Affiliations

Clinical Characteristics and Outcomes of Laboratory-Confirmed SARS-CoV-2 Cases Infected With Omicron Subvariants and the XBB Recombinant Variant

Rajesh P Karyakarte et al. Cureus. .

Abstract

Background SARS-CoV-2 has evolved to produce new variants causing successive waves of infection. Currently, six variants are being monitored by the World Health Organization that are replacing BA.5. These include BF.7 (BA.5 + R346T in spike), BQ.1 (and BQ.1.1, with BA.5 + R346T, K444T, N460K mutations in spike), BA.2.75 (including BA.2.75.2 and CH.1.1), and XBB (including XBB.1.5). BQ.1 and XBB variants are more immune evasive and have spread quickly throughout the world. Concerning the potential severity of infections caused by these variants, the present study describes the clinical characteristics and outcomes of these major variants in Maharashtra. Methodology A total of 1,141 reverse transcriptase-polymerase chain reaction (RT-PCR)-positive SARS-CoV-2 samples, with a cycle threshold (Ct) value of less than 25, were processed for SARS-CoV-2 whole genome sequencing between July 10, 2022, and January 12, 2023. All corresponding demographic and clinical data were recorded and analyzed using Microsoft® Excel and Epi Info™. Results Out of the 1,141 samples sequenced, BA.2.75* (63.78%) was the predominant Omicron variant, followed by the XBB* (18.88%), BA.2.38* (4.94%), BA.5* (4.06%), BA.2.10* (3.51%), and BQ.1* (1.65%). A total of 540 cases were contacted telephonically, of whom 494 (91.48%) were symptomatic with mild symptoms. Fever (77.73%) was the most common symptom, followed by cold (47.98%), cough (42.31%), and myalgia and fatigue (18.83%). Of the 540 cases, 414 (76.67%) cases recovered at home, and 126 (23.33%) were institutionally quarantined/hospitalized. Among the home-isolated and hospitalized cases, 416 (99.76%) and 108 (87.80%), respectively, recovered with symptomatic treatment, while one (0.24%) and 15 (12.20%), respectively, succumbed to the disease. Out of the 540 cases, 491 (90.93%) were vaccinated with at least one dose of the COVID-19 vaccine, 41 (7.59%) were unvaccinated, and for eight (1.48%) cases, vaccination data was not available. Conclusions The current study indicates that the XBB* variant is causing mild disease in India. However, as XBB* possesses both immune-escape and infectivity-enhancing mutations, it has the potential to spread to other parts of the world rapidly. Further, anti-SARS-CoV-2 vaccination improves survival rates in COVID-19.

Keywords: ba.2.10*; ba.2.38*; ba.2.75*; ba.5*; bq.1*; covid-19; sars-cov-2; xbb*; xbb.1.5.

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Conflict of interest statement

The authors have declared that no competing interests exist.

Figures

Figure 1
Figure 1. Geographical distribution of 1,141 RT-PCR-positive SARS-CoV-2 samples.
RT-PCR = reverse transcriptase-polymerase chain reaction; UCL = upper confidence limit; LCL = lower confidence limit
Figure 2
Figure 2. Age-wise distribution of 1,141 RT-PCR-positive SARS-CoV-2 samples.
RT-PCR = reverse transcriptase-polymerase chain reaction; UCL = upper confidence limit; LCL = lower confidence limit
Figure 3
Figure 3. Gender-wise distribution of 1,141 RT-PCR-positive SARS-CoV-2 samples.
RT-PCR = reverse transcriptase-polymerase chain reaction; UCL = upper confidence limit; LCL = lower confidence limit
Figure 4
Figure 4. Temporal distribution of SARS-CoV-2 variants during the study period (from July 10, 2022, to January 12, 2023).
Figure 5
Figure 5. Distribution of major SARS-CoV-2 variants detected during the study versus the area of residence.
Figure 6
Figure 6. Presence or absence of comorbidity versus the outcome of the disease.
Figure 7
Figure 7. Age-wise distribution of survived and dead cases.
Figure 8
Figure 8. Type of vaccine administered to the study population.
Figure 9
Figure 9. Vaccination status by age groups.
Figure 10
Figure 10. Impact of vaccination on the survival of cases.
Figure 11
Figure 11. Phylogenetic relatedness and convergent evolution of newer SARS-CoV-2 lineages.
This figure is taken from SARS-CoV-2 evolution, post-Omicron, available from https://virological.org/t/sars-cov-2-evolution-post-omicron/911 [11].
Figure 12
Figure 12. Mutation prevalence across lineages BJ.1, BM.1.1.1, and XBB* (mutations with >75% prevalence in at least one lineage).
This figure is generated and taken from Outbreak.info. Data represented is as of January 24, 2023 [15].
Figure 13
Figure 13. Prevalence of common lineages in India over the last 60 days.
This graph is generated and taken from Outbreak.info. Data represented is as of January 24, 2023 [23].
See this image and copyright information in PMC

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