Reinfection rate and disease severity of the BA.5 Omicron SARS-CoV-2 lineage compared to previously circulating variants of concern in the Canary Islands (Spain)

ABSTRACT

The emergence of the Omicron SARS-CoV-2 variant of concern has changed the COVID-19 scenario as this variant is characterized by high transmissibility and immune evasion ability. To evaluate the impact of this variant on the Canary Islands (Spain) population, we determined the reinfection rates and disease severity associated with the Omicron sublineages and the previously circulating variants of concern. We performed a retrospective observational study on 21,745 SARS-CoV-2 viral genomes collected from December 2020 to July 2022 in the Canary Islands (Spain). We compared the reinfection rates between lineages using pairwise proportion and Fisher’s exact tests. To assess disease severity, we studied the association of Alpha, Delta, BA.1, BA.2, BA.5, and other risk factors on 28-day hospital mortality using logistic regression and Cox proportional hazard models. We observed 127 bona fide reinfection cases throughout the study period. We found that BA.5 had the highest reinfection rate compared to other lineages (vs. Delta p = 2.89 × 10⁻²⁵; vs. BA.1 p = 5.17 × 10⁻¹¹; vs. BA.2 p = 0.002). Among the 1,094 hospitalized patients, multivariate logistic regression showed that Alpha (Odds Ratio [OR] =  0.45, 95% Confidence Interval [CI] =  0.23-0.87, p = 0.02), BA.2 (OR =   0.38, 95% CI = 0.22-0.63, p = 1.91 × 10⁻⁴), and BA.5 (OR = 0.30, 95% CI = 0.16-0.55, p = 1.05 × 10⁻⁴) had lower 28-day hospital mortality compared to Delta. These results were confirmed by using Cox proportional hazard models. Omicron lineages, and in particular BA.5, were associated with higher reinfection rates and lower disease severity (28-day hospital mortality) than previously circulating variants of concern.

KEYWORDS:

• SARS-CoV-2
• variants of concern
• Omicron lineage
• reinfection
• disease severity

Acknowledgements

We would like to deeply thank the patients participating in the study. JMLS, HRP, and AMB acknowledge the University of La Laguna for the training support during the PhD studies.

Disclosure statement

No potential conflicts of interest were reported by the authors.

Data availability statement

Sequences in FASTA format and associated metadata have been deposited in GISAID (https://gisaid.org) under identifiers EPI_SET_230213uw and EPI_SET_230322qh.

Additional information

Funding

This work was supported by the Cabildo Insular de Tenerife under grant [CGIEU0000219140 and “Apuestas científicas del ITER para colaborar en la lucha contra la COVID-19”]; Convenio Marco de Cooperación Consejería de Educación-Cabildo Insular de Tenerife 2021–2025 under grant [CGIAC0000014697]; Fundación Canaria Instituto de Investigación Sanitaria de Canarias under grant [PIFIISC21/37]; Instituto de Salud Carlos III under grant [FI18/00230, PI20/00876, and CD22/00138], co-funded by the European Regional Development Fund (ERDF), “A way of making Europe” from the European Union; Ministerio de Ciencia e Innovación under grant [PID2021-123031OB-1181 I00] and co-funded by ERDF; and the European Centre for Disease Prevention and Control under grant [ECDC/HERA/2021/024 ECD.12241].