INTRODUCTION In November 2021, omicron—a new SARS-CoV-2 variant—was identified in South Africa and almost immediately, WHO declared it a ‘variant of concern’. In view of its rapid worldwide spread and its imminent introduction in Cuba, genomic surveillance was strengthened.

OBJECTIVES Describe cases during the first eight epidemiological weeks (epiweeks) of SARS-CoV-2 infection attributable to omicron variant in Cuba by clinical and epidemiological variables.

METHODS From epiweek 48, 2021 to epiweek 4, 2022, 288 nasopharyngeal swabs were processed for sequencing of a 1836 bp fragment of the S gene. Variants were identified according to GISAID database and confirmed by phylogenetic analysis. Variants’ association with clinical and epidemiological outcomes was assessed.

RESULTS The first cases of omicron variant were imported, mostly from African countries and the United States. During the period studied, omicron was detected in 83.0% (239/288) of cases processed, while the delta variant was found in 17.0% (49/288). Most persons infected with omicron were symptomatic (63.2%; 151/239) and fully vaccinated (65.3%; 156/239); severe cases and deaths occurred mainly among patients aged ≥65 years (92.9%; 13/14), and 12 of these deaths occurred in fully vaccinated persons (92.3%; 12/13). Omicron spread rapidly throughout the country (from 10% of cases in epiweek 48, 2021, to 100% by epiweek 4, 2022), displacing the formerly predominant delta variant.

CONCLUSIONS Omicron’s rapid expansion in Cuba was associated with increased incidence but not with a higher case fatality rate. The relatively milder disease in those infected with this variant could be influenced by the high vaccination coverage, along with the natural immunity acquired as a consequence of previous virus infection.

KEYWORDS Pandemics, epidemiology, epidemiological monitoring, COVID-19 testing, COVID-19, SARS-CoV-2, COVID-19 vaccines, Cuba