Epidemiological Characterization of Patients in the First Eight Weeks Following Detection of SARS-CoV-2 B.1.1.529 (omicron) Variant in Cuba.

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. OBJECTIVE: 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.

Emergence and evolution of SARS-CoV-2 genetic variants during the Cuban epidemic.

The SARS CoV-2 D614G variant circulated in Cuba in 2020. New viral variants were detected after the opening of the border in November 2020. We show the results of the genomic surveillance in Cuba from December 28, 2020, to September 28, 2021 and their relationship to the epidemiological situation in the country. A total of 1,406 nasopharyngeal exudates from COVID-19 patients were processed for RNA extraction and the 1836 bp fragment of the spike gene was amplified and sequenced. The mutations present were determined using the GISAID database. Prevalence ratios were estimated by fitting Poisson univariate and multivariate regression models to investigate associations between SARS-CoV-2 variant group (VOC, non-VOC) and disease outcome. Seventeen genetic variants were detected including VOC Alpha, Beta, Gamma and Delta, one variant of interest (VOI) (Lambda) and two previous VOI (A.2.5.1 and Zeta/P.2). Beta (34.77%), Delta (24.89%) and D614G (19%) variants were the most frequently detected. By June, Delta increased in frequency, displacing Beta. Disease severity increased significantly with age and VOC (PR =1.98, IC 95%: 1.33-3.05, p <0.05). Genomic surveillance allowed us to identify the upsurge of novel variants. Coinciding with the higher epidemic period, multiple variants were co-circulating. Although we cannot rule out that failure in the transmission containment measures occurred, the increase in the number of cases associated with the circulation of several variants, particularly the Beta and Delta variants is highly suggestive. A greater association of Beta variant with clinical severity and Delta variant with a greater transmissibility was observed.

Clinical-Epidemiological Characteristics of the First Patients Diagnosed with COVID-19 in Cuba.

INTRODUCTION: COVID-19 is caused by the novel coronavirus SARS-CoV-2 and was declared a pandemic on March 11, 2020, the same day that the first cases in Cuba were diagnosed. In Cuba, all confirmed cases of COVID-19 were hospitalized from this point forward. OBJECTIVE: Characterize the first patients diagnosed with COVID-19 in Cuba. INTRODUCTION: METHODS We carried out a descriptive, cross-sectional study of 415 suspected cases of COVID-19 admitted to the Pedro Kourí Tropical Medicine Institute in Havana, Cuba, from March 11, 2020 through April 10, 2020. (In Cuba, all patients suspected of being COVID-19-positive were admitted to hospitals or isolation centers for observation and treatment.) Of these 415 individuals, 63 (15.2%) tested positive for SARS-CoV-2. Information was obtained from the Institute's databases as well as a standardized interview form for cases confirmed or suspected as infected with the novel coronavirus. We considered the following variables: age, sex, occupation at the time of interview, national origin, personal health history, time elapsed between symptom onset and hospital admission, signs and symptoms, diagnosis and status at discharge. We based our analysis on frequency distributions and double-entry contingency tables. RESULTS: The mean age was 50 years (range: 16-94 years). The 45-54 age group represented the largest share of cases (25.4%; 16/63); persons aged ≥65 years were 20.6% (13/63); there were more men than women (55.6% vs. 44.4%). Cubans represented 52.4% (33/63) of patients while 47.6% (30/63) were from 14 countries where COVID-19 had already been identified. All foreigners and Cubans who arrived from abroad were considered imported cases (54.0%; 34/63). Health personnel (10 doctors and 1 nurse) represented 17.5% (11/63) of cases. Cough (50.8%), fever (46.0%), sore throat (22.2%) and headache (19.0%) were the most frequently reported symptoms. Asymptomatic patients represented 25.4% (16/63) of cases. Hypertension was the most frequently associated chronic disease (28.6%), followed by asthma (25.0%) and diabetes (17.9%). Patients who were admitted to hospital ≥3 days after symptom onset represented 66.7% (42/63) of cases. Mean hospital stay was 13.7 days (range: 1-27 days). Factors associated with a higher risk of contracting the disease included occupation as a healthcare worker (OR: 1.85; 95%, CI: 0.88-3.87) and aged ≥65 years (OR: 1.68; 95% CI: 0.85-3.34). Five individuals died, for a fatality rate of 7.9% (three foreigners and two Cubans; four men and one woman). Four of these patients were infected outside of Cuba and one was identified as a contact of a confirmed case. All patients who died had significant comorbidities (diabetes, asthma and hypertension). Age of deceased patients ranged from 54 to 87 years. CONCLUSION: The first patients diagnosed with COVID-19 in Cuba were admitted to the Pedro Kourí Tropical Medicine Institute in Havana. They share characteristics with those reported by other countries: more men than women were affected, and comorbidities including hypertension, diabetes and asthma were all important risk factors, as was age ≥65 years. More than half of all cases were imported, and autochthonous patients were all contacts of confirmed cases.