SARS-CoV-2/influenza A (H3N2) virus coinfection: epidemiological surveillance in Northeast Brazil

In Brazil, more than 28 million coronavirus disease 2019 (COVID-19) cases and 649,000 associated deaths have been reported as of February 2022. Despite substantial reductions in hospitalizations and COVID-19 deaths and increased vaccine administration, the spread of the omicron variant led to a sharp increase in COVID-19 cases from January to February 2022. In addition, Brazil has faced an outbreak of nonseasonal flu cases caused by a new strain of influenza subtype A (H3N2) named Darwin. In most Brazilian states, the usual flu season is from May to July, and starts in the northeast region and spreads to the South¹. Identifying the so-called “twindemic” of COVID-19 and the flu is challenging because both infections cause similar respiratory manifestations, and Brazil's testing capacity is limited. In addition, evidence on the prevalence and outcomes associated with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and influenza virus coinfection in Brazil is lacking.

This descriptive report presents the results of epidemiological surveillance of patients with SARS-CoV-2 and influenza A (H3N2) virus coinfection in the State of Sergipe in northeastern Brazil from December 15, 2021 to January 14, 2022. The state of Sergipe is located in a region with the worst socioeconomic indicators in the country, with an estimated population of 2.3 million. This state has a Human Development Index of 0.665.

The first case of COVID-19 in Sergipe was confirmed on March 14, 2020 in a woman who traveled to Spain and was infected with SARS-CoV-2 lineage B.1. As of January 14, 2022, the State of Sergipe registered 279,587 confirmed COVID-19 cases and 6064 COVID-19-associated deaths. In addition, complete vaccination coverage against the disease with two doses of CoronaVac (Sinovac Biotech, Beijing, China), Covishield (AstraZeneca, Cambridge, UK), or ComiRNAty (Pfizer- BioNTech, New York, USA) vaccines or a single-dose of the Johnson & Johnson (Janssen) vaccine was estimated at 68%. The first out-of-season case of influenza A virus subtype H3N2 infection was confirmed on December 15, 2021. Approximately 75% of the at-risk and priority groups (older adults, pregnant and postpartum women, healthcare professionals, and children aged 6 months to 6 years) were vaccinated against influenza. Trivalent vaccines including the A/Victoria/2570/2019 (H1N1) pdm09-like virus, A/Hong Kong/2671/2019 (H3N2)-like virus, and B/Washington/02/2019 (B/Victoria lineage)-like virus were administered for flu vaccination in 2021.

All patients included in this analysis had laboratory-confirmed SARS-CoV-2 and/or influenza A virus subtype H3N2. Respiratory samples were analyzed by the Central Laboratory of Public Health, which has been used as the laboratory of reference for the diagnosis of public health diseases in each Brazilian state². Patient demographic data, including age, sex, COVID-19 vaccine status, and mortality were recorded. Case-fatality rates were calculated based on the number of deaths from SARS-CoV-2, influenza A (H3N2), and SARS-CoV-2/influenza A (H3N2) coinfection divided by the total number of confirmed cases for each condition.