Characterization of Respiratory Viruses in Patients with Acute Respiratory Infection in the City of Barranquilla during the SARS-CoV-2/COVID-19 Pandemic

Abstract

Introduction: Severe acute respiratory infection (SARI) is mainly caused by viral pathogens, with a high prevalence in high-risk populations such as infants and older adults. Coinfections by different viruses are frequent and, in some cases, associated with severe disease outcomes. Purpose: The main purpose of this study was to identify respiratory viruses circulating in Barranquilla during the peaks of the COVID-19 pandemic and estimate the prevalence of viral coinfections in samples from individuals with different degrees of respiratory infection. Methods: We received 5083 samples between epidemiological weeks 33–42 of 2021 submitted by the District Health Laboratory of Barranquilla and four local healthcare institutions during COVID-19 surveillance. Among them, we analyzed 101 samples from individuals presenting with influenza-like illness (ILI). Eighteen respiratory viruses, including SARS-CoV-2, were evaluated via qRT-PCR using nasal swabs or nasopharyngeal aspirate samples. Results: Of the 101 study individuals, 56 were male and 45 were female (55.5% and 44.5%, respectively); 25.7% of individuals were infected with at least one of the evaluated viruses. Respiratory syncytial virus (RSV) and human rhinovirus (HRV) were the two most frequently detected viruses (30.7% and 15.4% of total positives, respectively). Coinfections with two or more respiratory viruses accounted for 42% of the total positive cases. Discussion: Our findings indicate the presence of different respiratory viruses in swab or nasopharyngeal aspirate samples from individuals with ILI, including coinfections. These results reveal the circulation of several respiratory viruses in the city of Barranquilla, confirming their importance as potential causes of SARI in Colombia and the need for their active surveillance.