Background Acute respiratory infections are a major global burden, with pneumonia being the leading cause of death. However, very little information has been available on their causative agents in Africa. In Gabon, Central Africa, although COVID-19 has been extensively studied since the pandemic emerged, the other respiratory viral diseases have been paid less attention compared to COVID-19 and no surveillance study has been conducted in the country. Therefore, this study aimed to reveal the situation of respiratory viral diseases in Gabon during the COVID-19 pandemic.

Methods A total of 582 nasopharyngeal swab specimens were collected from SARS-CoV-2 negative patients with respiratory illness in several provinces of Gabon during the period from March to December, 2020. Viral RNA was extracted and screened by RT-qPCR for major 17 respiratory viruses. Epidemiological analysis was performed using patient demographic information and the detected viruses were analyzed genetically.

Results Of 582 samples, 156 were positive (26%) for eight viruses: enterovirus (EV), human rhinovirus (HRV), human coronavirus OC43, human parainfluenza virus 3 and 4a, adenovirus, influenza A virus (IAV) and human metapneumovirus. Genotyping of HRV based on 5’UTR and VP4/VP2 sequences identified all genotypes (A, B, and C). Gabonese hMPV and IAV strains were classified as group A and H3N2 respectively. Moreover, hMPV was detected for the first time in Gabon in this study.

Conclusion This study revealed the circulation and distribution of respiratory viruses during the COVID-19 pandemic in Gabon. In particular, detection rate of EV in this study was higher than that reported in 2014 in Gabon. This study reports for the first time in Gabon the molecular characterization of HRV, hMPV and whole genome of IAV strains. Further investigation would be required to validate the effect of the COVID-19 pandemic on the incidence of other respiratory viral diseases.

Funding source: JSPS