Circulating respiratory viruses including SARS-CoV-2 during 2021–2022 season in Tunisia: Epidemiological and dynamic changes

Changing patterns in community respiratory virus activity were reported in different geographical locations during the COVID-19 pandemic. In this study, we aimed to assess the prevalence of circulating respiratory viruses, including SARS-CoV-2, during the season 2021–2022 in Tunisia. We retrospectively enrolled 328 nasopharyngeal samples received at the Triage Center of Habib Bourguiba Hospital from patients with acute respiratory symptoms during September 2021–May 2022. All samples were screened for both SARS-CoV-2 and common respiratory viruses. This latter detection was performed using end-point multiplex RT-PCRs, Real-Time PCR, and AllplexTM Respiratory Panel 1 kit (Seegene) for Influenza Virus A (IFVA) and Respiratory Syncytial Virus (RSV) subtyping. Among included patients, at least one viral pathogen was identified in 118 (35.9 %) patients. The detection rate of SARS-CoV-2 was 21.6 %. A low viral coinfection rate was observed (3.3 %). The most prevalent pathogen among non-SARS-CoV-2 viruses was Enterovirus/Rhinovirus (HEV/HRV) (59.6 %) followed by IFVA (15.3 %) and Adenoviruses (ADV) (11.5 %). Only IFVA H3N2 was found to circulate during the study period. A negative virus interaction was eventually induced by SARS-CoV-2, as it was shown by lower levels of activity of non-SARS-CoV-2 viruses (not exceeding 17.7 %) while infections due to pandemic Omicron variants of concern became widespread. This study highlights the relative return of community IFVA circulation during the 2021–2022 season in Tunisia. A negative viral interaction between SARS-CoV-2 and other respiratory viruses is highly suggested, which explains, in addition to the easing of COVID-19 restriction measures, the epidemiological changes in non-SARS-CoV-2 viruses circulation.