Impact of the COVID-19 pandemic on the molecular epidemiology of respiratory rhinoviruses and enteroviruses in Tunisia

Abstract

Background: Rhinoviruses (RVs) and enteroviruses (EVs) are major causes of respiratory infections. The COVID-19 pandemic, marked by widespread public health interventions, disrupted viral circulation worldwide. This study assessed the impact of the pandemic on the molecular epidemiology and genetic diversity of RV/EVs in Tunisia.

Methods: We screened 883 nasopharyngeal samples collected between October 2020 and August 2022 for RV/EVs using commercial and/or in-house RT-PCR assays. Sequencing was performed to identify species and genotypes. For comparison, publicly available international sequences and pre-COVID-19 Tunisian sequences were included. Maximum-likelihood phylogeny and pairwise single nucleotide polymorphism distances were used to estimate genetic relationship. Rarefaction and extrapolation analyses were conducted to assess genotype diversity.

Results: RV/EVs maintained circulation during the pandemic with an overall detection rate of 16.5 %. RV-A was the predominant species (47.4 %), followed by RV-C (29.5 %) and RV-B (20.5 %), EV-B and EV-D (1.3 % each). RVs exhibited high genotype diversity, with 42 observed genotypes. Intra-genotype diversity was low during the pandemic in most cases, although a genetic divergence was observed from Tunisian sequences obtained few months before the outbreak. Rarefaction and extrapolation analyses suggested that genotype diversity increased during autumn 2021-summer 2022 compared to the earlier phase of the pandemic (autumn 2020-summer 2021). However, the overall genetic diversity during the pandemic was largely comparable to pre-pandemic levels.

Conclusion: This study provides the first analysis of RV/EV molecular epidemiology in North Africa during the COVID-19 pandemic. The continued circulation and high genetic diversity of RVs highlight their resilience to public health measures and potential viral interference.

Keywords: COVID-19; Enterovirus; Rhinovirus; Sequencing; Tunisia.