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.