Genomic surveillance and evolutionary dynamics of respiratory syncytial virus circulating in Tunisia post-COVID-19 pandemic lockdown restrictions

Abstract

Objectives: Human respiratory syncytial virus (hRSV) is the leading cause of severe respiratory infections in children worldwide. Severe cases often require intensive care. Respiratory syncytial virus (RSV) is classified into two main antigenic groups: RSV-A and RSV-B. Recent molecular advancements have significantly enhanced our ability to control and understand RSV infections. This study investigated the epidemiologic and genetic characteristics of the RSV in Tunisia, focusing on its evolutionary dynamics.

Methods: Between October and December 2021, 92 samples were collected from Tunisian patients hospitalized for mild-to-severe acute respiratory infections. Laboratory analyses, including real-time reverse transcription-polymerase chain reaction and whole genome sequencing (WGS), were performed to identify and characterize the RSV strains. Phylogenetic analyses were performed to compare the Tunisian sequences with the global RSV sequences from 2012 to 2022.

Results: Of the 92 patients (mean age 1 year and 6 months), 96.9% of the samples tested positive for RSV-A, and 22 samples exhibited co-infections with other respiratory viruses. WGS was successfully performed on the 74 samples. Phylogenetic analysis identified six distinct clades of RSV-A circulating in Tunisia, indicating multiple parallel introductions of the virus into the country. Specific Tunisian clades showed genetic similarities to RSV strains from Argentina, Belgium, and the Philippines.

Conclusions: This study underscores the genetic diversity of RSV in Tunisia, with multiple introductions after the lifting of COVID-19 restrictions in 2021. WGS revealed significant genetic heterogeneity within RSV-A, which could affect the effectiveness of vaccines and therapeutic strategies. Continued surveillance, particularly, in resource-limited regions, is crucial to inform and guide future interventions.

Keywords: Genetic diversity; Human respiratory syncytial virus (HRSV); Surveillance; Tunisia; Whole genome sequencing (WGS).

Figure 1

Distribution of the sequence data per country. The number of sequences collected between 2012 and 2022 and used in this study is displayed for the full-length data (left panel) and G gene data (right panel), with each segment color-coded by country of origin: green represents Asia, cyan represents Europe, red represents Africa, yellow represents the Americas, purple represents Oceania, and pink represents Tunisia.

Figure 2

Global phylogeny. The maximum likelihood trees of the respiratory syncytial virus-A full-length sequences (left) and G gene sequences (right) are shown. Branches are colored based on the country of origin, with Tunisian sequences highlighted in pink. For G gene sequences, the sampling year for Tunisian sequences is annotated on the right-hand side. Branch lengths represent nucleotide substitutions per site.

Figure 3

Phylogenetic tree of full-length strains from Tunisia. An extracted view of the tree from Figure 2 is shown, highlighting clades containing Tunisian data. The tips are color-coded by the Tunisian governorate and are annotated on the accompanying map. The five clades are indicated with arrows. Branch lengths represent nucleotide substitutions per site.

Figure 4

Analysis of the amino acid variance of the RSV-A sequences based on the G protein alignment. A total of 31 G protein sequences were selected based on the percentage of informative nucleotides (>95%) in the sequence. The figure was rendered using the Snipit tool with an improvement of the pipeline for amino acid visualization (https://github.com/aineniamh/snipit).