Molecular characterization of respiratory syncytial virus circulating in Tunisia between 2015 and 2018

Abstract

Introduction. Respiratory syncytial virus (RSV) is the most frequently identified viral agent in children with lower respiratory tract infection (LRTI). No data are available to date regarding RSV genotypes circulating in Tunisia. Aim. The aim of the present study was to investigate the genetic variability of the glycoprotein G gene in Tunisian RSV strains. Methodology. Nasopharyngeal aspirates were collected from infants hospitalized for LRTI in five Tunisian hospitals. All specimens were screened for RSV by a direct immunofluorescence assay (DIFA). To molecularly characterize Tunisian RSV strains, a phylogenetic analysis was conducted. Randomly selected positive samples were subjected to reverse transcription PCR amplifying the second hyper-variable region (HVR2) of the G gene. Results. Among a total of 1417 samples collected between 2015 and 2018, 394 (27.8 %) were positive for RSV by DIFA. Analysis of 61 randomly selected RSV strains revealed that group A RSV (78.7 %) predominated during the period of study as compared to group B RSV (21.3 %). The phylogenetic analysis showed that two genotypes of RSV-A were co-circulating: the ON1 genotype with a 72-nt duplication in HVR2 of the G gene was predominant (98.0 % of RSV-A strains), while one RSV-A strain clustered with the NA1 genotype (2.0 %). Concerning Tunisian group B RSV strains, all sequences contained a 60-nt insertion in HVR2 and a clustered BA10 genotype. Conclusion. These data suggest that RSV-A genotype ON1 and RSV-B genotype BA10, both with duplications in the G gene, were widely circulating in the Central coastal region of Tunisia between 2015 and 2018.

Full Genome Characterization of Respiratory Syncytial Virus Causing a Fatal Infection in an Immunocompromised Patient in Tunisia

“…These sequences differed by only nine non-synonymous substitutions, and none were present in the G or F gene (2 in NS2, 2 in M2, 5 in L). A second phylogenetic tree containing other Tunisian sequences [7] was estimated for the partial G gene region only (as only data for this region was available). For this phylogeny, sequences for all five isolates from the patient were used (Figure 2).…”

“…A second phylogenetic tree containing other Tunisian sequences [ 7 ] was estimated for the partial G gene region only (as only data for this region was available). For this phylogeny, sequences for all five isolates from the patient were used ( Figure 2 ).…”

“…An HRSV-B sequence was used as an outgroup (GenBank accession: MT107528). The HRV2 of the G gene (336 bp) was extracted from the global alignment and combined with the HRSV-A sequences from Jerbi et al [ 7 ] Identical global sequences were again removed, and the final data set consisted of 1070 sequences, including 36 sequences from Jerbi et al, and five sequences from the study here. Phylogenetic trees for the full genome were estimated using FastTree [ 19 , 20 ].…”

“…This classification is due to variations in one of the two hypervariable regions (HRV2) located at the C-terminal of the GPG. Based upon the HRV2 gene, at least 14 and 25 genotypes have been described globally for HRSV-A and HRSV-B, respectively [ 7 ]. In temperate regions, HRSV infections show a distinct seasonality with onset in late fall or early winter; usually the infection peak is between mid-December and early February [ 8 ].…”