Phylogeography and phylogeny of Rhinoviruses collected from Severe Acute Respiratory Infection (SARI) cases over successive epidemic periods in Tunisia.

Sondes Haddad-Boubaker,Amin Slim,Cherif Ben Hamda,Khaoula Mefteh,Hanen Smaoui,Kais Ghedira,Khaled Menif,Mohamed Ali Ben Hadj Kacem,Aida Bouafsoun,Henda Triki,Ilhem Boutiba-Ben Boubaker

doi:10.1371/journal.pone.0259859

Abstract

Rhinoviruses (RV) are a major cause of Severe Acute Respiratory Infection (SARI) in children, with high genotypic diversity in different regions. However, RV type diversity remains unknown in several regions of the world. In this study, the genetic variability of the frequently circulating RV types in Northern Tunisia was investigated, using phylogenetic and phylogeographic analyses with a specific focus on the most frequent RV types: RV-A101 and RV-C45. This study concerned 13 RV types frequently circulating in Northern Tunisia. They were obtained from respiratory samples collected in 271 pediatric SARI cases, between September 2015 and November 2017. A total of 37 RV VP4-VP2 sequences, selected among a total of 49 generated sequences, was compared to 359 sequences from different regions of the world. Evolutionary analysis of RV-A101 and RV-C45 showed high genetic relationship between different Tunisian strains and Malaysian strains. RV-A101 and C45 progenitor viruses’ dates were estimated in 1981 and 1995, respectively. Since the early 2000s, the two types had a wide spread throughout the world. Phylogenetic analyses of other frequently circulating strains showed significant homology of Tunisian strains from the same epidemic period, in contrast with earlier strains. The genetic relatedness of RV-A101 and RV-C45 might result from an introduction of viruses from different clades followed by local dissemination rather than a local persistence of an endemic clades along seasons. International traffic may play a key role in the spread of RV-A101, RV-C45, and other RVs.

Highlights

Rhinoviruses (RVs) are a common cause of upper respiratory diseases
As we have previously demonstrated, they correspond to the most frequent RV types A and C in Northern Tunisian between September 2015 and November 2017: RV-A (8 types) and RV-C (3 types), and all RV-B circulating in the same period (3 types) (Table 1) [16]
The Tunisian strains seem profoundly related to Malaysian ones

Summary

Introduction

Rhinoviruses (RVs) are a common cause of upper respiratory diseases In early childhood, they constitute a leading cause of severe lower respiratory infections causing important rates of hospitalization and mortality all around the world [1]. RVs are non-enveloped, positive-sense RNA viruses, classified within the Enterovirus genus of the family Picornaviridae [5, 6] They are characterized by a wide genetic diversity. Type identification is based on the VP4-VP2 coding region pairwise distances [9,10,11]. Using this approach, a significant number of RVs are still provisionally attributed. For accurate type identification, further genetic analysis using VP1 genomic coding region was recommended [10, 11]

Methods

Results

Discussion

Conclusion