High genotypic diversity of Rhinoviruses obtained from Tunisian children with severe acute respiratory infection

Abstract

Introduction: Rhinoviruses (HRV) are among the leading causes of Severe Acute Respiratory Infection (SARI). Their burden and genetic diversity vary from one region to another and little is known in Northern African regions. This study describes epidemiological patterns and genotypic diversity of HRV in SARI cases during a two and half year’s study, in Northern Tunisia.
 Methodology: A total of 271 SARI cases, admitted into the Pediatric Intensive Care Unit of Bechir Hamza Children's Hospital in Tunis, were collected between September 2015 and December 2017. The investigation concerned 104 samples positive for HRV and/or HEV (Human Enterovirus) obtained among these cases. Specific HRV and HEV detections were assessed by real-time PCRs. The HRV molecular typing was based on the VP4-VP2 genomic region analyses.
 Results: Among the viral SARI cases, 33.5% and 12.3% were positive for HRV and HEV respectively. Molecular investigations showed high prevalence of HRV-A (63.3%) followed by HRV-C (30.6%) and HRV-B (6.1%) and high genotypic diversity with 27 types. HRV cases were mostly detected in toddlers younger than 6 months. A total of 16 cases (28%) were found with bacterial and/or viral co-infection. HRV-C infection and HRV-A with bacterial co-infection were associated with complicated infection. Some of the detected types showed a continuous circulation or turnover during an extended period. HRV-A101 and HRV-C45 were the most frequently detected types.
 Conclusions: This study revealed, for the first time, the high HRV diversity in Tunisia, a North-African region. Specific phylogenetic investigations may help to evaluate their diversity and to trace their spread and epidemiological origin.

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

“…Thus, among the 49 generated sequences, 37 sequences, RV-A (n = 23); RV-B (n = 3) and RV-C (n = 11) were included. 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 ]. Viral RNA was extracted using the QIAamp MinElute Virus Spin Kit (Qiagen, GmbH, Hilden, Germany) according to the manufacturer’s recommendations.…”

“…In this study, phylogeographic analyses were conducted on the most frequently detected RV types in Northern Tunisia (RV-A101 and RV-C45), from September 2015 to November 2017 [ 16 ]. Both types belong to the most frequently circulating RV species in the world (A and C); they were detected in Europe, the USA, Asia, and Africa [ 11 ].…”

“…This hospital receives patients from Tunis (the capital), around 11 districts from northern Tunisia as well as complicated cases from other regions of the country. Among the 271 investigated samples, 57 were RV positive, using an in-house real-time PCR [ 16 , 17 ]. Among the RV positive samples, 49 had sufficient residual samples to be used for VP4-VP2 PCR amplification and sequencing [ 7 ] and the 49 VP4-VP2 sequences were generated [ 16 ].…”

“…Among the 271 investigated samples, 57 were RV positive, using an in-house real-time PCR [ 16 , 17 ]. Among the RV positive samples, 49 had sufficient residual samples to be used for VP4-VP2 PCR amplification and sequencing [ 7 ] and the 49 VP4-VP2 sequences were generated [ 16 ].…”

“…In Tunisia, we have recently described the circulation of 27 types of RV-A, B, and C, responsible for children’s SARI cases, between September 2015 and December 2017 [ 16 ]. Some of the circulating viruses were sporadic, while others circulated for long periods.…”