GENOTYPIC CHARACTERISATION OF HUMAN RESPIRATORY SYNCYTIAL VIRUS IN CHILDREN PRESENTING WITH RESPIRATORY TRACT INFECTIONS IN IBADAN, NIGERIA

Abstract

Human Respiratory Syncytial Virus (HRSV) is the most common viral cause of acute lower respiratory tract infections in infants and young children,however, effective vaccine is yet to be licensed for human use till date. Palivizumab, a Monoclonal Antibody (MAb) against the Fusion protein of the virus is used for prophylactic treatment in developed countries but not yet in Nigeria. Mutation at the binding site of this MAb may lead to drug resistance. Information on the circulating genotypes of HRSV from regions with high-burden of infection is vital in the global efforts towards the development of protective vaccine. This study was designed to determine the genotypes of HRSV circulating among children in Ibadan, and the presence of resistance mutation in the F gene of the strains identified. Nasopharyngeal and oropharyngeal swab samples were collected between March and October, 2015, from 231 children (aged 1 to 72 months) with symptoms of respiratory infections. The samples were collected at Oranyan and Omi-Adio primary health centres as well as Our Lady of Apostles Catholic Hospital, Oluyoro (a secondary health facility) in Ibadan. Viral RNA was extracted from the swab specimens and used to identify HRSV using primers targeting the conserved region of the matrix gene. The HRSV-positive samples were subtyped by PCR using subtype-specific primers targeting the second Hypervariable Region (HVR2) of the glycoprotein gene and then sequenced to determine the genotype(s). Antigenic site II of the F gene of HRSV-positive samples were also amplified, sequenced and analysed for amino acid substitutions. Demographic information and medical history were obtained using structured questionnaire. Data were analysed using Chi square at α0.05. The HRSV was detected in 41 specimens (17.8%), out of which 22 (53.7%) were subtype A and 11 (26.8%) were subtype B. Eight (19.5%) of the HRSV-positive samples could not be subtyped with primers used. Phylogenetic analysis showed that genotype ON1 with 72 nucleotide duplications was the major subgroup A virus detected alongside genotype NA2. All the detected HRSV subtype B belong to the BA genotype with characteristic 60 nucleotide duplications. Amino acid substitutions were found in the ON1 genotypes including threonine substituted with isoleucine at position 292 (T292I) in isolate NGR/OL76/15-RSVA. The NA2 genotype have mutation on all antigenic sites in the HVR2. Substitution of asparagine with serine at position 276 (N276S), previously reported to confer resistance against Palivizumab was detected in all the F gene analysed. Symptoms like cough (p=0.007), wheezing (p=0.001) and nasal congestion (p=0.001) were associated with HRSV positivity. Three genotypes of human respiratory syncytial viruswere detected among children in Ibadan, Nigeria. Substitution T292I found in one of the isolates has not been reported elsewhere although its significance is not yet known. The presence of the Palivizumab-resistance mutation on the circulating virus suggest the likelihood of treatment failure if the monoclonal antibody is introduced for use in Nigeria. Studies to determine the effect of the N276S mutation on Palivizumab is recommended to inform policy on the monoclonal antibody use in Nigeria.