Genotyping of Type A Human Respiratory Syncytial Virus Based on Direct F Gene Sequencing

An amplicon-based protocol for whole-genome sequencing of human respiratory syncytial virus subgroup A

It is convenient to study complete genome sequences of human respiratory syncytial virus (hRSV) for ongoing genomic characterization and identification of highly transmissible or pathogenic variants. Whole genome sequencing of hRSV has been challenging from respiratory tract specimens with low viral loads. Herein, we describe an amplicon-based protocol for whole genome sequencing of hRSV subgroup A validated with 24 isolates from nasopharyngeal swabs and infected cell cultures, which showed cycle threshold (Ct) values ranging from 10 to 31, as determined by quantitative reverse-transcription polymerase chain reaction. MinION nanopore generated 3200 to 5400 reads per sample to sequence over 93% of the hRSV-A genome. Coverage of each contig ranged from 130× to 200×. Samples with Ct values of 20.9, 25.2, 27.1, 27.7, 28.2, 28.8, and 29.6 led to the sequencing of over 99.0% of the virus genome, indicating high genome coverage even at high Ct values. This protocol enables the identification of hRSV subgroup A genotypes, as primers were designed to target highly conserved regions. Consequently, it holds potential for application in molecular epidemiology and surveillance of this hRSV subgroup.

Dominance of the ON1 Genotype of RSV-A and BA9 Genotype of RSV-B in Respiratory Cases from Jeddah, Saudi Arabia

Human respiratory syncytial virus (HRSV) is a main cause of hospital admission for lower respiratory tract infection. In previous studies from Saudi Arabia, higher prevalence of the NA1 genotype in group A was observed from Riyadh and Taif. This study recruited respiratory cases from Jeddah during January to December, 2017. RSV represented 13.4% in the recruited cases with 64% of them belonging to group A and 36% to group B. All group A cases in this study were ON1 type characterized by duplication of 72 nucleotides, 24 amino acids in the C-terminal in the second hypervariable region of the G gene. In addition, for group B all of the cases were clustered under BA9, which had uniquely characterized as duplication of 60 nucleotides in the G protein. Our sequences showed similarity with earlier sequences from Saudi Arabia, Kuwait, Thailand, South Africa, Spain, the USA and Cyprus. Some amino acid substitutions in the investigated sequences would cause a change in potential O-glycosylation and N-glycosylation profiles from prototype ON1. The predominance of the ON1 and BA9 genotype of RSV-A in Jeddah compared to previous Saudi studies showing predominance of the NA1 genotype for group A. This difference in genotype prevalence could be due to fast spread of the ON1 genotype worldwide or due to the flux of travelers through Jeddah during hajj/umrah compared to Riyadh and Taif. This shift in genotype distribution requires continuous surveillance for genetic characterization of circulating respiratory infections including RSV. These findings may contribute to the understanding of RSV evolution and to the potential development of a vaccine against RSV.

Respiratory syncytial virus A genotype classification based on systematic intergenotypic and intragenotypic sequence analysis

Respiratory syncytial virus (RSV), a leading cause of lower respiratory tract infections, is classified in two major groups (A and B) with multiple genotypes within them. Continuous changes in spatiotemporal distribution of RSV genotypes have been recorded since the identification of this virus. However, there are no established criteria for genotype definition, which affects the understanding of viral evolution, immunity, and development of vaccines. We conducted a phylogenetic analysis of 4,353 RSV-A G gene ectodomain sequences, and used 1,103 complete genome sequences to analyze the totallity of RSV-A genes. Intra- and intergenotype p-distance analysis and identification of molecular markers associated to specific genotypes were performed. Our results indicate that previously reported genotypes can be classified into nine distinct genotypes: GA1-GA7, SAA1, and NA1. We propose the analysis of the G gene ectodomain with a wide set of reference sequences of all genotypes for an accurate genotype identification.