Molecular epidemiology of human respiratory syncytial virus among children in Japan during three seasons and hospitalization risk of genotype ON1

Abstract

We investigated the genetic diversity, the circulation patterns, and risk for hospital admission of human respiratory syncytial virus (HRSV) strains in Japan between 2012 through 2015. During the study period, 744 HRSV-positive cases were identified by rapid diagnostic test. Of these, 572 samples were positive by real-time PCR; 400 (69.9%) were HRSV-A, and 172 (30.1%) were HRSV-B. HRSV-A and -B alternated as the dominant strain in the subsequent seasons. Phylogenetic tree analysis of the second hyper-variable region of the G protein classified the HRSV-A specimens into NA1 (n = 242) and ON1 (n = 114) genotypes and the HRSV-B specimens into BA9 (n = 60), and BA10 (n = 27). The ON1 genotype, containing a 72-nucleotide duplication in the G protein’s second hyper-variable region, was first detected in the 2012–2013 season but it predominated and replaced the older NA1 HRSV-A in the 2014–2015 season, which also coincided with a record number of HRSV cases reported to the National Infectious Disease Surveillance in Japan. The risk of hospitalization was 6.9 times higher for the ON1 genotype compared to NA1. In conclusion, our data showed that the emergence and predominance of the relatively new ON1 genotype in Japan was associated with a record high number of cases and increased risk for hospitalization.

Shifts in the epidemic season of human respiratory syncytial virus associated with inbound overseas travelers and meteorological conditions in Japan, 2014–2017: An ecological study

“…Of the 47 prefectures, 46 prefectures, excluding Okinawa prefecture, belong to the temperate zones [ 3 ]. Okinawa belongs to the subtropical region where the seasonality of HRSV is different [ 18 ]. Therefore, data for this study, only included the 46 prefectures which have temperate climates and excluded the subtropical Okinawa prefecture.…”

Detection of ON1 and novel genotypes of human respiratory syncytial virus and emergence of palivizumab resistance in Lebanon

“…Based on the variability within HVR2, at least 13 RSV-A and 22 RSV-B genotypic clades have been identified [6]. RSV-A ON1 and NA1 and RSV-B BA are the major circulating genotypes worldwide [7–9]. The RSV-A ON1 genotype, with its characteristic 72-nucleotide duplication in HVR2, emerged during the 2010/11 season in Canada and spread to other countries [10].…”

Factors Contributing to Symptom Duration and Viral Reduction in Outpatient Children With Respiratory Syncytial Virus Infection

“…We identified RSV serotype A or B from cDNA using TaqMan probes targeting the nucleic acid sequences unique to serotype A or B in F protein of human RSV. 11 The primer and probe set specific for either RSV-A or RSV-B were included in the real-time polymerase chain reaction (PCR) run using appropriate reaction mixtures and cDNA to identify RSV-A or RSV-B. Amplification was conducted as follows: 95°C for 10 seconds, followed by 50 cycles of 95°C for 5 seconds and 60°C for 30 seconds.…”

“…To quantify viral load in a clinical sample, another real-time PCR assay was performed using the primer and probe set targeting a standard sequence for RSV-A and -B in M gene of RSV. 11 Real-time PCR was run in 25 μL reaction mixtures using 12.5 μL 2 × Premix Taq solution, 1.25 U of TaKaRa Taq DNA Polymerase, 0.25 μL each of forward and reverse primers (20 pmol/mL each), 1 μL of 5 pmol/mL TaqMan probe, 1 μL of cDNA template and 10 μL nuclease-free water. The target sequence was cloned into a pM20-T vector (Takara Bio Inc., Shiga, Japan) using a Mighty TA cloning kit (Takara Bio Inc., Shiga, Japan) according to manufacturer’s protocol to obtain positive controls.…”