A multi-center study on Molecular Epidemiology of Human Respiratory Syncytial Virus from Children with Acute Lower Respiratory Tract Infections in the Mainland of China between 2015 and 2019

Abstract

Human respiratory syncytial virus (RSV) is a major pathogen of acute lower respiratory tract infection among young children. To investigate the prevalence and genetic characteristics of RSV in China, we performed a molecular epidemiological study during 2015-2019. A total of 964 RSV-positive specimens were identified from 5529 enrolled patients during a multi-center study. RSV subgroup A (RSV-A) was the predominant subgroup during this research period except in 2016. Totally, 535 sequences of the second hypervariable region (HVR-2) of the G gene were obtained. Combined with 182 Chinese sequences from GenBank, phylogenetic trees showed that 521 RSV-A sequences fell in genotypes ON1 (512), NA1 (6) and GA5 (3), respectively; while 196 RSV-B sequences fell in BA9 (193) and SAB4 (3). ON1 and BA9 were the only genotypes after December 2015. Genotypes ON1 and BA9 can be separated into 10 and 7 lineages, respectively. The HVR-2 of genotype ON1 had six amino acid changes with a frequency more than 10%, while two substitutions H258Q and H266L were co-occurrences. The HVR-2 of genotype BA9 had nine amino acid substitutions with a frequency more than 10%, while the sequences with T290I and T312I were all from 2018 to 2019. One N-glycosylation site at 237 was identified among ON1 sequences, while two N-glycosylation sites (296 and 310) were identified in the 60-nucleotide duplication region of BA9. To conclusion, ON1 and BA9 were the predominant genotypes in China during 2015-2019. For the genotypes ON1 and BA9, the G gene exhibited relatively high diversity and evolved continuously.

Keywords: Acute lower respiratory tract infection (ALRTI); Genetic characteristics; Genotype; Human respiratory syncytial virus (RSV); Molecular epidemiology.

Fig. 1

The phylogenetic dendrogram based on the Chinese RSV sequences from 2015 to 2019 and reference sequences with genotype information worldwide. A, B Detailed phylogenetic trees of the RSV-A and RSV-B taxa were analyzed, respectively. The neighbour-joining method was used to infer the topology by the MGEA 6.06 software. The percentage of bootstrap values (percentage of 1000 pseudoreplicate datasets) over 70% are shown at the nodes of the trees. Filled circles with different colors indicate the all the Chinese sequences from different years (red 2015, yellow 2016, purple 2017, green 2018, blue 2019). The scale bars represent substitutions per base pair per indicated horizontal distance.

Fig. 2

Summary of amino acid changes and frequencies in HVR-2 of the G gene of genotype GA5 (n = 3), NA1 (n = 6), ON1 (n = 512), SAB4 (n = 3), and BA9 (n = 193) comparing with their reference sequences. The earliest sequence of each genotype was used as the reference (GA5: Mon/1/01, AF516135; NA1: NG-016–04, AB470478; ON1: ON67-1210, JN257693; SAB4: Cam2009-0351, JN119976; BA9: BA/100/04, DQ227395). Only sites with a substitution frequency of more than 2% are indicated. For the RSV-A ON1 and RSV-B BA9 genotypes, these substitution frequency more than 5% or 10% were marked with orange and red label, respectively.