Molecular characterization of human respiratory syncytial virus in Seoul, South Korea, during 10 consecutive years, 2010–2019

Abstract

Respiratory syncytial virus (RSV) is the leading cause of lower respiratory tract infections and hospitalization in infants and young children. Here, we analyzed the genetic diversity of RSV using partial G gene sequences in 84 RSV-A and 78 RSV- B positive samples collected in Seoul, South Korea, for 10 consecutive years, from 2010 to 2019. Our phylogenetic analysis revealed that RSV-A strains were classified into either the ON1 (80.9%) or NA1 (19.0%) genotypes. On the other hand, RSV-B strains demonstrated diversified clusters within the BA genotype. Notably, some sequences designated as BA-SE, BA-SE1, and BA-DIS did not cluster with previously identified BA genotypes in the phylogenetic trees. Despite this, they did not meet the criteria for the assignment of a new genotype based on recent classification methods. Selection pressure analysis identified three positive selection sites (amino acid positions 273, 274, and 298) in RSV-A, and one possible positive selection site (amino acid position 296) in RSV-B, respectively. The mean evolutionary rates of Korean RSV-A from 1999 to 2019 and RSV-B strains from 1991 and 2019 were estimated at 3.51 × 10−3 nucleotides (nt) substitutions/site/year and 3.32 × 10−3 nt substitutions/site/year, respectively. The population dynamics in the Bayesian skyline plot revealed fluctuations corresponding to the emergence of dominant strains, including a switch of the dominant genotype from NA1 to ON1. Our study on time-scaled cumulative evolutionary analysis contributes to a better understanding of RSV epidemiology at the local level in South Korea.

Resurgence of respiratory syncytial virus with dominance of RSV-B during the 2022–2023 season

“…Among all the studied respiratory viruses, RSV was the most frequently identified etiologic agent of ARIs during the 2022–2023 season and the second most commonly detected respiratory virus after SARS-CoV-2 during the previous two seasons. Temporal and geographic variations exist in the incidence of RSV infection, depending on the study population, detection methods, climate, and other factors ( Gimferrer et al, 2019 ; Valley-Omar et al, 2022 ; Bimouhen et al, 2023 ; Kim et al, 2023 ). During the COVID-19 pandemic, the intensity of the applied anti-epidemic measures has played a crucial role in determining the spread of seasonal respiratory viruses.…”

“…Molecular analysis of RSV G genes revealed the presence of a 60-nucleotide duplication in HVR2, which is a landmark characteristic of BA strains initially described in Buenos Aires, Argentina, in 1999. Following its appearance, the BA genotype rapidly evolved and displayed significant diversification into at least 14 new genotypes ( Ábrego et al, 2017 ; Lee et al, 2021 ; Kim et al, 2023 ). Since 2006, RSV-B strains harboring this partial duplication have become globally predominant and have completely replaced all previously circulating RSV-B genotypes ( Trento et al, 2010 ).…”

“…The F protein is the major viral antigen and is relatively conserved, whereas the G protein contains two hypervariable regions (HVRs) in the superficial ectodomain and exhibits greater genetic diversity. The highly variable C-terminal region of the G gene (HVR2) is commonly used in molecular, epidemiological, and evolutionary studies ( Gimferrer et al, 2019 ; Sáez-López et al, 2019 ; Kim et al, 2023 ). The G and F proteins are heavily glycosylated with N-linked and O-linked sugars, which limit antibody access to the antigenic еpitopes, thereby facilitating RSV evasion from pre-existing immunity ( Holmes, 2013 ).…”

“… Goya et al (2020) proposed a new classification in which the number of genotypes was reduced to three for RSV-A (GA1–GA3) and seven for RSV-B (GB1–GB7), with two additional levels of classification defined as sub-genotypes and lineages ( Goya et al, 2020 ). Variations in the temporal and geographical distributions of individual RSV genotypes and the periodic replacement of predominant genotypes were observed ( Esposito et al, 2015 ; Sáez-López et al, 2019 ; Kamau et al, 2020 ; Lee et al, 2021 ; Tabatabai et al, 2022 ; Kim et al, 2023 ). Viruses of different genotypes can co-circulate during a single epidemic within the same community.…”

Identification of distinct genotypes in circulating RSV A strains based on variants on the virus replication-associated genes

“…The answer could be both. It has been established that the 2nd hypervariable region of G (HVR2) is highly variable and often used in determining RSV genotypes(51). However, in this study, we focused on a replication aspect starting with the polymerase L and observed variations majorly in the RdRP, CD, and MT domains.…”