Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2023 Jan 25;9(1):vead006.
doi: 10.1093/ve/vead006. eCollection 2023.

Evolutionary dynamics of respiratory syncytial virus in Buenos Aires: Viral diversity, migration, and subgroup replacement

Affiliations

Evolutionary dynamics of respiratory syncytial virus in Buenos Aires: Viral diversity, migration, and subgroup replacement

Stephanie Goya et al. Virus Evol. .

Abstract

Globally, the human respiratory syncytial virus (RSV) is one of the major causes of lower respiratory tract infections (LRTIs) in children. The scarcity of complete genome data limits our understanding of RSV spatiotemporal distribution, evolution, and viral variant emergence. Nasopharyngeal samples collected from hospitalized pediatric patients from Buenos Aires tested positive for RSV LRTI during four consecutive outbreaks (2014-2017) were randomly subsampled for RSV complete genome sequencing. Phylodynamic studies and viral population characterization of genomic variability, diversity, and migration of viruses to and from Argentina during the study period were performed. Our sequencing effort resulted in one of the largest collections of RSV genomes from a given location (141 RSV-A and 135 RSV-B) published so far. RSV-B was dominant during the 2014-2016 outbreaks (60 per cent of cases) but was abruptly replaced by RSV-A in 2017, with RSV-A accounting for 90 per cent of sequenced samples. A significant decrease in RSV genomic diversity-represented by both a reduction in genetic lineages detected and the predominance of viral variants defined by signature amino acids-was observed in Buenos Aires in 2016, the year prior to the RSV subgroup predominance replacement. Multiple introductions to Buenos Aires were detected, some with persistent detection over seasons, and also, RSV was observed to migrate from Buenos Aires to other countries. Our results suggest that the decrease in viral diversity may have allowed the dramatic predominance switch from RSV-B to RSV-A in 2017. The immune pressure generated against circulating viruses with limited diversity during a given outbreak may have created a fertile ground for an antigenically divergent RSV variant to be introduced and successfully spread in the subsequent outbreak. Overall, our RSV genomic analysis of intra- and inter-outbreak diversity provides an opportunity to better understand the epochal evolutionary dynamics of RSV.

Keywords: evolution; genome; genotype; migration; molecular epidemiology; next-generation sequencing (NGS); phylogeography; respiratory syncytial virus (RSV).

PubMed Disclaimer

Figures

Figure 1.
Figure 1.
Seasonality of RSV cases in children hospitalized with lower respiratory tract infection in Buenos Aires between 2014 and 2017. (A) A cumulative bar graph of the number of positive cases of respiratory viruses detected per month per year. Dotted lines represent the minimum and maximum temperatures recorded per month per year published by the Argentine National Weather Service. (B) The seasonality of the RSV-positive cases for subgroups A and B.
Figure 2.
Figure 2.
RSV-A and RSV-B genotyping. Maximum-likelihood trees for RSV genotyping based on the G gene for RSV-A (A) and RSV-B (B). Genotypes and sub-genotypes are detailed at the right of each tree. Color in branches denoted genetic lineages where Argentine sequences were associated. Colored dots at the tips indicate the Argentine sequences per year. Yellow highlight in phylogenetic clades denotes the RSV viral variants (see details in the manuscript). Statistical support (SH-alrt/ultrafast (UF)-Bootstrap) is shown in phylogenetic nodes of ON1 or BA clades, genetic lineages where Argentine sequences are associated, and the viral variants. Bar plots below the phylogenetic trees show the seasonality of the genetic lineages detected in Buenos Aires between 2014 and 2017 for RSV-A (C) and RSV-B (D). The number of cases of each genetic lineage detected per month per year is detailed.
Figure 3.
Figure 3.
The phylodynamics of RSV in Buenos Aires between 2014 and 2017. The reconstruction of the effective population size (Ne) concerning the time for RSV circulating in Buenos Aires. The lines show the median value, and the colored areas denote the 95 per cent HPD ranges (light blue: RSV-A and orange: RSV-B).
Figure 4.
Figure 4.
The Bayesian phylogeographic discrete analysis. Maximum clade credibility tree for RSV-A and RSV-B. The branches’ colors represent the MRCA’s location (described in the legend). Black dots in the nodes denote statistical support above 0.7 posterior probability. The time scale in years is detailed at the bottom. The viral introductions described in this study are marked with an arrow and identified with a number (details in Table 2). RSV viral variants discussed in the text are highlighted in orange, including the variant name at the top. Complete full-detailed phylogeographic trees are in the Supplementary material.

Similar articles

Cited by

References

    1. Agoti C. N. et al. (2012) ‘Genetic Relatedness of Infecting and Reinfecting Respiratory Syncytial Virus Strains Identified in a Birth Cohort from Rural Kenya’, The Journal of Infectious Diseases, 206: 1532–41. - PMC - PubMed
    1. Anderson L. J. et al. (1985) ‘Antigenic Characterization of Respiratory Syncytial Virus Strains with Monoclonal Antibodies’, Journal of Infectious Diseases, 151: 626–33. - PubMed
    1. Babraham Bioinformatics . FastQC A Quality Control Tool for High Throughput Sequence Data (cited 18 Feb 2022) <https://www.bioinformatics.babraham.ac.uk/projects/fastqc/> accessed 24 Sep 2022.
    1. Bakker S. E. et al. (2013) ‘The Respiratory Syncytial Virus Nucleoprotein-RNA Complex Forms a Left-Handed Helical Nucleocapsid’, Journal of General Virology, 94: 1734–8. - PMC - PubMed
    1. Beeler J. A., and van Wyke Coelingh K. (1989) ‘Neutralization Epitopes of the F Glycoprotein of Respiratory Syncytial Virus: Effect of Mutation upon Fusion Function’, Journal of Virology, 63: 2941–50. - PMC - PubMed