Genomic Epidemiology of Respiratory Syncytial Virus in a New England Hospital System, 2024

Abstract

Respiratory syncytial virus (RSV) is one of the main seasonal respiratory pathogens in the United States. Although several RSV vaccines were recently approved, vaccination rates remain low. We analyzed RSV-positive nasopharyngeal swabs from Boston Medical Center in 2024 using amplicon-based whole genome sequencing. We found that >80% of the samples were RSV-B, representing a major switch from 2022, when Boston RSV samples were approximately 90% RSV-A. Forty-five of 48 RSV-B samples mapped into a single clade (B.D.E.1), though not a single source within it, suggesting that the predominance of RSV-B is multifactorial. We also found examples of highly related genomes, suggesting clustered transmission. Mutations associated with vaccine escape were not observed. Our work highlights the importance of genomic surveillance for respiratory pathogens to monitor transmission dynamics, such as the unexpected switch from RSV-A to RSV-B dominance, and to understand the epidemiological changes that may be associated with RSV interventions.

Keywords: Massachusetts; genomic epidemiology; genomic surveillance; respiratory infections; respiratory syncytial virus.

Figure 1.

Patient ages and collection dates of respiratory syncytial virus samples received from Boston Medical Center in 2024. A, Number of samples, stratified by patient age group. B, Number of samples received per month (January–June 2024). N = 59.

Figure 2.

Genomic data generation and quality metrics of sequenced respiratory syncytial virus (RSV) samples. A, The sample processing pipeline from nasopharyngeal sample input to whole genome sequence data output. B, We aligned processed sequence data from each sample to both RSV-A and RSV-B reference genomes. “RSV-A Samples” describes samples amplified with the RSV-A primer sets, and “RSV-B” Samples” describes samples amplified with the RSV-B primer sets. The y-axis shows read depth + 1, to aid in plotting on a log scale. The dashed line is at 100 read-pairs. C, The y-axis represents the percent of nucleotides within the F or G gene that had >20× read depth for a given sample. The dashed line at 90% represents the threshold used to retain genomes for further analysis. D, Sample success tracker for the 59 original RSV samples received that proceeded through library preparation and sequencing. The y-axis represents the number of samples and their result at each step of the process. The x-axis shows samples as they proceeded through aliquoting, amplification, library construction, initial sequencing quality control, and subgroup confirmation (through alignment to reference genomes, as shown in panel B).

Figure 3.

Respiratory syncytial virus subgroup B (RSV-B) genomes from this study compared to global RSV-B genomes. A, Maximum likelihood phylogenetic tree of all RSV-B genomes sequenced in this study and all high-coverage, complete RSV-B genomes available in Global Initiative on Sharing All Influenza Data (GISAID) as of 8 November 2024 (n = 796). The inner ring denotes by each genome's clade (assigned by Nextclade), and the outer ring denotes genome source (genomes from this study, from United States samples in GISAID, or other GISAID samples). The dashed lines on the inside of the clade ring denote the regions of the tree that are expanded in (B) and (C). B, Expansion of the B.D.4 genomes within the larger tree in (A). All genomes are colored by location, and the 2 genomes labeled “Boston” and colored in orange are from this study. C, Expansion of a portion of the B.D.4.1.1 genomes within the larger tree in (A). All genomes are colored by location; the genome labeled “Boston” and colored in orange is from this study.

Figure 4.

Examination of respiratory syncytial virus subgroup B (RSV-B) genomes from this study alone. A, Maximum likelihood phylogenetic tree of all RSV-B genomes sequenced in this study, aligned to reference genome (EPI_ISL_1653999, labeled as “Reference” in the figure). Genomes clades were assigned by Nextclade. Genomes labeled by sample ID are specifically mentioned in the text. C1 and C2 denote genomes that are part of clusters 1 and 2, respectively. B, Pairwise comparisons of consensus sequences of all RSV-B genomes sequenced in this study. Each genome is represented by a row and column, and each tile is colored by the number of differences between the genomes intersecting at it. Only genome pairs with 0 differences between them are shown. Boxes denote the comparisons between genomes in C1 and C2, matching those indicated in (A).