The 2022 RSV surge was driven by multiple viral lineages [preprint]
Adams, Gordon ; Moreno, Gage K ; Petros, Brittany A ; Uddin, Rockib ; Levine, Zoe ; Kotzen, Ben ; Messer, Katelyn ; Dobbins, Sabrina T ; DeRuff, Katherine C ; Loreth, Christine ... show 10 more
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Moreno, Gage K
Petros, Brittany A
Uddin, Rockib
Levine, Zoe
Kotzen, Ben
Messer, Katelyn
Dobbins, Sabrina T
DeRuff, Katherine C
Loreth, Christine
Brock-Fisher, Taylor
Schaffner, Stephen F
Chaluvadi, Sushma
Kanjilal, Sanjat
Luban, Jeremy
Ozonoff, Al
Park, Daniel
Turbett, Sarah
Siddle, Katherine J
MacInnis, Bronwyn L
Sabeti, Pardis
Lemieux, Jacob
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Abstract
The US experienced an early and severe respiratory syncytial virus (RSV) surge in autumn 2022. Despite the pressure this has put on hospitals and care centers, the factors promoting the surge in cases are unknown. To investigate whether viral characteristics contributed to the extent or severity of the surge, we sequenced 105 RSV-positive specimens from symptomatic patients diagnosed with RSV who presented to the Massachusetts General Hospital (MGH) and its outpatient practices in the Greater Boston Area. Genomic analysis of the resulting 77 genomes (54 with >80% coverage, and 23 with >5% coverage) demonstrated that the surge was driven by multiple lineages of RSV-A (91%; 70/77) and RSV-B (9%; 7/77). Phylogenetic analysis of all US RSV-A revealed 12 clades, 4 of which contained Massachusetts and Washington genomes. These clades individually had times to most recent common ancestor (tMRCA) between 2014 and 2017, and together had a tMRCA of 2009, suggesting that they emerged well before the COVID-19 pandemic. Similarly, the RSV-B genomes had a tMRCA between 2016 and 2019. We found that the RSV-A and RSV-B genomes in our sample did not differ statistically from the estimated clock rate of the larger phylogenetic tree (10.6 and 12.4 substitutions per year, respectively). In summary, the polyphyletic nature of viral genomes sequenced in the US during the autumn 2022 surge is inconsistent with the emergence of a single, highly transmissible causal RSV lineage.
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Adams G, Moreno GK, Petros BA, Uddin R, Levine Z, Kotzen B, Messer K, Dobbins ST, DeRuff KC, Loreth C, Brock-Fisher T, Schaffner SF, Chaluvadi S, Kanjilal S, Luban J, Ozonoff A, Park D, Turbett S, Siddle KJ, MacInnis BL, Sabeti P, Lemieux J. The 2022 RSV surge was driven by multiple viral lineages. medRxiv [Preprint]. 2023 Jan 5:2023.01.04.23284195. doi: 10.1101/2023.01.04.23284195. Update in: N Engl J Med. 2023 Apr 6;388(14):1335-1337. doi: 10.1056/NEJMc2216153. PMID: 36656774; PMCID: PMC9844019.
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This article is a preprint. Preprints are preliminary reports of work that have not been certified by peer review.