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The 2022 RSV surge was driven by multiple viral lineages.

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.

SUBMITTER: Adams G

PROVIDER: S-EPMC9844019 | biostudies-literature | 2023 Jan

REPOSITORIES: biostudies-literature

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The 2022 RSV surge was driven by multiple viral lineages.

Adams Gordon G Moreno Gage K GK Petros Brittany A BA Uddin Rockib R Levine Zoe Z Kotzen Ben B Messer Katelyn K Dobbins Sabrina T ST DeRuff Katherine C KC Loreth Christine C Brock-Fisher Taylor T Schaffner Stephen F SF Chaluvadi Sushma S Kanjilal Sanjat S Luban Jeremy J Ozonoff Al A Park Daniel D Turbett Sarah S Siddle Katherine J KJ MacInnis Bronwyn L BL Sabeti Pardis P Lemieux Jacob J

medRxiv : the preprint server for health sciences 20230105

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 Bo ...[more]

PMID: 36656774

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Project description:ImportancePediatric readiness is essential for all emergency departments (EDs). Children's experience of care may differ according to operational challenges in children's hospitals, community hospitals, and rural EDs caused by recurring and sometimes unpredictable viral illness surges.ObjectiveTo describe wait times, lengths of stay (LOS), and ED revisits across diverse EDs participating in a statewide quality collaborative during a surge in visits in 2022.Design, setting, and participantsThis retrospective cohort study included 25 EDs from the Michigan Emergency Department Improvement Collaborative data registry from January 1, 2021, through December 31, 2022. Pediatric (patient age <18 years) encounters for viral and respiratory conditions were analyzed, comparing wait times, LOS, and ED revisit rates for children's hospital, urban pediatric high-volume (≥10% of overall visits), urban pediatric low-volume (<10% of overall visits), and rural EDs.ExposuresSurge in ED visit volumes for children with viral and respiratory illnesses from September 1 through December 31, 2022.Main outcomes and measuresProlonged ED visit wait times (arrival to clinician assigned, >4 hours), prolonged LOS (arrival to departure, >12 hours), and ED revisit rate (ED discharge and return within 72 hours).ResultsA total of 2 761 361 ED visits across 25 EDs in 2021 and 2022 were included. From September 1 to December 31, 2022, there were 301 688 pediatric visits for viral and respiratory illness, an increase of 71.8% over the 4 preceding months and 15.7% over the same period in 2021. At children's hospitals during the surge, 8.0% of visits had prolonged wait times longer than 4 hours, 8.6% had prolonged LOS longer than 12 hours, and 42 revisits occurred per 1000 ED visits. Prolonged wait times were rare among other sites. However, prolonged LOS affected 425 visits (2.2%) in urban high-pediatric volume EDs, 133 (2.6%) in urban pediatric low-volume EDs, and 176 (3.1%) in rural EDs. High visit volumes were associated with increased ED revisits across sites.Conclusions and relevanceIn this cohort study of more than 2.7 million ED visits, a pediatric viral illness surge was associated with different pediatric acute care across EDs in the state. Clinical management pathways and quality improvement efforts may more effectively mitigate dangerous clinical conditions with strong collaborative relationships across EDs and setting of care.

Project description:BackgroundA single viral variant is transmitted in the majority of HIV infections. However, about 20% of heterosexually transmitted HIV infections are caused by multiple viral variants. Detection of transmitted HIV variants is not trivial, as it involves analysis of multiple viral sequences representing intra-host HIV-1 quasispecies.MethodologyWe distinguish two types of multiple virus transmission in HIV infection: (1) HIV transmission from the same source, and (2) transmission from different sources. Viral sequences representing intra-host quasispecies in a longitudinally sampled cohort of 42 individuals with primary HIV-1C infection in Botswana were generated by single-genome amplification and sequencing and spanned the V1C5 region of HIV-1C env gp120. The Maximum Likelihood phylogeny and distribution of pairwise raw distances were assessed at each sampling time point (n = 217; 42 patients; median 5 (IQR: 4-6) time points per patient, range 2-12 time points per patient).ResultsTransmission of multiple viral variants from the same source (likely from the partner with established HIV infection) was found in 9 out of 42 individuals (21%; 95 CI 10-37%). HIV super-infection was identified in 2 patients (5%; 95% CI 1-17%) with an estimated rate of 3.9 per 100 person-years. Transmission of multiple viruses combined with HIV super-infection at a later time point was observed in one individual.ConclusionsMultiple HIV lineages transmitted from the same source produce a monophyletic clade in the inferred phylogenetic tree. Such a clade has transiently distinct sub-clusters in the early stage of HIV infection, and follows a predictable evolutionary pathway. Over time, the gap between initially distinct viral lineages fills in and initially distinct sub-clusters converge. Identification of cases with transmission of multiple viral lineages from the same source needs to be taken into account in cross-sectional estimation of HIV recency in epidemiological and population studies.

Project description:IntroductionIn the Northeast US, respiratory viruses such as influenza and respiratory syncytial virus (RSV), which were largely suppressed by COVID-19-related social distancing, made an unprecedented resurgence during 2022, leading to a substantial rise in viral co-infections. However, the relative rates of co-infection with seasonal respiratory viruses over this period have not been assessed.MethodsHere we reviewed multiplex respiratory viral PCR data (BioFire FilmArray™ Respiratory Panel v2.1 [RPP]) from patients with respiratory symptoms presenting to our medical center in New York City to assess co-infection rates of respiratory viruses, which were baselined to total rates of infection for each virus. We examined trends in monthly RPP data from adults and children during November 2021 through December 2022 to capture the full seasonal dynamics of respiratory viruses across periods of low and high prevalence.ResultsOf 50,022 RPPs performed for 34,610 patients, 44% were positive for at least one target, and 67% of these were from children. The overwhelming majority of co-infections (93%) were seen among children, for whom 21% of positive RPPs had two or more viruses detected, as compared to just 4% in adults. Relative to children for whom RPPs were ordered, children with co-infections were younger (3.0 vs 4.5 years) and more likely to be seen in the ED or outpatient settings than inpatient and ICU settings. In children, most viral co-infections were found at significantly reduced rates relative to that expected from the incidence of each virus, especially those involving SARS-CoV-2 and influenza. SARS-CoV-2 positive children had an 85%, 65% and 58% reduced rate of co-infection with influenza, RSV, and Rhino/enteroviruses, respectively, after compensating for the incidence of infection with each virus (p< 0.001).DiscussionOur results demonstrate that most respiratory viruses peaked in different months and present in co-infections less than would be expected based on overall rates of infection, suggesting a viral exclusionary effect between most seasonal respiratory viruses, including SARS-CoV-2, influenza and RSV. We also demonstrate the significant burden of respiratory viral co-infections among children. Further work is necessary to understand what predisposes certain patients for viral co-infection despite this exclusionary effect.

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The 2022 RSV surge was driven by multiple viral lineages.

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The 2022 RSV surge was driven by multiple viral lineages.

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