Dataset Information

Prevalence, variation, and transmission patterns of human respiratory syncytial virus from pediatric patients in Hubei, China during 2020-2021.

ABSTRACT: Human respiratory syncytial virus (RSV) is a severe threat to children and a main cause of acute lower respiratory tract infections. Nevertheless, the intra-host evolution and inter-regional diffusion of RSV are little known. In this study, we performed a systematic surveillance in hospitalized children in Hubei during 2020-2021, in which 106 RSV-positive samples were detected both clinically and by metagenomic next generation sequencing (mNGS). RSV-A and RSV-B groups co-circulated during surveillance with RSV-B being predominant. About 46 high-quality genomes were used for further analyses. A total of 163 intra-host nucleotide variation (iSNV) sites distributed in 34 samples were detected, and glycoprotein (G) gene was the most enriched gene for iSNVs, with non-synonymous substitutions more than synonymous substitutions. Evolutionary dynamic analysis showed that the evolutionary rates of G and NS2 genes were higher, and the population size of RSV groups changed over time. We also found evidences of inter-regional diffusion from Europe and Oceania to Hubei for RSV-A and RSV-B, respectively. This study highlighted the intra-host and inter-host evolution of RSV, and provided some evidences for understanding the evolution of RSV.

SUBMITTER: Yan Y

PROVIDER: S-EPMC10311268 | biostudies-literature | 2023 Jun

REPOSITORIES: biostudies-literature

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Prevalence, variation, and transmission patterns of human respiratory syncytial virus from pediatric patients in Hubei, China during 2020-2021.

Yan Yi Y Wang Decheng D Li Ying Y Wu Zhiyong Z Liu Haizhou H Shi Yue Y Lu Xiaoxia X Liu Di D

Virologica Sinica 20230503 3

Human respiratory syncytial virus (RSV) is a severe threat to children and a main cause of acute lower respiratory tract infections. Nevertheless, the intra-host evolution and inter-regional diffusion of RSV are little known. In this study, we performed a systematic surveillance in hospitalized children in Hubei during 2020-2021, in which 106 RSV-positive samples were detected both clinically and by metagenomic next generation sequencing (mNGS). RSV-A and RSV-B groups co-circulated during survei ...[more]

PMID: 37146717

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Project description:Detailed information on the source, spread and evolution of respiratory syncytial virus (RSV) during seasonal community outbreaks remains sparse. Molecular analyses of attachment (G) gene sequences from hospitalized cases suggest that multiple genotypes and variants co-circulate during epidemics and that RSV persistence over successive seasons is characterized by replacement and multiple new introductions of variants. No studies have defined the patterns of introduction, spread and evolution of RSV at the local community and household level. We present a whole genome sequence analysis of 131 RSV group A viruses collected during 6-month household-based RSV infection surveillance in Coastal Kenya, 2010 within an area of 12 km2. RSV infections were identified by regular symptom-independent screening of all household members twice weekly. Phylogenetic analysis revealed that the RSV A viruses in nine households were closely related to genotype GA2 and fell within a single branch of the global phylogeny. Genomic analysis allowed the detection of household-specific variation in seven households. For comparison, using only G gene analysis, household-specific variation was found only in one of the nine households. Nucleotide changes were observed both intra-host (viruses identified from same individual in follow-up sampling) and inter-host (viruses identified from different household members) and these coupled with sampling dates enabled a partial reconstruction of the within household transmission chains. The genomic evolutionary rate for the household dataset was estimated as 2.307 × 10 - 3 (95% highest posterior density: 0.935-4.165× 10 - 3) substitutions/site/year. We conclude that (i) at the household level, most RSV infections arise from the introduction of a single virus variant followed by accumulation of household specific variation and (ii) analysis of complete virus genomes is crucial to better understand viral transmission in the community. A key question arising is whether prevention of RSV introduction or spread within the household by vaccinating key transmitting household members would lead to a reduced onward community-wide transmission.

Project description:ImportanceBronchiolitis is the most common diagnosis necessitating respiratory support and pediatric intensive care, and respiratory syncytial virus (RSV) is the most common cause of bronchiolitis. In 2023, the monoclonal antibody nirsevimab and the maternal RSVpreF vaccine were implemented to prevent RSV in infants.ObjectiveTo determine the potential association of novel RSV prevention strategies with pediatric intensive care unit (ICU) utilization.Design, setting, and participantsThis retrospective cross-sectional study examined US pediatric ICU encounters with and without RSV from January 1, 2017, to June 1, 2023. Data were from Oracle Cerner RealWorld Data, a national electronic health record database. All children (aged >1 day and <18 years) admitted to an ICU during the study period were included in the analysis. Statistical analysis was performed from February to May 2024.Main outcomes and measuresThe primary outcomes were ICU encounters with RSV and ICU encounters with RSV eligible for RSV prevention.ResultsThere were 119 782 ICU encounters from 53 hospitals; 65 757 encounters (54.9%) were male; median (IQR) age was 4.5 (1.1-12.5) years, median (IQR) ICU length of stay was 1.8 (1.0-3.9) days; 13 702 ICU encounters (11.4%) had RSV, of which 38.6% (5217) were eligible for prevention (4.4% of total ICU encounters). Encounters with RSV accounted for 21.1% (109 334) of ICU days, of which 43.8% (47 888) were eligible for prevention (9.2% of total ICU days). Encounters with RSV were associated with a greater use of positive pressure ventilation (4074 [29.7%] vs 18 821 [17.7%]; P < .001) and vasoactive medications (3057 [22.3%] vs 18 570 [17.5%]; P < .001) compared with those without RSV.Conclusions and relevanceThe findings of this retrospective cross-sectional study of RSV and US pediatric intensive care utilization suggest that if 65% to 85% of eligible children received RSV prevention, an estimated 2.1% to 2.8% reduction in pediatric ICU encounters and an estimated 4.5% to 5.9% reduction in pediatric ICU days could be achieved.

Dataset Information

Prevalence, variation, and transmission patterns of human respiratory syncytial virus from pediatric patients in Hubei, China during 2020-2021.

Publications

Prevalence, variation, and transmission patterns of human respiratory syncytial virus from pediatric patients in Hubei, China during 2020-2021.

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