Respiratory Syncytial Virus Genotypes Research Articles

Sewage surveillance revealed the seasonality and prevalence of respiratory syncytial virus and its implications for seasonal immunization strategy in low and middle-income regions of China

Respiratory syncytial virus (RSV) represents a significant global health threat, with a disproportionately high disease burden in low and middle-income regions (LMIRs). Estimating the prevalence of RSV infection at the community levels remains a huge challenge, particularly in LMIRs where clinical data are scarce. In this study, we first detected RSV RNA in the fecal samples from 300 patients to understand the fecal shedding patterns of RSV. Meanwhile, we conducted sewage surveillance of RSV in four geographically distinct LMIRs in China from April 2023 to June 2024. Real-time reverse transcription quantitative Polymerase Chain Reaction (RT-qPCR) was employed to monitor the dynamics of sewage RSV concentration in a typical sewershed from Yingkou, Xi'an, Nanchang, and Nanning, respectively. Subsequent amplicon sequencing was conducted to understand the genotype and mutations of sewage RSV. Through RT-qPCR, we observed two RSV epidemics that lasted from late April to May and October to February in both Yingkou and Xi'an. For Nanchang, only one RSV epidemic was observed which emerged from September to February. Notably, in Nanning, a prolonged RSV epidemic was observed from August to April, suggesting RSV vaccination in Nanning faced more challenges. Amplicon sequencing revealed that sewage RSV found in four LMIRs is genetically distinct, highlighting the need for local initiatives for wastewater monitoring of RSV. This study filled the gaps in previous assessment of suitability of RSV vaccination in LMIRs based on clinical surveillance, demonstrating the effectiveness of wastewater surveillance in guiding public health interventions.

Differences Between RSVA and RSVB Subgroups and Implications for Pharmaceutical Preventive Measures.

Understanding the differences between respiratory syncytial virus (RSV) subgroupsA and B provides insights for the development of prevention strategies and public health interventions. We aimed to describe the structural differences of RSV subgroups, their epidemiology, and genomic diversity. The associated immune response and differences in clinical severity were also investigated. A literature review from PubMed and Google Scholar (1985-2023) was performed and extended using snowballing from references in captured publications. RSV has two major antigenic subgroups, A and B, defined by the Gglycoprotein. The RSVF fusion glycoprotein in the prefusion conformation is a major target of virus neutralizing antibodies and differs in surface exposed regions between RSVA and RSVB. The subgroups co-circulate annually, but there is considerable debate as to whether clinical severity is impacted by the subgroup of the infecting RSV strain. Large variations between the studies reporting RSV subgroup impact on clinical severity were observed. A tendency for higher disease severity may be attributed to RSVA but no consensus could be reached as to whether infection by one of the subgroup caused more severe outcomes. RSV genotype diversity decreased over the last two decades, and ON and BA have become the sole lineages detected for RSVA and RSVB, since 2014. No studies with data obtained after 2014 reported a difference in disease severity between the two subgroups. RSVF is relatively well conserved and highly similar between RSVA and B, but changes in the amino acid sequence have been observed. Some of these changes led to differences in F antigenic sites compared to reference F sequences (e.g., RSV/A Long strain), which are more pronounced in antigenic sites of the prefusion conformation of RSVB. Initial results from the second season after vaccination suggest specific RSVB efficacy wanes more rapidly than RSVA for RSV PreF-based monovalent vaccines. RSVA and RSVB both contribute substantially to the global RSV burden. Both RSV subgroups cause severe disease and none of the available evidence to date suggests any differences in clinical severity between the subgroups. Therefore, it is important to implement measures effective at preventing disease due to both RSVA and RSVB to ensure impactful public health interventions. Monitoring overtime will be needed to assess the impact of waning antibody levels on subgroup-specific efficacy.

Targeted metagenomics reveals association between severity and pathogen co-detection in infants with respiratory syncytial virus

Respiratory syncytial virus (RSV) is the leading cause of hospitalisation for respiratory infection in young children. RSV disease severity is known to be age-dependent and highest in young infants, but other correlates of severity, particularly the presence of additional respiratory pathogens, are less well understood. In this study, nasopharyngeal swabs were collected from two cohorts of RSV-positive infants <12 months in Spain, the UK, and the Netherlands during 2017–20. We show, using targeted metagenomic sequencing of >100 pathogens, including all common respiratory viruses and bacteria, from samples collected from 433 infants, that burden of additional viruses is common (111/433, 26%) but only modestly correlates with RSV disease severity. In contrast, there is strong evidence in both cohorts and across age groups that presence of Haemophilus bacteria (194/433, 45%) is associated with higher severity, including much higher rates of hospitalisation (odds ratio 4.25, 95% CI 2.03–9.31). There is no evidence for association between higher severity and other detected bacteria, and no difference in severity between RSV genotypes. Our findings reveal the genomic diversity of additional pathogens during RSV infection in infants, and provide an evidence base for future causal investigations of the impact of co-infection on RSV disease severity.

A robust, scalable, and cost-efficient approach to whole genome sequencing of RSV directly from clinical samples.

Respiratory syncytial virus (RSV) is a leading cause of severe acute respiratory tract infections in children and the elderly, and its prevention has become an increasing priority. Recently, vaccines and a long-acting monoclonal antibody to protect effectively against severe disease have been approved for the first time. Hence, there is an urgent need for genomic surveillance of RSV at the global scale to monitor virus evolution, especially with an eye toward immune evasion. However, robust, cost-effective methods for RSV whole genome sequencing that are suitable for high-throughput of clinical samples are currently scarce. Therefore, we have developed Next-RSV-SEQ, an experimental and computational pipeline that produces reliably high-quality RSV genomes directly from clinical specimens and isolates.

Clinical, Genomic, and Immunological Characterization of RSV Surge in Sydney, Australia, 2022.

The 2022 seasonal respiratory syncytial virus (RSV) epidemic in Sydney, Australia saw an unprecedented number of RSV detections. We aimed to characterize genomic and immunologic factors associated with the surge in RSV cases. Whole genome sequences of RSV were generated from 264 RSV-infected infants and linked to case-matched clinical data from the 2022 southern hemisphere RSV season. We then performed an immunologic analysis of baseline RSV-specific humoral immunity in women of childbearing age before and throughout the coronavirus disease 2019 pandemic. Clinical analysis revealed a high burden of disease across patients of all health backgrounds. More than one-half of RSV-related health care visits by infants resulted in hospitalization, and one-quarter required high-flow respiratory support or a higher level of care. Viral phylogenetic analyses revealed that 2022 Sydney RSV sequences were closely related to viruses that had been circulating globally since 2017, including those detected in recent US outbreaks. Nonsynonymous mutations within the palivizumab and nirsevimab binding sites were detected at low frequencies. There was no difference in baseline RSV-neutralizing antibody titers between 2020 and 2022. Collectively, these findings suggest that neither the emergence of a novel RSV genotype nor hypothesized immune debt was associated with the surge of RSV cases and hospitalizations in 2022. Continued genomic and immunologic surveillance is required to further understand the factors driving outbreaks of RSV globally, and to inform guidelines for the rollout and ongoing use of recently developed immunotherapeutics and vaccines.

2608. Circulating Respiratory Syncytial Virus Genotypes in Hospitalized Children with Bronchiolitis in the United Arab Emirates

Abstract Background Respiratory syncytial virus (RSV) is a major cause of acute respiratory illness in young children and elderly people worldwide. It has a complex molecular epidemiology with multiple strains cocirculating during a single epidemic. Whole genome sequencing is a valuable tool for monitoring genetic diversity and providing genomic information essential for antiviral and vaccine development. In the United Arab Emirates (UAE), little is known about the RSV circulating genotypes, their evolution, and transmission dynamics. Using next-generation sequencing, this study aims to identify RSV genotypes circulating among young children with bronchiolitis in Al Ain City, UAE. Methods This cross-sectional study involved 100 children under two years of age who were hospitalized at a tertiary care facility between April and December 2021 with RSV-positive bronchiolitis. Nasopharyngeal samples were obtained, within 24 hours of hospitalization, for RSV genotyping. MinION nanopore sequencer was used to analyze the whole viral genome. We only sequenced samples with cycle threshold (Ct) &amp;lt; 30 (n=70). After sequencing, 7 samples were not analyzed due to long gaps and small lengths. The remaining 63 samples included 59 RSV-A and 4 RSV-B isolates. Results The median age of the studied children was 4.3 months, interquartile range (2.1-10.4), with 56% below the age of 6 months. There was no significant difference in the clinical characteristics of children having RSV-A compared to those infected with RSV-B. Phylogenetic analysis showed that out of the 59 RSV-A sequences, 58 clustered with the NA1 genotype, and 1 sequence clustered with the GA1 genotype. All RSV-B sequences were classified as BA2 genotypes. The amino acid sequence alignment of the G gene revealed that all 58 NA1 genotypes had 24 amino acid duplication regions from 247 to 282 amino acid positions. We also found four substitutional changes at L248I, H258Q, L274P, and P276Q. Conclusion Phylogenetic analysis revealed that the subtype A NA1 genotype was the dominant strain among the studied children in Al Ain, UAE during the 2021 season. As vaccine development advances, further sequencing of RSV is needed to better understand viral origin, transmission, and genetic recombination, particularly in under-studied populations. Disclosures All Authors: No reported disclosures

Molecular epidemiology and characteristics of respiratory syncytial virus among hospitalized children in Guangzhou, China

BackgroundHuman respiratory syncytial virus (RSV) is a leading cause of acute lower respiratory tract infection and hospitalization, especially in children. Highly mutagenic nature and antigenic diversity enable the RSV to successfully survive in human population. We conducted a molecular epidemiological study during 2017–2021 to investigate the prevalence and genetic characteristics of RSV.MethodsA total of 6499 nasopharyngeal (NP) swabs were collected from hospitalized children at Department of Pediatrics, Guangdong Provincial Hospital of Traditional Chinese Medicine, Guangzhou, Guangdong, China. All NP swab specimens were preliminary screened for common respiratory viruses and then tested for RSV using specific PCR assays. Partial G genes of RSV were amplified for phylogenetic analysis and genetic characterization.ResultsThe overall detection rate for common respiratory viruses was 16.12% (1048/6499). Among those, 405 specimens (6.20%, 405/6499) were found positive for RSV. The monthly distribution of RSV and other respiratory viruses was variable, and the highest incidence was recorded in Autumn and Winter. Based on the sequencing of hypervariable region of G gene, 93 RSV sequences were sub-grouped into RSV-A (56, 60.2%) and RSV-B (37, 39.8%). There was no coinfection of RSV-A and RSV-B in the tested samples. Phylogenetic analysis revealed that RSV-A and RSV-B strains belonged to ON1 and BA9 genotypes respectively, indicating predominance of these genotypes in Guangzhou. Several substitutions were observed which may likely change the antigenicity and pathogenicity of RSV. Multiple glycosylation sites were noticed, demonstrating high selection pressure on these genotypes.ConclusionThis study illustrated useful information about epidemiology, genetic characteristics, and circulating genotypes of RSV in Guangzhou China. Regular monitoring of the circulating strains of RSV in different parts of China could assist in the development of more effective vaccines and preventive measures.

Circulation of human respiratory syncytial virus and new ON1 genotype in northern Viet Nam, 2017-2020.

Human respiratory syncytial virus (RSV) is a primary cause of paediatric severe acute respiratory infection (SARI) worldwide, especially in developing countries. We investigated the genetic characteristics of RSV in northern Viet Nam to determine the prevalence and distribution of subtypes as well as the diversity and transmission patterns of genotypes. In two facilities, from January 2017 to December 2020, 1563 clinical specimens were collected from paediatric patients hospitalized with SARI and tested for RSV. Selected positive samples underwent sequencing analysis targeting the second hypervariable region of the G gene using next-generation sequencing. The RSV positivity rate was 28.02% (438/1563 samples), and prevalence was highest in children aged <1year (43.84%; 192/438). Subtype RSV-A accounted for 53.42% (234/438) of cases, RSV-B for 45.89% (201/438), and there was coinfection in 0.68% (3/438). Both subtypes cocirculated and peaked during August-September in each year of the study. Phylogenetic analysis showed that RSV-A samples belonged to the ON1 genotype, which has three subgenotypes: ON1.1, ON1.2 and ON1.3. However, we did not find the 72-nucleotide duplication in the second hypervariable region of the G gene, a characteristic of genotype ON1, in any RSV-A samples. RSV-B samples belonged to genotype BA9. Our results provide additional molecular characterization of RSV infections in Viet Nam. Specially, our study is the first to report the absence of the 72-nucleotide duplication in the G gene of RSV-A genotype ON1 in Viet Nam, which may help in understanding the genetic evolution of RSV and be useful for vaccine development in the future.

Genomic characterization of respiratory syncytial virus genotypes circulating in the paediatric population of Sydney, NSW, Australia.

Respiratory syncytial virus (RSV), or human orthopneumovirus, is a major cause of acute lower respiratory infection (ALRI), particularly in young children, causing significant morbidity and mortality. We used pathogen genomics to characterize the population structure and genetic signatures of RSV isolates circulating in children in New South Wales between 2016 and 2018 and to understand the evolutionary dynamics of these strains in the context of publicly available RSV genomes from the region and globally. Whole-genome phylogenetic analysis demonstrated the co-circulation of a few major RSV clades in the paediatric population from Sydney. The whole-genome-based genotypes A23 (RSV-A ON1-like genotype) and B6 (RSV-B BA9-like genotype) were the predominant RSV-A and RSV-B genotypes circulating during the study period, respectively. These genotypes were characterized with high levels of diversity of predicted N- and O-linked glycosylation patterns in both the G and F glycoproteins. Interestingly, a novel 72-nucleotide triplication in the sequence that corresponds to the C-terminal region of the G gene was identified in four of the A23 genotype sequenced in this study. Consistently, the population dynamics analysis demonstrated a continuous increase in the effective population size of A23 and B6 genotypes globally. Further investigations including functional mapping of mutations and identifying the impact of sequence changes on virus fitness are highly required. This study highlights the potential impact of an integrated approach that uses WG-based phylogeny and studying selective pressure events in understanding the emergence and dissemination of RSV genotypes.

Impact of public health measures and new introducing variants on Respiratory syncytial virus recrudescence in Taiwan during the COVID-19 pandemic.

Respiratory syncytial virus (RSV) causes clinically significant distress in children and adults. Non-pharmaceutical interventions against SARS-CoV-2 have affected the seasonal activity of common respiratory pathogens. This seems exceptionally true regarding RSV's seasonal circulation, hence we have investigated the changes in the epidemiology of RSV in Taiwan during the pandemic. A prospective surveillance of RSV among hospitalized children was carried out between 2020 and 2022 in central Taiwan. Of all PCR-detected RSV, genotype and evolutionary analysis were further investigated. Demographics and clinical features were compared between each outbreak. Throughout the consecutive three years of the SARS-CoV-2 pandemic, RSV outbreaks took place in Taiwan first in 2020 and a second time in 2022. We enrolled 80 and 105 hospitalized child cases, in each surge respectively. The RSV G protein genomic analysis revealed that RSV ON1 and RSV BA9 were separately contributing to these two outbreaks, and evolutionary evidence indicated these RSV variants are new to Taiwan, with their own featured sets of mutations. Clinically, a shift in age of RSV infected children was found, but the clinical severity was not worse and remained independent of RSV genotype. There were two delayed RSV surges after the relaxation of public measures during the pandemic in Taiwan, and both outbreaks were driven by new RSV genetic variants rather than cryptic circulation of the previous genetic clusters in Taiwan. These findings highlight the importance of continued surveillance on the trend and evolution of RSV after the COVID-19 pandemic.

Predominance of ON1 and BA9 genotypes of human respiratory syncytial virus in children with acute respiratory infection in Chiang Mai, Thailand, 2020–2021

BackgroundHuman respiratory syncytial virus (hRSV) is an important cause of acute respiratory infection, especially in children. Few studies have investigated molecular epidemiology of hRSV infection in Thailand. The aims of this study were to investigate the prevalence and genotype diversity of hRSV in children with acute respiratory infection (ARI) in Thailand. MethodsA total of 383 nasopharyngeal swabs collected from children with ARI from October 2020 to September 2021 were screened for hRSV and nucleotide sequences of the hypervariable region 2 (HVR2) of G gene of the detected hRSV were analysed. ResultsOf 383 nasopharyngeal swabs, 104 (27.2 %) were positive for hRSV, of which 51 (49.0 %), 43 (41.3 %), and 10 (9.6 %) were hRSV-A, hRSV-B, and untypeable strains, respectively. All hRSV-A and hRSV-B were ON1 genotype and BA9 genotype, respectively. Most of the hRSV strains were detected in the cool months, November 2020 to February 2021. Phylogenetic analysis of the HVR2 sequence of G gene revealed three clusters of hRSV-A (ON1 genotype) and two clusters of hRSV-B (BA9 genotype). The hRSV-A strains in cluster 1 and 3 were closely related to the hRSV-A reference strains reported previously from other regions of Thailand whereas those in cluster 2 were closely related to the hRSV-A reference strains reported previously from Europe and Africa. For the hRSV-B strains, both clusters 1 and 2 were closely related to the hRSV-B reference strains reported previously from Europe, Australia, and Taiwan. The predicted N- and O-linked glycosylation sites were found along the length of HVR2 of G protein, mostly in the hRSV-B strains. ConclusionsThe ON1 and BA9 were the only two hRSV genotypes that were co-predominant and solely detected in this study. The findings indicated that the ON1 and BA9 are the only two hRSV genotypes currently circulating in children with ARI in northern Thailand.

Changes in HRSV Epidemiology but Not Circulating Variants in Hospitalized Children due to the Emergence of SARS-CoV-2.

This study assesses the circulation of human respiratory syncytial virus (HRSV) genotypes before, during, and toward the end of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic in children and determines the influence of the pandemic on HRSV circulation patterns and evolution. Phylogenetic analysis of the hypervariable glycoprotein G gene was performed on 221/261 (84.7%) HRSV-positive samples and shows two separated clusters, one belonging to HRSV-A (129/221) and another to HRSV-B (92/221). All Slovenian HRSV-A strains contained the 72-nucleotide-long duplicated region in the attachment glycoprotein G gene and were classified as lineage GA2.3.5. All Slovenian HRSV-B strains similarly contained a 60-nucleotide-long duplicated region in the attachment glycoprotein G gene and were classified as lineage GB5.0.5a. During the 3-year period (2018-2021) covered by the study, no significant differences were observed within strains detected before the SARS-CoV-2 pandemic, during it, and after the implementation of nonpharmaceutical preventive measures. Slovenian HRSV-A strains seem to be more diverse than HRSV-B strains. Therefore, further whole-genome investigations would be required for better monitoring of the long-term impact of SARS-CoV-2 endemic circulation and the formation of new HRSV lineages and epidemiological patterns.

Influence of Sex on Respiratory Syncytial Virus Genotype Infection Frequency and Nasopharyngeal Microbiome.

Respiratory syncytial virus (RSV) has a significant health burden in children, older adults, and the immunocompromised. However, limited effort has been made to identify emergence of new RSV genotypes' frequency of infection and how the combination of nasopharyngeal microbiome and viral genotypes impact RSV disease outcomes. In an observational cohort designed to capture the first infant RSV infection, we employed multi-omics approaches to sequence 349 RSV complete genomes and matched nasopharyngeal microbiomes, during which the 2012/2013 season was dominated by RSV-A, whereas 2013 and 2014 was dominated by RSV-B. We found non-G-72nt-duplicated RSV-A strains were more frequent in male infants (P = 0.02), whereas G-72nt-duplicated genotypes (which is ON1 lineage) were seen equally in both males and females. DESeq2 testing of the nasal microbiome showed Haemophilus was significantly more abundant in infants with RSV-A infection compared to infants with RSV-B infection (adjusted P = 0.002). In addition, the broad microbial clustering of the abundant genera was significantly associated with infant sex (P = 0.03). Overall, we show sex differences in infection by RSV genotype and host nasopharyngeal microbiome, suggesting an interaction between host genetics, virus genotype, and associated nasopharyngeal microbiome. IMPORTANCE Respiratory syncytial virus (RSV) is one of the leading causes of lower respiratory tract infections in young children and is responsible for high hospitalization rates and morbidity in infants and the elderly. To understand how the emergence of RSV viral genotypes and viral-respiratory microbiome interactions contribute to infection frequency and severity, we utilized an observational cohort designed to capture the first infant RSV infection we employed multi-omics approaches to sequence 349 RSV complete genomes and matched nasopharyngeal microbiomes. We found non-G-72nt-duplicated RSV-A genotypes were more frequent in male infants, whereas G-72nt-duplicated RSV-A strains (ON1 lineage) were seen equally in both males and females. Microbiome analysis show Haemophilus was significantly more abundant in infants with RSV-A compared to infants with RSV-B infection and the microbial clustering of the abundant genera was associated with infant sex. Overall, we show sex differences in RSV genotype-nasopharyngeal microbiome, suggesting an interaction host genetics-virus-microbiome interaction.

Immune escaping of the novel genotypes of human respiratory syncytial virus based on gene sequence variation.

Immune escaping from host herd immunity has been related to changes in viral genomic sequences. The study aimed to understand the diverse immune responses to different subtypes or genotypes of human respiratory syncytial virus (RSV) in pediatric patients. The genomic sequences of different subtypes or RSV genotypes, isolated from Beijing patients, were sequenced and systematically analyzed. Specifically, the antiviral effects of Palivizumab and the cross-reactivity of human sera from RSV-positive patients to different subtypes or genotypes of RSV were determined. Then, the level of 38 cytokines and chemokines in respiratory and serum samples from RSV-positive patients was evaluated. The highest nucleotide and amino acid variations and the secondary and tertiary structure diversities among different subtypes or genotypes of RSV were found in G, especially for genotype ON1 with a 72bp-insertion compared to NA1 in subtype A, while more mutations of F protein were found in the NH-2 terminal, including the antigenic site II, the target of Palivizumab, containing one change N276S. Palivizumab inhibited subtype A with higher efficiency than subtype B and had stronger inhibitory effects on the reference strains than on isolated strains. However, RSV-positive sera had stronger inhibitory effects on the strains in the same subtypes or genotypes of RSV. The level of IFN-α2, IL-1α, and IL-1β in respiratory specimens from patients with NA1 was lower than those with ON1, while there were higher TNFα, IFNγ, IL-1α, and IL-1β in the first serum samples from patients with ON1 compared to those with BA9 of subtype B. Diverse host immune responses were correlated with differential subtypes and genotypes of RSV in pediatric patients, demonstrating the impact of viral genetics on host immunity.

Reclassification of respiratory syncytial virus genotypes in India.

The online version contains supplementary material available at 10.1007/s13337-022-00802-x.

Genome analysis of human respiratory syncytial virus in Fujian Province, Southeast China.

Respiratory syncytial virus (RSV) is one of the main causes of acute respiratory infections (ARI)leading to a heavy disease burden. Reports on RSV in China are limited, especially in Fujian Province, and RSV whole-genome sequences in Fujian Province are not reported. This study aimed to explore the genomic characteristics of RSV to provide evidence for the development of vaccines and medicines. Reverse transcription-polymerase chain reaction (RT-PCR) was used to amplify and obtain the attachment (G) gene and whole-genome fragments from the positive samples. Genetic evolution as well as nucleotide and amino acid homology analyses of the virus sequences were conducted to identify any amino acid mutations. A total of 72 RSV-positive cases were collected, and 53G gene sequences were obtained using polymerase chain reaction (PCR) amplification. The ON1 and BA11 genotypes were found to be dominant using the Basic Local Alignment Search Tool (BLAST) on the NCBI website. The 40 genotype ON1 sequences had high nucleotide identity (95.3%-99.8%) and amino acid similarity (92.5%-100%), whereas the 13 BA11 genotype sequenceshad 97.3%-99.6% nucleotide identity and 94.8%-99.7% amino acid similarity. Compared to the ON1 prototype (JN257693) and BA11 prototype (AY333364), the obtained sequences had no nucleotide insertions or deletions, indicating high similarity among the samples. A total of 17 RSV whole genome sequences were obtained, 10 of which were genotype ON1 and seven were genotype BA11. Certain amino acid mutations were found in the antigen site and epitope of the fusion (F) protein but not in the G protein. Glycosylation analyses of specific RSV genes revealed high positive selection rates for the gene, and the N- and O-linked glycosylation sequences in the F gene were relatively conserved. From July 2018 to January 2020, ON1 and BA11 were the most prevalent RSV genotypes in Fujian Province. A high nucleotide identity and amino acid similarity were observed between the reference strain and the obtained strains, as well as among the sequences of the obtained isotypes. Certain amino acid mutations occur at the antigen site and the epitope of the F protein.

Genotyping of respiratory syncytial virus among influenza-like illness and severe acute respiratory infection cases of children in the Philippines from 2006 to 2016.

ObjectiveRespiratory syncytial virus (RSV) is a leading cause of severe lower respiratory infection, and therefore, a major threat to global health. This study determined the epidemiological and molecular characteristics of RSV among cases of influenza‐like illness (ILI) and severe acute respiratory infection (SARI) among children in the Philippines.MethodThe study included archived nasopharyngeal swab and oropharyngeal swab samples collected from patients under the age of five who are presented with ILI or SARI for the period of 2006–2016. Swabs were examined for RSV subgroup by multiplex real‐time qRT‐PCR. Partial genome sequencing and phylogenetic analyses of the second hypervariable region (HVR) of the G gene were used to determine the genotype of RSV isolates.ResultsA total of 1036 representative samples from all sites were selected and tested. Of these samples, 122 were RSV‐positive at 11.8% prevalence rate, and 58.2% (71/122) were classified as RSV‐A. Six genotypes were identified, which include NA1 (27/122, 22.1%), ON1 (5/122, 4.1%), GA2 (1/122, 0.8%), and GA5 (1/122, 0.8%) for RSV‐A; and BA2 (13/122, 10.7%) and BA9 (1/122, 0.8%) for RSV‐B. Most RSV‐related cases were significantly associated with clinical characteristics such as runny nose (88.1% RSV vs. 11.9% non‐RSV: p value = 0.021), pneumonia (80.6% RSV vs. 19.4% non‐RSV; p value = 0.015), and bronchitis (71.7% RSV vs. 28.3% non‐RSV; p value < 0.001). Increased RSV‐related cases were observed among children below 24 months old.ConclusionThe RSV trend and genetic variability in the Philippines resembles a similar pattern of transmission globally.

Genetic diversity and epidemiological features of respiratory syncytial virus, Beijing, 2015–2019: A multicenter and all-age groups study

To investigate the genetic variability and the epidemiological features of respiratory syncytial virus (RSV) in Beijing during five consecutive seasons from 2015 to 2019. We collected 36,927 samples (ages ranged from 1 day to 101 years old) from cases with acute respiratory tract infections (ARTI) using the Respiratory Pathogens Surveillance System (RPSS) in Beijing, 2015-2019. G gene sequencing and phylogenetic analysis were performed to identify RSV genotypes, clusters, and amino acid (aa) changes. In total, 764 (2.1%, 764/36927) cases were RSV positive, 52.1% cases were children under 5 years old, and 25.8% were elderly ≥ 60 years old. We obtained 369 sequences of the G gene. ON1 and BA9 were the dominant genotypes in Beijing. Sub-lineage 4 of ON1, which contains four aa substitutions (T113I, N178G, H258Q, and H266L), emerged in 2017 and became the predominant variant in 2018-2019. Sub-lineage 4 of BA9, which contains two aa changes (A131T, T137I), emerged in 2017 and became the predominant variant in 2019. We also observed 10 rarely reported nucleotide deletions in the 3' end of the G gene from five sequences of the ON1 genotype. With the exception of children < 5 years old, RSV infection mainly occurred in the elderly ≥ 60 years old. Newly emerged sub-lineages have replaced existing sub-lineage over time and become predominant in Beijing. Continued surveillance of the genetic diversity of RSV is necessary.

Molecular epidemiology of respiratory syncytial virus in hospitalised children in Heidelberg, Southern Germany, 2014-2017.

Respiratory syncytial virus (RSV) is the leading cause of hopitalisation in young children with respiratory tract infections (RTI). The aim of this research project was to analyse RSV genotypes and the diversification of RSV strains among hospitalised children in Heidelberg, Germany. We prospectively analysed nasopharyngeal swabs (NPS) from children who were hospitalised with acute RTI at the University Hospital Heidelberg, Germany, during winter seasons 2014 to 2017. RSV RT-PCR and RSV sequence analysis of the G gene coding for the attachment glycoprotein were performed. Clinical data was obtained using a standardised questionnaire. RSV was detected in 405 out of 946 samples from hospitalised children. Most RSV positive children were below the age of two years (84.4%) and had a lower RTI (78.8%). The majority of RSV positive children was male, significantly younger than RSV negative children with a median age of 0.39years and with more severe respiratory symptoms. Out of 405 positive samples, 317 RSV strains were successfully sub-grouped into RSV subtypes A (57.4%; 182/317) and B (42.6%; 135/317). Both RSV subtypes cocirculated in all analysed winter seasons. Phylogenetic analysis of 317 isolates revealed that the majority of RSV-A strains (180/182) belonged to the ON1 genotype, most RSV-B strains could be attributed to the BAIX genotype (132/135). ON1 and BAIX strains showed a sub-differentiation into different lineages and we were able to identify new (sub)genotypes. Analysis of the molecular epidemiology of RSV from different seasons revealed the cocirculation and diversification of RSV genotypes ON1 and BAIX.

Clinical and biological consequences of respiratory syncytial virus genetic diversity.

Respiratory syncytial virus (RSV) is one of the most common etiological agents of global acute respiratory tract infections with a disproportionate burden among infants, individuals over the age of 65, and immunocompromised populations. The two major subtypes of RSV (A and B) co-circulate with a predominance of either group during different epidemic seasons, with frequently emerging genotypes due to RSV’s high genetic variability. Global surveillance systems have improved our understanding of seasonality, disease burden, and genomic evolution of RSV through genotyping by sequencing of attachment (G) glycoprotein. However, the integration of these systems into international infrastructures is in its infancy, resulting in a relatively low number (~2200) of publicly available RSV genomes. These limitations in surveillance hinder our ability to contextualize RSV evolution past current canonical attachment glycoprotein (G)-oriented understanding, thus resulting in gaps in understanding of how genetic diversity can play a role in clinical outcome, therapeutic efficacy, and the host immune response. Furthermore, utilizing emerging RSV genotype information from surveillance and testing the impact of viral evolution using molecular techniques allows us to establish causation between the clinical and biological consequences of arising genotypes, which subsequently aids in informed vaccine design and future vaccination strategy. In this review, we aim to discuss the findings from current molecular surveillance efforts and the gaps in knowledge surrounding the consequence of RSV genetic diversity on disease severity, therapeutic efficacy, and RSV–host interactions.