Molecular epidemiology of respiratory syncytial virus for 28 consecutive seasons (1990-2018) and genetic variability of the duplication region in the G gene of genotypes ON1 and BA in South Korea

Epidemiology and Disease Burden of Respiratory Syncytial Virus Infection in Adults

Respiratory syncytial virus (RSV) constitutes a significant cause of respiratory illness and mortality among older adults, a demographic that is expanding with considerable impact on healthcare systems worldwide. The actual burden of RSV in this population may still be underestimated, owing to factors such as low awareness and suboptimal diagnostic sensitivity in adults, the lack of robust RSV surveillance systems, and the infrequent use of diagnostic testing. Recent advancements in respiratory virus detection have spurred further exploration into appropriate preventive and therapeutic strategies. The recent approval of two vaccines highlights the critical need for the precise estimation of the RSV disease burden to optimize the effectiveness and cost-efficiency of immunization programs. This narrative review aimed to summarize the existing knowledge of the RSV burden in adults with a particular focus on older adults, incorporating data from Korea. Overall, current estimates indicate that the annual RSV attack rate in the general adult population ranges from 1 - 7%, increasing to approximately 4 - 10% among elderly and high-risk groups. The in-hospital mortality rate can be estimated to be around 7 - 10%, rising up to 40% among intensive care unit-admitted patients. To elucidate RSV's disease burden, further continuing research, including population-based studies, is necessary.

Etiology and Clinical Characteristics of Community-Acquired Pneumonia in Korean Children During the Pre-COVID-19 Period, 2015-2020

BACKGROUND

There have been many epidemiologic studies on community-acquired pneumonia (CAP) among children, most of which had substantial limitations. This study investigated the etiologic distribution and clinical characteristics of CAP in Korean children for 5 years before the coronavirus disease 2019 (COVID-19) pandemic.

METHODS

A retrospective analysis of children hospitalized for CAP at 4 referral hospitals during 2015-2020 was performed. Cases in which bronchiolitis was suspected or pulmonary infiltration was not evident on chest radiography (CXR) were excluded. Viruses and atypical bacteria were defined as detected when positive in the polymerase chain reaction test performed for respiratory specimens. Serologic testing result for Mycoplasma pneumoniae was incorporated with strict interpretation. Pyogenic bacteria were included only when cultured in blood, pleural fluid, or bronchoalveolar lavage, but those cultured in endotracheal aspirate or sputum when the case was clinically evident bacterial pneumonia were also included.

RESULTS

A total of 2,864 cases of suspected pneumonia were selected by diagnosis code and CXR findings. Medical chart and CXR review excluded nosocomial pneumonia and cases without evident infiltration, resulting in 517 (18.1%) CAP cases among 489 children. Regarding clinical symptoms, high fever was present in 59.4% and dyspnea in 19.9% of cases. Respiratory support was required for 29.2% of patients, including mechanical ventilation for 3.9%. Pathogens were detected in 49.9% of cases, with viruses in 32.3%, atypical bacteria in 17.8%, and pyogenic bacteria in 2.3% of cases. As single pathogens, M. pneumoniae (16.8%) and respiratory syncytial virus (RSV, 13.7%) were the most common. Parenteral β-lactam and macrolide antibiotics were administered in 81.6% and 50.7% of cases, respectively. A total of 12 (2.3%) cases resulted in poor outcomes, including 3 deaths.

CONCLUSION

M. pneumoniae and RSV were the most commonly detected pathogens of pediatric CAP, which was selected by strict clinical and radiologic criteria. It is necessary to carefully decide whether to use parenteral antibiotics based on the epidemiology and clinical features of CAP in children.

Molecular Epidemiology and Genetic Diversity of Human Respiratory Syncytial Virus in Sicily during Pre- and Post-COVID-19 Surveillance Seasons

Human respiratory syncytial virus (hRSV) is an important pathogen of acute respiratory tract infection of global significance. In this study, we investigated the molecular epidemiology and the genetic variability of hRSV over seven surveillance seasons between 2015 and 2023 in Sicily, Italy. hRSV subgroups co-circulated through every season, although hRSV-B mostly prevailed. After the considerable reduction in the circulation of hRSV due to the widespread implementation of non-pharmaceutical preventive measures during the COVID-19 pandemic, hRSV rapidly re-emerged at a high intensity in 2022-2023. The G gene was sequenced for genotyping and analysis of deduced amino acids. A total of 128 hRSV-A and 179 hRSV-B G gene sequences were obtained. The phylogenetic analysis revealed that the GA2.3.5a (ON1) and GB5.0.5a (BA9) genotypes were responsible for the hRSV epidemics in Sicily.; only one strain belonged to the genotype GB5.0.4a. No differences were observed in the circulating genotypes during pre- and post-pandemic years. Amino acid sequence alignment revealed the continuous evolution of the G gene, with a combination of amino acid changes specifically appearing in 2022-2023. The predicted N-glycosylation sites were relatively conserved in ON1 and BA9 genotype strains. Our findings augment the understanding and prediction of the seasonal evolution of hRSV at the local level and its implication in the monitoring of novel variants worth considering in better design of candidate vaccines.

Global distribution of respiratory syncytial virus A and B infections: a systematic review

Respiratory syncytial virus (RSV) is the main cause of severe respiratory infections in young children. The need for global epidemiologic data regarding RSV has been increasingly recognized. RSV A infections are reported more frequently than RSV B. Nonetheless, the temporal distribution of infections caused by both RSV groups has not been investigated globally. A systematic review was carried out regarding published studies on RSV A and B epidemiology, as well as RSV G gene ectodomain sequence data available at GenBank. A total of 76,668 [45,990 (60%) RSV A and 30,678 (40%) RSV B] positive samples from 83 countries were identified and included in the analysis. Genotype assignment was obtained in 5,340 RSV A and 2,518 RSV B sequences. Two patterns of RSV circulation were observed: continuous seasons with RSV A predominance and alternate predominance of RSV A and B. These patterns were observed in all regions, but the predominant RSV group seldom coincided in all continents during a given year or season. The most frequently identified RSV A genotype was NA1 (including ON1 viruses) (76.30%), and the most frequently identified RSV B genotype was BA (70.65%). Multiple genotypes circulated simultaneously throughout the evolutionary history of RSV, but genotype diversity decreased after the year 2000. The classification of RSV group and genotype is important for the development of vaccines, as well as to understand viral dynamics. This study displays the global and continental RSV circulation patterns from the first report of human RSV infection until the end of 2020.

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

BACKGROUND

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.

METHODS

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.

RESULTS

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 0.39 years 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.

CONCLUSION

Analysis of the molecular epidemiology of RSV from different seasons revealed the cocirculation and diversification of RSV genotypes ON1 and BAIX.

Genetic Diversity and Molecular Epidemiology of Circulating Respiratory Syncytial Virus in Central Taiwan, 2008-2017

In this study, we investigated the molecular evolution and phylodynamics of respiratory syncytial virus (RSV) over 10 consecutive seasons (2008–2017) and the genetic variability of the RSV genotypes ON1 and BA in central Taiwan. The ectodomain region of the G gene was sequenced for genotyping. The nucleotide and deduced amino acid sequences of the second hypervariable region of the G protein in RSV ON1 and BA were analyzed. A total of 132 RSV-A and 81 RSV-B isolates were obtained. Phylogenetic analysis revealed that the NA1, ON1, and BA9 genotypes were responsible for the RSV epidemics in central Taiwan in the study period. For RSV-A, the NA1 genotype predominated during the 2008–2011 seasons. The ON1 genotype was first detected in 2011 and replaced NA1 after 2012. For RSV-B, the BA9 and BA10 genotypes cocirculated from 2008 to 2010, but the BA9 genotype has predominated since 2012. Amino acid sequence alignments revealed the continuous evolution of the G gene in the ectodomain region. The predicted N-glycosylation sites were relatively conserved in the ON1 (site 237 and 318) and BA9 (site 296 and 310) genotype strains. Our results contribute to the understanding and prediction of the temporal evolution of RSV at the local level.

The spatial-temporal dynamics of respiratory syncytial virus infections across the east-west coasts of Australia during 2016-17

Respiratory syncytial virus (RSV) is an important human respiratory pathogen. In temperate regions, a distinct seasonality is observed, where peaks of infections typically occur in early winter, often preceding the annual influenza season. Infections are associated with high rates of morbidity and mortality and in some populations exceed that of influenza. Two subtypes, RSV-A and RSV-B, have been described, and molecular epidemiological studies have shown that both viruses mostly co-circulate. This trend also appears to be the case for Australia; however, previous genomic studies have been limited to cases from one Eastern state—New South Wales. As such, the broader spatial patterns and viral traffic networks across the continent are not known. Here, we conducted a whole-genome study of RSV comparing strains across eastern and Western Australia during the period January 2016 to June 2017. In total, 96 new RSV genomes were sequenced, compiled with previously generated data, and examined using a phylodynamic approach. This analysis revealed that both RSV-A and RSV-B strains were circulating, and each subtype was dominated by a single genotype, RSV-A ON1-like and RSV-B BA10-like viruses. Some geographical clustering was evident in strains from both states with multiple distinct sub-lineages observed and relatively low mixing across jurisdictions, suggesting that endemic transmission was likely seeded from imported, unsampled locations. Overall, the RSV phylogenies reflected a complex pattern of interactions across multiple epidemiological scales from fluid virus traffic across global and regional networks to fine-scale local transmission events.

Molecular epidemiology of respiratory syncytial virus among children and adults in India 2016 to 2018

Respiratory syncytial virus (RSV) is a common cause of respiratory tract infections among children less than 5 years of age and the elderly. This study intended to determine the circulating genotypes of RSV among severe acute respiratory illness (SARI) cases during the period 2016–2018 in India, among hospitalized acute febrile illness cases of age ranging from 1 to 65 years. Throat/nasopharyngeal swab samples were subjected for testing RSV and subgroups by real-time reverse transcriptase polymerase chain reaction (RT-PCR), further sequencing and phylogenetic analysis were performed for the second hypervariable region of the G gene. RSV-A and B subtypes co-circulated during the years 2016, 2017, and 2018, with RSV-A as the dominant subtype in 2016, and RSV-B as the dominant subgroup in 2017 and 2018. Phylogenetic analysis revealed that the circulating genotypes of RSV were GA2 (16/16), of RSV-A, and GB5 (23/23) of RSV-B in the South, North, and Northeast region of India during the period between 2016 and 2018. Here we report the first study comprising the distribution of RSV-A and B genotypes in the different geographic regions of India among children and adults during the year 2016 to 2018. We also report GA2.3.7 lineage of GA2 genotype for the first time in India to the best of our knowledge.

Evolutionary analysis of human respiratory syncytial virus collected in Myanmar between 2015 and 2018

We studied genetic variation in the second hypervariable region (HVR) of the G gene of human respiratory syncytial virus (HRSV) from 1701 nasal swab samples collected from outpatients with acute respiratory infections at two general hospitals in the cities Yangon and Pyinmana in Myanmar from 2015 to 2018. HRSV genotypes were characterized using phylogenetic trees constructed using the maximum likelihood method. Time-scale phylogenetic tree analyses were performed using the Bayesian Markov chain Monte Carlo method. In total, 244 (14.3%) samples were HRSV-positive and were classified as HRSV-A (n = 84, 34.4%), HRSV-B (n = 158, 64.8%), and co-detection of HRSV-A/HRSV-B (n = 2, 0.8%). HRSV epidemics occurred seasonally between July (1.9%, 15/785) and August (10.5%, 108/1028), with peak infections in September (35.8%, 149/416) and October (58.2%, 89/153). HRSV infection rate was higher in children ≥1 year of age than in those <1 year of age (70.5% vs. 29.5%). The most common HRSV symptoms in children were cough (80%-90%) and rhinorrhea (70%-100%). The predominant genotypes were ON1for HRSV-A (78%) and BA9 for HRSV-B (64%). Time to the most recent common ancestor was 2014 (95% highest posterior density [HPD], 2012-2015) for HRSV-A ON1 and 2009 (95% HPD, 2004-2012) for HRSV-B BA9. The mean evolutionary rate (substitutions/site/year) for HRSV-B (2.12 × 10^-2, 95% HPD, 8.53 × 10^-3-3.63 × 10^-2) was slightly higher than that for HRSV-A (1.39 × 10^-2, 95% HPD, 6.03 × 10^-3-2.12 × 10^-2). The estimated effective population size (diversity) for HRSV-A increased from 2015 to 2016 and declined in mid-2018, whereas HRSV-B diversity was constant in 2015 and 2016 and increased in mid-2017. In conclusion, the dominant HRSV-A and HRSV-B genotypes in Myanmar were ON1 and BA9, respectively, between 2015 and 2018. HRSV-B evolved slightly faster than HRSV-A and exhibited unique phylogenetic characteristics.

Reverse genetics systems for contemporary isolates of respiratory syncytial virus enable rapid evaluation of antibody escape mutants

Human respiratory syncytial virus (RSV) is the leading cause of acute lower respiratory infection in children under 5 y of age. In the absence of a safe and effective vaccine and with limited options for therapeutic interventions, uncontrolled epidemics of RSV occur annually worldwide. Existing RSV reverse genetics systems have been predominantly based on older laboratory-adapted strains such as A2 or Long. These strains are not representative of currently circulating genotypes and have a convoluted passage history, complicating their use in studies on molecular determinants of viral pathogenesis and intervention strategies. In this study, we have generated reverse genetics systems for clinical isolates of RSV-A (ON1, 0594 strain) and RSV-B (BA9, 9671 strain) in which the full-length complementary DNA (cDNA) copy of the viral antigenome is cloned into a bacterial artificial chromosome (BAC). Additional recombinant (r) RSVs were rescued expressing enhanced green fluorescent protein (EGFP), mScarlet, or NanoLuc luciferase from an additional transcription unit inserted between the P and M genes. Mutations in antigenic site II of the F protein conferring escape from palivizumab neutralization (K272E, K272Q, S275L) were investigated using quantitative cell-fusion assays and rRSVs via the use of BAC recombineering protocols. These mutations enabled RSV-A and -B to escape palivizumab neutralization but had differential impacts on cell-to-cell fusion, as the S275L mutation resulted in an almost-complete ablation of syncytium formation. These reverse genetics systems will facilitate future cross-validation efficacy studies of novel RSV therapeutic intervention strategies and investigations into viral and host factors necessary for virus entry and cell-to-cell spread.

Circulating Respiratory Syncytial Virus Genotypes and Genetic Variability of the G Gene during 2017 and 2018/2019 Seasonal Epidemics Isolated from Children with Lower Respiratory Tract Infections in Daejeon, Korea

BACKGROUND

Respiratory syncytial virus (RSV) is a major pathogen causing respiratory tract infections in infants and young children. The aim of this study was to confirm the genetic evolution of RSV causing respiratory infections in children at Daejeon in Korea, through G gene analysis of RSV-A and RSV-B strains that were prevalent from 2017 to 2019.

METHODS

Pediatric patients admitted for lower respiratory tract infections at The Catholic University of Korea Daejeon St. Mary's Hospital in the 2017 and 2018/2019 RSV seasonal epidemics, who had RSV detected via multiplex polymerase chain reaction (PCR) were included. The nucleic acid containing RSV-RNA isolated from each of the patients' nasal discharge during standard multiplex PCR testing was stored. The G gene was sequenced and phylogenetic analysis was performed using MEGA X program and the genotype was confirmed.

RESULTS

A total of 155 specimens including 49 specimens from 2017 and 106 specimens from 2018-2019 were tested. The genotype was confirmed in 18 specimens (RSV-A:RSV-B = 4:14) from 2017 and 8 specimens (RSV-A:RSV-B = 7:1) from 2018/2019. In the phylogenetic analysis, all RSV-A type showed ON1 genotype and RSV-B showed BA9 genotype.

CONCLUSION

RSV-B belonging to BA9 in 2017, and RSV-A belonging to ON1 genotype in 2018/2019 was the most prevalent circulating genotypes during the two RSV seasons in Daejeon, Korea.

Results from the WHO external quality assessment for the respiratory syncytial virus pilot, 2016-17

Background

External quality assessments (EQAs) for the molecular detection of respiratory syncytial virus (RSV) are necessary to ensure the provision of reliable and accurate results. One of the objectives of the pilot of the World Health Organization (WHO) Global RSV Surveillance, 2016‐2017, was to evaluate and standardize RSV molecular tests used by participating countries. This paper describes the first WHO RSV EQA for the molecular detection of RSV.

Methods

The WHO implemented the pilot of Global RSV Surveillance based on the WHO Global Influenza Surveillance and Response System (GISRS) from 2016 to 2018 in 14 countries. To ensure standardization of tests, 13 participating laboratories were required to complete a 12 panel RSV EQA prepared and distributed by the Centers for Disease Control and Prevention (CDC), USA. The 14th laboratory joined the pilot late and participated in a separate EQA. Laboratories evaluated a RSV rRT‐PCR assay developed by CDC and compared where applicable, other Laboratory Developed Tests (LDTs) or commercial assays already in use at their laboratories.

Results

Laboratories performed well using the CDC RSV rRT‐PCR in comparison with LDTs and commercial assays. Using the CDC assay, 11 of 13 laboratories reported correct results. Two laboratories each reported one false‐positive finding. Of the laboratories using LDTs or commercial assays, results as assessed by Ct values were 100% correct for 1/5 (20%). With corrective actions, all laboratories achieved satisfactory outputs.

Conclusions

These findings indicate that reliable results can be expected from this pilot. Continued participation in EQAs for the molecular detection of RSV is recommended.