Toward unified molecular surveillance of RSV: A proposal for genotype definition

Functional implications of respiratory syncytial virus F sequence variability: a comparative analysis using contemporary RSV isolates

Respiratory syncytial virus (RSV) remains a major global health issue. Therapeutic options are limited, but new prophylactics, all targeting the fusion (F) glycoprotein, were recently licensed. Although F sequence variation is limited, it is unclear if and how this variability translates to phenotypical differences. We analyzed full F sequences of 105 contemporary RSV isolates, gathered from children presenting with acute lower respiratory tract infections. Based on F antigenic site variation, 20 isolates were selected for functional characterization. Although RSV F diversity is generally low, the overall mean pairwise distance between RSV-A strains is higher than RSV-B (0.014 vs 0.008, P < 0.001). Sequence variability in the known monoclonal antibody (mAb)-binding sites seems insufficient to explain the divergent and often subgroup-dependent sensitivity to mAb neutralization. Despite comparable growth rates, mean syncytium size was higher (mean 61.68 [SD 24.51] vs 31.72 [SD 11.64], P < 0.001), and mean syncytium frequency was lower (mean 25.37 [SD 9.20] vs 47.85 [11.52], P < 0.001) in RSV-A strains. For all isolates, higher temperatures were associated with increased inactivation, although some RSV-A isolates displayed manifestly higher stability. Genomic and phenotypic variability among our contemporary RSV isolates was limited, with noticeable exceptions. The availability of new prophylactics targeting RSV F corroborates the importance of continued RSV surveillance to identify changes in the F sequence, including mutations that reduce mAb efficacy or lead to escape mutants. Surveillance should include both sequencing data and an evaluation of sensitivity to prophylactic antibodies, using contemporary clinical isolates.IMPORTANCERespiratory syncytial virus (RSV) is a major cause of respiratory infections in young children worldwide. Recent progress has led to new ways to prevent serious RSV-associated disease. The virus's fusion (F) protein is a key focus for vaccine development because it helps the virus enter host cells and is well conserved across different virus strains. However, it is unclear if small differences in the F protein sequence could affect how the virus behaves in vitro. In this study, we, therefore, analyzed 105 RSV samples from children under two who presented with respiratory infections. We selected 20 samples (12 RSV-A and 8 RSV-B) for functional testing, based on their F protein sequences. Phenotypic differences between clinical isolates and reference strains, such as virus stability at 4°C and susceptibility to monoclonal antibody neutralization, highlight the importance of using viruses isolated from recent clinical samples. Although significant functional differences were observed in traits related to the F protein, both between the RSV subgroups and within, the underlying molecular mechanisms remain unclear. Ongoing monitoring of RSV is critical to ensure current and future vaccines remain effective.

Genetic and Clinical-epidemiologic Profile of hRSV in Pediatric Patients in Southern Brazil: A Four-year Hospital Surveillance Study

BACKGROUND

Respiratory syncytial virus (hRSV) infections primarily cause acute respiratory illness and pediatric hospitalizations. We examined the hRSV molecular epidemiology in a pediatric cohort over a 4-year period and described the interrelationship with clinical data.

METHODS

A cross-sectional study was conducted from 2014 to 2017 on children with acute respiratory illness. Respiratory viruses were detected using a multiplex real-time polymerase chain reaction and molecular typing was performed by nucleotide sequencing.

RESULTS

Three hundred fifty-three children with hRSV were included; 207 (36%) samples were submitted to partial G gene sequencing. A total of 58.3% (n = 120) were males, the median age was 2.3 months (interquartile range 1-4), and 36.4% (n = 75) of the children required intensive care unit assistance. Coinfection was detected in 27 (5.7%) children, mainly hRSV and rhinovirus (14.2%). A total of 95.6% of patients had no comorbidities, and prematurity (4.4%) was more frequent among those with comorbidities. hRSV-B was detected in 109 patients (53%) and hRSV-A in 98 patients (47%), with changes in incidence over the period. All the hRSV-A sequences were classified as ON1-like, with genetic lineage GA2.3.5 forming distinct clusters. hRSV-B sequences were identified as BA-like, comprising 3 genetic lineages, GB5.0.2, GB5.0.4a and GB5.0.5a, with variation over time, and a higher severity was associated with hRSV type B GB5.0.2 and GB5.0.4a lineages compared with the GB5.0.5a.

CONCLUSIONS

Both hRSV subtypes showed similar severity and were not linked to comorbidities. Severe cases were more common in young patients and those infected with GB5.0.2 and GB5.0.4a genotypes. Understanding hRSV's molecular evolution is crucial for tracking new variants and assessing their impact on the effectiveness of emerging vaccines and monoclonal antibodies.

Genotypic Characterization of Human Respiratory Syncytial Viruses Detected in Mexico Between 2021 and 2024

Human respiratory syncytial virus (HRSV) is a leading cause of severe respiratory infections among children, older adults, and immunocompromised individuals. The COVID-19 pandemic and the non-pharmacological interventions to mitigate it resulted in significant changes in HRSV epidemiology and seasonality patterns. Worldwide, there was a considerable reduction in the number of HRSV infections during that period, and the impact of those changes on genotype distribution is still not fully understood. In this work, we analyzed the genotypic characteristics of HRSV strains detected between 2021 and 2024 in Mexico with the aim of identifying changes in circulating lineages. HRSV positive samples collected in five states in Mexico were used. The complete viral attachment glycoprotein gene was sequenced, and phylogenetic inference was performed using datasets including all sequences available at GenBank and GISAID until 30 June 2024. We obtained 114 HRSV sequences (63.2% HRSV-A and 36.8% HRSV-B); 19 were from the 2021-2022 season, 53 from 2022-2023, and 42 from 2023-2024. All HRSV-A sequences clustered with sequences from other countries within A.D lineages, including A.D.1, A.D.3, A.D.5.1, and A.D.5.2 lineages. All HRSV-B sequences clustered in the B.D.E.1 lineage with sequences collected between 2020 and 2024. In conclusion, the characterization of HRSV viruses circulating in Mexico during and after the SARS-CoV-2 pandemic and comparison to all available sequences reported to date corroborates that, on a global scale, HRSV-A viruses of several A.D lineages circulate simultaneously, while HRSV-B viruses are restricted to the B.D.E.1 lineage.

Molecular epidemiological surveillance of respiratory syncytial virus infection in Myanmar from 2019 to 2023

To evaluate genetic changes in respiratory syncytial virus (RSV) between 2019 and 2023, we analyzed RSV strains from Myanmar before and after the COVID- 19 pandemic. Real-time polymerase chain reaction (RT-PCR) positive samples from children presenting with acute respiratory infections at outpatient clinics in Yangon were sequenced to determine the genotype. Phylogenetic and molecular evolutionary analyses were conducted using the Bayesian Markov Chain Monte Carlo method to construct the time-scale Maximum Clade Credibility tree. Of 1127 samples, 104 (9.2%) RSV-A and 233 (20.7%) RSV-B were positive by RT-PCR. There was an absence of a notable epidemic in 2020, a temporal shift with a surge of RSV-A in the 2021 outbreak, a lack of expected cases in 2022 and a substantial resurgence of RSV-B in 2023. The genotype of RSV-A was mainly A.D.3 lineage through the study period, while RSV-B were B.D.4.1.1 and B.D.E.1. RSV-A showed that the same lineage persisted within Myanmar throughout the pandemic, leading to a large outbreak post-COVID. In contrast, RSV-B strains appear to have temporarily disappeared during the pandemic, but subsequently, globally circulating strains likely entered Myanmar, resulting in a major outbreak in 2023. The estimated evolutionary rate at the G-ectodomain for RSV-A was 7.76 × 10⁻³ and RSV-B was 5.67 × 10⁻³ substitutions/site/year. Strengthening genomic surveillance will likely support comparisons of circulating strains with those in other countries and facilitate the introduction of vaccines and other interventions.

Early Experience on Universal Prophylaxis in Infants against Respiratory Syncytial Virus: Facts and Expectations

During the 2023/24 season, nirsevimab significantly reduced the risk of bronchiolitis and confirmed respiratory syncytial virus (RSV) infections in primary care, hospital, and pediatric intensive care unit admissions among infants aged 0 to 11 months, even in a season with a high community RSV burden, particularly for older infants. These findings are very useful for public health authorities to continue to implement immunization campaigns against RSV in the coming seasons. Moreover, universal immunization against RSV represents a transformative step toward reducing the burden of RSV in infants. With promising evidence from recently published studies, the expectations for a reduction of RSV-associated hospitalizations, alongside the improvement of public health outcomes and equitable access to these measures, are high. However, achieving these goals will require addressing challenges related to vaccine uptake, funding, and RSV surveillance to prompt detect resistances due to mutations of the virus. These interventions need to be integrated into public health strategies because they hold the potential to make a significant impact on infant's health worldwide.

Human respiratory syncytial virus genetic diversity and lineage replacement in Ireland pre- and post-COVID-19 pandemic

Human respiratory syncytial virus (HRSV) is a common cause of lower respiratory tract infections globally, and changes in viral epidemiology have been observed in many jurisdictions following the coronavirus disease 2019 (COVID-19) pandemic. Newly licensed vaccines and monoclonal antibodies are anticipated to alleviate the burden on healthcare systems, though such interventions may exert selective pressures on viral evolution. To evaluate the diversity of HRSV in Ireland pre- and post-COVID-19 pandemic, whole-genome sequencing was performed on HRSV-A (n=123) and -B (n=110) samples collected from community and hospitalized cases, during three HRSV seasons between 2021 and 2024. Additionally, G gene sequences, from HRSV-A (n=141) and -B (n=141), collected in the 2015-2019 period were examined. Lineages were assigned by phylogenetic analyses including reference lineages. Phylogenetic trees inferred with the G gene and whole genomes were consistent. Changes in the prevalence of certain lineages post-COVID-19 reflected the impact of non-pharmaceutical interventions (NPIs) introduced to reduce severe acute respiratory syndrome coronavirus 2 transmission, with A.D.1 and A.D.5 the dominant HRSV-A lineages and B.D.E.1 the most prevalent HRSV-B lineage. Similar trends were observed in HRSV lineages circulating across Europe during this time. The emergence of a new lineage was identified as a descendant from A.D.1, with eight distinctive substitutions in proteins G, F and L. Other circulating lineages with aa substitutions were observed in the F glycoprotein, which could impact nirsevimab binding. We provide the first comprehensive analysis of HRSV genomic diversity and evolution in Ireland over the last decade and the impact of the NPIs introduced during the COVID-19 pandemic. This study provides a foundation for future public health surveillance employing pathogen genomics to enable an evidence-based assessment of the impact of pharmaceutical interventions on HRSV evolution and disease severity.

Utility of hypervariable region in hepatitis E virus for genetic evolution analysis and epidemiological studies

Clinical and experimental studies have advanced our understanding of hepatitis E virus (HEV) infection; however, translating the findings to improve prevention and clinical outcomes remains challenging. Phylogenetic analyses of HEV show inconsistencies due to variations in the nucleotide regions studied. This study examined specific HEV regions to facilitate comprehensive molecular and phylogenetic analyses by examining the complete genome and commonly studied partial genome regions. We compared topological similarities between phylogenetic trees and evaluated evolutionary divergence using base substitutions and pairwise distances. The hypervariable region (HVR) showed the closest topology (Robinson-Foulds, Jaccard Robinson-Foulds and clustering information) to the complete genome and a higher mutation rate, resulting in longer branch lengths and clearer genotypic distinctions. Pairwise analysis revealed greater intra- and intergenotypic diversity in the HVR than in other regions. The higher base substitution rate and longer branch lengths of HVR suggest its key role in genotype evolution. Classifying HEV using HVR instead of the other partial genomic regions can reveal subtypes that more accurately reflect the genetic characteristics of HEV. Future research could focus on HVRs to better compare clinical symptoms and genetic features of HEV.

Molecular Analysis of Human Respiratory Syncytial Virus Group B Strains Isolated in Kenya Before and During the Emergence of Pandemic Influenza A/H1N1

BACKGROUND

We conducted a retrospective study to explore molecular insights into human respiratory syncytial virus (HRSV) group B strains among patients attending outpatient clinics at government medical facilities both prior and during the onset of Influenza A/H1N1/2009 pandemic outbreak.

METHODS

We screened 2300 nasopharyngeal swabs using multiplex real time reverse transcriptase polymerase chain reaction. We amplified a segment of the first and second hypervariable regions, as well as the conserved portion of the third domain of the G-gene using HRSV-B specific primers, sequenced by Sanger di-deoxy chain termination method and thereafter analyzed the sequences.

RESULTS

We characterized the circulating strains into three known genotypes: SAB4 (1.4%), BA7 (1.4%), and multiple variants of BA9 (97.2%). The majority of BA9 viruses were uniquely Kenyan with only 4% aligning with BA9 lineages found elsewhere. The mean evolutionary rate of the HRSV-B was estimated to be 3.08 × 10-3 substitutions per site per year.

CONCLUSION

Our findings indicate that the circulating HRSV-B viruses in Kenya underwent a slower evolution during the period of 2007-2010. Additionally, our findings reveal the existence of a unique lineage as well as new variants that have not been reported elsewhere to date.

Epidemiology and genetic diversity of human respiratory syncytial virus in Belgium between 2011 and 2019

BACKGROUND

Human respiratory syncytial virus (HRSV) is worldwide one of the leading causes of acute respiratory tract infections in young children and the elderly population. Two distinct subtypes of HRSV (A and B) and a multitude of genotypes have been described. The laboratory of Clinical and Epidemiological Virology (KU Leuven/University Hospitals Leuven) has a long-standing history of HRSV surveillance in Belgium.

METHODS

In this study, the seasonal circulation of HRSV in Belgium was monitored during 8 consecutive seasons prior to the SARS-CoV-2 pandemic (2011-2012 until 2018-2019). By use of a multiplex quantitative real time PCR panel, 27,386 respiratory samples were tested for HRSV. Further subtyping and sequencing of the HRSV positive samples was performed by PCR and Sanger sequencing. The prevalence and positivity rate were estimated in 4 distinct age groups and the circulating strains of each subtype were situated in a global context and in reference to the described genotypes in literature.

RESULTS

HRSV circulated in Belgium in a yearly re-occurring pattern during the winter months and both HRSV subtypes co-circulated simultaneously. All HRSV-B strains contained the 60 nt duplication in the HVR2 region of the G gene. Strains of subtype HRSV-A with a 72 nt duplication in the HVR2 region were first observed during the 2011-2012 season and replaced all other circulating strains from 2014 to 2015 onwards.

Genomic Analysis and Surveillance of Respiratory Syncytial Virus Using Wastewater-Based Epidemiology

Respiratory syncytial virus (RSV) causes severe infections in infants, immunocompromised or elderly individuals resulting in annual epidemics of respiratory disease. Currently, limited clinical surveillance and the lack of predictable seasonal dynamics limit the public health response. Wastewater-based epidemiology (WBE) has recently been used globally as a key metric in determining prevalence of severe acute respiratory syndrome coronavirus 2 in the community, but its application to other respiratory viruses is limited. In this study, we present an integrated genomic WBE approach, applying reverse-transcription quantitative polymerase chain reaction and partial G-gene sequencing to track RSV levels and variants in the community. We report increasing detection of RSV in wastewater concomitant with increasing numbers of positive clinical cases. Analysis of wastewater-derived RSV sequences permitted identification of distinct circulating lineages within and between seasons. Altogether, our genomic WBE platform has the potential to complement ongoing global surveillance and aid the management of RSV by informing the timely deployment of pharmaceutical and nonpharmaceutical interventions.

Inno4Vac Workshop Report Part 2: RSV-Controlled Human Infection Model (CHIM) Strain Selection and Immune Assays for RSV CHIM Studies, November 2021, MHRA, UK

Controlled human infection models (CHIMs) are a critical tool for the understanding of infectious disease progression, characterising immune responses to infection and rapid assessment of vaccines or drug treatments. There is increasing interest in using CHIMs for vaccine development and an obvious need for widely available and fit-for-purpose challenge agents. Inno4Vac is a large European consortium working towards accelerating and de-risking the development of new vaccines, including development of CHIMs for influenza, respiratory syncytial virus and Clostridium difficile. This report (in two parts) summarises a workshop held at the MHRA in 2021, focused on how to select CHIM candidate strains of influenza and respiratory syncytial virus (RSV) based on desirable virus characteristics and which immune assays would provide relevant information for assessing pre-existing and post-infection immune responses and defining correlates of protection. This manuscript (part 2) summarises presentations and discussions centred around RSV CHIMs and immune assays (an additional manuscript summarises influenza CHIM and immune assays: Inno4Vac workshop report Part 1: Controlled human influenza virus infection model (CHIVIM) strain selection and immune assays for CHIVIM studies, November 2021, MHRA, UK).

The Role of the CX3CR1-CX3CL1 Axis in Respiratory Syncytial Virus Infection and the Triggered Immune Response

Respiratory syncytial virus (RSV) is a common respiratory pathogen that causes respiratory illnesses, ranging from mild symptoms to severe lower respiratory tract infections in infants and older adults. This virus is responsible for one-third of pneumonia deaths in the pediatric population; however, there are currently only a few effective vaccines. A better understanding of the RSV-host relationship at the molecular level may lead to a more effective management of RSV-related symptoms. The fractalkine (CX3CL1) receptor (CX3CR1) is a co-receptor for RSV expressed by airway epithelial cells and diverse immune cells. RSV G protein binds to the CX3CR1 receptor via a highly conserved amino acid motif (CX3C motif), which is also present in CX3CL1. The CX3CL1-CX3CR1 axis is involved in the activation and infiltration of immune cells into the infected lung. The presence of the RSV G protein alters the natural functions of the CX3CR1-CX3CL1 axis and modifies the host's immune response, an aspects that need to be considered in the development of an efficient vaccine and specific pharmacological treatment.

Characterizing human respiratory syncytial virus among children admitted with acute respiratory tract infections from 2019 to 2022

Respiratory syncytial virus is a major causative agent of lower respiratory tract infection in children, especially infants with substantial morbidity and mortality implications. The virus undergoes continuous evolution documented by accumulation of mutations in the glycoprotein gene necessitating vigilant surveillance to provide essential data to epidemiologists and researchers involved in development of vaccines. This study was aimed to perform molecular characterization of respiratory syncytial virus (RSV) among children ≤ 5 years admitted in hospital. In the current study we observed RSV-A (2019 (n = 95) and 2021 (n = 61) seasons) and RSV-B (2022 season (n = 68)). Phylogenetic analysis revealed all RSV-A strains (n = 47) to be GA.2.3.5 and RSV-B (n = 22) were classified as GB.5.0.5a. Selection pressure analysis identified one positive (P274L/V) and one negative site (P230T) in RSV-A, while in RSV-B there was only one negatively selected site (S295). This study spanning over three seasons contributes to RSV evolutionary dynamics in India emphasizing the importance of on-going surveillance to inform effective public health strategies and vaccine development efforts.

Whole genome molecular analysis of respiratory syncytial virus pre and during the COVID-19 pandemic in Free State province, South Africa

Respiratory syncytial virus (RSV) is the most predominant viral pathogen worldwide in children with lower respiratory tract infections. The Coronavirus disease 2019 (COVID-19) pandemic and resulting nonpharmaceutical interventions perturbed the transmission pattern of respiratory pathogens in South Africa. A seasonality shift and RSV resurgence was observed in 2020 and 2021, with several infected children observed. Conventional RSV-positive nasopharyngeal swabs were collected from various hospitals in the Free State province, Bloemfontein, South Africa, from children suffering from respiratory distress and severe acute respiratory infection between 2020 to 2021. Overlapping genome fragments were amplified and complete genomes were sequenced using the Illumina MiSeq platform. Maximum likelihood phylogenetic and evolutionary analysis were performed on both RSV-A/-B G-genes with published reference sequences from GISAID and GenBank. Our study strains belonged to the RSV-A GA2.3.2 and RSV-B GB5.0.5a clades. The upsurge of RSV was due to pre-existing strains that predominated in South Africa and circulating globally also driving these off-season RSV outbreaks during the COVID-19 pandemic. The variants responsible for the resurgence were phylogenetically related to pre-pandemic strains and could have contributed to the immune debt resulting from pandemic imposed restrictions. The deviation of the RSV season from the usual pattern affected by the COVID-19 pandemic highlights the need for ongoing genomic surveillance and the identification of genetic variants to prevent unforeseen outbreaks in the future.

Identification of distinct genotypes in circulating RSV A strains based on variants in the virus replication-associated genes

Respiratory syncytial virus (RSV) is a common cause of respiratory infection that often leads to hospitalization of infected younger children and older adults. RSV is classified into two strains, A and B, each with several subgroups or genotypes. One issue with the definition of these subgroups is the lack of a unified method of identification or genotyping. We propose that genotyping strategies based on the genes coding for replication-associated proteins could provide critical information on the replication capacity of the distinct subgroups, while clearly distinguishing genotypes. Here, we analyzed the virus replication-associated genes N, P, M2, and L from de novo assembled RSV A sequences obtained from 31 newly sequenced samples from hospitalized patients in Philadelphia and 78 additional publicly available sequences from different geographic locations within the United States. In-depth analysis and annotation of variants in the replication-associated proteins identified the polymerase protein L as a robust target for genotyping RSV subgroups. Importantly, our analysis revealed non-synonymous variations in L that were consistently accompanied by conserved changes in its co-factor P or the M2-2 protein, suggesting associations and interactions between specific domains of these proteins. Similar associations were seen among sequences of the related human metapneumovirus. These results highlight L as an alternative to other RSV genotyping targets and demonstrate the value of in-depth analyses and annotations of RSV sequences as it can serve as a foundation for subsequent in vitro and clinical studies on the efficiency of the polymerase and fitness of different virus isolates.IMPORTANCEGiven the historical heterogeneity of respiratory syncytial virus (RSV) and the disease it causes, there is a need to understand the properties of the circulating RSV strains each season. This information would benefit from an informative and consensus method of genotyping the virus. Here, we carried out a variant analysis that shows a pattern of specific variations among the replication-associated genes of RSV A across different seasons. Interestingly, these variation patterns, which were also seen in human metapneumovirus sequences, point to previously defined interactions of domains within these genes, suggesting co-variation in the replication-associated genes. Our results also suggest a genotyping strategy that can prove to be particularly important in understanding the genotype-phenotype correlation in the era of RSV vaccination, where selective pressure on the virus to evolve is anticipated. More importantly, the categorization of pneumoviruses based on these patterns may be of prognostic value.

Circulation of new lineages of RSV-A and RSV-B in Kuwait shows high diversity in the N- and O-linked glycosylation sites in the G protein between 2020 and 2022

The human respiratory syncytial virus (RSV) is a significant health concern, particularly for infants, young children, and the elderly. This virus is known to evolve continuously due to environmental factors and herd immunity. In light of this, our study aimed to analyze the genetic variability of the G protein in RSV-A and RSV-B genotypes in Kuwait from 2020 to 2022. Between January 2020 and September 2022, we collected 490 respiratory samples from hospitalized patients with acute respiratory tract infections. These samples were tested and confirmed positive for RSV using multiplex Real-Time PCR. Subsequently, the samples underwent nucleic acid sequencing using the advanced Nanopore sequencing technology to analyze the full-length G gene. Sequence analysis showed that 64 isolates (76%) were RSV-A, and 20 isolates (24%) were RSV-B. The G genes of RSV-A belonged to genotype GA2.3.5, while all the RSV-B genotypes belonged to GB5.0.5a. New lineages and sub-lineages of RSV-A and RSV-B were detected, indicating the circulation of new strains in Kuwait. Many unique and new amino acid changes, including insertions, were found in the G proteins of Kuwaiti isolates, with the highest variability in the second hypervariable region. An increased number of N and O-linked glycosylation sites were also identified in the G protein, which could speculate to alter the antigenicity of RSV. The identified changes in the G protein of RSV-A and RSV-B genotypes might result from immune pressure and could affect the antigenic characteristics of circulating strains in Kuwait. This could potentially lead to new RSV variants that can evade the immune response. Our in-depth analysis of the G proteins of both RSV-A and RSV-B could aid in the development of more potent treatments and vaccines.

Sequence analysis of respiratory syncytial virus cases reveals a novel subgroup -B strain circulating in north-central Italy after pandemic restrictions

BACKGROUND

Following the pandemic restrictions, the epidemiology of respiratory syncytial virus (RSV) has changed, leading to intense hospitalization peaks.

OBJECTIVES

This study, conducted at multiple sites in Italy, aimed to describe the temporal dynamics of two post-COVID-19 RSV epidemics. Additionally, the circulating RSV-A and -B lineages were characterized and compared to those found in 2018 and 2019.

STUDY DESIGN

Respiratory specimens and data were collected from RSV-positive patients, both inpatients, and outpatients, of all ages at three sites in north-central Italy. To analyze these samples, roughly one-sixth were sequenced in the attachment glycoprotein G gene and subjected to phylogenetic and mutational analyses, including pre-pandemic sequences from north-central Italy.

RESULTS

The first post-pandemic surge of RSV cases was quite intense, occurring from October 2021 to early January 2022. The subsequent RSV epidemic (from November 2022 to early March 2023) also had a high impact, characterized by a rise in elderly patient cases. Post-pandemic cases of RSV-A were caused by various strains present in Italy prior to COVID-19. In contrast, a distinct RSV-B lineage, which was concurrently spreading in other countries, was identified as the main cause of the surge in 2022-2023 but remained undetected in Italy before the pandemic.

CONCLUSIONS

This study describes the temporal dynamics of post-pandemic RSV subgroups and uncovers a lineage of RSV-B with high genetic divergence that may have increased the impact of decreased population immunity.

Standardized Phylogenetic Classification of Human Respiratory Syncytial Virus below the Subgroup Level

A globally implemented unified phylogenetic classification for human respiratory syncytial virus (HRSV) below the subgroup level remains elusive. We formulated global consensus of HRSV classification on the basis of the challenges and limitations of our previous proposals and the future of genomic surveillance. From a high-quality curated dataset of 1,480 HRSV-A and 1,385 HRSV-B genomes submitted to GenBank and GISAID (https://www.gisaid.org) public sequence databases through March 2023, we categorized HRSV-A/B sequences into lineages based on phylogenetic clades and amino acid markers. We defined 24 lineages within HRSV-A and 16 within HRSV-B and provided guidelines for defining prospective lineages. Our classification demonstrated robustness in its applicability to both complete and partial genomes. We envision that this unified HRSV classification proposal will strengthen HRSV molecular epidemiology on a global scale.

Genetic characterization of respiratory syncytial virus surface glycoproteins F and G in Taiwan, 2017-2021

BACKGROUND

Respiratory syncytial virus (RSV) infection imposes substantial health burden and disproportionally affects young infants, elderly, and immunocompromised hosts. RSV harbors key surface glycoproteins F and G, both crucial for viral infection and evolution.

METHODS

In this study, we examined the genetic characteaistics of 179 RSV isolates collected between 2017 and 2021 in Taiwan. G ectodomain and whole F gene were sequenced and aligned with available references from GenBank.

RESULTS

RSV ON1 and BA9 were two predominant genotypes throughout the study period. Genetic variations of G protein accumulated over time. New ON1 strains containing E257K and K204R-V225A-T238I-Y280H in combination emerged in 2019 and contributed to a local endemic in 2020. RSV-B strain with A131T and T137I substitution in G protein emerged in 2018. On the other hand, F protein of both RSV genotypes was generally conserved but some feature changes should be noted: RSV-B in Taiwan harbored 100% of I206M and Q209R in site Ø, and L172Q and S173L in site V. These amino acid changes do not affect the susceptibility of Nirsevimab but imply no effectiveness of Suptavumab.

CONCLUSION

RSV continuously evolves in Taiwan and accumulated signature genetic changes over time. Vigilant RSV genomic surveillance is important to monitor the viral evolution in the upcoming future of new RSV vaccines and prophylaxis.

Genomic Evolution and Surveillance of Respiratory Syncytial Virus during the 2023-2024 Season

Respiratory syncytial virus (RSV) is a significant cause of morbidity, particularly in infants. This study describes RSV genomic diversity and disease outcomes during the 2023-2024 season in the Johns Hopkins Hospital System (JHHS). Between August and December 2023, 406 patient samples were sequenced, showing that RSV-B GB5.0.5a was the dominant genotype detected. RSV-A genotype GA2.3.5 was detected less frequently. Metadata analysis of patient data revealed that, although RSV-B was more commonly detected, patients with RSV-A infections were more frequently hospitalized. Analysis of both the G- and F-genes revealed multiple amino acid substitutions in both RSV-A and RSV-B, with some positions within the F-protein that could be associated with evasion of antibody responses. Phylogenetic analysis revealed the genetic diversity of circulating GB5.0.5a and GA2.3.5 genotypes. This study serves as an important baseline for genomic surveillance of RSV within the JHHS and will assist in characterizing the impact of the newly approved RSV vaccines on RSV genomic evolution and the emergence of escape mutations.

Genomic characterization of circulating human respiratory syncytial viruses A and B in Kuwait using whole-genome sequencing

The human respiratory syncytial virus (RSV) is considered one of the most common viruses that infect children globally. The virus is known to have extensive gene sequence variability within and between RSV groups A and B globally; however, there is no information on the whole-genome characterization and diversity of RSV in Kuwait. Therefore, this study aimed to sequence the entire genome of RSV strains isolated from patients with acute respiratory tract infection (ARTI) in Kuwait. Therefore, this study aimed to sequence the entire genome of RSV strains isolated from patients with ARTI in Kuwait. Between January 2020 and September 2022, 7,093 respiratory samples were collected from hospitalized infants, children, and adults and were analyzed for respiratory viruses by multiplex real-time PCR. Whole-genome sequencing using the Oxford Nanopore sequencing technology was performed on 84 RSV-positive samples. The results revealed a higher prevalence of group A (76%) than group B (24%) RSV isolates. Phylogenetic analysis showed that RSV-A strains clustered with the GA2.3.5 sub-genotype and RSV-B strains clustered with the GB5.0.5a sub-genotype; however, forming new lineages of RSV-A and RSV-B circulated in Kuwait during this period. Genetic variability was higher among the group A viruses than group B viruses, and the rate of synonymous and missense mutations was high in genes other than the G protein-coding gene. We also detected several known and unique molecular markers in different protein-coding genes. This is the first study in Kuwait to characterize the whole genomes of RSV A and B to identify the circulating genotypes, comprehend the genetic diversity and the evolution of the virus, and identify important genetic markers associated with specific genotypes.IMPORTANCEWhole-genome sequencing of respiratory syncytial virus (RSV) strains in Kuwait using MinION Nanopore technology was used to characterize and analyze the genotypes and sub-genotypes of the RSV circulating among patients with acute respiratory tract infections in Kuwait. This study also identified known and unknown gene mutations and imported genetic markers associated with specific genotypes. These results will assist in establishing a framework for RSV classification and allow for a better consideration of the mechanisms leading to the generation of diversity of RSV. In addition, these data will allow a comparison of vaccine viruses with those in Kuwait, providing useful insights into future vaccine and therapy strategies for RSV in Kuwait.

Association of disease severity and genetic variation during primary Respiratory Syncytial Virus infections

BACKGROUND

Respiratory Syncytial Virus (RSV) disease in young children ranges from mild cold symptoms to severe symptoms that require hospitalization and sometimes result in death. Studies have shown a statistical association between RSV subtype or phylogenic lineage and RSV disease severity, although these results have been inconsistent. Associations between variation within RSV gene coding regions or residues and RSV disease severity has been largely unexplored.

METHODS

Nasal swabs from children (< 8 months-old) infected with RSV in Rochester, NY between 1977-1998 clinically presenting with either mild or severe disease during their first cold-season were used. Whole-genome RSV sequences were obtained using overlapping PCR and next-generation sequencing. Both whole-genome phylogenetic and non-phylogenetic statistical approaches were performed to associate RSV genotype with disease severity.

RESULTS

The RSVB subtype was statistically associated with disease severity. A significant association between phylogenetic clustering of mild/severe traits and disease severity was also found. GA1 clade sequences were associated with severe disease while GB1 was significantly associated with mild disease. Both G and M2-2 gene variation was significantly associated with disease severity. We identified 16 residues in the G gene and 3 in the M2-2 RSV gene associated with disease severity.

CONCLUSION

These results suggest that phylogenetic lineage and the genetic variability in G or M2-2 genes of RSV may contribute to disease severity in young children undergoing their first infection.

Respiratory Syncytial Virus in Adult Patients at a Tertiary Care Hospital in Germany: Clinical Features and Molecular Epidemiology of the Fusion Protein in the Severe Respiratory Season of 2022/2023

Following an interseasonal rise in mainly pediatric respiratory syncytial virus (RSV) cases in Germany in 2021, an exceptionally high number of adult cases was observed in the subsequent respiratory season of 2022/2023. The aim of this study was to compare the clinical presentation of RSV infections in the pre- and post-SARS-CoV-2 pandemic periods. Additionally, the local epidemiology of the RSV fusion protein was analyzed at a molecular genetic and amino acid level. RSV detections in adults peaked in calendar week 1 of 2023, 8 weeks earlier than the earliest peak observed in the three pre-pandemic seasons. Although the median age of the adult patients was not different (66.5 vs. 65 years), subtle differences between both periods regarding comorbidities and the clinical presentation of RSV cases were noted. High rates of comorbidities prevailed; however, significantly lower numbers of patients with a history of lung transplantation (p = 0.009), chronic kidney disease (p = 0.013), and immunosuppression (p = 0.038) were observed in the 2022/2023 season. In contrast, significantly more lower respiratory tract infections (p < 0.001), in particular in the form of pneumonia (p = 0.015) and exacerbations of obstructive lung diseases (p = 0.008), were detected. An ICU admission was noted for 23.7% of all patients throughout the study period. Sequence analysis of the fusion protein gene revealed a close phylogenetic relatedness, regardless of the season of origin. However, especially for RSV-B, an accumulation of amino acid point substitutions was noted, including in antigenic site Ø. The SARS-CoV-2 pandemic had a tremendous impact on the seasonality of RSV, and the introduction of new vaccination and immunization strategies against RSV warrants further epidemiologic studies of this important pathogen.

Microbiological and epidemiological features of respiratory syncytial virus

The properties of the main surface proteins and the viral cycle of the respiratory syncytial virus (RSV) make it an attractive pathogen from the perspective of microbiology. The virus gets its name from the manner it infects cells, which enables it to produce syncytia, which allow the virus' genetic material to move across cells without having to release viral offspring to the cellular exterior, reducing immune system identification. This causes a disease with a high impact in both children and adults over 60, which has sparked the development of several preventive interventions based on vaccines and monoclonal antibodies for both age groups. The epidemiological characteristics of this virus, which circulates in epidemics throughout the coldest months of the year and exhibits a marked genetic and antigenic drift due to its high mutation capability, must be taken into consideration while using these preventive methods. The most important microbiological and epidemiological elements of RSV are covered in this study, along with how they have affected the creation of preventive medications and their use in the future.

RSV-GenoScan: An automated pipeline for whole-genome human respiratory syncytial virus (RSV) sequence analysis

BACKGROUND

Advances in high-throughput sequencing (HTS) technologies and reductions in sequencing costs have revolutionised the study of genomics and molecular biology by making whole-genome sequencing (WGS) accessible to many laboratories. However, the analysis of WGS data requires significant computational effort, which is the major drawback in implementing WGS as a routine laboratory technique.

OBJECTIVE

Automated pipelines have been developed to overcome this issue, but they do not exist for all organisms. This is the case for human respiratory syncytial virus (RSV), which is a leading cause of lower respiratory tract infections in infants, the elderly, and immunocompromised adults.

RESULTS

We present RSV-GenoScan, a fast and easy-to-use pipeline for WGS analysis of RSV generated by HTS on Illumina or Nanopore platforms. RSV-GenoScan automates the WGS analysis steps directly from the raw sequence data. The pipeline filters the sequence data, maps the reads to the RSV reference genomes, generates a consensus sequence, identifies the RSV subgroup, and lists amino acid mutations, insertions and deletions in the F and G viral genes. This enables the rapid identification of mutations in these coding genes that are known to confer resistance to monoclonal antibodies.

AVAILABILITY

RSV-GenoScan is freely available at https://github.com/AlexandreD-bio/RSV-GenoScan.

Characterization of human respiratory syncytial virus in children with severe acute respiratory infection before and during the COVID-19 pandemic

Objectives

Annual outbreaks of human respiratory syncytial virus (HRSV) are caused by newly introduced and locally persistent strains. During the COVID-19 pandemic, global and local circulation of HRSV significantly decreased. This study was conducted to characterize HRSV in 2018-2022 and to analyze the impact of COVID-19 on the evolution of HRSV.

Design/methods

Combined oropharyngeal and nasopharyngeal swabs were collected from children hospitalized with severe acute respiratory infection at two hospitals in Zambia. The second hypervariable region of the attachment gene G was targeted for phylogenetic analysis.

Results

Of 3113 specimens, 504 (16.2%) were positive for HRSV, of which 131 (26.0%) and 66 (13.1%) were identified as HRSVA and HRSVB, respectively. In early 2021, an increase in HRSV was detected, caused by multiple distinct clades of HRSVA and HRSVB. Some were newly introduced, whereas others resulted from local persistence.

Conclusions

This study provides insights into the evolution of HRSV, driven by global and local circulation. The COVID-19 pandemic had a temporal impact on the evolution pattern of HRSV. Understanding the evolution of HRSV is vital for developing strategies for its control.

Whole-Genome Sequencing and Genetic Diversity of Human Respiratory Syncytial Virus in Patients with Influenza-like Illness in Sicily (Italy) from 2017 to 2023

Monitoring the genetic variability of human respiratory syncytial virus (hRSV) is of paramount importance, especially for the potential implication of key antigenic mutations on the emergence of immune escape variants. Thus, to describe the genetic diversity and evolutionary dynamics of hRSV circulating in Sicily (Italy), a total of 153 hRSV whole-genome sequences collected from 770 hRSV-positive subjects between 2017 and 2023, before the introduction of expanded immunization programs into the population, were investigated. The phylogenetic analyses indicated that the genotypes GA.2.3.5 (ON1) for hRSV-A and GB.5.0.5a (BA9) for hRSV-B co-circulated in our region. Amino acid (AA) substitutions in the surface and internal proteins were evaluated, including the F protein antigenic sites, as the major targets of immunoprophylactic monoclonal antibodies and vaccines. Overall, the proportion of AA changes ranged between 1.5% and 22.6% among hRSV-A, whereas hRSV-B varied in the range 0.8-16.9%; the latter was more polymorphic than hRSV-A within the key antigenic sites. No AA substitutions were found at site III of both subgroups. Although several non-synonymous mutations were found, none of the polymorphisms known to potentially affect the efficacy of current preventive measures were documented. These findings provide new insights into the global hRSV molecular epidemiology and highlight the importance of defining a baseline genomic picture to monitor for future changes that might be induced by the selective pressures of immunological preventive measures, which will soon become widely available.

Impact of COVID-19 Pandemic Restrictions on Respiratory Virus Patterns: Insights from RSV Surveillance in Gwangju, South Korea

The social restriction measures implemented due to the COVID-19 pandemic have impacted the pattern of occurrences of respiratory viruses. According to surveillance results in the Gwangju region of South Korea, respiratory syncytial virus (RSV) did not occur during the 2020/2021 season. However, there was a delayed resurgence in the 2021/2022 season, peaking until January 2022. To analyze this, a total of 474 RSV positive samples were investigated before and after the COVID-19 pandemic. Among them, 73 samples were selected for whole-genome sequencing. The incidence rate of RSV in the 2021/2022 season after COVID-19 was found to be approximately three-fold higher compared to before the pandemic, with a significant increase observed in the age group from under 2 years old to under 5 years old. Phylogenetic analysis revealed that, for RSV-A, whereas four lineages were observed before COVID-19, only the A.D.3.1 lineage was observed during the 2021/2022 season post-pandemic. Additionally, during the 2022/2023 season, the A.D.1, A.D.3, and A.D.3.1 lineages co-circulated. For RSV-B, while the B.D.4.1.1 lineage existed before COVID-19, both the B.D.4.1.1 and B.D.E.1 lineages circulated after the pandemic. Although atypical RSV occurrences were not due to new lineages, there was an increase in the frequency of mutations in the F protein of RSV after COVID-19. These findings highlight the need to continue monitoring changes in RSV occurrence patterns in the aftermath of the COVID-19 pandemic to develop and manage strategies in response.

Genetic Diversity of Human Respiratory Syncytial Virus during COVID-19 Pandemic in Yaoundé, Cameroon, 2020-2021

Worldwide, human respiratory syncytial virus (HRSV) is a major cause of severe infections of the lower respiratory system, affecting individuals of all ages. This study investigated the genetic variability of HRSV during the COVID-19 outbreak in Yaoundé; nasopharyngeal samples positive for HRSV were collected from different age groups between July 2020 and October 2021. A semi-nested RT-PCR was performed on the second hypervariable region of the G gene of detected HRSV, followed by sequencing and phylogenetic assessment. Throughout the study, 40 (37.7%) of the 106 HRSV-positive samples successfully underwent G-gene amplification. HRSV A and HRSV B co-circulated at rates of 47.5% and 52.5%, respectively. HRSV A clustered in the GA2.3.5 genetic lineage (ON1) and HRSV B clustered in the GB5.0.5a genetic lineage (BA9). Differences in circulating genotypes were observed between pre- and post-pandemic years for HRSV A. Predictions revealed potential N-glycosylation sites at positions 237-318 of HRSV A and positions 228-232-294 of HRSV B. This study reports the molecular epidemiology of HRSV in Cameroon during the COVID-19 pandemic. It describes the exclusive co-circulation of two genetic lineages. These findings highlight the importance of implementing comprehensive molecular surveillance to prevent the unexpected emergence of other diseases.

Respiratory Syncytial Virus and Influenza Infections in Children in Ulaanbaatar, Mongolia, 2015-2021

BACKGROUND

Data available for RSV and influenza infections among children < 2 years in Mongolia are limited. We present data from four districts of Ulaanbaatar from April 2015 to June 2021.

METHODS

This study was nested in an enhanced surveillance project evaluating pneumococcal conjugate vaccine (PCV13) impact on the incidence of hospitalized lower respiratory tract infections (LRTIs). Our study was restricted to children aged < 2 years with arterial O2 saturation < 93% and children with radiological pneumonia. Nasopharyngeal (NP) swabs collected at admission were tested for RSV and influenza using qRT-PCR. NP swabs of all patients with radiological pneumonia and of a subset of randomly selected NP swabs were tested for S. pneumoniae (S.p.) by qPCR and for serotypes by culture and DNA microarray.

RESULTS

Among 5705 patients, 2113 (37.0%) and 386 (6.8%) had RSV and influenza infections, respectively. Children aged 2-6 months had a higher percentage of very severe RSV infection compared to those older than 6 months (42.2% versus 31.4%, p-value Fisher's exact = 0.001). S.p. carriage was detected in 1073/2281 (47.0%) patients. Among S.p. carriage cases, 363/1073 (33.8%) had S.p. and RSV codetection, and 82/1073 (7.6%) had S.p. and influenza codetection. S.p. codetection with RSV/influenza was not associated with more severe LRTIs, compared to only RSV/influenza cases.

CONCLUSION

In Mongolia, RSV is an important pathogen causing more severe LRTI in children under 6 months of age. Codetection of RSV or influenza virus and S.p. was not associated with increased severity.

Genomic evolution of human respiratory syncytial virus during a decade (2013-2023): bridging the path to monoclonal antibody surveillance

OBJECTIVES

This study investigated the prevalence, genetic diversity, and evolution of human respiratory syncytial virus (HRSV) in Barcelona from 2013 to 2023.

METHODS

Respiratory specimens from patients with RTI suspicion at Hospital Universitari Vall d'Hebron were collected from October 2013 to May 2023 for laboratory-confirmation of respiratory viruses. Next-generation sequencing was performed in randomly-selected samples with Illumina technology. Phylogenetic analyses of whole genome sequences were performed with BEAST v1.10.4. Signals of selection and evolutionary pressures were inferred by population dynamics and evolutionary analyses. Mutations in major surface proteins were genetic and structurally characterised, emphasizing those within antigenic epitopes.

RESULTS

Analyzing 139,625 samples, 5.3% were HRSV-positive (3008 HRSV-A, 3882 HRSV-B, 56 HRSV-A and -B, and 495 unsubtyped HRSV), with a higher prevalence observed in the paediatric population. Pandemic-related shifts in seasonal patterns returned to normal in 2022-2023. A total of 198 whole-genome sequences were obtained for HRSV-A (6.6% of the HRSV-A positive samples) belonging to GA2.3.5 lineage. For HRSV-B, 167 samples were sequenced (4.3% of the HRSV-B positive samples), belonging to GB5.0.2, GB5.0.4a and GB5.0.5a. HRSV-B exhibited a higher evolution rate. Post-SARS-CoV-2 pandemic, both subtypes showed increased evolutionary rates and decreased effective population size initially, followed by a sharp increase. Analyses indicated negative selective pressure on HRSV. Mutations in antigenic epitopes, including S276N and M274I in palivizumab-targeted site II, and I206M, Q209R, and S211N in nirsevimab-targeted site Ø, were identified.

DISCUSSION

Particularly in the context of the large-scale use in 2023-2024 season of nirsevimab, continuous epidemiological and genomic surveillance is crucial.

Identification of distinct genotypes in circulating RSV A strains based on variants on the virus replication-associated genes

Respiratory syncytial virus is a common cause of respiratory infection that often leads to hospitalization of infected younger children and older adults. RSV is classified into two strains, A and B, each with several subgroups or genotypes. One issue with the definition of these subgroups is the lack of a unified method of identification or genotyping. We propose that genotyping strategies based on the genes coding for replication-associated proteins could provide critical information on the replication capacity of the distinct subgroup, while clearly distinguishing genotypes. Here, we analyzed the virus replication-associated genes N, P, M2, and L from de novo assembled RSV A sequences obtained from 31 newly sequenced samples from hospitalized patients in Philadelphia and 78 additional publicly available sequences from different geographic locations within the US. In-depth analysis and annotation of the protein variants in L and the other replication-associated proteins N, P, M2-1, and M2-2 identified the polymerase protein L as a robust target for genotyping RSV subgroups. Importantly, our analysis revealed non-synonymous variations in L that were consistently accompanied by conserved changes in its co-factor P or the M2-2 protein, suggesting associations and interactions between specific domains of these proteins. These results highlight L as an alternative to other RSV genotyping targets and demonstrate the value of in-depth analyses and annotations of RSV sequences as it can serve as a foundation for subsequent in vitro and clinical studies on the efficiency of the polymerase and fitness of different virus isolates.

Genomic characterization of human respiratory syncytial virus circulating in Islamabad, Pakistan, during an outbreak in 2022-2023

In this study, conducted at the National Institute of Health, Islamabad, during an outbreak of human respiratory syncytial virus (hRSV) from December 2022 to January 2023, the first whole-genome sequences of hRSV isolates from Islamabad, Pakistan, were determined. Out of 10 positive samples, five were sequenced, revealing the presence of two genotypes: RSV-A (GA2.3.5, ON1 strain) and RSV-B (GB5.0.5.a, BA-10 strain). A rare non-synonymous substitution (E232G) in G the protein and N276S in the F protein were found in RSV-A. In RSV-B, the unique mutations K191R, Q209R, and I206M were found in the F protein. These mutations could potentially influence vaccine efficacy and viral pathogenicity. This research underscores the importance of genomic surveillance for understanding RSV diversity and guiding public health responses in Pakistan.

Deviations in RSV epidemiological patterns and population structures in the United States following the COVID-19 pandemic

Respiratory Syncytial Virus (RSV) is a leading cause of acute respiratory tract infection, with the greatest impact on infants, immunocompromised individuals, and older adults. RSV prevalence decreased substantially in the United States (US) following the implementation of COVID-19-related non-pharmaceutical interventions but later rebounded with abnormal seasonality. The biological and epidemiological factors underlying this altered behavior remain poorly defined. In this retrospective cohort study from 2009 to 2023 in Chicago, Illinois, US, we examined RSV epidemiology, clinical severity, and genetic diversity. We found that changes in RSV diagnostic platforms drove increased detections in outpatient settings post-2020 and that hospitalized adults infected with RSV-A were at higher risk of intensive care admission than those with RSV-B. While population structures of RSV-A remained unchanged, RSV-B exhibited a genetic shift into geographically distinct clusters. Mutations in the antigenic regions of the fusion protein suggest convergent evolution with potential implications for vaccine and therapeutic development.

Resurgence of respiratory syncytial virus with dominance of RSV-B during the 2022-2023 season

Background

Respiratory syncytial virus (RSV) is a common cause of upper and lower respiratory tract infections. This study aimed to explore the prevalence of respiratory syncytial virus (RSV) and other respiratory viruses in Bulgaria, characterize the genetic diversity of RSV strains, and perform amino acid sequence analyses of RSV surface and internal proteins.

Methods

Clinical and epidemiological data and nasopharyngeal swabs were prospectively collected from patients with acute respiratory infections between October 2020 and May 2023. Real-time PCR for 13 respiratory viruses, whole-genome sequencing, phylogenetic, and amino acid analyses were performed.

Results

This study included three epidemic seasons (2020-2021, 2021-2022, and 2022-2023) from week 40 of the previous year to week 20 of the following year. Of the 3,047 patients examined, 1,813 (59.5%) tested positive for at least one viral respiratory pathogen. RSV was the second most detected virus (10.9%) after SARS-CoV-2 (22%). Coinfections between RSV and other respiratory viruses were detected in 68 cases, including 14 with SARS-CoV-2. After two seasons of low circulation, RSV activity increased significantly during the 2022-2023 season. The detection rates of RSV were 3.2, 6.6, and 13.7% in the first, second, and third seasons, respectively. RSV was the most common virus found in children under 5 years old with bronchiolitis (40%) and pneumonia (24.5%). RSV-B drove the 2022-2023 epidemic. Phylogenetic analysis indicated that the sequenced RSV-B strains belonged to the GB5.0.5a and GB5.0.6a genotypes. Amino acid substitutions in the surface and internal proteins, including the F protein antigenic sites were identified compared to the BA prototype strain.

Conclusion

This study revealed a strong resurgence of RSV in the autumn of 2022 after the lifting of anti-COVID-19 measures, the leading role of RSV as a causative agent of serious respiratory illnesses in early childhood, and relatively low genetic diversity in circulating RSV strains.

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 acute lower respiratory tract infections causing significant morbidity and mortality among children and the elderly; two RSV vaccines and a monoclonal antibody have recently been approved. Thus, there is an increasing need for a detailed and continuous genomic surveillance of RSV circulating in resource-rich and resource-limited settings worldwide. However, robust, cost-effective methods for whole genome sequencing of RSV from clinical samples that are amenable to high-throughput are still scarce. We developed Next-RSV-SEQ, an experimental and computational pipeline to generate whole genome sequences of historic and current RSV genotypes by in-solution hybridization capture-based next generation sequencing. We optimized this workflow by automating library preparation and pooling libraries prior to enrichment in order to reduce hands-on time and cost, thereby augmenting scalability. Next-RSV-SEQ yielded near-complete to complete genome sequences for 98% of specimens with Cp values ≤31, at median on-target reads >93%, and mean coverage depths between ~1,000 and >5,000, depending on viral load. Whole genomes were successfully recovered from samples with viral loads as low as 230 copies per microliter RNA. We demonstrate that the method can be expanded to other respiratory viruses like parainfluenza virus and human metapneumovirus. Next-RSV-SEQ produces high-quality RSV genomes directly from culture isolates and, more importantly, clinical specimens of all genotypes in circulation. It is cost-efficient, scalable, and can be extended to other respiratory viruses, thereby opening new perspectives for a future effective and broad genomic surveillance of respiratory viruses.

IMPORTANCE

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.

Atypical age distribution and high disease severity in children with RSV infections during two irregular epidemic seasons throughout the COVID-19 pandemic, Germany, 2021 to 2023

BackgroundNon-pharmaceutical interventions (NPIs) during the COVID-19 pandemic affected respiratory syncytial virus (RSV) circulation worldwide.AimTo describe, for children aged < 5 years, the 2021 and 2022/23 RSV seasons in Germany.MethodsThrough data and 16,754 specimens from outpatient sentinel surveillance, we investigated RSV seasonality, circulating lineages, and affected children's age distributions in 2021 and 2022/23. Available information about disease severity from hospital surveillance was analysed for patients with RSV-specific diagnosis codes (n = 13,104). Differences between RSV seasons were assessed by chi-squared test and age distributions trends by Mann-Kendall test.ResultsRSV seasonality was irregular in 2021 (weeks 35-50) and 2022/23 (weeks 41-3) compared to pre-COVID-19 2011/12-2019/20 seasons (median weeks 51-12). RSV positivity rates (RSV-PR) were higher in 2021 (40% (522/1,291); p < 0.001) and 2022/23 (30% (299/990); p = 0.005) than in prior seasons (26% (1,430/5,511)). Known globally circulating RSV-A (lineages GA2.3.5 and GA2.3.6b) and RSV-B (lineage GB5.0.5a) strains, respectively, dominated in 2021 and 2022/23. In 2021, RSV-PRs were similar in 1 - < 2, 2 - < 3, 3 - < 4, and 4 - < 5-year-olds. RSV hospitalisation incidence in 2021 (1,114/100,000, p < 0.001) and in 2022/23 (1,034/100,000, p < 0.001) was approximately double that of previous seasons' average (2014/15-2019/20: 584/100,000). In 2022/23, proportions of RSV patients admitted to intensive care units rose (8.5% (206/2,413)) relative to pre-COVID-19 seasons (6.8% (551/8,114); p = 0.004), as did those needing ventilator support (6.1% (146/2,413) vs 3.8% (310/8,114); p < 0.001).ConclusionsHigh RSV-infection risk in 2-4-year-olds in 2021 and increased disease severity in 2022/23 possibly result from lower baseline population immunity, after NPIs diminished exposure to RSV.

Resurgence of human respiratory syncytial virus during COVID-19 pandemic in Southern Brazil

Respiratory Syncytial Virus (RSV) is an important cause of respiratory infection in humans. Severe cases are common in children ≤2 years old, immunocompromised individuals, and the elderly. In 2020, RSV infection reduced in Rio Grande do Sul (RS), southern Brazil; however, in 2021 resurgence of RSV was observed. This study analyzed epidemiological and genetic features of RSV infection cases reported in 2021 in RS. Nasopharyngeal samples collected from individuals with respiratory infection negative for SARS-CoV-2, Influenza A and B viruses were assessed for the presence of RSV by real time RT-qPCR. RSV-A and RSV-B genomic sequencing and phylogenetic reconstructions were performed for genotyping and clade characterization. Among 21,035 respiratory samples analyzed, 2,947 were positive for RSV, 947 of which were hospitalized patients. Positive cases were detected year-round, with the highest number in June-July (winter). Children <1 year comprised 56.28% (n = 533) of the hospitalized patients infected with RSV, whereas 14.46% (n = 137) were individuals >60 years. Of a total of 361 deaths, 14.68% (n = 53) were RSV positive, mostly patients >60 years old (73.58%, n = 39). Chronic kidney disease, cardiopathy, Down syndrome and neurological diseases were associated with RSV infection. RSV-A was identified in 58.5% (n = 117/200) of the patients, and RSV-B in 41.5% (n = 83/200). Of 95 RSV genomes recovered from SARI cases, 66 were RSV-A GA.2.3.5 genotype, while 29 were RSV-B GB.5.0.5a genotype. This study provides epidemiological and molecular data on RSV cases in RS during the COVID-19 pandemic and highlights that investigation of different respiratory viruses is essential for decision-making and disease prevention and control measures.

Respiratory Syncytial Virus European Laboratory Network 2022 Survey: Need for Harmonization and Enhanced Molecular Surveillance

Respiratory syncytial virus (RSV) is a common pathogen causing mostly cold-like symptoms, but in very young infants and elderly individuals it can lead to severe disease and even death. There are currently promising developments both in vaccine development and in therapeutics that are expected to be approved soon. To get an impression within European countries of the laboratory diagnostics and surveillance activities, in anticipation of these developments, we queried the members of the European Respiratory Syncytial Virus Laboratory Network (RSV-LabNet, under the umbrella of the PROMISE project) via an online survey. The answers from the consortium members showed scattered monitoring and the application of a broad array of techniques in the laboratories. A majority of the members expressed strong interest in harmonization and collaboration for setting up surveillance programs and the need for sharing laboratory protocols. The additional value of RSV whole-genome sequencing is broadly appreciated, but implementation requires further development and closer collaboration. The RSV-LabNet can have an important responsibility in establishing contacts and exchange of expertise and providing a platform for communication to advance diagnostics, preparedness, and surveillance.

An amplicon-based protocol for whole-genome sequencing of human respiratory syncytial virus subgroup A

It is convenient to study complete genome sequences of human respiratory syncytial virus (hRSV) for ongoing genomic characterization and identification of highly transmissible or pathogenic variants. Whole genome sequencing of hRSV has been challenging from respiratory tract specimens with low viral loads. Herein, we describe an amplicon-based protocol for whole genome sequencing of hRSV subgroup A validated with 24 isolates from nasopharyngeal swabs and infected cell cultures, which showed cycle threshold (Ct) values ranging from 10 to 31, as determined by quantitative reverse-transcription polymerase chain reaction. MinION nanopore generated 3200 to 5400 reads per sample to sequence over 93% of the hRSV-A genome. Coverage of each contig ranged from 130× to 200×. Samples with Ct values of 20.9, 25.2, 27.1, 27.7, 28.2, 28.8, and 29.6 led to the sequencing of over 99.0% of the virus genome, indicating high genome coverage even at high Ct values. This protocol enables the identification of hRSV subgroup A genotypes, as primers were designed to target highly conserved regions. Consequently, it holds potential for application in molecular epidemiology and surveillance of this hRSV subgroup.

Epidemiology and molecular analyses of respiratory syncytial virus in the 2021-2022 season in northern Italy

Background

Human respiratory syncytial virus (RSV) is the leading cause of acute lower respiratory tract infection among infants and young children worldwide, with seasonal peaks in January and February. This study aimed to characterize the RSV samples from a pediatric cohort in the 2021-2022 season in Italy.

Methods

In total, 104 samples were collected from pediatric patients attending the "Vittore Buzzi" Children's Hospital in Milan, Italy in the 2021-2022 season. RT-PCR and next-generation sequencing were used to discriminate subgroups and obtain whole genomes. Maximum likelihood and Bayesian phylogenetic methods were used to analyze Italian sequences in the European contest and date Italian clusters.

Results

The median age was 78 days, and 76.9% of subjects required hospitalization, with a higher proportion of patients under 3 months of age. An equal proportion of subgroups A (GA2.3.5) and B (GB5.0.5a) was found, with significant differences in length of hospitalization, days of supplemental oxygen treatment, and intravenous hydration duration. Phylogeny highlighted 26 and 37 clusters containing quite the total of Italian sequences for RSV-A and -B, respectively. Clusters presented a tMRCA between December 2011-February 2017 and May 2014-December 2016 for A and B subgroups, respectively. Compared to European sequences, specific mutations were observed in Italian strains.

Conclusion

These data confirmed a more severe clinical course of RSV-A, particularly in young children. This study permitted the characterization of recent Italian RSV whole genomes, highlighting the peculiar pattern of mutations that needs to be investigated further and monitored.

Controlled Human Infection Challenge Studies with RSV

Despite considerable momentum in the development of RSV vaccines and therapeutics, there remain substantial barriers to the development and licensing of effective agents, particularly in high-risk populations. The unique immunobiology of RSV and lack of clear protective immunological correlates has held back RSV vaccine development, which, therefore, depends on large and costly clinical trials to demonstrate efficacy. Studies involving the deliberate infection of human volunteers offer an intermediate step between pre-clinical and large-scale studies of natural infection. Human challenge has been used to demonstrate the potential efficacy of vaccines and antivirals while improving our understanding of the protective immunity against RSV infection. Early RSV human infection challenge studies determined the role of routes of administration and size of inoculum on the disease. However, inherent limitations, the use of highly attenuated/laboratory-adapted RSV strains and the continued evolutionary adaptation of RSV limits extrapolation of results to present-day vaccine testing. With advances in technology, it is now possible to perform more detailed investigations of human mucosal immunity against RSV in experimentally infected adults and, more recently, older adults to optimise the design of vaccines and novel therapies. These studies identified defects in RSV-induced humoral and CD8+ T cell immunity that may partly explain susceptibility to recurrent RSV infection. We discuss the insights from human infection challenge models, ethical and logistical considerations, potential benefits, and role in streamlining and accelerating novel antivirals and vaccines against RSV. Finally, we consider how human challenges might be extended to include relevant at-risk populations.

Altered RSV Epidemiology and Genetic Diversity Following the COVID-19 Pandemic

Respiratory Syncytial Virus (RSV) is a leading cause of acute respiratory tract infection, with greatest impact on infants, immunocompromised individuals, and older adults. RSV prevalence decreased substantially following the implementation of non-pharmaceutical interventions to mitigate the COVID-19 pandemic but later rebounded with initially abnormal seasonality. The biological and epidemiological factors underlying this altered behavior remain poorly defined. In this retrospective cohort study, we examined RSV epidemiology, clinical severity, and genetic diversity in the years surrounding the COVID-19 pandemic. We found that changes in RSV diagnostic platforms drove increased detections in outpatient settings after 2020 and that hospitalized adults with RSV-A were at higher risk of needing intensive care than those with RSV-B. While the population structure of RSV-A remained unchanged, the population structure of RSV-B shifted in geographically distinct clusters. Mutations in the antigenic regions of the fusion protein suggest convergent evolution with potential implications for vaccine and therapeutic development.

Molecular Epidemiology of Respiratory Syncytial Virus during 2019-2022 and Surviving Genotypes after the COVID-19 Pandemic in Japan

To evaluate the changes in respiratory syncytial virus (RSV) collected between 2019 and 2022, we analyzed RSV-A and RSV-B strains from various prefectures in Japan before and after the COVID-19 pandemic. RT-PCR-positive samples collected from children with rapid test positivity at outpatient clinics in 11 prefectures in Japan were sequenced for the ectodomain of the G gene to determine the genotype. Time-aware phylogeographic analyses were performed using the second hypervariable region (HVR) of the G gene from 2012 to 2022. Of 967 samples, 739 (76.4%) were found to be RSV-positive using RT-PCR. RSV peaked in September 2019 but was not detected in 2020, except in Okinawa. Nationwide epidemics occurred with peaks in July 2021 and 2022. The genotype remained the same, ON1 for RSV-A and BA9 for RSV-B during 2019-2022. Phylogeographic analysis of HVR revealed that at least seven clusters of RSV-A had circulated previously but decreased to two clusters after the pandemic, whereas RSV-B had a single monophyletic cluster over the 10 years. Both RSV-A and RSV-B were transferred from Okinawa into other prefectures after the pandemic. The RSV epidemic was suppressed due to pandemic restrictions; however, pre-pandemic genotypes spread nationwide after the pandemic.

Genomic characterisation of respiratory syncytial virus: a novel system for whole genome sequencing and full-length G and F gene sequences

To advance our understanding of respiratory syncytial virus (RSV) impact through genomic surveillance, we describe two PCR-based sequencing systems, (i) RSVAB-WGS for generic whole-genome sequencing and (ii) RSVAB-GF, which targets major viral antigens, G and F, and is used as a complement for challenging cases with low viral load. These methods monitor RSV genetic diversity to inform molecular epidemiology, vaccine effectiveness and treatment strategies, contributing also to the standardisation of surveillance in a new era of vaccines.

Respiratory syncytial virus in pediatric patients with severe acute respiratory infections in Senegal: findings from the 2022 sentinel surveillance season

In 2022, many regions around the world experienced a severe respiratory syncytial virus (RSV) epidemic with an earlier-than-usual start and increased numbers of paediatric patients in emergency departments. Here we carried out this study to describe the epidemiology and genetic characteristics of RSV infection in patients hospitalized with severe acute respiratory infections in 2022. Samples were tested for RSV by multiplex real time reverse transcription polymerase chain reaction. Subsequently, a subset of RSV positive samples was selected for NGS sequencing. RSV was detected in 16.04%, among which RSV-A was confirmed in 7.5% and RSV-B in 76.7%. RSV infection were more identified in infants aged ≤ 11 months (83.3%) and a shift in the circulation pattern was observed, with highest incidences between September-November. Phylogenetic analyses revealed that all RSV-A strains belonged to GA2.3.5 genotype and all RSV-B strains to GB5.0.5a genotype. Three putative N-glycosylation sites at amino acid positions 103, 135, 237 were predicted among RSV-A strains, while four N-linked glycosylation sites at positions 81, 86, 231 and 294 were identified in RSV-B strains. Globally, our findings reveal an exclusive co-circulation of two genetic lineages of RSV within the pediatric population in Senegal, especially in infants aged ≤ 11 months.

The Modification of the Illumina® CovidSeq™ Workflow for RSV Genomic Surveillance: The Genetic Variability of RSV during the 2022-2023 Season in Northwest Spain

There is growing interest in the molecular surveillance of the Respiratory Syncytial Virus and the monitorization of emerging mutations that could impair the efficacy of antiviral prophylaxis and treatments. A simple, scalable protocol for viral nucleic acid enrichment could improve the surveillance of RSV. We developed a protocol for RSV-A and B amplification based on the Illumina CovidSeq workflow using an RSV primer panel. A total of 135 viral genomes were sequenced from nasopharyngeal samples through the optimization steps of this panel, while an additional 15 samples were used to test the final version. Full coverage of the G gene and over 95% of the coverage of the F gene, the target of the available RSV antivirals or monoclonal antibodies, were obtained. The F:K68N mutation, associated with decreased nirsevimab activity, was detected in our facility. Additionally, phylogenetic analysis showed several sublineages in the 2022-2023 influenza season in Europe. Our protocol allows for a simple and scalable simultaneous amplification of the RSV-A and B whole genome, increasing the yield of RSV sequencing and reducing costs. Its application would allow the world to be ready for the detection of arising mutations in relation to the widespread use of nirsevimab for RSV prevention.

Genetic diversity and its impact on disease severity in respiratory syncytial virus subtype-A and -B bronchiolitis before and after pandemic restrictions in Rome

OBJECTIVES

To scrutinize whether the high circulation of respiratory syncytial virus (RSV) observed in 2021-2022 and 2022-2023 was due to viral diversity, we characterized RSV-A and -B strains causing bronchiolitis in Rome, before and after the COVID-19 pandemic.

METHODS

RSV-positive samples, prospectively collected from infants hospitalized for bronchiolitis from 2017-2018 to 2022-2023, were sequenced in the G gene; phylogenetic results and amino acid substitutions were analyzed. Subtype-specific data were compared among seasons.

RESULTS

Predominance of RSV-A and -B alternated in the pre-pandemic seasons; RSV-A dominated in 2021-2022 whereas RSV-B was predominant in 2022-2023. RSV-A sequences were ON1 genotype but quite distant from the ancestor; two divergent clades included sequences from pre- and post-pandemic seasons. Nearly all RSV-B were BA10 genotype; a divergent clade included only strains from 2021-2022 to 2022-2023. RSV-A cases had lower need of O2 therapy and of intensive care during 2021-2022 with respect to all other seasons. RSV-B infected infants were more frequently admitted to intensive care units and needed O2 in 2022-2023.

CONCLUSIONS

The intense RSV peak in 2021-2022, driven by RSV-A phylogenetically related to pre-pandemic strains is attributable to the immune debt created by pandemic restrictions. The RSV-B genetic divergence observed in post-pandemic strains may have increased the RSV-B specific immune debt, being a possible contributor to bronchiolitis severity in 2022-2023.

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.

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.