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

Molecular epidemiology and phylogenetic analysis of human respiratory syncytial virus type B in Riyadh, Saudi Arabia

The human respiratory syncytial virus (HRSV), recently known as the human orthopneumovirus (HOPV), continues to generate new variants with the ability to cause recurrent infections. Data regarding HRSV-B evolution and genetic diversity in Riyadh, Saudi Arabia, are very limited. Therefore, the current study was designed to investigate the prevalence, genetic diversity, and evolution of HRSV-B. A total of 200 nasopharyngeal aspirate (NPA) samples from hospitalized children at King Khaled University Hospital were screened for the presence of HRSV-B. The second hypervariable region (2nd HVR) of the G gene from all 37 HRSV-B genotypes was used to study sequences and family trees. Of the 200 screened nasopharyngeal samples (NPAs), 16 (8%) were positive for HRSV-B, with a high incidence rate in the age group of 2 to 5 months. The analysis of the 2nd HVR region's sequence showed several differences, such as point mutations, different protein lengths, sequence gaps, duplication regions, and glycosylation sites. A total of 46-point mutations were reported, of which 29 changed their corresponding amino acid residues. N-linked glycosylation sites in Riyadh strains were 3, whereas O-linked glycosylation sites ranged from 22 to 32. Phylogenetic analysis revealed that Riyadh strains from the seasons 2019/20 and 2022/23 are grouped into the subclade BA-11. Other Riyadh strains from different previous seasons were clustered into different sub-genotypes (BA-9, -10, and -12). Seasonal surveillance and molecular evolution tracking of HRSV-B is essential for the early detection of viral genotypes that might cause severe illness consequences and widespread transmission.

Epidemiological and clinical profile of viral respiratory infections in children under 5 years at pre- and post-COVID-19 era in Praia, Cabo Verde

BACKGROUND

The coronavirus disease-19 (COVID-19) pandemic has affected global health, influencing the prevalence of different respiratory pathogens. The aim of this study is to evaluate the distribution of agents causing acute respiratory infections in children under 5 years old before and after the COVID-19 pandemic in Praia, Cabo Verde, and to describe associated clinical variables.

METHODS

Conducted at the University Hospital Dr. Agostinho Neto, this study replicated methods from a previous work from 2019 (Correia et al. 2021). Nasopharyngeal samples were analysed using FilmArray® Respiratory Panel 2.1 (BioFire) to identify agents of acute respiratory infections. Molecular identification of human respiratory syncytial virus subtypes was performed using a real-time duplex reverse transcription polymerase chain reaction. Statistical analysis was performed using IBM SPSS version 29 and R 3.5.1 software.

RESULTS

In 2022, 86.5% (83/96) of nasopharyngeal samples were positive for at least one pathogen. Human rhinovirus/human enterovirus was the most frequent agent, followed by human respiratory syncytial virus, adenovirus and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Co-infections were observed in 43.3% of positive cases. Infection rates were significantly higher in children under 1 year of age, particularly for SARS-CoV-2 and human respiratory syncytial virus. Seasonal variations were observed, with human respiratory syncytial virus predominating in November, SARS-CoV-2 in January and human parainfluenza virus-4 in May. Molecular analysis of human respiratory syncytial virus revealed a shift in subtype prevalence, with both human respiratory syncytial virus-A and -B co-circulating in the pre-pandemic period, whereas only human respiratory syncytial virus-B was detected in the post-pandemic period.

CONCLUSION

Our data indicate changes in the distribution of respiratory viruses in the post-pandemic period compared to pre-pandemic period. The high prevalence of co-infections highlights the complexity of acute respiratory infection aetiology, emphasising the need for enhanced respiratory virus surveillance systems in Cabo Verde. Identifying seasonal trends and risk factors can contribute to targeted interventions and improved public health strategies to mitigate the burden of acute respiratory infections in young children.

Genome-Wide Analyses of Human Respiratory Syncytial Viruses Provide Insights into Evolutionary Dynamics

Human Respiratory syncytial virus (HRSV) is a leading cause of acute lower respiratory tract infections. It is essential to monitor its genomic characteristics. In this study, we analyzed the variation and evolutionary features of HRSV A and HRSV B using whole-genome data, with a focus on their evolutionary features post-COVID-19. Our findings revealed: (i) the mutation rates of HRSV A genes were generally higher than those of HRSV B genes, with the primary mutation directions for both subtypes being C to T, T to C, G to A, and A to G; (ii) multiple lineages of both subtypes that were prevalent during the pandemic are no longer circulating, likely related to the founder effect caused by non-pharmaceutical interventions; (iii) the lineage-defining amino acids on the neutralizing antigens F and G of the circulating lineages post SARS-CoV-2 pandemic exhibited significant temporal specificity; (iv) HRSV B predominated over A in 2023, and the lineage-defining amino acids of the HRSV B F protein located on or very close to major neutralizing antigenic sites, and several lineage-defining amino acids of the G protein were under strong positive selection. These observations suggested that the HRSV B showed stronger adaptive evolutionary features compared to HRSV A post-pandemic. Combining with the fact that several lineage-defining amino acids are located in the replication-related proteins, we hypothesized a potential model of synergistic evolution mediated by multi-protein mutations in the adaptive evolution of circulating strains. However, the impact of these amino acid changes on the viral properties requires further experimental validation.

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.

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.

Microevolution and phylogenomic study of Respiratory Syncytial Virus type A

Communal respiratory syncytial virus (RSV) causes mild to severe illnesses, predominantly in older adults, or people with certain chronic medical conditions, and in children. Symptoms may include rhinorrhea, cough, fever, and dyspnea. In most cases, the infection is mild and resolves on its own, but in some cases, it can lead to more serious illness such as bronchiolitis or pneumonia. The RSV genome codes for ten proteins, NS1, NS2, N, P, M, SH, G, F, M2 and L. We aimed to identify the RSV geographical transmission pattern based on parsimony and investigate hotspot regions across the complete RSV genomes. We employed Viral Evolutionary Network Analysis System on full-length available RSV genomes and with HyPhy for elucidating type of selection pressure. These results indicated that RSV strains circulating in South and North America are not mixed to the European samples, however, genomes reported from Australia are the direct decedents of European samples. Samples reported from the United Kingdom exhibited significant diversity, spanning almost every cluster. This report provides a complete mutational analysis of all the individual RSV genes, and particularly the 31 hotspot substituting regions circulating across the globe in RSV type A samples. Further, protein G and L displayed higher level of codons experienced positive selection. This analysis of RSV type A highlights mutational frequencies across the whole genome, offering valuable insights for epidemiological control and drug development.

Respiratory Syncytial Virus Disease Burden and Nirsevimab Effectiveness in Young Children From 2023-2024

Importance

During the 2023-2024 respiratory syncytial virus (RSV) season in the United States, 2 new RSV prevention products were recommended to protect infants in their first RSV season: nirsevimab and Pfizer's maternal RSV vaccine. Postlicensure studies are needed to assess prevention product impact and effectiveness.

Objective

To compare the epidemiology and disease burden of medically attended RSV-associated acute respiratory illness (ARI) among children younger than 5 years during the 2023-2024 RSV season with 3 prepandemic RSV seasons (2017-2020), estimate nirsevimab effectiveness against medically attended RSV-associated ARI, and compare nirsevimab binding site mutations among circulating RSV in infants with and without nirsevimab receipt.

Design, Setting, and Participants

This study included prospective population-based surveillance for medically attended ARI with systematic molecular testing for RSV and whole-genome sequencing of RSV positive samples, as well as a test-negative case-control design to estimate nirsevimab effectiveness. The study was conducted in 7 academic pediatric medical centers in the United States with data from RSV seasons (September 1 through April 30) in 2017 through 2020. Participants were children younger than 5 years with medically attended ARI.

Exposure

For the nirsevimab effectiveness analyses, nirsevimab receipt among infants younger than 8 months as of or born after October 1, 2023.

Main Outcome and Measure

Medically attended RSV-associated ARI.

Results

Overall, 28 689 children younger than 5 years with medically attended ARI were enrolled, including 9536 during September 1, 2023, through April 30, 2024, and 19 153 during the same calendar period of 2017-2020. Of these children, 16 196 (57%) were male, and 12 444 (43.4) were female; the median (IQR) age was 15 (6-29) months. During 2023-2024, the proportion of children with RSV was 23% (2199/9490) among all medically attended episodes, similar to 2017-2020. RSV-associated hospitalization rates in 2023-2024 were similar to average 2017-2020 seasonal rates with 5.0 (95% CI, 4.6-5.3) per 1000 among children younger than 5 years; the highest rates were among children aged 0 to 2 months (26.6; 95% CI, 23.0-30.2). Low maternal RSV vaccine uptake precluded assessment of effectiveness. Overall, 10 of 765 case patients (1%) who were RSV positive and 126 of 851 control patients (15%) who were RSV negative received nirsevimab. Nirsevimab effectiveness was 89% (95% CI, 79%-94%) against medically attended RSV-associated ARI and 93% (95% CI, 82%-97%) against RSV-associated hospitalization. Among 229 sequenced specimens, there were no differences in nirsevimab binding site mutations by infant nirsevimab receipt status.

Conclusions and Relevance

This analysis documented the continued high burden of medically attended RSV-associated ARI among young children in the US. There is a potential for substantial public health impact with increased and equitable prevention product coverage in future seasons.

The recent landscape of RSV vaccine research

Respiratory syncytial virus (RSV) causes a significant burden of acute respiratory illness across all ages, particularly for infants and older adults. Infants, especially those born prematurely or with underlying health conditions, face a high risk of severe RSV-related lower respiratory tract infections (LRTIs). Globally, RSV contributes to millions of LRTI cases annually, with a disproportionate burden in low- and middle-income countries (LMICs). The RSV virion outer capsule contains glycoproteins G and F which are essential for viral entry into respiratory epithelial cells and represent key targets for therapeutics development. The F-glycoprotein has several highly conserved antigenic sites that have proven useful targets for the development of monoclonal antibodies (mAbs) against RSV. Historically, prevention in infants was limited to the mAb palivizumab, which, despite its efficacy, was costly and inaccessible in many regions. Recent advancements include nirsevimab, a long-acting mAb that has shown substantial efficacy in reducing medically attended RSV-related disease in infants, in phase III clinical trials, early regional and national real-world data. In addition, three new vaccines have been approved: two protein subunit vaccines and a messenger RNA vaccine. The vaccines are all licenced for use in older adults, with one also approved as a maternal vaccine. Promising candidates in development include the mAb clesrovimab, which has an extended half-life and high levels in the nasal epithelial lining and high safety and efficacy profiles in late-stage trials. There are also a wide range of vaccine candidates currently in late-stage clinical trials. These developments signify a major advancement in RSV prevention strategies, offering improved protection for high-risk populations. With the ongoing rollout of the recently licenced vaccines and mAbs internationally, the landscape of RSV care is rapidly changing. We also must ensure these advances reach those in LMICs who need these therapies most.

Landscape of respiratory syncytial virus

ABSTRACT

Respiratory syncytial virus (RSV) is an enveloped, negative-sense, single-stranded RNA virus of the Orthopneumovirus  genus of the Pneumoviridae family in the order Mononegavirales. RSV can cause acute upper and lower respiratory tract infections, sometimes with extrapulmonary complications. The disease burden of RSV infection is enormous, mainly affecting infants and older adults aged 75 years or above. Currently, treatment options for RSV are largely supportive. Prevention strategies remain a critical focus, with efforts centered on vaccine development and the use of prophylactic monoclonal antibodies. To date, three RSV vaccines have been approved for active immunization among individuals aged 60 years and above. For children who are not eligible for these vaccines, passive immunization is recommended. A newly approved prophylactic monoclonal antibody, Nirsevimab, which offers enhanced neutralizing activity and an extended half-life, provides exceptional protection for high-risk infants and young children. This review provides a comprehensive and detailed exploration of RSV's virology, immunology, pathogenesis, epidemiology, clinical manifestations, treatment options, and prevention strategies.

Vaccine and therapeutic agents against the respiratory syncytial virus: resolved and unresolved issue

Respiratory syncytial virus (RSV) is a predominant pathogen responsible for respiratory tract infections among infants, the elderly, and immunocompromised individuals. In recent years, significant progress has been made in innovative vaccines and therapeutic agents targeting RSV. Nevertheless, numerous challenges and bottlenecks persist in the prevention and treatment of RSV infections. This review will provide an overview of the resolved and unresolved issues surrounding the development of vaccines and therapeutic agents against RSV. As of September 2024, three RSV vaccines against acute lower respiratory infections (ALRI) have been approved globally. Additionally, there have been notable progress in the realm of passive immunoprophylactic antibodies, with the monoclonal antibody nirsevimab receiving regulatory approval for the prevention of RSV infections in infants. Furthermore, a variety of RSV therapeutic agents are currently under clinical investigation, with the potential to yield breakthrough advancements in the foreseeable future. This review delineates the advancements and challenges faced in vaccines and therapeutic agents targeting RSV. It aims to provide insights that will guide the development of effective preventive and control measures for RSV.

Respiratory Syncytial Virus: A WAidid Consensus Document on New Preventive Options

Background/Objectives: Respiratory syncytial virus (RSV) is a leading cause of respiratory infections, particularly affecting young infants, older adults, and individuals with comorbidities. Methods: This document, developed as a consensus by an international group of experts affiliated with the World Association of Infectious Diseases and Immunological Disorders (WAidid), focuses on recent advancements in RSV prevention, highlighting the introduction of monoclonal antibodies (mAbs) and vaccines. Results: Historically, RSV treatment options were limited to supportive care and the monoclonal antibody palivizumab, which required multiple doses. Recent innovations have led to the development of long-acting mAbs, such as nirsevimab, which provide season-long protection with a single dose. Nirsevimab has shown high efficacy in preventing severe RSV-related lower respiratory tract infections (LRTIs) in infants, reducing hospitalizations and ICU admissions. Additionally, new vaccines, such as RSVpreF and RSVpreF3, target older adults and have demonstrated significant efficacy in preventing LRTIs in clinical trials. Maternal vaccination strategies also show promise in providing passive immunity to newborns, protecting them during the most vulnerable early months of life. This document further discusses the global burden of RSV, its economic impact, and the challenges of implementing these preventative strategies in different healthcare settings. Conclusions: The evidence supports the integration of both passive (mAbs) and active (vaccines) immunization approaches as effective tools to mitigate the public health impact of RSV. The combined use of these interventions could substantially reduce RSV-related morbidity and mortality across various age groups and populations, emphasizing the importance of widespread immunization efforts.

Respiratory Syncytial Virus Risk Profile in Hospitalized Infants and Comparison with Influenza and COVID-19 Controls in Valladolid, Spain, 2010-2022

INTRODUCTION

We aimed to describe the risk profile of RSV infections among children aged ≤ 24 months in Valladolid from January 2010 to August 2022 and to compare them with influenza and COVID-19 controls.

METHODS

We conducted a retrospective cohort study of all laboratory-confirmed RSV, influenza, and COVID-19 infections. We analyzed risk factors for RSV hospitalization and severity (length-of-stay ≥ 8 days, intensive-care-unit admission, in-hospital death or readmission < 30 days) and compared severity between hospitalized RSV patients vs. influenza and COVID-19 controls using multivariable logistic regression models.

RESULTS

We included 1507 patients with RSV (1274 inpatient), 32 with influenza, and 52 COVID-19 controls. Hospitalized RSV (mean age 5.3 months) and COVID-19 (4 months) were younger than influenza (9.1 months) patients. Sixteen percent of patients had RSV within the first month of life. Most infants did not have comorbidities (74% RSV, 56% influenza, and 69% COVID-19). Forty-one percent of patients with RSV and influenza were coinfected vs. 27% COVID-19 (p = 0.04). Among RSV, hospitalization risk factors were prematurity (adjusted OR 3.11 [95% CI 1.66, 4.44]) and coinfection (2.03 [1.45, 2.85]). Risks for higher severity were maternal smoking (1.89 [1.07, 3.33]), prematurity (2.31 [1.59, 3.34]), chronic lung disease (2.20 [1.06, 4.58]), neurodevelopmental condition (4.28 [2.10, 8.73]), and coinfection (2.67 [2.09, 3.40]). Breastfeeding was protective against hospitalization (0.87 [0.80, 0.95]) and severity (0.81 [0.74, 0.88]), while complete vaccination schedule was protective against severity (0.51 [0.27, 0.97]). RSV had 2.47 (1.03, 5.96) higher risk of experiencing any severe outcome compared to influenza and did not show significant differences vs. COVID-19.

CONCLUSIONS

RSV hospitalizations were more frequent and severe than influenza, while severity was comparable to the early pandemic COVID-19. Currently, both influenza and COVID-19 vaccines are included in the maternal and childhood Spanish immunization schedule between the ages of 6 and 59 months. RSV monoclonal antibody is recommended for ≤ 6 months but a third of patients were aged 6-24 months. Maternal RSV vaccination can protect their children directly from birth and indirectly through breastfeeding.