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Sondlane H, Ogunbayo A, Donato C, Mogotsi M, Esona M, Hallbauer U, Bester P, Goedhals D, Nyaga M. Whole genome molecular analysis of respiratory syncytial virus pre and during the COVID-19 pandemic in Free State province, South Africa. Virus Res 2024; 347:199421. [PMID: 38942296 PMCID: PMC11283024 DOI: 10.1016/j.virusres.2024.199421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 05/14/2024] [Accepted: 06/16/2024] [Indexed: 06/30/2024]
Abstract
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.
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Affiliation(s)
- Hlengiwe Sondlane
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa
| | - Ayodeji Ogunbayo
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa
| | - Celeste Donato
- Enteric Diseases Group, Murdoch Children's Research Institute, Parkville, VIC, Australia; Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia; The Centre for Pathogen Genomics, The Doherty Institute, University of Melbourne, Australia
| | - Milton Mogotsi
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa
| | - Mathew Esona
- Diarrheal Pathogens Research Unit, Sefako Makgatho Health Sciences University, Medunsa 0204, Pretoria, South Africa
| | - Ute Hallbauer
- Department of Paediatrics and Child Health, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa
| | - Phillip Bester
- Division of Virology, School of Pathology, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa
| | - Dominique Goedhals
- Division of Virology, School of Pathology, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa; PathCare, Pretoria, South Africa
| | - Martin Nyaga
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa.
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2
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Musa AO, Faber SR, Forrest K, Smith KP, Sengupta S, López CB. Identification of distinct genotypes in circulating RSV A strains based on variants in the virus replication-associated genes. J Virol 2024; 98:e0099024. [PMID: 39007617 DOI: 10.1128/jvi.00990-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Accepted: 06/16/2024] [Indexed: 07/16/2024] Open
Abstract
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.
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Affiliation(s)
- Abdulafiz O Musa
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, Missouri, USA
- Center for Women's Infectious Diseases Research, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Sydney R Faber
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, Missouri, USA
- Center for Women's Infectious Diseases Research, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Kaitlyn Forrest
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Division of Neonatology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Kenneth P Smith
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Infectious Disease Diagnostics Laboratory, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Shaon Sengupta
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Division of Neonatology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Carolina B López
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, Missouri, USA
- Center for Women's Infectious Diseases Research, Washington University School of Medicine, Saint Louis, Missouri, USA
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3
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Nuttens C, Moyersoen J, Curcio D, Aponte-Torres Z, Baay M, Vroling H, Gessner BD, Begier E. Differences Between RSV A and RSV B Subgroups and Implications for Pharmaceutical Preventive Measures. Infect Dis Ther 2024; 13:1725-1742. [PMID: 38971918 PMCID: PMC11266343 DOI: 10.1007/s40121-024-01012-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 06/21/2024] [Indexed: 07/08/2024] Open
Abstract
INTRODUCTION Understanding the differences between respiratory syncytial virus (RSV) subgroups A and B provides insights for the development of prevention strategies and public health interventions. We aimed to describe the structural differences of RSV subgroups, their epidemiology, and genomic diversity. The associated immune response and differences in clinical severity were also investigated. METHODS A literature review from PubMed and Google Scholar (1985-2023) was performed and extended using snowballing from references in captured publications. RESULTS RSV has two major antigenic subgroups, A and B, defined by the G glycoprotein. The RSV F fusion glycoprotein in the prefusion conformation is a major target of virus neutralizing antibodies and differs in surface exposed regions between RSV A and RSV B. The subgroups co-circulate annually, but there is considerable debate as to whether clinical severity is impacted by the subgroup of the infecting RSV strain. Large variations between the studies reporting RSV subgroup impact on clinical severity were observed. A tendency for higher disease severity may be attributed to RSV A but no consensus could be reached as to whether infection by one of the subgroup caused more severe outcomes. RSV genotype diversity decreased over the last two decades, and ON and BA have become the sole lineages detected for RSV A and RSV B, since 2014. No studies with data obtained after 2014 reported a difference in disease severity between the two subgroups. RSV F is relatively well conserved and highly similar between RSV A and B, but changes in the amino acid sequence have been observed. Some of these changes led to differences in F antigenic sites compared to reference F sequences (e.g., RSV/A Long strain), which are more pronounced in antigenic sites of the prefusion conformation of RSV B. Initial results from the second season after vaccination suggest specific RSV B efficacy wanes more rapidly than RSV A for RSV PreF-based monovalent vaccines. CONCLUSIONS RSV A and RSV B both contribute substantially to the global RSV burden. Both RSV subgroups cause severe disease and none of the available evidence to date suggests any differences in clinical severity between the subgroups. Therefore, it is important to implement measures effective at preventing disease due to both RSV A and RSV B to ensure impactful public health interventions. Monitoring overtime will be needed to assess the impact of waning antibody levels on subgroup-specific efficacy.
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Affiliation(s)
| | | | | | | | - Marc Baay
- Epidemiology & Pharmacovigilance, P95, Louvain, Belgium
| | - Hilde Vroling
- Epidemiology & Pharmacovigilance, P95, Louvain, Belgium
| | | | - Elizabeth Begier
- Scientific Affairs, Older Adult RSV Vaccine Program, Global Medical Development Scientific and Clinical Affairs, Pfizer Vaccines, 9 Riverwalk, Citywest Business Campus, Dublin 24, Dublin, Ireland.
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4
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Pierangeli A, Midulla F, Piralla A, Ferrari G, Nenna R, Pitrolo AMG, Licari A, Marseglia GL, Abruzzese D, Pellegrinelli L, Galli C, Binda S, Cereda D, Fracella M, Oliveto G, Campagna R, Petrarca L, Pariani E, Antonelli G, Baldanti F. Sequence analysis of respiratory syncytial virus cases reveals a novel subgroup -B strain circulating in north-central Italy after pandemic restrictions. J Clin Virol 2024; 173:105681. [PMID: 38733664 DOI: 10.1016/j.jcv.2024.105681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 03/08/2024] [Accepted: 04/28/2024] [Indexed: 05/13/2024]
Abstract
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.
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Affiliation(s)
- Alessandra Pierangeli
- Virology Laboratory, Department of Molecular Medicine, Sapienza University, V.le Porta Tiburtina, 28, 00185 Rome, Italy.
| | - Fabio Midulla
- Department of Pediatrics and Infantile Neuropsychiatry, Sapienza University, V.le Regina Elena, 299, 00161, Rome, Italy
| | - Antonio Piralla
- Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Viale C. Golgi, 19, 27100 Pavia, Italy
| | - Guglielmo Ferrari
- Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Viale C. Golgi, 19, 27100 Pavia, Italy
| | - Raffaella Nenna
- Department of Pediatrics and Infantile Neuropsychiatry, Sapienza University, V.le Regina Elena, 299, 00161, Rome, Italy
| | | | - Amelia Licari
- Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, via S. da Nuova, 65, 27100 Pavia, Italy; Pediatric Clinic, Fondazione IRCCS Policlinico San Matteo, Viale C. Golgi, 19, 27100 Pavia, Italy
| | - Gian Luigi Marseglia
- Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, via S. da Nuova, 65, 27100 Pavia, Italy; Pediatric Clinic, Fondazione IRCCS Policlinico San Matteo, Viale C. Golgi, 19, 27100 Pavia, Italy
| | - Dario Abruzzese
- Pediatric Clinic, Fondazione IRCCS Policlinico San Matteo, Viale C. Golgi, 19, 27100 Pavia, Italy
| | - Laura Pellegrinelli
- Department of Biomedical Sciences for Health, University of Milan, via C. Pascal, 36, 20133 Milan, Italy
| | - Cristina Galli
- Department of Biomedical Sciences for Health, University of Milan, via C. Pascal, 36, 20133 Milan, Italy
| | - Sandro Binda
- Department of Biomedical Sciences for Health, University of Milan, via C. Pascal, 36, 20133 Milan, Italy
| | - Danilo Cereda
- DG Welfare, Regione Lombardia, Piazza Città di Lombardia, 1, 20124, Milan, Italy
| | - Matteo Fracella
- Virology Laboratory, Department of Molecular Medicine, Sapienza University, V.le Porta Tiburtina, 28, 00185 Rome, Italy
| | - Giuseppe Oliveto
- Virology Laboratory, Department of Molecular Medicine, Sapienza University, V.le Porta Tiburtina, 28, 00185 Rome, Italy
| | - Roberta Campagna
- Virology Laboratory, Department of Molecular Medicine, Sapienza University, V.le Porta Tiburtina, 28, 00185 Rome, Italy
| | - Laura Petrarca
- Department of Pediatrics and Infantile Neuropsychiatry, Sapienza University, V.le Regina Elena, 299, 00161, Rome, Italy
| | - Elena Pariani
- Department of Biomedical Sciences for Health, University of Milan, via C. Pascal, 36, 20133 Milan, Italy
| | - Guido Antonelli
- Virology Laboratory, Department of Molecular Medicine, Sapienza University, V.le Porta Tiburtina, 28, 00185 Rome, Italy; University Hospital Policlinico Umberto I, Sapienza University, V.le del Policlinico 155, 00161 Rome, Italy
| | - Fausto Baldanti
- Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Viale C. Golgi, 19, 27100 Pavia, Italy; Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, via S. da Nuova, 65, 27100 Pavia, Italy
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5
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Goya S, Ruis C, Neher RA, Meijer A, Aziz A, Hinrichs AS, von Gottberg A, Roemer C, Amoako DG, Acuña D, McBroome J, Otieno JR, Bhiman JN, Everatt J, Muñoz-Escalante JC, Ramaekers K, Duggan K, Presser LD, Urbanska L, Venter M, Wolter N, Peret TC, Salimi V, Potdar V, Borges V, Viegas M. Standardized Phylogenetic Classification of Human Respiratory Syncytial Virus below the Subgroup Level. Emerg Infect Dis 2024; 30:1631-1641. [PMID: 39043393 PMCID: PMC11286072 DOI: 10.3201/eid3008.240209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2024] Open
Abstract
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.
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Affiliation(s)
| | | | | | - Adam Meijer
- University of Washington, Seattle, Washington, USA (S. Goya)
- University of Cambridge, Cambridge, UK (C. Ruis); University of Basel and SIB, Basel, Switzerland (R.A. Neher, C. Roemer, L. Urbanska)
- National Institute for Public Health and the Environment, Bilthoven, the Netherlands (A. Meijer, L.D. Presser)
- World Health Organization Collaborating Centre for Reference and Research on Influenza, Melbourne, Victoria, Australia (A. Aziz)
- University of California Santa Cruz, Santa Cruz, California, USA (A.S. Hinrichs, J. McBroome)
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, J. Everatt, N. Wolter)
- University of Witwatersrand, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, N. Wolter)
- University of KwaZulu-Natal, Durban, South Africa (D.G. Amoako)
- Universidad Nacional de La Plata, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- National Scientific and Technical Research Council, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- Theiagen Genomics, Highlands Ranch, Colorado, USA (J.R. Otieno)
- Autonomous University of San Luis Potosí, San Luis Potosí, Mexico (J.C. Muñoz-Escalante)
- Rega Institute for Medical Research, Leuven, Belgium (K. Ramaekers)
- University of Edinburgh, Edinburgh, Scotland, UK (K. Duggan)
- University of Pretoria, Pretoria, South Africa (M. Venter)
- University of Texas Medical Branch, Galveston, Texas, USA (T.C.T. Peret)
- Tehran University of Medical Sciences, Tehran, Iran (V. Salimi)
- ICMR National Institute of Virology, Pune, India (V. Potdar)
- National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal (V. Borges)
| | - Ammar Aziz
- University of Washington, Seattle, Washington, USA (S. Goya)
- University of Cambridge, Cambridge, UK (C. Ruis); University of Basel and SIB, Basel, Switzerland (R.A. Neher, C. Roemer, L. Urbanska)
- National Institute for Public Health and the Environment, Bilthoven, the Netherlands (A. Meijer, L.D. Presser)
- World Health Organization Collaborating Centre for Reference and Research on Influenza, Melbourne, Victoria, Australia (A. Aziz)
- University of California Santa Cruz, Santa Cruz, California, USA (A.S. Hinrichs, J. McBroome)
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, J. Everatt, N. Wolter)
- University of Witwatersrand, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, N. Wolter)
- University of KwaZulu-Natal, Durban, South Africa (D.G. Amoako)
- Universidad Nacional de La Plata, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- National Scientific and Technical Research Council, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- Theiagen Genomics, Highlands Ranch, Colorado, USA (J.R. Otieno)
- Autonomous University of San Luis Potosí, San Luis Potosí, Mexico (J.C. Muñoz-Escalante)
- Rega Institute for Medical Research, Leuven, Belgium (K. Ramaekers)
- University of Edinburgh, Edinburgh, Scotland, UK (K. Duggan)
- University of Pretoria, Pretoria, South Africa (M. Venter)
- University of Texas Medical Branch, Galveston, Texas, USA (T.C.T. Peret)
- Tehran University of Medical Sciences, Tehran, Iran (V. Salimi)
- ICMR National Institute of Virology, Pune, India (V. Potdar)
- National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal (V. Borges)
| | - Angie S. Hinrichs
- University of Washington, Seattle, Washington, USA (S. Goya)
- University of Cambridge, Cambridge, UK (C. Ruis); University of Basel and SIB, Basel, Switzerland (R.A. Neher, C. Roemer, L. Urbanska)
- National Institute for Public Health and the Environment, Bilthoven, the Netherlands (A. Meijer, L.D. Presser)
- World Health Organization Collaborating Centre for Reference and Research on Influenza, Melbourne, Victoria, Australia (A. Aziz)
- University of California Santa Cruz, Santa Cruz, California, USA (A.S. Hinrichs, J. McBroome)
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, J. Everatt, N. Wolter)
- University of Witwatersrand, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, N. Wolter)
- University of KwaZulu-Natal, Durban, South Africa (D.G. Amoako)
- Universidad Nacional de La Plata, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- National Scientific and Technical Research Council, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- Theiagen Genomics, Highlands Ranch, Colorado, USA (J.R. Otieno)
- Autonomous University of San Luis Potosí, San Luis Potosí, Mexico (J.C. Muñoz-Escalante)
- Rega Institute for Medical Research, Leuven, Belgium (K. Ramaekers)
- University of Edinburgh, Edinburgh, Scotland, UK (K. Duggan)
- University of Pretoria, Pretoria, South Africa (M. Venter)
- University of Texas Medical Branch, Galveston, Texas, USA (T.C.T. Peret)
- Tehran University of Medical Sciences, Tehran, Iran (V. Salimi)
- ICMR National Institute of Virology, Pune, India (V. Potdar)
- National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal (V. Borges)
| | - Anne von Gottberg
- University of Washington, Seattle, Washington, USA (S. Goya)
- University of Cambridge, Cambridge, UK (C. Ruis); University of Basel and SIB, Basel, Switzerland (R.A. Neher, C. Roemer, L. Urbanska)
- National Institute for Public Health and the Environment, Bilthoven, the Netherlands (A. Meijer, L.D. Presser)
- World Health Organization Collaborating Centre for Reference and Research on Influenza, Melbourne, Victoria, Australia (A. Aziz)
- University of California Santa Cruz, Santa Cruz, California, USA (A.S. Hinrichs, J. McBroome)
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, J. Everatt, N. Wolter)
- University of Witwatersrand, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, N. Wolter)
- University of KwaZulu-Natal, Durban, South Africa (D.G. Amoako)
- Universidad Nacional de La Plata, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- National Scientific and Technical Research Council, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- Theiagen Genomics, Highlands Ranch, Colorado, USA (J.R. Otieno)
- Autonomous University of San Luis Potosí, San Luis Potosí, Mexico (J.C. Muñoz-Escalante)
- Rega Institute for Medical Research, Leuven, Belgium (K. Ramaekers)
- University of Edinburgh, Edinburgh, Scotland, UK (K. Duggan)
- University of Pretoria, Pretoria, South Africa (M. Venter)
- University of Texas Medical Branch, Galveston, Texas, USA (T.C.T. Peret)
- Tehran University of Medical Sciences, Tehran, Iran (V. Salimi)
- ICMR National Institute of Virology, Pune, India (V. Potdar)
- National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal (V. Borges)
| | - Cornelius Roemer
- University of Washington, Seattle, Washington, USA (S. Goya)
- University of Cambridge, Cambridge, UK (C. Ruis); University of Basel and SIB, Basel, Switzerland (R.A. Neher, C. Roemer, L. Urbanska)
- National Institute for Public Health and the Environment, Bilthoven, the Netherlands (A. Meijer, L.D. Presser)
- World Health Organization Collaborating Centre for Reference and Research on Influenza, Melbourne, Victoria, Australia (A. Aziz)
- University of California Santa Cruz, Santa Cruz, California, USA (A.S. Hinrichs, J. McBroome)
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, J. Everatt, N. Wolter)
- University of Witwatersrand, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, N. Wolter)
- University of KwaZulu-Natal, Durban, South Africa (D.G. Amoako)
- Universidad Nacional de La Plata, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- National Scientific and Technical Research Council, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- Theiagen Genomics, Highlands Ranch, Colorado, USA (J.R. Otieno)
- Autonomous University of San Luis Potosí, San Luis Potosí, Mexico (J.C. Muñoz-Escalante)
- Rega Institute for Medical Research, Leuven, Belgium (K. Ramaekers)
- University of Edinburgh, Edinburgh, Scotland, UK (K. Duggan)
- University of Pretoria, Pretoria, South Africa (M. Venter)
- University of Texas Medical Branch, Galveston, Texas, USA (T.C.T. Peret)
- Tehran University of Medical Sciences, Tehran, Iran (V. Salimi)
- ICMR National Institute of Virology, Pune, India (V. Potdar)
- National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal (V. Borges)
| | | | - Dolores Acuña
- University of Washington, Seattle, Washington, USA (S. Goya)
- University of Cambridge, Cambridge, UK (C. Ruis); University of Basel and SIB, Basel, Switzerland (R.A. Neher, C. Roemer, L. Urbanska)
- National Institute for Public Health and the Environment, Bilthoven, the Netherlands (A. Meijer, L.D. Presser)
- World Health Organization Collaborating Centre for Reference and Research on Influenza, Melbourne, Victoria, Australia (A. Aziz)
- University of California Santa Cruz, Santa Cruz, California, USA (A.S. Hinrichs, J. McBroome)
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, J. Everatt, N. Wolter)
- University of Witwatersrand, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, N. Wolter)
- University of KwaZulu-Natal, Durban, South Africa (D.G. Amoako)
- Universidad Nacional de La Plata, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- National Scientific and Technical Research Council, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- Theiagen Genomics, Highlands Ranch, Colorado, USA (J.R. Otieno)
- Autonomous University of San Luis Potosí, San Luis Potosí, Mexico (J.C. Muñoz-Escalante)
- Rega Institute for Medical Research, Leuven, Belgium (K. Ramaekers)
- University of Edinburgh, Edinburgh, Scotland, UK (K. Duggan)
- University of Pretoria, Pretoria, South Africa (M. Venter)
- University of Texas Medical Branch, Galveston, Texas, USA (T.C.T. Peret)
- Tehran University of Medical Sciences, Tehran, Iran (V. Salimi)
- ICMR National Institute of Virology, Pune, India (V. Potdar)
- National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal (V. Borges)
| | - Jakob McBroome
- University of Washington, Seattle, Washington, USA (S. Goya)
- University of Cambridge, Cambridge, UK (C. Ruis); University of Basel and SIB, Basel, Switzerland (R.A. Neher, C. Roemer, L. Urbanska)
- National Institute for Public Health and the Environment, Bilthoven, the Netherlands (A. Meijer, L.D. Presser)
- World Health Organization Collaborating Centre for Reference and Research on Influenza, Melbourne, Victoria, Australia (A. Aziz)
- University of California Santa Cruz, Santa Cruz, California, USA (A.S. Hinrichs, J. McBroome)
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, J. Everatt, N. Wolter)
- University of Witwatersrand, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, N. Wolter)
- University of KwaZulu-Natal, Durban, South Africa (D.G. Amoako)
- Universidad Nacional de La Plata, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- National Scientific and Technical Research Council, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- Theiagen Genomics, Highlands Ranch, Colorado, USA (J.R. Otieno)
- Autonomous University of San Luis Potosí, San Luis Potosí, Mexico (J.C. Muñoz-Escalante)
- Rega Institute for Medical Research, Leuven, Belgium (K. Ramaekers)
- University of Edinburgh, Edinburgh, Scotland, UK (K. Duggan)
- University of Pretoria, Pretoria, South Africa (M. Venter)
- University of Texas Medical Branch, Galveston, Texas, USA (T.C.T. Peret)
- Tehran University of Medical Sciences, Tehran, Iran (V. Salimi)
- ICMR National Institute of Virology, Pune, India (V. Potdar)
- National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal (V. Borges)
| | - James R. Otieno
- University of Washington, Seattle, Washington, USA (S. Goya)
- University of Cambridge, Cambridge, UK (C. Ruis); University of Basel and SIB, Basel, Switzerland (R.A. Neher, C. Roemer, L. Urbanska)
- National Institute for Public Health and the Environment, Bilthoven, the Netherlands (A. Meijer, L.D. Presser)
- World Health Organization Collaborating Centre for Reference and Research on Influenza, Melbourne, Victoria, Australia (A. Aziz)
- University of California Santa Cruz, Santa Cruz, California, USA (A.S. Hinrichs, J. McBroome)
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, J. Everatt, N. Wolter)
- University of Witwatersrand, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, N. Wolter)
- University of KwaZulu-Natal, Durban, South Africa (D.G. Amoako)
- Universidad Nacional de La Plata, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- National Scientific and Technical Research Council, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- Theiagen Genomics, Highlands Ranch, Colorado, USA (J.R. Otieno)
- Autonomous University of San Luis Potosí, San Luis Potosí, Mexico (J.C. Muñoz-Escalante)
- Rega Institute for Medical Research, Leuven, Belgium (K. Ramaekers)
- University of Edinburgh, Edinburgh, Scotland, UK (K. Duggan)
- University of Pretoria, Pretoria, South Africa (M. Venter)
- University of Texas Medical Branch, Galveston, Texas, USA (T.C.T. Peret)
- Tehran University of Medical Sciences, Tehran, Iran (V. Salimi)
- ICMR National Institute of Virology, Pune, India (V. Potdar)
- National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal (V. Borges)
| | - Jinal N. Bhiman
- University of Washington, Seattle, Washington, USA (S. Goya)
- University of Cambridge, Cambridge, UK (C. Ruis); University of Basel and SIB, Basel, Switzerland (R.A. Neher, C. Roemer, L. Urbanska)
- National Institute for Public Health and the Environment, Bilthoven, the Netherlands (A. Meijer, L.D. Presser)
- World Health Organization Collaborating Centre for Reference and Research on Influenza, Melbourne, Victoria, Australia (A. Aziz)
- University of California Santa Cruz, Santa Cruz, California, USA (A.S. Hinrichs, J. McBroome)
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, J. Everatt, N. Wolter)
- University of Witwatersrand, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, N. Wolter)
- University of KwaZulu-Natal, Durban, South Africa (D.G. Amoako)
- Universidad Nacional de La Plata, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- National Scientific and Technical Research Council, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- Theiagen Genomics, Highlands Ranch, Colorado, USA (J.R. Otieno)
- Autonomous University of San Luis Potosí, San Luis Potosí, Mexico (J.C. Muñoz-Escalante)
- Rega Institute for Medical Research, Leuven, Belgium (K. Ramaekers)
- University of Edinburgh, Edinburgh, Scotland, UK (K. Duggan)
- University of Pretoria, Pretoria, South Africa (M. Venter)
- University of Texas Medical Branch, Galveston, Texas, USA (T.C.T. Peret)
- Tehran University of Medical Sciences, Tehran, Iran (V. Salimi)
- ICMR National Institute of Virology, Pune, India (V. Potdar)
- National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal (V. Borges)
| | - Josie Everatt
- University of Washington, Seattle, Washington, USA (S. Goya)
- University of Cambridge, Cambridge, UK (C. Ruis); University of Basel and SIB, Basel, Switzerland (R.A. Neher, C. Roemer, L. Urbanska)
- National Institute for Public Health and the Environment, Bilthoven, the Netherlands (A. Meijer, L.D. Presser)
- World Health Organization Collaborating Centre for Reference and Research on Influenza, Melbourne, Victoria, Australia (A. Aziz)
- University of California Santa Cruz, Santa Cruz, California, USA (A.S. Hinrichs, J. McBroome)
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, J. Everatt, N. Wolter)
- University of Witwatersrand, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, N. Wolter)
- University of KwaZulu-Natal, Durban, South Africa (D.G. Amoako)
- Universidad Nacional de La Plata, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- National Scientific and Technical Research Council, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- Theiagen Genomics, Highlands Ranch, Colorado, USA (J.R. Otieno)
- Autonomous University of San Luis Potosí, San Luis Potosí, Mexico (J.C. Muñoz-Escalante)
- Rega Institute for Medical Research, Leuven, Belgium (K. Ramaekers)
- University of Edinburgh, Edinburgh, Scotland, UK (K. Duggan)
- University of Pretoria, Pretoria, South Africa (M. Venter)
- University of Texas Medical Branch, Galveston, Texas, USA (T.C.T. Peret)
- Tehran University of Medical Sciences, Tehran, Iran (V. Salimi)
- ICMR National Institute of Virology, Pune, India (V. Potdar)
- National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal (V. Borges)
| | - Juan C. Muñoz-Escalante
- University of Washington, Seattle, Washington, USA (S. Goya)
- University of Cambridge, Cambridge, UK (C. Ruis); University of Basel and SIB, Basel, Switzerland (R.A. Neher, C. Roemer, L. Urbanska)
- National Institute for Public Health and the Environment, Bilthoven, the Netherlands (A. Meijer, L.D. Presser)
- World Health Organization Collaborating Centre for Reference and Research on Influenza, Melbourne, Victoria, Australia (A. Aziz)
- University of California Santa Cruz, Santa Cruz, California, USA (A.S. Hinrichs, J. McBroome)
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, J. Everatt, N. Wolter)
- University of Witwatersrand, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, N. Wolter)
- University of KwaZulu-Natal, Durban, South Africa (D.G. Amoako)
- Universidad Nacional de La Plata, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- National Scientific and Technical Research Council, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- Theiagen Genomics, Highlands Ranch, Colorado, USA (J.R. Otieno)
- Autonomous University of San Luis Potosí, San Luis Potosí, Mexico (J.C. Muñoz-Escalante)
- Rega Institute for Medical Research, Leuven, Belgium (K. Ramaekers)
- University of Edinburgh, Edinburgh, Scotland, UK (K. Duggan)
- University of Pretoria, Pretoria, South Africa (M. Venter)
- University of Texas Medical Branch, Galveston, Texas, USA (T.C.T. Peret)
- Tehran University of Medical Sciences, Tehran, Iran (V. Salimi)
- ICMR National Institute of Virology, Pune, India (V. Potdar)
- National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal (V. Borges)
| | | | - Kate Duggan
- University of Washington, Seattle, Washington, USA (S. Goya)
- University of Cambridge, Cambridge, UK (C. Ruis); University of Basel and SIB, Basel, Switzerland (R.A. Neher, C. Roemer, L. Urbanska)
- National Institute for Public Health and the Environment, Bilthoven, the Netherlands (A. Meijer, L.D. Presser)
- World Health Organization Collaborating Centre for Reference and Research on Influenza, Melbourne, Victoria, Australia (A. Aziz)
- University of California Santa Cruz, Santa Cruz, California, USA (A.S. Hinrichs, J. McBroome)
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, J. Everatt, N. Wolter)
- University of Witwatersrand, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, N. Wolter)
- University of KwaZulu-Natal, Durban, South Africa (D.G. Amoako)
- Universidad Nacional de La Plata, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- National Scientific and Technical Research Council, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- Theiagen Genomics, Highlands Ranch, Colorado, USA (J.R. Otieno)
- Autonomous University of San Luis Potosí, San Luis Potosí, Mexico (J.C. Muñoz-Escalante)
- Rega Institute for Medical Research, Leuven, Belgium (K. Ramaekers)
- University of Edinburgh, Edinburgh, Scotland, UK (K. Duggan)
- University of Pretoria, Pretoria, South Africa (M. Venter)
- University of Texas Medical Branch, Galveston, Texas, USA (T.C.T. Peret)
- Tehran University of Medical Sciences, Tehran, Iran (V. Salimi)
- ICMR National Institute of Virology, Pune, India (V. Potdar)
- National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal (V. Borges)
| | - Lance D. Presser
- University of Washington, Seattle, Washington, USA (S. Goya)
- University of Cambridge, Cambridge, UK (C. Ruis); University of Basel and SIB, Basel, Switzerland (R.A. Neher, C. Roemer, L. Urbanska)
- National Institute for Public Health and the Environment, Bilthoven, the Netherlands (A. Meijer, L.D. Presser)
- World Health Organization Collaborating Centre for Reference and Research on Influenza, Melbourne, Victoria, Australia (A. Aziz)
- University of California Santa Cruz, Santa Cruz, California, USA (A.S. Hinrichs, J. McBroome)
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, J. Everatt, N. Wolter)
- University of Witwatersrand, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, N. Wolter)
- University of KwaZulu-Natal, Durban, South Africa (D.G. Amoako)
- Universidad Nacional de La Plata, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- National Scientific and Technical Research Council, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- Theiagen Genomics, Highlands Ranch, Colorado, USA (J.R. Otieno)
- Autonomous University of San Luis Potosí, San Luis Potosí, Mexico (J.C. Muñoz-Escalante)
- Rega Institute for Medical Research, Leuven, Belgium (K. Ramaekers)
- University of Edinburgh, Edinburgh, Scotland, UK (K. Duggan)
- University of Pretoria, Pretoria, South Africa (M. Venter)
- University of Texas Medical Branch, Galveston, Texas, USA (T.C.T. Peret)
- Tehran University of Medical Sciences, Tehran, Iran (V. Salimi)
- ICMR National Institute of Virology, Pune, India (V. Potdar)
- National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal (V. Borges)
| | - Laura Urbanska
- University of Washington, Seattle, Washington, USA (S. Goya)
- University of Cambridge, Cambridge, UK (C. Ruis); University of Basel and SIB, Basel, Switzerland (R.A. Neher, C. Roemer, L. Urbanska)
- National Institute for Public Health and the Environment, Bilthoven, the Netherlands (A. Meijer, L.D. Presser)
- World Health Organization Collaborating Centre for Reference and Research on Influenza, Melbourne, Victoria, Australia (A. Aziz)
- University of California Santa Cruz, Santa Cruz, California, USA (A.S. Hinrichs, J. McBroome)
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, J. Everatt, N. Wolter)
- University of Witwatersrand, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, N. Wolter)
- University of KwaZulu-Natal, Durban, South Africa (D.G. Amoako)
- Universidad Nacional de La Plata, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- National Scientific and Technical Research Council, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- Theiagen Genomics, Highlands Ranch, Colorado, USA (J.R. Otieno)
- Autonomous University of San Luis Potosí, San Luis Potosí, Mexico (J.C. Muñoz-Escalante)
- Rega Institute for Medical Research, Leuven, Belgium (K. Ramaekers)
- University of Edinburgh, Edinburgh, Scotland, UK (K. Duggan)
- University of Pretoria, Pretoria, South Africa (M. Venter)
- University of Texas Medical Branch, Galveston, Texas, USA (T.C.T. Peret)
- Tehran University of Medical Sciences, Tehran, Iran (V. Salimi)
- ICMR National Institute of Virology, Pune, India (V. Potdar)
- National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal (V. Borges)
| | - Marietjie Venter
- University of Washington, Seattle, Washington, USA (S. Goya)
- University of Cambridge, Cambridge, UK (C. Ruis); University of Basel and SIB, Basel, Switzerland (R.A. Neher, C. Roemer, L. Urbanska)
- National Institute for Public Health and the Environment, Bilthoven, the Netherlands (A. Meijer, L.D. Presser)
- World Health Organization Collaborating Centre for Reference and Research on Influenza, Melbourne, Victoria, Australia (A. Aziz)
- University of California Santa Cruz, Santa Cruz, California, USA (A.S. Hinrichs, J. McBroome)
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, J. Everatt, N. Wolter)
- University of Witwatersrand, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, N. Wolter)
- University of KwaZulu-Natal, Durban, South Africa (D.G. Amoako)
- Universidad Nacional de La Plata, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- National Scientific and Technical Research Council, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- Theiagen Genomics, Highlands Ranch, Colorado, USA (J.R. Otieno)
- Autonomous University of San Luis Potosí, San Luis Potosí, Mexico (J.C. Muñoz-Escalante)
- Rega Institute for Medical Research, Leuven, Belgium (K. Ramaekers)
- University of Edinburgh, Edinburgh, Scotland, UK (K. Duggan)
- University of Pretoria, Pretoria, South Africa (M. Venter)
- University of Texas Medical Branch, Galveston, Texas, USA (T.C.T. Peret)
- Tehran University of Medical Sciences, Tehran, Iran (V. Salimi)
- ICMR National Institute of Virology, Pune, India (V. Potdar)
- National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal (V. Borges)
| | - Nicole Wolter
- University of Washington, Seattle, Washington, USA (S. Goya)
- University of Cambridge, Cambridge, UK (C. Ruis); University of Basel and SIB, Basel, Switzerland (R.A. Neher, C. Roemer, L. Urbanska)
- National Institute for Public Health and the Environment, Bilthoven, the Netherlands (A. Meijer, L.D. Presser)
- World Health Organization Collaborating Centre for Reference and Research on Influenza, Melbourne, Victoria, Australia (A. Aziz)
- University of California Santa Cruz, Santa Cruz, California, USA (A.S. Hinrichs, J. McBroome)
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, J. Everatt, N. Wolter)
- University of Witwatersrand, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, N. Wolter)
- University of KwaZulu-Natal, Durban, South Africa (D.G. Amoako)
- Universidad Nacional de La Plata, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- National Scientific and Technical Research Council, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- Theiagen Genomics, Highlands Ranch, Colorado, USA (J.R. Otieno)
- Autonomous University of San Luis Potosí, San Luis Potosí, Mexico (J.C. Muñoz-Escalante)
- Rega Institute for Medical Research, Leuven, Belgium (K. Ramaekers)
- University of Edinburgh, Edinburgh, Scotland, UK (K. Duggan)
- University of Pretoria, Pretoria, South Africa (M. Venter)
- University of Texas Medical Branch, Galveston, Texas, USA (T.C.T. Peret)
- Tehran University of Medical Sciences, Tehran, Iran (V. Salimi)
- ICMR National Institute of Virology, Pune, India (V. Potdar)
- National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal (V. Borges)
| | - Teresa C.T. Peret
- University of Washington, Seattle, Washington, USA (S. Goya)
- University of Cambridge, Cambridge, UK (C. Ruis); University of Basel and SIB, Basel, Switzerland (R.A. Neher, C. Roemer, L. Urbanska)
- National Institute for Public Health and the Environment, Bilthoven, the Netherlands (A. Meijer, L.D. Presser)
- World Health Organization Collaborating Centre for Reference and Research on Influenza, Melbourne, Victoria, Australia (A. Aziz)
- University of California Santa Cruz, Santa Cruz, California, USA (A.S. Hinrichs, J. McBroome)
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, J. Everatt, N. Wolter)
- University of Witwatersrand, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, N. Wolter)
- University of KwaZulu-Natal, Durban, South Africa (D.G. Amoako)
- Universidad Nacional de La Plata, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- National Scientific and Technical Research Council, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- Theiagen Genomics, Highlands Ranch, Colorado, USA (J.R. Otieno)
- Autonomous University of San Luis Potosí, San Luis Potosí, Mexico (J.C. Muñoz-Escalante)
- Rega Institute for Medical Research, Leuven, Belgium (K. Ramaekers)
- University of Edinburgh, Edinburgh, Scotland, UK (K. Duggan)
- University of Pretoria, Pretoria, South Africa (M. Venter)
- University of Texas Medical Branch, Galveston, Texas, USA (T.C.T. Peret)
- Tehran University of Medical Sciences, Tehran, Iran (V. Salimi)
- ICMR National Institute of Virology, Pune, India (V. Potdar)
- National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal (V. Borges)
| | - Vahid Salimi
- University of Washington, Seattle, Washington, USA (S. Goya)
- University of Cambridge, Cambridge, UK (C. Ruis); University of Basel and SIB, Basel, Switzerland (R.A. Neher, C. Roemer, L. Urbanska)
- National Institute for Public Health and the Environment, Bilthoven, the Netherlands (A. Meijer, L.D. Presser)
- World Health Organization Collaborating Centre for Reference and Research on Influenza, Melbourne, Victoria, Australia (A. Aziz)
- University of California Santa Cruz, Santa Cruz, California, USA (A.S. Hinrichs, J. McBroome)
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, J. Everatt, N. Wolter)
- University of Witwatersrand, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, N. Wolter)
- University of KwaZulu-Natal, Durban, South Africa (D.G. Amoako)
- Universidad Nacional de La Plata, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- National Scientific and Technical Research Council, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- Theiagen Genomics, Highlands Ranch, Colorado, USA (J.R. Otieno)
- Autonomous University of San Luis Potosí, San Luis Potosí, Mexico (J.C. Muñoz-Escalante)
- Rega Institute for Medical Research, Leuven, Belgium (K. Ramaekers)
- University of Edinburgh, Edinburgh, Scotland, UK (K. Duggan)
- University of Pretoria, Pretoria, South Africa (M. Venter)
- University of Texas Medical Branch, Galveston, Texas, USA (T.C.T. Peret)
- Tehran University of Medical Sciences, Tehran, Iran (V. Salimi)
- ICMR National Institute of Virology, Pune, India (V. Potdar)
- National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal (V. Borges)
| | - Varsha Potdar
- University of Washington, Seattle, Washington, USA (S. Goya)
- University of Cambridge, Cambridge, UK (C. Ruis); University of Basel and SIB, Basel, Switzerland (R.A. Neher, C. Roemer, L. Urbanska)
- National Institute for Public Health and the Environment, Bilthoven, the Netherlands (A. Meijer, L.D. Presser)
- World Health Organization Collaborating Centre for Reference and Research on Influenza, Melbourne, Victoria, Australia (A. Aziz)
- University of California Santa Cruz, Santa Cruz, California, USA (A.S. Hinrichs, J. McBroome)
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, J. Everatt, N. Wolter)
- University of Witwatersrand, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, N. Wolter)
- University of KwaZulu-Natal, Durban, South Africa (D.G. Amoako)
- Universidad Nacional de La Plata, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- National Scientific and Technical Research Council, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- Theiagen Genomics, Highlands Ranch, Colorado, USA (J.R. Otieno)
- Autonomous University of San Luis Potosí, San Luis Potosí, Mexico (J.C. Muñoz-Escalante)
- Rega Institute for Medical Research, Leuven, Belgium (K. Ramaekers)
- University of Edinburgh, Edinburgh, Scotland, UK (K. Duggan)
- University of Pretoria, Pretoria, South Africa (M. Venter)
- University of Texas Medical Branch, Galveston, Texas, USA (T.C.T. Peret)
- Tehran University of Medical Sciences, Tehran, Iran (V. Salimi)
- ICMR National Institute of Virology, Pune, India (V. Potdar)
- National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal (V. Borges)
| | - Vítor Borges
- University of Washington, Seattle, Washington, USA (S. Goya)
- University of Cambridge, Cambridge, UK (C. Ruis); University of Basel and SIB, Basel, Switzerland (R.A. Neher, C. Roemer, L. Urbanska)
- National Institute for Public Health and the Environment, Bilthoven, the Netherlands (A. Meijer, L.D. Presser)
- World Health Organization Collaborating Centre for Reference and Research on Influenza, Melbourne, Victoria, Australia (A. Aziz)
- University of California Santa Cruz, Santa Cruz, California, USA (A.S. Hinrichs, J. McBroome)
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, J. Everatt, N. Wolter)
- University of Witwatersrand, Johannesburg, South Africa (A. von Gottberg, J.N. Bhiman, N. Wolter)
- University of KwaZulu-Natal, Durban, South Africa (D.G. Amoako)
- Universidad Nacional de La Plata, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- National Scientific and Technical Research Council, Buenos Aires, Argentina (D. Acuña, M. Viegas)
- Theiagen Genomics, Highlands Ranch, Colorado, USA (J.R. Otieno)
- Autonomous University of San Luis Potosí, San Luis Potosí, Mexico (J.C. Muñoz-Escalante)
- Rega Institute for Medical Research, Leuven, Belgium (K. Ramaekers)
- University of Edinburgh, Edinburgh, Scotland, UK (K. Duggan)
- University of Pretoria, Pretoria, South Africa (M. Venter)
- University of Texas Medical Branch, Galveston, Texas, USA (T.C.T. Peret)
- Tehran University of Medical Sciences, Tehran, Iran (V. Salimi)
- ICMR National Institute of Virology, Pune, India (V. Potdar)
- National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal (V. Borges)
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6
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Fang YP, Chang CC, Lai DW, Lee CY. Genetic characterization of respiratory syncytial virus surface glycoproteins F and G in Taiwan, 2017-2021. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2024; 57:564-572. [PMID: 38937186 DOI: 10.1016/j.jmii.2024.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 05/11/2024] [Accepted: 06/15/2024] [Indexed: 06/29/2024]
Abstract
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.
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Affiliation(s)
- Yu Ping Fang
- Department of Pediatrics, Chang Bing Show Chwan Memorial Hospital, Changhua, Taiwan
| | - Chun Chin Chang
- Department of Pathology and Laboratory Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - De Wei Lai
- Experimental Animal Center, Department of Molecular Biology and Cell Research, Chang Bing Show Chwan Memorial Hospital, Changhua, Taiwan; Department of Pharmacy and Master Program, Tajen University, Pingtung, Taiwan
| | - Chun Yi Lee
- Department of Pediatrics, Chang Bing Show Chwan Memorial Hospital, Changhua, Taiwan; College of Medicine, National Chung Hsing University, Taiwan.
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Hou M, Liu G, Meng C, Dong L, Fang Y, Wang L, Wang N, Cai C, Wang H. Circulation patterns and molecular characteristics of respiratory syncytial virus among hospitalized children in Tianjin, China, before and during the COVID-19 pandemic (2017-2022). Virol Sin 2024:S1995-820X(24)00114-7. [PMID: 39067791 DOI: 10.1016/j.virs.2024.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 07/24/2024] [Indexed: 07/30/2024] Open
Abstract
Respiratory syncytial virus (RSV) is the main pathogen that causes hospitalization for acute lower respiratory tract infections (ALRIs) in children. With the reopening of communities and schools, the resurgence of RSV in the COVID-19 post-pandemic era has become a major concern. To understand the circulation patterns and genotype variability of RSV in Tianjin before and during the COVID-19 pandemic, a total of 19,531 nasopharyngeal aspirate samples from hospitalized children in Tianjin from July 2017 to June 2022 were evaluated. Direct immunofluorescence and polymerase chain reaction (PCR) were used for screening RSV-positive samples and subtyping, respectively. Further analysis of mutations in the second hypervariable region (HVR2) of the G gene was performed through Sanger sequencing. Our results showed that 16.46% (3,215/19,531) samples were RSV positive and a delayed increase in the RSV infection rates occurred in the winter season from December 2020 to February 2021, with the average RSV-positive rate of 35.77% (519/1,451). The ON1, with H258Q and H266L substitutions, and the BA9, with T290I and T312I substitutions, are dominant strains that alternately circulate every 1-2 years in Tianjin, China, from July 2017 to June 2022. In addition, novel substitutions, such as N296Y, K221T, N230K, V251A in the BA9 genotype, and L226I in the ON1 genotype, emerged during the COVID-19 pandemic. Analysis of clinical characteristics indicated no significant differences between RSV-A and RSV-B groups. This study provides a theoretical basis for clinical prevention and treatment. However, further studies are needed to explore the regulatory mechanism of host immune responses to different lineages of ON1 and BA9 in the future.
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Affiliation(s)
- Mengzhu Hou
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin, 300134, China
| | - Guangping Liu
- Graduate School, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
| | - Chao Meng
- Department of Medical Laboratory, Tianjin Second People's Hospital, Tianjin, 300192, China
| | - Lili Dong
- Department of Respiratory, Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin, 300134, China
| | - Yulian Fang
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin, 300134, China
| | - Lu Wang
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin, 300134, China
| | - Ning Wang
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin, 300134, China
| | - Chunquan Cai
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital (Children's Hospital of Tianjin University), Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin, 300134, China.
| | - Hanjie Wang
- School of Life Sciences, Tianjin University and Tianjin Engineering Center of Micro-Nano Biomaterials and Detection-Treatment Technology, Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, Tianjin, 300072, China.
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Jelley L, Douglas J, O'Neill M, Berquist K, Claasen A, Wang J, Utekar S, Johnston H, Judy B, Allais M, de Ligt J, Tan CE, Seeds R, Wood T, Aminisani N, Jennings T, Welch D, Turner N, McIntyre P, Dowell T, Trenholme A, Byrnes C, Webby R, French N, Winter D, Huang QS, Geoghegan JL. Spatial and temporal transmission dynamics of respiratory syncytial virus in New Zealand before and after the COVID-19 pandemic. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.07.15.24310412. [PMID: 39072023 PMCID: PMC11275701 DOI: 10.1101/2024.07.15.24310412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Human respiratory syncytial virus (RSV) is a major cause of acute respiratory infection. In 2020, RSV was effectively eliminated from the community in New Zealand due to non-pharmaceutical interventions (NPI) used to control the spread of COVID-19. However, in April 2021, following a brief quarantine-free travel agreement with Australia, there was a large-scale nationwide outbreak of RSV that led to reported cases more than five times higher, and hospitalisations more than three times higher, than the typical seasonal pattern. In this study, we generated 1,471 viral genomes of both RSV-A and RSV-B sampled between 2015 and 2022 from across New Zealand. Using a phylodynamics approach, we used these data to better understand RSV transmission patterns in New Zealand prior to 2020, and how RSV became re-established in the community following the relaxation of COVID-19 restrictions. We found that in 2021, there was a large epidemic of RSV in New Zealand that affected a broader age group range compared to the usual pattern of RSV infections. This epidemic was due to an increase in RSV importations, leading to several large genomic clusters of both RSV-A ON1 and RSV-B BA9 genotypes in New Zealand. However, while a number of importations were detected, there was also a major reduction in RSV genetic diversity compared to pre-pandemic seasonal outbreaks. These genomic clusters were temporally associated with the increase of migration in 2021 due to quarantine-free travel from Australia at the time. The closest genetic relatives to the New Zealand RSV genomes, when sampled, were viral genomes sampled in Australia during a large, off-season summer outbreak several months prior, rather than cryptic lineages that were sustained but not detected in New Zealand. These data reveal the impact of NPI used during the COVID-19 pandemic on other respiratory infections and highlight the important insights that can be gained from viral genomes.
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Bender W, Zhang Y, Corbett A, Chu C, Grier A, Wang L, Qiu X, McCall MN, Topham DJ, Walsh EE, Mariani TJ, Scheuermann R, Caserta MT, Anderson CS. Association of disease severity and genetic variation during primary Respiratory Syncytial Virus infections. BMC Med Genomics 2024; 17:165. [PMID: 38898440 PMCID: PMC11188216 DOI: 10.1186/s12920-024-01930-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 06/11/2024] [Indexed: 06/21/2024] Open
Abstract
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.
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Affiliation(s)
- William Bender
- Division of Infectious Disease, Department of Medicine, School of Medicine and Dentistry, University of Rochester, University of Rochester Medical Center, Rochester, NY, USA
| | - Yun Zhang
- J. Craig Venter Institute, San Diego, CA, USA
| | - Anthony Corbett
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, NY, USA
| | - Chinyi Chu
- Division of Neonatology, Department of Pediatrics, University of Rochester Medical Center, Rochester, NY, USA
| | - Alexander Grier
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, USA
| | - Lu Wang
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, NY, USA
| | - Xing Qiu
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, NY, USA
| | - Matthew N McCall
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, NY, USA
| | - David J Topham
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, USA
| | - Edward E Walsh
- Division of Infectious Disease, Department of Medicine, School of Medicine and Dentistry, University of Rochester, University of Rochester Medical Center, Rochester, NY, USA
| | - Thomas J Mariani
- Division of Neonatology, Department of Pediatrics, University of Rochester Medical Center, Rochester, NY, USA
| | | | - Mary T Caserta
- Division of Infectious Diseases, Department of Pediatrics, University of Rochester Medical Center, Rochester, NY, USA
| | - Christopher S Anderson
- Division of Infectious Disease, Department of Medicine, School of Medicine and Dentistry, University of Rochester, University of Rochester Medical Center, Rochester, NY, USA.
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Mojarrad S, Tavakoli Movaghar N, Edalat F, Letafati A, Kargar Jahromi Z, Moattari A. Epidemiological and phylogenetic assessment of human respiratory syncytial virus among pediatric patients presenting acute respiratory infections in Shiraz, Iran during 2015-2016. IRANIAN JOURNAL OF MICROBIOLOGY 2024; 16:411-420. [PMID: 39005603 PMCID: PMC11245347 DOI: 10.18502/ijm.v16i3.15798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Background and Objectives The pediatric population worldwide bears a significant morbidity and death burden due to acute respiratory infections (ARIs). Human Orthopneumovirus, sometimes referred to as the Human Respiratory Syncytial Virus (HRSV), is one of the main causes of ARIs in infants. The main goal of this study was to identify the genetic diversity of HRSV strains that were circulating in the Iranian population at a certain time of year. Materials and Methods Two hundred youngsters less than 12 years old with acute respiratory infections had samples taken from their throat and pharynx secretions. Then, external and hemi-nested PCR were employed, using specific primers targeting the G gene region to detect HRSV. Subsequently, nine randomly selected positive samples were subjected to sequencing. The results were then compared with reference strains cataloged in GeneBank, and phylogenetic tree was constructed using Chromes and MEGA7. Results Out of 200 samples, 34 were identified as containing HRSV. Subgroup A was predominant, accounting for 61.76% of cases, followed by subgroup BA (35.29%) and subgroup B (2.94%). Phylogenetic analysis revealed five samples associated with subtype B and four with genotype A. Genomic analysis showed three samples under the GA2 subgroup and one under GA1 for subtype A, and four samples in subgroup BA and one in GB2 for subtype B. Conclusion In this study, subgroup A strains, particularly genotype GA2, exhibited a higher prevalence compared to subgroup B strains during the specific period under investigation, shedding light on the genetic landscape of HRSV in this region.
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Affiliation(s)
- Saber Mojarrad
- Department of Bacteriology & Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Nahid Tavakoli Movaghar
- Department of Bacteriology & Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Fahime Edalat
- Department of Bacteriology & Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Arash Letafati
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Zahra Kargar Jahromi
- Department of Bacteriology & Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Afagh Moattari
- Department of Bacteriology & Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
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Simusika P, Okamoto M, Dapat C, Muleya W, Malisheni M, Azam S, Imamura T, Saito M, Mwape I, Mpabalwani E, Monze M, Oshitani H. Characterization of human respiratory syncytial virus in children with severe acute respiratory infection before and during the COVID-19 pandemic. IJID REGIONS 2024; 11:100354. [PMID: 38596821 PMCID: PMC11002793 DOI: 10.1016/j.ijregi.2024.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 03/13/2024] [Indexed: 04/11/2024]
Abstract
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.
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Affiliation(s)
- Paul Simusika
- Tohoku University Graduate School of Medicine, Department of Virology, Sendai, Japan
- University Teaching Hospitals, Pathology and Microbiology Department, Virology Laboratory, Lusaka, Zambia
- Levy Mwanawasa Medical University, Institute of Basic and Biomedical Sciences ,Lusaka, Zambia
| | - Michiko Okamoto
- Tohoku University Graduate School of Medicine, Department of Virology, Sendai, Japan
| | - Clyde Dapat
- Tohoku University Graduate School of Medicine, Department of Virology, Sendai, Japan
| | - Walter Muleya
- University of Zambia, School of Veterinary Medicine, Department of Biomedical Sciences, Lusaka, Zambia
| | - Moffat Malisheni
- University Teaching Hospitals, Pathology and Microbiology Department, Virology Laboratory, Lusaka, Zambia
| | - Sikandar Azam
- Tohoku University Graduate School of Medicine, Department of Virology, Sendai, Japan
| | - Takeaki Imamura
- Tohoku University Graduate School of Medicine, Department of Virology, Sendai, Japan
| | - Mayuko Saito
- Tohoku University Graduate School of Medicine, Department of Virology, Sendai, Japan
| | - Innocent Mwape
- Center for Infectious Disease Research in Zambia, Lusaka, Zambia
| | - Evans Mpabalwani
- University of Zambia, School of Medicine, Department of Pediatrics and Child Health, Lusaka, Zambia
| | - Mwaka Monze
- University Teaching Hospitals, Pathology and Microbiology Department, Virology Laboratory, Lusaka, Zambia
| | - Hitoshi Oshitani
- Tohoku University Graduate School of Medicine, Department of Virology, Sendai, Japan
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Tramuto F, Maida CM, Randazzo G, Guzzetta V, Santino A, Li Muli R, Costantino C, Graziano G, Amodio E, Mazzucco W, Vitale F. Whole-Genome Sequencing and Genetic Diversity of Human Respiratory Syncytial Virus in Patients with Influenza-like Illness in Sicily (Italy) from 2017 to 2023. Viruses 2024; 16:851. [PMID: 38932144 PMCID: PMC11209242 DOI: 10.3390/v16060851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Revised: 05/21/2024] [Accepted: 05/24/2024] [Indexed: 06/28/2024] Open
Abstract
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.
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Affiliation(s)
- Fabio Tramuto
- Department of Health Promotion Sciences Maternal and Infant Care, Internal Medicine and Medical Specialties “G. D’Alessandro”—Hygiene Section, University of Palermo, 90133 Palermo, Italy; (C.M.M.); (C.C.); (E.A.); (W.M.); (F.V.)
- Regional Reference Laboratory for Molecular Surveillance of Influenza, Clinical Epidemiology Unit, University Hospital “Paolo Giaccone”, 90133 Palermo, Italy; (G.R.); (V.G.); (A.S.); (R.L.M.); (G.G.)
| | - Carmelo Massimo Maida
- Department of Health Promotion Sciences Maternal and Infant Care, Internal Medicine and Medical Specialties “G. D’Alessandro”—Hygiene Section, University of Palermo, 90133 Palermo, Italy; (C.M.M.); (C.C.); (E.A.); (W.M.); (F.V.)
- Regional Reference Laboratory for Molecular Surveillance of Influenza, Clinical Epidemiology Unit, University Hospital “Paolo Giaccone”, 90133 Palermo, Italy; (G.R.); (V.G.); (A.S.); (R.L.M.); (G.G.)
| | - Giulia Randazzo
- Regional Reference Laboratory for Molecular Surveillance of Influenza, Clinical Epidemiology Unit, University Hospital “Paolo Giaccone”, 90133 Palermo, Italy; (G.R.); (V.G.); (A.S.); (R.L.M.); (G.G.)
| | - Valeria Guzzetta
- Regional Reference Laboratory for Molecular Surveillance of Influenza, Clinical Epidemiology Unit, University Hospital “Paolo Giaccone”, 90133 Palermo, Italy; (G.R.); (V.G.); (A.S.); (R.L.M.); (G.G.)
| | - Arianna Santino
- Regional Reference Laboratory for Molecular Surveillance of Influenza, Clinical Epidemiology Unit, University Hospital “Paolo Giaccone”, 90133 Palermo, Italy; (G.R.); (V.G.); (A.S.); (R.L.M.); (G.G.)
| | - Rita Li Muli
- Regional Reference Laboratory for Molecular Surveillance of Influenza, Clinical Epidemiology Unit, University Hospital “Paolo Giaccone”, 90133 Palermo, Italy; (G.R.); (V.G.); (A.S.); (R.L.M.); (G.G.)
| | - Claudio Costantino
- Department of Health Promotion Sciences Maternal and Infant Care, Internal Medicine and Medical Specialties “G. D’Alessandro”—Hygiene Section, University of Palermo, 90133 Palermo, Italy; (C.M.M.); (C.C.); (E.A.); (W.M.); (F.V.)
- Regional Reference Laboratory for Molecular Surveillance of Influenza, Clinical Epidemiology Unit, University Hospital “Paolo Giaccone”, 90133 Palermo, Italy; (G.R.); (V.G.); (A.S.); (R.L.M.); (G.G.)
| | - Giorgio Graziano
- Regional Reference Laboratory for Molecular Surveillance of Influenza, Clinical Epidemiology Unit, University Hospital “Paolo Giaccone”, 90133 Palermo, Italy; (G.R.); (V.G.); (A.S.); (R.L.M.); (G.G.)
| | - Emanuele Amodio
- Department of Health Promotion Sciences Maternal and Infant Care, Internal Medicine and Medical Specialties “G. D’Alessandro”—Hygiene Section, University of Palermo, 90133 Palermo, Italy; (C.M.M.); (C.C.); (E.A.); (W.M.); (F.V.)
| | - Walter Mazzucco
- Department of Health Promotion Sciences Maternal and Infant Care, Internal Medicine and Medical Specialties “G. D’Alessandro”—Hygiene Section, University of Palermo, 90133 Palermo, Italy; (C.M.M.); (C.C.); (E.A.); (W.M.); (F.V.)
- Regional Reference Laboratory for Molecular Surveillance of Influenza, Clinical Epidemiology Unit, University Hospital “Paolo Giaccone”, 90133 Palermo, Italy; (G.R.); (V.G.); (A.S.); (R.L.M.); (G.G.)
| | - Francesco Vitale
- Department of Health Promotion Sciences Maternal and Infant Care, Internal Medicine and Medical Specialties “G. D’Alessandro”—Hygiene Section, University of Palermo, 90133 Palermo, Italy; (C.M.M.); (C.C.); (E.A.); (W.M.); (F.V.)
- Regional Reference Laboratory for Molecular Surveillance of Influenza, Clinical Epidemiology Unit, University Hospital “Paolo Giaccone”, 90133 Palermo, Italy; (G.R.); (V.G.); (A.S.); (R.L.M.); (G.G.)
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Cho SJ, Kim SH, Mun J, Yun JE, Park S, Park J, Lee YU, Park JS, Yun H, Lee CM, Kim JP, Seo JM. Impact of COVID-19 Pandemic Restrictions on Respiratory Virus Patterns: Insights from RSV Surveillance in Gwangju, South Korea. Viruses 2024; 16:850. [PMID: 38932143 PMCID: PMC11209132 DOI: 10.3390/v16060850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 05/23/2024] [Accepted: 05/23/2024] [Indexed: 06/28/2024] Open
Abstract
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.
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Affiliation(s)
- Sun-Ju Cho
- Division of Emerging Infectious Disease, Department of Infectious Disease Research, Health and Environment Research Institute of Gwangju, Gwangju 61954, Republic of Korea; (S.-H.K.); (J.M.); (J.-e.Y.); (S.P.); (J.P.); (Y.-U.L.); (J.-s.P.); (H.Y.); (C.-m.L.); (J.-P.K.); (J.-M.S.)
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Moumbeket Yifomnjou MH, Monamele GC, Modiyinji AF, Njankouo-Ripa M, Onana B, Njouom R. Genetic Diversity of Human Respiratory Syncytial Virus during COVID-19 Pandemic in Yaoundé, Cameroon, 2020-2021. Microorganisms 2024; 12:952. [PMID: 38792782 PMCID: PMC11123827 DOI: 10.3390/microorganisms12050952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 04/03/2024] [Accepted: 04/19/2024] [Indexed: 05/26/2024] Open
Abstract
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.
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Affiliation(s)
- Moïse Henri Moumbeket Yifomnjou
- Virology Unit, Centre Pasteur du Cameroun, 451 Rue 2005, Yaoundé P.O. Box 1274, Cameroon; (M.H.M.Y.); (G.C.M.); (A.F.M.); (M.N.-R.)
- Laboratory of Microbiology, University of Yaoundé I, Yaoundé P.O. Box 812, Cameroon;
| | - Gwladys Chavely Monamele
- Virology Unit, Centre Pasteur du Cameroun, 451 Rue 2005, Yaoundé P.O. Box 1274, Cameroon; (M.H.M.Y.); (G.C.M.); (A.F.M.); (M.N.-R.)
| | - Abdou Fatawou Modiyinji
- Virology Unit, Centre Pasteur du Cameroun, 451 Rue 2005, Yaoundé P.O. Box 1274, Cameroon; (M.H.M.Y.); (G.C.M.); (A.F.M.); (M.N.-R.)
| | - Mohamadou Njankouo-Ripa
- Virology Unit, Centre Pasteur du Cameroun, 451 Rue 2005, Yaoundé P.O. Box 1274, Cameroon; (M.H.M.Y.); (G.C.M.); (A.F.M.); (M.N.-R.)
| | - Boyomo Onana
- Laboratory of Microbiology, University of Yaoundé I, Yaoundé P.O. Box 812, Cameroon;
| | - Richard Njouom
- Virology Unit, Centre Pasteur du Cameroun, 451 Rue 2005, Yaoundé P.O. Box 1274, Cameroon; (M.H.M.Y.); (G.C.M.); (A.F.M.); (M.N.-R.)
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15
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Musa AO, Faber SR, Forrest K, Smith KP, Sengupta S, López CB. Identification of distinct genotypes in circulating RSV A strains based on variants on the virus replication-associated genes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.22.590570. [PMID: 38712045 PMCID: PMC11071361 DOI: 10.1101/2024.04.22.590570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
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.
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Affiliation(s)
- Abdulafiz O. Musa
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, Missouri, USA
- Center for Womeńs Infectious Diseases Research, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Sydney R. Faber
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, Missouri, USA
- Center for Womeńs Infectious Diseases Research, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Kaitlyn Forrest
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Division of Neonatology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Kenneth P. Smith
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Infectious Disease Diagnostics Laboratory, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Shaon Sengupta
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Division of Neonatology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Carolina B. López
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, Missouri, USA
- Center for Womeńs Infectious Diseases Research, Washington University School of Medicine, Saint Louis, Missouri, USA
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16
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Fröhlich GC, Gregianini TS, Pinheiro FG, Nascimento R, Cezar TM, Pscheidt VM, Selayaran T, Martins LG, Gomes MFDC, Salvato RS, Pereira EC, Guimarães-Ribeiro V, Scalioni LDP, Siqueira MM, Resende PC, Veiga ABG. Resurgence of human respiratory syncytial virus during COVID-19 pandemic in Southern Brazil. J Med Virol 2024; 96:e29551. [PMID: 38506236 DOI: 10.1002/jmv.29551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 02/16/2024] [Accepted: 03/10/2024] [Indexed: 03/21/2024]
Abstract
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.
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Affiliation(s)
- Guilherme C Fröhlich
- Laboratório Central de Saúde Pública, Centro Estadual de Vigilância em Saúde da Secretaria de Saúde do Estado do Rio Grande do Sul-LACEN/CEVS/SES-RS, Porto Alegre, Brazil
- Universidade Federal de Ciências da Saúde de Porto Alegre-UFCSPA, Porto Alegre, Brazil
| | - Tatiana S Gregianini
- Laboratório Central de Saúde Pública, Centro Estadual de Vigilância em Saúde da Secretaria de Saúde do Estado do Rio Grande do Sul-LACEN/CEVS/SES-RS, Porto Alegre, Brazil
| | - Felipe G Pinheiro
- Universidade Federal de Ciências da Saúde de Porto Alegre-UFCSPA, Porto Alegre, Brazil
| | - Rodrigo Nascimento
- Universidade Federal de Ciências da Saúde de Porto Alegre-UFCSPA, Porto Alegre, Brazil
| | - Thiago M Cezar
- Universidade Federal de Ciências da Saúde de Porto Alegre-UFCSPA, Porto Alegre, Brazil
| | - Veridiane M Pscheidt
- Universidade Federal de Ciências da Saúde de Porto Alegre-UFCSPA, Porto Alegre, Brazil
| | - Tainá Selayaran
- Universidade Federal de Ciências da Saúde de Porto Alegre-UFCSPA, Porto Alegre, Brazil
- Centro de Desenvolvimento Científico e Tecnológico, Centro Estadual de Vigilância em Saúde da Secretaria de Saúde do Estado do Rio Grande do Sul-CDCT/CEVS/SES-RS, Porto Alegre, Brazil
| | - Letícia G Martins
- Centro Estadual de Vigilância em Saúde da Secretaria de Saúde do Estado do Rio Grande do Sul-CEVS/SES-RS, Porto Alegre, Brazil
| | | | - Richard S Salvato
- Centro de Desenvolvimento Científico e Tecnológico, Centro Estadual de Vigilância em Saúde da Secretaria de Saúde do Estado do Rio Grande do Sul-CDCT/CEVS/SES-RS, Porto Alegre, Brazil
| | - Elisa C Pereira
- Laboratório Vírus Respiratórios, Exantemáticos, Enterovírus e Emergências Virais - LVRE/FIOCRUZ-RJ, Porto Alegre, Brazil
| | - Victor Guimarães-Ribeiro
- Laboratório Vírus Respiratórios, Exantemáticos, Enterovírus e Emergências Virais - LVRE/FIOCRUZ-RJ, Porto Alegre, Brazil
| | - Letícia de Paula Scalioni
- Laboratório Vírus Respiratórios, Exantemáticos, Enterovírus e Emergências Virais - LVRE/FIOCRUZ-RJ, Porto Alegre, Brazil
| | - Marilda M Siqueira
- Laboratório Vírus Respiratórios, Exantemáticos, Enterovírus e Emergências Virais - LVRE/FIOCRUZ-RJ, Porto Alegre, Brazil
| | - Paola C Resende
- Laboratório Vírus Respiratórios, Exantemáticos, Enterovírus e Emergências Virais - LVRE/FIOCRUZ-RJ, Porto Alegre, Brazil
| | - Ana B G Veiga
- Universidade Federal de Ciências da Saúde de Porto Alegre-UFCSPA, Porto Alegre, Brazil
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Huang L, Xu Y, Yang Y, Dong H, Luo Q, Chen Z, Du H, Mei G, Wang X, Guan Y, Zhao C, Han J, Lu G. Molecular epidemiology and clinical characteristics of respiratory syncytial virus in hospitalized children during winter 2021-2022 in Bengbu, China. Front Public Health 2024; 11:1310293. [PMID: 38235154 PMCID: PMC10791987 DOI: 10.3389/fpubh.2023.1310293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 12/01/2023] [Indexed: 01/19/2024] Open
Abstract
Objective This study aimed to study the molecular epidemiology and clinical characteristics of respiratory syncytial virus (RSV) infection from hospitalized children with ARTI in Bengbu. Methods One hundred twenty-four nasopharyngeal swab specimens and clinical data from children with ARTI cases were collected in Bengbu, China, during winter 2021-2022. The samples were detected by qPCR of 13 respiratory viruses. Phylogenetic analysis was constructed using MEGA 7.0. All analyses were performed using SAS software, version 9.4. Results In winter 2021-2022, URTI, NSCAP, SCAP, and bronchiolitis accounted for 41.03%, 27.35%, 17.09%, and 14.53% of hospitalized children in Bengbu, China. The detection rates of the top three were RSV (41.94%), ADV (5.65%), and FluB (5.65%) in hospitalized children through 13 virus detection. RSV is the main pathogen of hospitalized children under 2 years old. Forty-eight sequences of G protein of RSV were obtained through PCR amplification, including RSV-A 37 strains and RSV-B 11 strains. Phylogenetic analysis showed that all RSV-A and RSV-B were ON1 and BA9 genotypes, respectively. ON1 genotypes were further divided into two clades. The majority of ON1 strains formed a unique genetic clade with T113I, V131D, N178 G, and H258Q mutations. Furthermore, RSV infection was an independent risk factor for ventilator use (OR = 9.55, 95% CI 1.87-48.64). Conclusion There was a high incidence of RSV among hospitalized children during winter 2021-2022 in Bengbu with ON1 and BA9 being the dominant strains. This study demonstrated the molecular epidemiological characteristics of RSV in children with respiratory infections in Bengbu, China.
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Affiliation(s)
- Limin Huang
- The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui, China
- Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Yuanyou Xu
- The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui, China
| | - Yanqing Yang
- Chinese Center for Disease Control and Prevention, Beijing, China
| | - Hongming Dong
- School of Basic Medicine, North China University of Science and Technology, Tangshan, China
| | - Qin Luo
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Zhen Chen
- Chinese Center for Disease Control and Prevention, Beijing, China
| | - Haijun Du
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Guoyong Mei
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xinyue Wang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- College of Life Science and Agriculture and Forestry, Qiqihar University, Qiqihar, China
| | - Yake Guan
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Chihong Zhao
- Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jun Han
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Guoyu Lu
- The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui, China
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18
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Umar S, Yang R, Wang X, Liu Y, Ke P, Qin S. Molecular epidemiology and characteristics of respiratory syncytial virus among hospitalized children in Guangzhou, China. Virol J 2023; 20:272. [PMID: 37993935 PMCID: PMC10666375 DOI: 10.1186/s12985-023-02227-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 11/03/2023] [Indexed: 11/24/2023] Open
Abstract
BACKGROUND Human respiratory syncytial virus (RSV) is a leading cause of acute lower respiratory tract infection and hospitalization, especially in children. Highly mutagenic nature and antigenic diversity enable the RSV to successfully survive in human population. We conducted a molecular epidemiological study during 2017-2021 to investigate the prevalence and genetic characteristics of RSV. METHODS A total of 6499 nasopharyngeal (NP) swabs were collected from hospitalized children at Department of Pediatrics, Guangdong Provincial Hospital of Traditional Chinese Medicine, Guangzhou, Guangdong, China. All NP swab specimens were preliminary screened for common respiratory viruses and then tested for RSV using specific PCR assays. Partial G genes of RSV were amplified for phylogenetic analysis and genetic characterization. RESULTS The overall detection rate for common respiratory viruses was 16.12% (1048/6499). Among those, 405 specimens (6.20%, 405/6499) were found positive for RSV. The monthly distribution of RSV and other respiratory viruses was variable, and the highest incidence was recorded in Autumn and Winter. Based on the sequencing of hypervariable region of G gene, 93 RSV sequences were sub-grouped into RSV-A (56, 60.2%) and RSV-B (37, 39.8%). There was no coinfection of RSV-A and RSV-B in the tested samples. Phylogenetic analysis revealed that RSV-A and RSV-B strains belonged to ON1 and BA9 genotypes respectively, indicating predominance of these genotypes in Guangzhou. Several substitutions were observed which may likely change the antigenicity and pathogenicity of RSV. Multiple glycosylation sites were noticed, demonstrating high selection pressure on these genotypes. CONCLUSION This study illustrated useful information about epidemiology, genetic characteristics, and circulating genotypes of RSV in Guangzhou China. Regular monitoring of the circulating strains of RSV in different parts of China could assist in the development of more effective vaccines and preventive measures.
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Affiliation(s)
- Sajid Umar
- Global Health Research Center, Duke Kunshan University, Kunshan, China
- Division of Natural and Applied Sciences (DNAS), Duke Kunshan University, Kunshan, China
| | - Rongyuan Yang
- Key Laboratory for Infectious Disease, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xinye Wang
- School of Biomedical Sciences, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Yuntao Liu
- Emergency Department, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Peifeng Ke
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, No. 111 Dade Road, Yuexiu District, Guangzhou, China.
| | - Sheng Qin
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, No. 111 Dade Road, Yuexiu District, Guangzhou, China.
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19
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Jallow MM, Diagne MM, Sagne SN, Tall F, Diouf JBN, Boiro D, Mendy MP, Ndiaye NK, Kiori D, Sy S, Goudiaby D, Loucoubar C, Fall G, Barry MA, Dia N. Respiratory syncytial virus in pediatric patients with severe acute respiratory infections in Senegal: findings from the 2022 sentinel surveillance season. Sci Rep 2023; 13:20404. [PMID: 37990112 PMCID: PMC10663443 DOI: 10.1038/s41598-023-47015-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 11/08/2023] [Indexed: 11/23/2023] Open
Abstract
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.
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Affiliation(s)
| | | | - Samba Niang Sagne
- Institut Pasteur de Dakar, Unité d'Epidémiologie Des Maladies Infectieuses, 36, Avenue Pasteur, B.P. 220, Dakar, Senegal
| | - Fatime Tall
- Hôpital Des Enfants Albert Royer de Fann, Dakar, Senegal
| | | | | | | | | | - Davy Kiori
- Département de Virologie, Institut Pasteur de Dakar, Dakar, Senegal
| | - Sara Sy
- Département de Virologie, Institut Pasteur de Dakar, Dakar, Senegal
| | - Déborah Goudiaby
- Département de Virologie, Institut Pasteur de Dakar, Dakar, Senegal
| | - Cheikh Loucoubar
- Institut Pasteur de Dakar, Unité d'Epidémiologie Des Maladies Infectieuses, 36, Avenue Pasteur, B.P. 220, Dakar, Senegal
| | - Gamou Fall
- Département de Virologie, Institut Pasteur de Dakar, Dakar, Senegal
| | - Mamadou Aliou Barry
- Institut Pasteur de Dakar, Unité d'Epidémiologie Des Maladies Infectieuses, 36, Avenue Pasteur, B.P. 220, Dakar, Senegal
| | - Ndongo Dia
- Département de Virologie, Institut Pasteur de Dakar, Dakar, Senegal.
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20
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Davina-Nunez C, Perez-Castro S, Cabrera-Alvargonzalez JJ, Montano-Barrientos J, Godoy-Diz M, Regueiro B. The Modification of the Illumina ® CovidSeq™ Workflow for RSV Genomic Surveillance: The Genetic Variability of RSV during the 2022-2023 Season in Northwest Spain. Int J Mol Sci 2023; 24:16055. [PMID: 38003246 PMCID: PMC10671726 DOI: 10.3390/ijms242216055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 10/27/2023] [Accepted: 11/02/2023] [Indexed: 11/26/2023] Open
Abstract
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.
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Affiliation(s)
- Carlos Davina-Nunez
- Microbiology and Infectology Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur), 36312 Vigo, Spain; (C.D.-N.); (J.J.C.-A.); (B.R.)
- Faculty of Biology, Universidade de Vigo, 36310 Vigo, Spain
| | - Sonia Perez-Castro
- Microbiology and Infectology Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur), 36312 Vigo, Spain; (C.D.-N.); (J.J.C.-A.); (B.R.)
- Microbiology Department, Complexo Hospitalario Universitario de Vigo (CHUVI), Servizo Galego de Saúde (SERGAS), 36214 Vigo, Spain; (J.M.-B.); (M.G.-D.)
| | - Jorge Julio Cabrera-Alvargonzalez
- Microbiology and Infectology Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur), 36312 Vigo, Spain; (C.D.-N.); (J.J.C.-A.); (B.R.)
- Microbiology Department, Complexo Hospitalario Universitario de Vigo (CHUVI), Servizo Galego de Saúde (SERGAS), 36214 Vigo, Spain; (J.M.-B.); (M.G.-D.)
| | - Jhon Montano-Barrientos
- Microbiology Department, Complexo Hospitalario Universitario de Vigo (CHUVI), Servizo Galego de Saúde (SERGAS), 36214 Vigo, Spain; (J.M.-B.); (M.G.-D.)
| | - Montse Godoy-Diz
- Microbiology Department, Complexo Hospitalario Universitario de Vigo (CHUVI), Servizo Galego de Saúde (SERGAS), 36214 Vigo, Spain; (J.M.-B.); (M.G.-D.)
| | - Benito Regueiro
- Microbiology and Infectology Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur), 36312 Vigo, Spain; (C.D.-N.); (J.J.C.-A.); (B.R.)
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21
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Pierangeli A, Piralla A, Uceda Renteria S, Giacomel G, Lunghi G, Pagani E, Giacobazzi E, Vian E, Biscaro V, Piccirilli G, Lazzarotto T, Menzo S, Ferreri ML, Novazzi F, Petrarca L, Licari A, Ferrari G, Oliveto G, Antonelli G, Binda S, Galli C, Pellegrinelli L, Pariani E, Baldanti F. Multicenter epidemiological investigation and genetic characterization of respiratory syncytial virus and metapneumovirus infections in the pre-pandemic 2018-2019 season in northern and central Italy. Clin Exp Med 2023; 23:2725-2737. [PMID: 36522554 PMCID: PMC9754777 DOI: 10.1007/s10238-022-00973-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022]
Abstract
Respiratory syncytial virus (RSV) and human metapneumovirus (HMPV) cause a high burden of disease, particularly in children and the elderly. With the aim to add knowledge on RSV and HMPV infections in Italy, a prospective, multicenter study was conducted by eight centers of the Working Group on Respiratory Virus Infections (GLIViRe), from December 2018-April 2019. Weekly distribution and patients' demographic and clinical data were compared in 1300 RSV and 222 HMPV-positive cases. Phylogenetic analysis of the G-glycoprotein coding region was performed to characterize circulating strains. RSV positivity ranged from 6.4% in outpatients of all ages to 31.7% in hospitalized children; HMPV positivity was 4-1.2% with no age-association. RSV season peaked in February and ended in mid-April: HMPV circulation was higher when RSV decreased in early spring. RSV was more frequent in infants, whereas HMPV infected comparatively more elderly adults; despite, their clinical course was similar. RSV-B cases were two-thirds of the total and had similar clinical severity compared to RSV-A. Phylogenetic analysis showed the circulation of RSV-A ON1 variants and the predominance of RSV-B genotype BA10. HMPV genotype A2c was the prevalent one and presented insertions of different lengths in G. This first multicenter Italian report on seasonality, age-specific distribution, and clinical presentation of RSV and HMPV demonstrated their substantial disease burden in young patients but also in the elderly. These data may provide the basis for a national respiratory virus surveillance network.
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Affiliation(s)
- Alessandra Pierangeli
- Virology Laboratory, Department of Molecular Medicine, Sapienza University of Rome, V.Le Porta Tiburtina, 28; 00185, Rome, Italy
| | - Antonio Piralla
- Microbiology and Virology Unit, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Sara Uceda Renteria
- Virology Unit, Clinical Laboratory, Foundation IRCCS Ca’ Granda Ospedale Maggiore, Milan, Italy
| | - Giovanni Giacomel
- Virology Unit, Clinical Laboratory, Foundation IRCCS Ca’ Granda Ospedale Maggiore, Milan, Italy
| | - Giovanna Lunghi
- Virology Unit, Clinical Laboratory, Foundation IRCCS Ca’ Granda Ospedale Maggiore, Milan, Italy
| | - Elisabetta Pagani
- Laboratorio Aziendale Di Microbiologia E Virologia, Hospital of Bolzano (SABES-ASDAA), Bolzano, Italy
| | - Elisabetta Giacobazzi
- Laboratorio Aziendale Di Microbiologia E Virologia, Hospital of Bolzano (SABES-ASDAA), Bolzano, Italy
| | - Elisa Vian
- Microbiology Unit, Hospital of Treviso (AULSS2), Treviso, Italy
| | - Valeria Biscaro
- Microbiology Unit, Hospital of Treviso (AULSS2), Treviso, Italy
| | - Giulia Piccirilli
- Microbiology Unit, IRCCS Azienda Ospedaliero-Universitaria, Bologna, Italy
| | - Tiziana Lazzarotto
- Section of Microbiology, Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
| | - Stefano Menzo
- Department of Biomedical Sciences and Public Health, Università Politecnica Delle Marche, Ancona, Italy
| | - Monica Lucia Ferreri
- Virology Laboratory, Azienda Ospedaliera Ospedali Riuniti Di Ancona, Ancona, Italy
| | - Federica Novazzi
- Ospedale Di Circolo E Fondazione Macchi, ASST Sette Laghi, Varese, Italy
| | - Laura Petrarca
- Department of Maternal Infantile and Urological Sciences, Sapienza University of Rome, Rome, Italy
| | - Amelia Licari
- Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, Pavia, Italy
| | - Guglielmo Ferrari
- Microbiology and Virology Unit, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Giuseppe Oliveto
- Virology Laboratory, Department of Molecular Medicine, Sapienza University of Rome, V.Le Porta Tiburtina, 28; 00185, Rome, Italy
| | - Guido Antonelli
- Virology Laboratory, Department of Molecular Medicine, Sapienza University of Rome, V.Le Porta Tiburtina, 28; 00185, Rome, Italy
| | - Sandro Binda
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Cristina Galli
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Laura Pellegrinelli
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Elena Pariani
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Fausto Baldanti
- Microbiology and Virology Unit, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
- Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, Pavia, Italy
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22
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Bimouhen A, Regragui Z, El Falaki F, Ihazmade H, Benkerroum S, Barakat A, Rguig A, Benamar T, Triki S, Bakri Y, Oumzil H. Circulation patterns and molecular epidemiology of human respiratory syncytial virus over five consecutive seasons in Morocco. Influenza Other Respir Viruses 2023; 17:e13203. [PMID: 37859975 PMCID: PMC10582604 DOI: 10.1111/irv.13203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 09/05/2023] [Accepted: 09/10/2023] [Indexed: 10/21/2023] Open
Abstract
Background Respiratory syncytial virus (HRSV) is the leading cause of respiratory tract infections in infants and young children. we investigated the prevalence and characteristics of HRSV in Morocco and explored trends in circulating genotypes through partial G gene analysis of HRSV strains prevalent from 2012 to 2017. Methods Respiratory samples were gathered from both outpatients and inpatients meeting ILI or SARI case definitions. The patients' ages varied from 1 month to 99 years old. Nucleic acids were extracted and HRSV type/subtype was detected by RT-qPCR. A subset of positive samples was randomly selected in each epidemic year, the complete viral genome was sequenced, phylogenetic analysis was performed using the MEGA7 program and the genotypes were confirmed. Results The 3679 specimens were collected from 2012 to 2017, of which 726 (19.7%) were positive for HRSV. The 35% (257/726) of HRSV-positives were of the HRSV-A subtype, while the HRSV-B subtype accounted for 61% (442/726). The co-infection rate was 3.7% (27/726). The virus circulates in a periodic pattern, where epidemics occur during the fall months through early spring. HRSV genotype was confirmed in 127 specimens (56 HRSV-A and 71 HRSV-B). Based on phylogenetic analysis, all HRSV-A were ON1 genotype, and HRSV-B were mostly BA9 genotype. HRSV-B belonging to the BA10 genotype was detected in 2012 exclusively. Conclusions BA9, BA10, and ON1 were the only HRSV genotypes detected between 2012 and 2017. Variations in the G gene amino acid chain were identified in local strains, which suggests an increased need for continuous genomic surveillance.
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Affiliation(s)
- Abderrahman Bimouhen
- Laboratory of Human Pathologies Biology, Faculty of SciencesMohammed V University in RabatRabatMorocco
- National Influenza Center, Virology DepartmentNational Institute of Hygiene, Ministry of HealthRabatMorocco
| | - Zakia Regragui
- National Influenza Center, Virology DepartmentNational Institute of Hygiene, Ministry of HealthRabatMorocco
| | - Fatima El Falaki
- National Influenza Center, Virology DepartmentNational Institute of Hygiene, Ministry of HealthRabatMorocco
| | - Hassan Ihazmade
- National Influenza Center, Virology DepartmentNational Institute of Hygiene, Ministry of HealthRabatMorocco
| | - Samira Benkerroum
- National Influenza Center, Virology DepartmentNational Institute of Hygiene, Ministry of HealthRabatMorocco
| | - Amal Barakat
- World Health Organization Regional Office for the Eastern MediterraneanCairoEgypt
| | - Ahmed Rguig
- Directorate of Epidemiology and Disease ControlMinistry of HealthRabatMorocco
| | - Touria Benamar
- Directorate of Epidemiology and Disease ControlMinistry of HealthRabatMorocco
| | - Soumia Triki
- World Health Organization Country Office of MoroccoRabatMorocco
| | - Youssef Bakri
- Laboratory of Human Pathologies Biology, Faculty of SciencesMohammed V University in RabatRabatMorocco
- Center of human pathologies genomic, faculty of Medicine and PharmacyMohammed V university in RabatRabatMorocco
| | - Hicham Oumzil
- National Influenza Center, Virology DepartmentNational Institute of Hygiene, Ministry of HealthRabatMorocco
- Pedagogy and Research Unit of Microbiology, School of Medicine and PharmacyMohammed V University in RabatRabatMorocco
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23
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Pierangeli A, Nenna R, Fracella M, Scagnolari C, Oliveto G, Sorrentino L, Frasca F, Conti MG, Petrarca L, Papoff P, Turriziani O, Antonelli G, Stefanelli P, Palamara AT, Midulla F. Genetic diversity and its impact on disease severity in respiratory syncytial virus subtype-A and -B bronchiolitis before and after pandemic restrictions in Rome. J Infect 2023; 87:305-314. [PMID: 37495189 DOI: 10.1016/j.jinf.2023.07.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 07/07/2023] [Accepted: 07/18/2023] [Indexed: 07/28/2023]
Abstract
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.
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Affiliation(s)
- A Pierangeli
- Virology Laboratory, Department of Molecular Medicine, Sapienza University, V.le Porta Tiburtina, 28, 00185 Rome, Italy.
| | - R Nenna
- Department of Pediatrics and Infantile Neuropsychiatry, Sapienza University, V.le Regina Elena, 299, 00161 Rome, Italy.
| | - M Fracella
- Virology Laboratory, Department of Molecular Medicine, Sapienza University, V.le Porta Tiburtina, 28, 00185 Rome, Italy.
| | - C Scagnolari
- Virology Laboratory, Department of Molecular Medicine, Sapienza University, V.le Porta Tiburtina, 28, 00185 Rome, Italy.
| | - G Oliveto
- Virology Laboratory, Department of Molecular Medicine, Sapienza University, V.le Porta Tiburtina, 28, 00185 Rome, Italy.
| | - L Sorrentino
- Virology Laboratory, Department of Molecular Medicine, Sapienza University, V.le Porta Tiburtina, 28, 00185 Rome, Italy.
| | - F Frasca
- Virology Laboratory, Department of Molecular Medicine, Sapienza University, V.le Porta Tiburtina, 28, 00185 Rome, Italy.
| | - M G Conti
- Department of Pediatrics and Infantile Neuropsychiatry, Sapienza University, V.le Regina Elena, 299, 00161 Rome, Italy.
| | - L Petrarca
- Department of Pediatrics and Infantile Neuropsychiatry, Sapienza University, V.le Regina Elena, 299, 00161 Rome, Italy.
| | - P Papoff
- Department of Pediatrics and Infantile Neuropsychiatry, Sapienza University, V.le Regina Elena, 299, 00161 Rome, Italy.
| | - O Turriziani
- Virology Laboratory, Department of Molecular Medicine, Sapienza University, V.le Porta Tiburtina, 28, 00185 Rome, Italy.
| | - G Antonelli
- Virology Laboratory, Department of Molecular Medicine, Sapienza University, V.le Porta Tiburtina, 28, 00185 Rome, Italy.
| | - P Stefanelli
- Department of Infectious Diseases, Istituto Superiore di Sanità, V.le Regina Elena, 299, 00161 Rome, Italy.
| | - A T Palamara
- Department of Infectious Diseases, Istituto Superiore di Sanità, V.le Regina Elena, 299, 00161 Rome, Italy.
| | - F Midulla
- Department of Pediatrics and Infantile Neuropsychiatry, Sapienza University, V.le Regina Elena, 299, 00161 Rome, Italy.
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24
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Malasao R, Chaiut W, Tantipetcharawan W, Tongphung R, Charoensri N, Takarn P, Sudjaritruk T, Maneekarn N. Predominance of ON1 and BA9 genotypes of human respiratory syncytial virus in children with acute respiratory infection in Chiang Mai, Thailand, 2020-2021. J Infect Public Health 2023; 16:1418-1426. [PMID: 37482015 DOI: 10.1016/j.jiph.2023.07.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 07/06/2023] [Accepted: 07/17/2023] [Indexed: 07/25/2023] Open
Abstract
BACKGROUND Human respiratory syncytial virus (hRSV) is an important cause of acute respiratory infection, especially in children. Few studies have investigated molecular epidemiology of hRSV infection in Thailand. The aims of this study were to investigate the prevalence and genotype diversity of hRSV in children with acute respiratory infection (ARI) in Thailand. METHODS A total of 383 nasopharyngeal swabs collected from children with ARI from October 2020 to September 2021 were screened for hRSV and nucleotide sequences of the hypervariable region 2 (HVR2) of G gene of the detected hRSV were analysed. RESULTS Of 383 nasopharyngeal swabs, 104 (27.2 %) were positive for hRSV, of which 51 (49.0 %), 43 (41.3 %), and 10 (9.6 %) were hRSV-A, hRSV-B, and untypeable strains, respectively. All hRSV-A and hRSV-B were ON1 genotype and BA9 genotype, respectively. Most of the hRSV strains were detected in the cool months, November 2020 to February 2021. Phylogenetic analysis of the HVR2 sequence of G gene revealed three clusters of hRSV-A (ON1 genotype) and two clusters of hRSV-B (BA9 genotype). The hRSV-A strains in cluster 1 and 3 were closely related to the hRSV-A reference strains reported previously from other regions of Thailand whereas those in cluster 2 were closely related to the hRSV-A reference strains reported previously from Europe and Africa. For the hRSV-B strains, both clusters 1 and 2 were closely related to the hRSV-B reference strains reported previously from Europe, Australia, and Taiwan. The predicted N- and O-linked glycosylation sites were found along the length of HVR2 of G protein, mostly in the hRSV-B strains. CONCLUSIONS The ON1 and BA9 were the only two hRSV genotypes that were co-predominant and solely detected in this study. The findings indicated that the ON1 and BA9 are the only two hRSV genotypes currently circulating in children with ARI in northern Thailand.
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Affiliation(s)
- Rungnapa Malasao
- Department of Community Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Wilawan Chaiut
- Department of Community Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand; School of Integrative Medicine, Mae Fah Luang University, Chiang Rai 57100, Thailand
| | - Wanwisa Tantipetcharawan
- Microbiology unit, Diagnostic laboratory, Maharaj Nakorn Chiang Mai Hospital, Chiang Mai 50200, Thailand
| | - Ratchanu Tongphung
- Microbiology unit, Diagnostic laboratory, Maharaj Nakorn Chiang Mai Hospital, Chiang Mai 50200, Thailand
| | - Nicha Charoensri
- Centre for Research and Development of Medical Diagnostic Laboratories (CMDL), Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Piyawan Takarn
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Tavitiya Sudjaritruk
- Division of Infectious Diseases, Department of Pediatrics, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Niwat Maneekarn
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand.
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25
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Shishir TA, Saha O, Rajia S, Mondol SM, Masum MHU, Rahaman MM, Hossen F, Bahadur NM, Ahmed F, Naser IB, Amin MR. Genome-wide study of globally distributed respiratory syncytial virus (RSV) strains implicates diversification utilizing phylodynamics and mutational analysis. Sci Rep 2023; 13:13531. [PMID: 37598270 PMCID: PMC10439963 DOI: 10.1038/s41598-023-40760-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 08/16/2023] [Indexed: 08/21/2023] Open
Abstract
Respiratory syncytial virus (RSV) is a common respiratory pathogen that causes mild cold-like symptoms and severe lower respiratory tract infections, causing hospitalizations in children, the elderly and immunocompromised individuals. Due to genetic variability, this virus causes life-threatening pneumonia and bronchiolitis in young infants. Thus, we examined 3600 whole genome sequences submitted to GISAID by 31 December 2022 to examine the genetic variability of RSV. While RSVA and RSVB coexist throughout RSV seasons, RSVA is more prevalent, fatal, and epidemic-prone in several countries, including the United States, the United Kingdom, Australia, and China. Additionally, the virus's attachment glycoprotein and fusion protein were highly mutated, with RSVA having higher Shannon entropy than RSVB. The genetic makeup of these viruses contributes significantly to their prevalence and epidemic potential. Several strain-specific SNPs co-occurred with specific haplotypes of RSVA and RSVB, followed by different haplotypes of the viruses. RSVA and RSVB have the highest linkage probability at loci T12844A/T3483C and G13959T/C2198T, respectively. The results indicate that specific haplotypes and SNPs may significantly affect their spread. Overall, this analysis presents a promising strategy for tracking the evolving epidemic situation and genetic variants of RSV, which could aid in developing effective control, prophylactic, and treatment strategies.
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Affiliation(s)
- Tushar Ahmed Shishir
- Department of Mathematics and Natural Sciences, BRAC University, Dhaka, Bangladesh
| | - Otun Saha
- Department of Microbiology, Noakhali Science and Technology University, Noakhali, Bangladesh.
| | - Sultana Rajia
- Department of Microbiology, Noakhali Science and Technology University, Noakhali, Bangladesh
| | | | - Md Habib Ullah Masum
- Department of Microbiology, Noakhali Science and Technology University, Noakhali, Bangladesh
| | | | - Foysal Hossen
- Department of Microbiology, Noakhali Science and Technology University, Noakhali, Bangladesh
| | | | - Firoz Ahmed
- Department of Microbiology, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Iftekhar Bin Naser
- Department of Mathematics and Natural Sciences, BRAC University, Dhaka, Bangladesh
| | - Mohammad Ruhul Amin
- Department of Microbiology, Noakhali Science and Technology University, Noakhali, Bangladesh.
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26
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Ono T, Hashimoto K, Kume Y, Chishiki M, Okabe H, Sato M, Norito S, Aso J, Sada M, Mochizuki I, Mashiyama F, Ishibashi N, Suzuki S, Sakuma H, Suwa R, Kawase M, Takeda M, Shirato K, Kimura H, Hosoya M. Molecular Diversity of Human Respiratory Syncytial Virus before and during the COVID-19 Pandemic in Two Neighboring Japanese Cities. Microbiol Spectr 2023; 11:e0260622. [PMID: 37409937 PMCID: PMC10433803 DOI: 10.1128/spectrum.02606-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 06/20/2023] [Indexed: 07/07/2023] Open
Abstract
Human respiratory syncytial viruses (HRSVs) are divided into subgroups A and B, which are further divided based on the nucleotide sequence of the second hypervariable region (HVR) of the attachment glycoprotein (G) gene. Understanding the molecular diversity of HRSV before and during the coronavirus disease 2019 (COVID-19) pandemic can provide insights into the effects of the pandemic on HRSV dissemination and guide vaccine development. Here, we analyzed HRSVs isolated in Fukushima Prefecture from September 2017 to December 2021. Specimens from pediatric patients were collected at two medical institutions in neighboring cities. A phylogenetic tree based on the second HVR nucleotide sequences was constructed using the Bayesian Markov chain Monte Carlo method. HRSV-A (ON1 genotype) and HRSV-B (BA9 genotype) were detected in 183 and 108 specimens, respectively. There were differences in the number of HRSV strains within clusters prevalent at the same time between the two hospitals. The genetic characteristics of HRSVs in 2021 after the COVID-19 outbreak were similar to those in 2019. HRSVs within a cluster may circulate within a region for several years, causing an epidemic cycle. Our findings add to the existing knowledge of the molecular epidemiology of HRSV in Japan. IMPORTANCE Understanding the molecular diversity of human respiratory syncytial viruses during pandemics caused by different viruses can provide insights that can guide public health decisions and vaccine development.
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Affiliation(s)
- Takashi Ono
- Department of Pediatrics, Fukushima Medical University, Fukushima, Fukushima, Japan
| | - Koichi Hashimoto
- Department of Pediatrics, Fukushima Medical University, Fukushima, Fukushima, Japan
| | - Yohei Kume
- Department of Pediatrics, Fukushima Medical University, Fukushima, Fukushima, Japan
| | - Mina Chishiki
- Department of Pediatrics, Fukushima Medical University, Fukushima, Fukushima, Japan
| | - Hisao Okabe
- Department of Pediatrics, Fukushima Medical University, Fukushima, Fukushima, Japan
| | - Masatoki Sato
- Department of Pediatrics, Fukushima Medical University, Fukushima, Fukushima, Japan
| | - Sakurako Norito
- Department of Pediatrics, Fukushima Medical University, Fukushima, Fukushima, Japan
| | - Jumpei Aso
- Department of Respiratory Medicine, Kyorin University School of Medicine, Tokyo, Japan
| | - Mitsuru Sada
- Department of Respiratory Medicine, Kyorin University School of Medicine, Tokyo, Japan
| | - Izumi Mochizuki
- Department of Pediatrics, Ohara General Hospital, Fukushima, Fukushima, Japan
| | - Fumi Mashiyama
- Department of Pediatrics, Hoshi General Hospital, Koriyama, Fukushima, Japan
| | - Naohisa Ishibashi
- Department of Pediatrics, Ohara General Hospital, Fukushima, Fukushima, Japan
| | - Shigeo Suzuki
- Department of Pediatrics, Ohara General Hospital, Fukushima, Fukushima, Japan
| | - Hiroko Sakuma
- Department of Pediatrics, Hoshi General Hospital, Koriyama, Fukushima, Japan
| | - Reiko Suwa
- Department of Virology 3, National Institute of Infectious Diseases, Tokyo, Japan
| | - Miyuki Kawase
- Department of Virology 3, National Institute of Infectious Diseases, Tokyo, Japan
| | - Makoto Takeda
- Department of Microbiology, Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kazuya Shirato
- Department of Virology 3, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hirokazu Kimura
- Gunma Paz University, Graduate School of Health Sciences, Takasaki, Gunma, Japan
| | - Mitsuaki Hosoya
- Department of Pediatrics, Fukushima Medical University, Fukushima, Fukushima, Japan
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27
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Lara-Hernandez I, Muñoz-Escalante JC, Bernal-Silva S, Noyola DE, Wong-Chew RM, Comas-García A, Comas-Garcia M. Ultrastructural and Functional Characterization of Mitochondrial Dynamics Induced by Human Respiratory Syncytial Virus Infection in HEp-2 Cells. Viruses 2023; 15:1518. [PMID: 37515204 PMCID: PMC10386036 DOI: 10.3390/v15071518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 06/27/2023] [Accepted: 07/05/2023] [Indexed: 07/30/2023] Open
Abstract
Human respiratory syncytial virus (hRSV) is the leading cause of acute lower respiratory tract infections in children under five years of age and older adults worldwide. During hRSV infection, host cells undergo changes in endomembrane organelles, including mitochondria. This organelle is responsible for energy production in the cell and plays an important role in the antiviral response. The present study focuses on characterizing the ultrastructural and functional changes during hRSV infection using thin-section transmission electron microscopy and RT-qPCR. Here we report that hRSV infection alters mitochondrial morphodynamics by regulating the expression of key genes in the antiviral response process, such as Mfn1, VDAC2, and PINK1. Our results suggest that hRSV alters mitochondrial morphology during infection, producing a mitochondrial phenotype with shortened cristae, swollen matrix, and damaged membrane. We also observed that hRSV infection modulates the expression of the aforementioned genes, possibly as an evasion mechanism in the face of cellular antiviral response. Taken together, these results advance our knowledge of the ultrastructural alterations associated with hRSV infection and might guide future therapeutic efforts to develop effective antiviral drugs for hRSV treatment.
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Affiliation(s)
- Ignacio Lara-Hernandez
- High-Resolution Microscopy Section, Center for Research in Health Sciences and Biomedicine, Autonomous University of San Luis Potosí, San Luis Potosí 78210, Mexico
| | - Juan Carlos Muñoz-Escalante
- Center for Research in Health Sciences and Biomedicine, Autonomous University of San Luis Potosí, San Luis Potosí 78210, Mexico
- Department of Microbiology, School of Medicine, Autonomous University of San Luis Potosí, San Luis Potosí 78210, Mexico
| | - Sofía Bernal-Silva
- Department of Microbiology, School of Medicine, Autonomous University of San Luis Potosí, San Luis Potosí 78210, Mexico
- Genomic Medicine Section, Center for Research in Health Sciences and Biomedicine, Autonomous University of San Luis Potosí, San Luis Potosí 78210, Mexico
| | - Daniel E Noyola
- Center for Research in Health Sciences and Biomedicine, Autonomous University of San Luis Potosí, San Luis Potosí 78210, Mexico
- Department of Microbiology, School of Medicine, Autonomous University of San Luis Potosí, San Luis Potosí 78210, Mexico
| | - Rosa María Wong-Chew
- Research Division, School of Medicine, National Autonomous University of Mexico, Mexico City 04360, Mexico
| | - Andreu Comas-García
- Department of Microbiology, School of Medicine, Autonomous University of San Luis Potosí, San Luis Potosí 78210, Mexico
| | - Mauricio Comas-Garcia
- High-Resolution Microscopy Section, Center for Research in Health Sciences and Biomedicine, Autonomous University of San Luis Potosí, San Luis Potosí 78210, Mexico
- Science Department, Autonomous University of San Luis Potosí, San Luis Potosí 78210, Mexico
- Molecular and Translation Medicine Section, Center for Research in Health Sciences and Biomedicine, Autonomous University of San Luis Potosí, San Luis Potosí 78210, Mexico
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28
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Virant MJ, Luštrek M, Kogoj R, Petrovec M, Uršič T. Changes in HRSV Epidemiology but Not Circulating Variants in Hospitalized Children due to the Emergence of SARS-CoV-2. Viruses 2023; 15:1218. [PMID: 37376518 DOI: 10.3390/v15061218] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/17/2023] [Accepted: 05/21/2023] [Indexed: 06/29/2023] Open
Abstract
This study assesses the circulation of human respiratory syncytial virus (HRSV) genotypes before, during, and toward the end of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic in children and determines the influence of the pandemic on HRSV circulation patterns and evolution. Phylogenetic analysis of the hypervariable glycoprotein G gene was performed on 221/261 (84.7%) HRSV-positive samples and shows two separated clusters, one belonging to HRSV-A (129/221) and another to HRSV-B (92/221). All Slovenian HRSV-A strains contained the 72-nucleotide-long duplicated region in the attachment glycoprotein G gene and were classified as lineage GA2.3.5. All Slovenian HRSV-B strains similarly contained a 60-nucleotide-long duplicated region in the attachment glycoprotein G gene and were classified as lineage GB5.0.5a. During the 3-year period (2018-2021) covered by the study, no significant differences were observed within strains detected before the SARS-CoV-2 pandemic, during it, and after the implementation of nonpharmaceutical preventive measures. Slovenian HRSV-A strains seem to be more diverse than HRSV-B strains. Therefore, further whole-genome investigations would be required for better monitoring of the long-term impact of SARS-CoV-2 endemic circulation and the formation of new HRSV lineages and epidemiological patterns.
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Affiliation(s)
- Monika Jevšnik Virant
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška 4, 1000 Ljubljana, Slovenia
| | - Manca Luštrek
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška 4, 1000 Ljubljana, Slovenia
| | - Rok Kogoj
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška 4, 1000 Ljubljana, Slovenia
| | - Miroslav Petrovec
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška 4, 1000 Ljubljana, Slovenia
| | - Tina Uršič
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška 4, 1000 Ljubljana, Slovenia
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29
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Kim HN, Hwang J, Yoon SY, Lim CS, Cho Y, Lee CK, Nam MH. Molecular characterization of human respiratory syncytial virus in Seoul, South Korea, during 10 consecutive years, 2010-2019. PLoS One 2023; 18:e0283873. [PMID: 37023101 PMCID: PMC10079039 DOI: 10.1371/journal.pone.0283873] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Accepted: 03/19/2023] [Indexed: 04/07/2023] Open
Abstract
Respiratory syncytial virus (RSV) is the leading cause of lower respiratory tract infections and hospitalization in infants and young children. Here, we analyzed the genetic diversity of RSV using partial G gene sequences in 84 RSV-A and 78 RSV- B positive samples collected in Seoul, South Korea, for 10 consecutive years, from 2010 to 2019. Our phylogenetic analysis revealed that RSV-A strains were classified into either the ON1 (80.9%) or NA1 (19.0%) genotypes. On the other hand, RSV-B strains demonstrated diversified clusters within the BA genotype. Notably, some sequences designated as BA-SE, BA-SE1, and BA-DIS did not cluster with previously identified BA genotypes in the phylogenetic trees. Despite this, they did not meet the criteria for the assignment of a new genotype based on recent classification methods. Selection pressure analysis identified three positive selection sites (amino acid positions 273, 274, and 298) in RSV-A, and one possible positive selection site (amino acid position 296) in RSV-B, respectively. The mean evolutionary rates of Korean RSV-A from 1999 to 2019 and RSV-B strains from 1991 and 2019 were estimated at 3.51 × 10-3 nucleotides (nt) substitutions/site/year and 3.32 × 10-3 nt substitutions/site/year, respectively. The population dynamics in the Bayesian skyline plot revealed fluctuations corresponding to the emergence of dominant strains, including a switch of the dominant genotype from NA1 to ON1. Our study on time-scaled cumulative evolutionary analysis contributes to a better understanding of RSV epidemiology at the local level in South Korea.
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Affiliation(s)
- Ha Nui Kim
- Department of Laboratory Medicine, Korea University College of Medicine, Seoul, Korea
| | - Jinha Hwang
- Department of Laboratory Medicine, Korea University College of Medicine, Seoul, Korea
| | - Soo-Young Yoon
- Department of Laboratory Medicine, Korea University College of Medicine, Seoul, Korea
| | - Chae Seung Lim
- Department of Laboratory Medicine, Korea University College of Medicine, Seoul, Korea
| | - Yunjung Cho
- Department of Laboratory Medicine, Korea University College of Medicine, Seoul, Korea
| | - Chang-Kyu Lee
- Department of Laboratory Medicine, Korea University College of Medicine, Seoul, Korea
| | - Myung-Hyun Nam
- Department of Laboratory Medicine, Korea University College of Medicine, Seoul, Korea
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30
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Che Y, Gribenko AV, Song X, Handke LD, Efferen KS, Tompkins K, Kodali S, Nunez L, Prasad AK, Phelan LM, Ammirati M, Yu X, Lees JA, Chen W, Martinez L, Roopchand V, Han S, Qiu X, DeVincenzo JP, Jansen KU, Dormitzer PR, Swanson KA. Rational Design of a Highly Immunogenic Prefusion-Stabilized F Glycoprotein Antigen for a Respiratory Syncytial Virus Vaccine. Sci Transl Med 2023; 15:eade6422. [PMID: 37023209 DOI: 10.1126/scitranslmed.ade6422] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
Abstract
Respiratory syncytial virus (RSV) is the leading, global cause of serious respiratory disease in infants and is an important cause of respiratory illness in older adults. No RSV vaccine is currently available. The RSV fusion (F) glycoprotein is a key antigen for vaccine development, and its prefusion conformation is the target of the most potent neutralizing antibodies. Here, we describe a computational and experimental strategy for designing immunogens that enhance the conformational stability and immunogenicity of RSV prefusion F. We obtained an optimized vaccine antigen after screening nearly 400 engineered F constructs. Through in vitro and in vivo characterization studies, we identified F constructs that are more stable in the prefusion conformation and elicit ~10-fold higher serum neutralizing titers in cotton rats than DS-Cav1. The stabilizing mutations of the lead construct (847) were introduced onto F glycoprotein backbones of strains representing the dominant circulating genotypes of the two major RSV subgroups, A and B. Immunization of cotton rats with a bivalent vaccine formulation of these antigens conferred complete protection against RSV challenge, with no evidence of disease enhancement. The resulting bivalent RSV prefusion F investigational vaccine has recently been shown to be efficacious against RSV disease in two pivotal phase 3 efficacy trials, one for passive protection of infants by immunization of pregnant women and the second for active protection of older adults by direct immunization.
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Affiliation(s)
- Ye Che
- Discovery Sciences, Pfizer Inc; Groton, CT 06340, USA
| | - Alexey V Gribenko
- Vaccine Research and Development, Pfizer Inc; Pearl River, NY 10965, USA
| | - Xi Song
- Discovery Sciences, Pfizer Inc; Groton, CT 06340, USA
| | - Luke D Handke
- Vaccine Research and Development, Pfizer Inc; Pearl River, NY 10965, USA
| | - Kari S Efferen
- Vaccine Research and Development, Pfizer Inc; Pearl River, NY 10965, USA
| | - Kristin Tompkins
- Vaccine Research and Development, Pfizer Inc; Pearl River, NY 10965, USA
| | - Srinivas Kodali
- Vaccine Research and Development, Pfizer Inc; Pearl River, NY 10965, USA
| | - Lorna Nunez
- Vaccine Research and Development, Pfizer Inc; Pearl River, NY 10965, USA
| | - A Krishna Prasad
- Vaccine Research and Development, Pfizer Inc; Pearl River, NY 10965, USA
| | - Lynn M Phelan
- Vaccine Research and Development, Pfizer Inc; Pearl River, NY 10965, USA
| | - Mark Ammirati
- Discovery Sciences, Pfizer Inc; Groton, CT 06340, USA
| | - Xiaodi Yu
- Discovery Sciences, Pfizer Inc; Groton, CT 06340, USA
| | - Joshua A Lees
- Discovery Sciences, Pfizer Inc; Groton, CT 06340, USA
| | - Wei Chen
- Vaccine Research and Development, Pfizer Inc; Pearl River, NY 10965, USA
| | - Lyndsey Martinez
- Vaccine Research and Development, Pfizer Inc; Pearl River, NY 10965, USA
| | - Vidia Roopchand
- Vaccine Research and Development, Pfizer Inc; Pearl River, NY 10965, USA
| | - Seungil Han
- Discovery Sciences, Pfizer Inc; Groton, CT 06340, USA
| | - Xiayang Qiu
- Discovery Sciences, Pfizer Inc; Groton, CT 06340, USA
| | - John P DeVincenzo
- Children's Foundation Research Institute at Le Bonheur Children's Hospital; Memphis, TN 38103, USA
| | - Kathrin U Jansen
- Vaccine Research and Development, Pfizer Inc; Pearl River, NY 10965, USA
| | - Philip R Dormitzer
- Vaccine Research and Development, Pfizer Inc; Pearl River, NY 10965, USA
| | - Kena A Swanson
- Vaccine Research and Development, Pfizer Inc; Pearl River, NY 10965, USA
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Hönemann M, Thiem S, Bergs S, Berthold T, Propach C, Siekmeyer M, Frille A, Wallborn T, Maier M, Pietsch C. In-Depth Analysis of the Re-Emergence of Respiratory Syncytial Virus at a Tertiary Care Hospital in Germany in the Summer of 2021 after the Alleviation of Non-Pharmaceutical Interventions Due to the SARS-CoV-2 Pandemic. Viruses 2023; 15:v15040877. [PMID: 37112857 PMCID: PMC10144477 DOI: 10.3390/v15040877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 03/24/2023] [Accepted: 03/28/2023] [Indexed: 04/29/2023] Open
Abstract
Following the extensive non-pharmaceutical interventions (NPIs) and behavioral changes in the wake of the SARS-CoV-2 pandemic, an interseasonal rise in respiratory syncytial virus (RSV) cases was observed in Germany in 2021. The aim of this study was to characterize the local molecular epidemiology of RSV infections in comparison to the three pre-pandemic seasons. Additionally, clinical data were retrieved from patient charts to determine the clinical significance of RSV infections. RSV detections peaked in calendar week 40 of 2021, 18 weeks earlier than the usual peak observed in the three pre-pandemic seasons. Sequence analysis revealed a close phylogenetic relatedness regardless of the season of origin. A significantly higher amount of pediatric cases (88.9% of all cases, p < 0.001) was observed for season 2021/2022. For the pediatric cases, significant differences were observed for an increased number of siblings in the household (p = 0.004), a lower rate of fever (p = 0.007), and a reduced amount of co-infections (p = 0.001). Although the mean age of the adult patients was significantly younger (47.1 vs. 64.7, p < 0.001), high rates of comorbidities, lower respiratory tract infections and intensive care unit admissions prevailed. The NPIs in the wake of the SARS-CoV-2 pandemic had a tremendous impact on the epidemiologic characteristics and seasonality of RSV and warrant further epidemiologic studies of this important pathogen.
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Affiliation(s)
- Mario Hönemann
- Virology Department, Institute of Medical Microbiology and Virology, University of Leipzig, Johannisallee 30, 04103 Leipzig, Germany
| | - Stephanie Thiem
- Virology Department, Institute of Medical Microbiology and Virology, University of Leipzig, Johannisallee 30, 04103 Leipzig, Germany
| | - Sandra Bergs
- Virology Department, Institute of Medical Microbiology and Virology, University of Leipzig, Johannisallee 30, 04103 Leipzig, Germany
| | - Tom Berthold
- Virology Department, Institute of Medical Microbiology and Virology, University of Leipzig, Johannisallee 30, 04103 Leipzig, Germany
| | - Christian Propach
- Virology Department, Institute of Medical Microbiology and Virology, University of Leipzig, Johannisallee 30, 04103 Leipzig, Germany
| | - Manuela Siekmeyer
- Department of Pediatrics, University of Leipzig, Liebigstrasse 20a, 04103 Leipzig, Germany
| | - Armin Frille
- Department of Respiratory Medicine, University of Leipzig, Liebigstrasse 20, 04103 Leipzig, Germany
| | - Tillmann Wallborn
- Department of Pediatrics, Klinikum St. Georg, Delitzscher Strasse 141, 04129 Leipzig, Germany
| | - Melanie Maier
- Virology Department, Institute of Medical Microbiology and Virology, University of Leipzig, Johannisallee 30, 04103 Leipzig, Germany
| | - Corinna Pietsch
- Virology Department, Institute of Medical Microbiology and Virology, University of Leipzig, Johannisallee 30, 04103 Leipzig, Germany
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da Costa VG, Gomes AJC, Bittar C, Geraldini DB, Previdelli da Conceição PJ, Cabral ÁS, Carvalho T, Biselli JM, Provazzi PJS, Campos GRF, Sanches PRDS, Costa PI, Nogueira ML, Araujo JP, Spilki FR, Calmon MF, Rahal P. Burden of Influenza and Respiratory Syncytial Viruses in Suspected COVID-19 Patients: A Cross-Sectional and Meta-Analysis Study. Viruses 2023; 15:665. [PMID: 36992374 PMCID: PMC10055802 DOI: 10.3390/v15030665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/11/2023] [Accepted: 02/27/2023] [Indexed: 03/06/2023] Open
Abstract
Non-SARS-CoV-2 respiratory viral infections, such as influenza virus (FluV) and human respiratory syncytial virus (RSV), have contributed considerably to the burden of infectious diseases in the non-COVID-19 era. While the rates of co-infection in SARS-CoV-2-positive group (SCPG) patients have been determined, the burden of other respiratory viruses in the SARS-CoV-2-negative group (SCNG) remains unclear. Here, we conducted a cross-sectional study (São José do Rio Preto county, Brazil), and we collected our data using a meta-analysis to evaluate the pooled prevalence of FluV and RSV among SCNG patients. Out of the 901 patients suspected of COVID-19, our molecular results showed positivity of FluV and RSV in the SCNG was 2% (15/733) and 0.27% (2/733), respectively. Co-infection with SARS-CoV-2 and FluV, or RSV, was identified in 1.7% of the patients (3/168). Following our meta-analysis, 28 studies were selected (n = 114,318 suspected COVID-19 patients), with a pooled prevalence of 4% (95% CI: 3-6) for FluV and 2% (95% CI: 1-3) for RSV among SCNG patients were observed. Interestingly, FluV positivity in the SCNG was four times higher (OR = 4, 95% CI: 3.6-5.4, p < 0.01) than in the SCPG. Similarly, RSV positivity was significantly associated with SCNG patients (OR = 2.9, 95% CI: 2-4, p < 0.01). For subgroup analysis, cold-like symptoms, including fever, cough, sore throat, headache, myalgia, diarrhea, and nausea/vomiting, were positively associated (p < 0.05) with the SCPG. In conclusion, these results show that the pooled prevalence of FluV and RSV were significantly higher in the SCNG than in the SCPG during the early phase of the COVID-19 pandemic.
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Affiliation(s)
- Vivaldo Gomes da Costa
- Laboratório de Estudos Genômicos, Departamento de Biologia, Instituto de Biociências Letras e Ciências Exatas, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), São José do Rio Preto 15054-000, SP, Brazil
| | - Ana Júlia Chaves Gomes
- Laboratório de Estudos Genômicos, Departamento de Biologia, Instituto de Biociências Letras e Ciências Exatas, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), São José do Rio Preto 15054-000, SP, Brazil
| | - Cíntia Bittar
- Laboratório de Estudos Genômicos, Departamento de Biologia, Instituto de Biociências Letras e Ciências Exatas, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), São José do Rio Preto 15054-000, SP, Brazil
| | - Dayla Bott Geraldini
- Laboratório de Estudos Genômicos, Departamento de Biologia, Instituto de Biociências Letras e Ciências Exatas, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), São José do Rio Preto 15054-000, SP, Brazil
| | - Pâmela Jóyce Previdelli da Conceição
- Laboratório de Estudos Genômicos, Departamento de Biologia, Instituto de Biociências Letras e Ciências Exatas, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), São José do Rio Preto 15054-000, SP, Brazil
| | - Ágata Silva Cabral
- Laboratório de Estudos Genômicos, Departamento de Biologia, Instituto de Biociências Letras e Ciências Exatas, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), São José do Rio Preto 15054-000, SP, Brazil
| | - Tamara Carvalho
- Laboratório de Estudos Genômicos, Departamento de Biologia, Instituto de Biociências Letras e Ciências Exatas, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), São José do Rio Preto 15054-000, SP, Brazil
| | - Joice Matos Biselli
- Laboratório de Estudos Genômicos, Departamento de Biologia, Instituto de Biociências Letras e Ciências Exatas, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), São José do Rio Preto 15054-000, SP, Brazil
| | - Paola Jocelan Scarin Provazzi
- Laboratório de Estudos Genômicos, Departamento de Biologia, Instituto de Biociências Letras e Ciências Exatas, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), São José do Rio Preto 15054-000, SP, Brazil
| | - Guilherme Rodrigues Fernandes Campos
- Laboratório de Pesquisas em Virologia (LPV), Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto (FAMERP), São José do Rio Preto 15090-000, SP, Brazil
| | - Paulo Ricardo da Silva Sanches
- Laboratório de Virologia Molecular, Departamento de Ciências Biológicas, Faculdade de Ciências Farmacêuticas (UNESP), Araraquara 14800-903, SP, Brazil
| | - Paulo Inácio Costa
- Departamento de Análises Clínicas, Faculdade de Ciências Farmacêuticas (UNESP), Araraquara 14801-360, SP, Brazil
| | - Maurício Lacerda Nogueira
- Laboratório de Pesquisas em Virologia (LPV), Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto (FAMERP), São José do Rio Preto 15090-000, SP, Brazil
| | - João Pessoa Araujo
- Instituto de Biotecnologia, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Botucatu 18607-440, SP, Brazil
| | - Fernando Rosado Spilki
- Laboratório de Microbiologia Molecular, Instituto de Ciências da Saúde, Universidade Feevale, Novo Hamburgo 93525-075, RS, Brazil
| | - Marília Freitas Calmon
- Laboratório de Estudos Genômicos, Departamento de Biologia, Instituto de Biociências Letras e Ciências Exatas, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), São José do Rio Preto 15054-000, SP, Brazil
| | - Paula Rahal
- Laboratório de Estudos Genômicos, Departamento de Biologia, Instituto de Biociências Letras e Ciências Exatas, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), São José do Rio Preto 15054-000, SP, Brazil
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Bandla SS, Bhatt R, Devadiga S. Reclassification of respiratory syncytial virus genotypes in India. Virusdisease 2023; 34:1-14. [PMID: 37009257 PMCID: PMC10050612 DOI: 10.1007/s13337-022-00802-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Accepted: 11/13/2022] [Indexed: 11/28/2022] Open
Abstract
Respiratory syncytial virus (RSV) is known to be the major cause of lower respiratory tract infections in infants and in the elderly. RSV was recently reclassified and simplified into three genotypes of the RSV-A subgroup (GA1-GA3) and into seven genotypes of the RSV-B subgroup (GB1-GB7). This classification strategy was not implemented globally. This study intended to reclassify the sequences that were submitted in GenBank till September 2021 from India. The gene sequences of the ectodomain region, second hypervariable region (SHR), and the partial second hypervariable region (PSHR) of the G gene were selected for the analysis. 25 ectodomain, 36 s hypervariable, and 19 partial second hypervariable regions of the RSV-A subgroup and 42-ectodomain, 49-s hypervariable region and 11-partial second hypervariable region of RSV-B subgroup were used for phylogenetic analysis. P-distance was calculated to support the genotype determination done by phylogenetic analysis. Phylogenetic analysis revealed that GA2.3.1, GA2.3.3, GA2.3.4, GA2.3.5, and GA2.3.6b lineages of GA2 genotype for RSV-A; and GB5.0.1, GB5.0.2, GB5.0.3, GB5.0.4a, GB5.0.4c, GB5.0.5a, GB5.0.5c lineages of GB5 genotype and GB7 genotype for RSV-B were that circulated in India. This work has implication for RSV vaccine research, and also for strategies for the prevention and control of RSV infection in humans. Supplementary Information The online version contains supplementary material available at 10.1007/s13337-022-00802-x.
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Affiliation(s)
- Sai Suresh Bandla
- Father Muller Research Centre, Father Muller Medical College, Kankanady, Mangalore, 575002 Karnataka India
- Independent Researcher, Hyderabad, India
| | - Rushil Bhatt
- Father Muller Research Centre, Father Muller Medical College, Kankanady, Mangalore, 575002 Karnataka India
- Independent Researcher, Pune, India
| | - Santhosha Devadiga
- Father Muller Research Centre, Father Muller Medical College, Kankanady, Mangalore, 575002 Karnataka India
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34
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Parida P, N S, E R S, Jagadesh A, Marate S, Govindakaranavar A. The emergence of human metapneumovirus G gene duplication in hospitalized patients with respiratory tract infection, India, 2016-2018. Mol Biol Rep 2023; 50:1109-1116. [PMID: 36399244 PMCID: PMC9889522 DOI: 10.1007/s11033-022-08092-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 11/04/2022] [Indexed: 11/19/2022]
Abstract
BACKGROUND Human metapneumovirus (HMPV) belongs to the family Pneumoviridae. It is one of the emerging respiratory viruses causing both upper and lower respiratory tract illnesses. HMPV has two genotypes: A and B. These genotypes are classified into lineage A1, A2, B1 and B2. Lineage-A2 is further classified as A2a, A2b and A2c. Similarly, B2 is classified as B2a and B2b. Studies have shown the circulation of A2b, B1 and B2 lineages in India. However, a limited amount of data is available on the current circulating genotypes of HMPV in India. METHODS Throat swab samples positive for HMPV by real-time RT- PCR, archived at Manipal Institute of Virology as a part of a hospital-based acute febrile illness surveillance study, was used from April 2016 to August 2018 by purposive sampling method. We performed the conventional reverse transcriptase-polymerase chain reaction for twenty samples targeting the G gene and then subjected them to sequencing. Phylogenetic analysis was done using MEGA X software by the Maximum Likelihood method. RESULTS All the twenty sequences belonged to the A2c subgroup. Phylogenetic analysis showed that strains from the study have genetic relation with circulating strains in Japan, China and Croatia. Seven out of the twenty sequences showed 180-nucleotide duplication and eleven sequences showed 111-nucleotide duplication. Two sequences did not show any duplications. CONCLUSION In the current study, we report that A2c is the sub-lineage in India from April 2016 to August 2018. This study is the first retrospective study reporting the circulation of the A2c sub-lineage among adults in India with 180- and 111-nucleotide duplications in the G gene of human metapneumovirus.
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Affiliation(s)
- Preetiparna Parida
- Manipal Institute of Virology (MIV), Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, 576104, India
| | - Sudheesh N
- Manipal Institute of Virology (MIV), Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, 576104, India.
| | - Sanjay E R
- Manipal Institute of Virology (MIV), Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, 576104, India
| | - Anitha Jagadesh
- Manipal Institute of Virology (MIV), Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, 576104, India
| | - Srilatha Marate
- Manipal Institute of Virology (MIV), Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, 576104, India
| | - Arunkumar Govindakaranavar
- Manipal Institute of Virology (MIV), Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, 576104, India.
- , 2-49, Vaikathu, Maratithota Road, MooduAthradi, Athradi PO, Udupi, Karnataka, 576107, India.
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35
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Goya S, Lucion MF, Shilts MH, Juárez MDV, Gentile A, Mistchenko AS, Viegas M, Das SR. Evolutionary dynamics of respiratory syncytial virus in Buenos Aires: Viral diversity, migration, and subgroup replacement. Virus Evol 2023; 9:vead006. [PMID: 36880065 PMCID: PMC9985318 DOI: 10.1093/ve/vead006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 09/25/2022] [Accepted: 01/24/2023] [Indexed: 01/26/2023] Open
Abstract
Globally, the human respiratory syncytial virus (RSV) is one of the major causes of lower respiratory tract infections (LRTIs) in children. The scarcity of complete genome data limits our understanding of RSV spatiotemporal distribution, evolution, and viral variant emergence. Nasopharyngeal samples collected from hospitalized pediatric patients from Buenos Aires tested positive for RSV LRTI during four consecutive outbreaks (2014-2017) were randomly subsampled for RSV complete genome sequencing. Phylodynamic studies and viral population characterization of genomic variability, diversity, and migration of viruses to and from Argentina during the study period were performed. Our sequencing effort resulted in one of the largest collections of RSV genomes from a given location (141 RSV-A and 135 RSV-B) published so far. RSV-B was dominant during the 2014-2016 outbreaks (60 per cent of cases) but was abruptly replaced by RSV-A in 2017, with RSV-A accounting for 90 per cent of sequenced samples. A significant decrease in RSV genomic diversity-represented by both a reduction in genetic lineages detected and the predominance of viral variants defined by signature amino acids-was observed in Buenos Aires in 2016, the year prior to the RSV subgroup predominance replacement. Multiple introductions to Buenos Aires were detected, some with persistent detection over seasons, and also, RSV was observed to migrate from Buenos Aires to other countries. Our results suggest that the decrease in viral diversity may have allowed the dramatic predominance switch from RSV-B to RSV-A in 2017. The immune pressure generated against circulating viruses with limited diversity during a given outbreak may have created a fertile ground for an antigenically divergent RSV variant to be introduced and successfully spread in the subsequent outbreak. Overall, our RSV genomic analysis of intra- and inter-outbreak diversity provides an opportunity to better understand the epochal evolutionary dynamics of RSV.
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Affiliation(s)
- Stephanie Goya
- Virology Laboratory, Ricardo Gutiérrez Children’s Hospital, Gallo 1330, Buenos Aires 1425, Argentina
- National Scientific and Technical Research Council, Godoy Cruz 2290, Buenos Aires 1425, Argentina
- Department of Medicine, Vanderbilt University Medical Center, 1161 21st Ave S, Nashville, TN 37232, USA
| | - Maria Florencia Lucion
- Department of Epidemiology, Ricardo Gutiérrez Children’s Hospital, Gallo 1330, Buenos Aires 1425, Argentina
| | - Meghan H Shilts
- Department of Medicine, Vanderbilt University Medical Center, 1161 21st Ave S, Nashville, TN 37232, USA
| | - María del Valle Juárez
- Department of Epidemiology, Ricardo Gutiérrez Children’s Hospital, Gallo 1330, Buenos Aires 1425, Argentina
| | - Angela Gentile
- Department of Epidemiology, Ricardo Gutiérrez Children’s Hospital, Gallo 1330, Buenos Aires 1425, Argentina
| | - Alicia S Mistchenko
- Virology Laboratory, Ricardo Gutiérrez Children’s Hospital, Gallo 1330, Buenos Aires 1425, Argentina
| | - Mariana Viegas
- Virology Laboratory, Ricardo Gutiérrez Children’s Hospital, Gallo 1330, Buenos Aires 1425, Argentina
- National Scientific and Technical Research Council, Godoy Cruz 2290, Buenos Aires 1425, Argentina
| | - Suman R Das
- Department of Medicine, Vanderbilt University Medical Center, 1161 21st Ave S, Nashville, TN 37232, USA
- Department Otolaryngology—Head and Neck Surgery, Vanderbilt University Medical Center, 1215 21st Ave S, Nashville, TN 37232, USA
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36
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Coppée R, Chenane HR, Bridier-Nahmias A, Tcherakian C, Catherinot E, Collin G, Lebourgeois S, Visseaux B, Descamps D, Vasse M, Farfour E. Temporal dynamics of RSV shedding and genetic diversity in adults during the COVID-19 pandemic in a French hospital, early 2021. Virus Res 2023; 323:198950. [PMID: 36181977 PMCID: PMC9519364 DOI: 10.1016/j.virusres.2022.198950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 09/03/2022] [Accepted: 09/27/2022] [Indexed: 01/25/2023]
Abstract
Human respiratory syncytial virus (RSV) is responsible of lower respiratory tract infections which may be severe in infants, elderly and immunocompromised adults. Europe and North-American countries have observed a massive reduction of RSV incidence during the 2020-2021 winter season. Using a systematic RSV detection coupled to SARS-CoV-2 for all adult patients admitted at the Foch hospital (Suresnes, France) between January and March 2021 (n = 11,324), only eight RSV infections in patients with prolonged RNA shedding were diagnosed. RSV whole-genome sequencing revealed that six and two patients were infected by RSV groups A and B, respectively. RSV carriage lasted from 7 to at least 30 days disregarding of RSV lineage. The most prolonged RSV shedding was observed in an asymptomatic patient. We detected novel patient-specific non-synonymous mutations in the G glycoprotein gene, including a double identical mutation in the repeated region for one patient. No additional mutation occurred in the RSV genome over the course of infection in the four patients tested for. In conclusion, our results suggest that the temporal shift in the RSV epidemic is not likely to be explained by the emergence of a high frequency, unreported variant. Moreover, prolonged RSV carriages in asymptomatic patients could play a role in virus spread.
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Affiliation(s)
- Romain Coppée
- Université Paris Cité and Sorbonne Paris Nord, Inserm, IAME, F-75018 Paris, France
| | | | | | | | | | - Gilles Collin
- Université Paris Cité and Sorbonne Paris Nord, Inserm, IAME, F-75018 Paris, France; Laboratoire de Virologie, Hôpital Bichat-Claude Bernard, AP-HP, F-75018 Paris, France
| | - Samuel Lebourgeois
- Université Paris Cité and Sorbonne Paris Nord, Inserm, IAME, F-75018 Paris, France
| | - Benoit Visseaux
- Université Paris Cité and Sorbonne Paris Nord, Inserm, IAME, F-75018 Paris, France; Laboratoire de Virologie, Hôpital Bichat-Claude Bernard, AP-HP, F-75018 Paris, France
| | - Diane Descamps
- Université Paris Cité and Sorbonne Paris Nord, Inserm, IAME, F-75018 Paris, France; Laboratoire de Virologie, Hôpital Bichat-Claude Bernard, AP-HP, F-75018 Paris, France
| | - Marc Vasse
- Service de Biologie Clinique, Hôpital Foch, F-92150 Suresnes, France
| | - Eric Farfour
- Service de Biologie Clinique, Hôpital Foch, F-92150 Suresnes, France
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ON-1 and BA-IX Are the Dominant Sub-Genotypes of Human Orthopneumovirus A&B in Riyadh, Saudi Arabia. Genes (Basel) 2022; 13:genes13122288. [PMID: 36553555 PMCID: PMC9778264 DOI: 10.3390/genes13122288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/29/2022] [Accepted: 11/30/2022] [Indexed: 12/11/2022] Open
Abstract
Human orthopneumovirus (HOPV) is the major viral pathogen responsible for lower respiratory tract infections (LRTIs) in infants and young children in Riyadh, Saudi Arabia. Yet, predominant HOPV subtypes circulating in this region and their molecular and epidemiological characteristics are not fully ascertained. A total of 300 clinical samples involving nasopharyngeal aspirates (NPAs), throat swabs, and sputum were collected during winter seasons of 2019/2020 and 2021/2022 for HOPV subtyping and genotyping. Of the 300 samples, HOPV was identified in 55 samples (18.3%) with a distinct predominance of type A viruses (81.8%) compared to type B viruses (18.2%). Importantly, the ON1 strain of HOPV-A and BA-IX strain of HOPV-B groups were found to be responsible for all the infections. Sequence analysis revealed a duplication region within 2nd HVR of G protein gene of ON1 and BA-IX strains. This nucleotide duplication exerted a profound effect on protein length and affinity towards cell receptors. Further, these modifications may aid the HOPV in immune evasion and recurrent infections. Data from this study showed that ON-1 genotype of HOPV-A and BA-IX genotype of HOPV-B were dominant in Riyadh, Saudi Arabia. Further, a duplication of sequence within 2nd HVR of G protein gene was found.
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Lin WH, Wu FT, Chen YY, Wang CW, Lin HC, Kuo CC, Lai WC, Lin FJ, Tiew WT, Tsai AL, Ho KT, Kuo TY, Li CH, Wu CY, Pan YJ, Tsao KC, Hsieh YC. Unprecedented outbreak of respiratory syncytial virus in Taiwan associated with ON1 variant emergence between 2010 and 2020. Emerg Microbes Infect 2022; 11:1000-1009. [PMID: 35293267 PMCID: PMC8979508 DOI: 10.1080/22221751.2022.2054365] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
An outbreak of respiratory syncytial virus (RSV) has been observed in Taiwan since August 2020. We reviewed a central laboratory-based surveillance network established over 20 years by Taiwan Centres for Disease Control for respiratory viral pathogens between 2010 and 2020.A retrospective study of children <5 years old hospitalized with RSV infection at Chang Gung Memorial Hospital between 2018 and 2020 was conducted, and samples positive for RSV-A were sequenced. Clinical data were obtained and stratified by genotype and year.Data from 2020 showed an approximately 4-fold surge in RSV cases compared to 2010 in Taiwan, surpassing previous years during which ON1 was prevalent. Phylogenetic analysis of G protein showed that novel ON1 variants were clustered separately from those of 2018 and 2019 seasons and ON1 reference strains. The variant G protein carried six amino acid changes that emerged gradually in 2019; high consistency was observed in 2020. A unique substitution, E257K, was observed in 2020 exclusively. The F protein of the variant carried T12I and H514N substitutions, which weren't at antigenic sites. In terms of multivariate analysis, age (OR: 0.97; 95% CI: 0.94-0.99; p = 0.02) and 2020 ON1 variant (OR:2.52; 95% CI:1.13-5.63; p = 0.025) were independently associated with oxygen saturation <94% during hospitalization.The 2020 ON1 variant didn't show higher replication or virulence compared with those in 2018 in our study. The unprecedented 2020 RSV epidemic may attribute to antigenic changes and lack of interferon-stimulated immunity induced by seasonal circulating virus under non-pharmaceutical intervention.
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Affiliation(s)
- Wei-Hsuan Lin
- Department of Pediatrics, Chang Gung Children's Hospital, Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Fang-Tzy Wu
- Center for Diagnostics and Vaccine Development, Centres for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan
| | - Yi-Yin Chen
- Department of Pediatrics, Chang Gung Children's Hospital, Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Chih-Wei Wang
- Departments of Anatomic Pathology, Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Ho-Chen Lin
- Department of Pediatrics, Chang Gung Children's Hospital, Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Ching-Chia Kuo
- Department of Pediatrics, Chang Gung Children's Hospital, Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Wan-Chun Lai
- Department of Pediatrics, Chang Gung Children's Hospital, Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Fang-Ju Lin
- Department of Pediatrics, Chang Gung Children's Hospital, Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, Kaohsiung, Taiwan
| | - Wan-Tin Tiew
- Department of Pediatrics, Chang Gung Children's Hospital, Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - An-Li Tsai
- Department of Pediatrics, Chang Gung Children's Hospital, Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Kuan-Ta Ho
- Department of Pediatrics, Chang Gung Children's Hospital, Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Ting-Yu Kuo
- Center for Diagnostics and Vaccine Development, Centres for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan
| | - Chung-Hao Li
- Center for Diagnostics and Vaccine Development, Centres for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan
| | - Ching-Yi Wu
- Center for Diagnostics and Vaccine Development, Centres for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan
| | - Yi-Jiun Pan
- Department of Microbiology and Immunology, School of Medicine, College of Medicine, China Medical University, Taichung, Taiwan
| | - Kuo-Chien Tsao
- Research Centre for Emerging Viral Infections, Chang Gung University, Taoyuan, Taiwan.,Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Yu-Chia Hsieh
- Department of Pediatrics, Chang Gung Children's Hospital, Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, Taoyuan, Taiwan
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Lin TY, Chi H, Kuo CY, Tsai HP, Wang JR, Liu CC, Shen CF. Outbreak of respiratory syncytial virus subtype ON1 among children during COVID-19 pandemic in Southern Taiwan. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2022; 55:1168-1179. [PMID: 36137926 DOI: 10.1016/j.jmii.2022.08.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 08/24/2022] [Accepted: 08/28/2022] [Indexed: 12/27/2022]
Abstract
BACKGROUND The regional respiratory syncytial virus (RSV) outbreak in southern Taiwan in late 2020 followed the surge of RSV cases in the national surveillance data and displayed distinct clinical features. This study investigated RSV epidemiology in the most recent five years and compared the clinical manifestations of this outbreak with non-outbreak period. METHODS Medical records of RSV-infected children at the National Cheng Kung University Hospital from January 2016 to December 2020 were retrospectively retrieved from hospital-based electronic medical database. Cases of RSV infection were identified by RSV antigen positive and/or RSV isolated from respiratory specimens. The demographic, clinical presentations, and laboratory data were recorded. The RSV isolates in 2020 was sequenced for phylogenetic analysis. RESULTS Overall, 442 RSV-infected cases were retrieved and 42.1% (186 cases) clustered in late 2020. The 2020 outbreak started in September, peaked in November, and lasted for 3 months. 2020 RSV-infected children were older (2.3 ± 2.2 years vs. 1.0 ± 1.0 years), more likely to be diagnosed with bronchopneumonia (57.5% vs. 31.6%), but also had a lower hospitalization rate, shorter hospital stay, less oxygen use, and less respiratory distress than those in 2016-2019 (all p value < 0.05). The RSV isolates in 2020 belonged to RSV-A subtype ON1 but were phylogenetically distinct from the ON1 strains prevalent in Taiwan previously. CONCLUSION The 2020 RSV outbreak was led by the novel RSV-A subtype ON1 variant with clinical manifestations distinct from previous years. Continuous surveillance of new emerging variants of respiratory viruses in the post-pandemic era is warranted.
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Affiliation(s)
- Ting-Yu Lin
- Department of Pediatrics, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Hsin Chi
- Department of Medicine, MacKay Medicine College, New Taipei, Taiwan; Department of Pediatrics, MacKay Children's Hospital and MacKay Memorial Hospital, Taipei, Taiwan
| | - Cheng-Yen Kuo
- Department of Pediatrics, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Huey-Pin Tsai
- Department of Pathology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Jen-Ren Wang
- Department of Pathology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Ching-Chuan Liu
- Department of Pediatrics, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan, Taiwan.
| | - Ching-Fen Shen
- Department of Pediatrics, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan.
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Donovan-Banfield I, Milligan R, Hall S, Gao T, Murphy E, Li J, Shawli GT, Hiscox J, Zhuang X, McKeating JA, Fearns R, Matthews DA. Direct RNA sequencing of respiratory syncytial virus infected human cells generates a detailed overview of RSV polycistronic mRNA and transcript abundance. PLoS One 2022; 17:e0276697. [PMID: 36355791 PMCID: PMC9648745 DOI: 10.1371/journal.pone.0276697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 10/11/2022] [Indexed: 11/12/2022] Open
Abstract
To characterize species of viral mRNA transcripts generated during respiratory syncytial virus (RSV) infection, human fibroblast-like MRC-5 lung cells were infected with subgroup A RSV for 6, 16 and 24 hours. In addition, we characterised the viral transcriptome in infected Calu-3 lung epithelial cells at 48 hours post infection. Total RNA was harvested and polyadenylated mRNA was enriched and sequenced by direct RNA sequencing using an Oxford nanopore device. This platform yielded over 450,000 direct mRNA transcript reads which were mapped to the viral genome and analysed to determine the relative mRNA levels of viral genes using our in-house ORF-centric pipeline. We examined the frequency of polycistronic readthrough mRNAs were generated and assessed the length of the polyadenylated tails for each group of transcripts. We show a general but non-linear decline in gene transcript abundance across the viral genome, as predicted by the model of RSV gene transcription. However, the decline in transcript abundance is not uniform. The polyadenylate tails generated by the viral polymerase are similar in length to those generated by the host polyadenylation machinery and broadly declined in length for most transcripts as the infection progressed. Finally, we observed that the steady state abundance of transcripts with very short polyadenylate tails less than 20 nucleotides is less for N, SH and G transcripts in both cell lines compared to NS1, NS2, P, M, F and M2 which may reflect differences in mRNA stability and/or translation rates within and between the cell lines.
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Affiliation(s)
- I’ah Donovan-Banfield
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University of Bristol, Bristol, United Kingdom
- Department of Infection Biology and Microbiome, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Rachel Milligan
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University of Bristol, Bristol, United Kingdom
| | - Sophie Hall
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University of Bristol, Bristol, United Kingdom
| | - Tianyi Gao
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University of Bristol, Bristol, United Kingdom
| | - Eleanor Murphy
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University of Bristol, Bristol, United Kingdom
| | - Jack Li
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University of Bristol, Bristol, United Kingdom
| | - Ghada T. Shawli
- Department of Infection Biology and Microbiome, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Julian Hiscox
- Department of Infection Biology and Microbiome, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Xiaodong Zhuang
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Jane A. McKeating
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, United Kingdom
| | - Rachel Fearns
- Department of Microbiology, National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston, Massachusetts, United States of America
- * E-mail: (DAM); (RF)
| | - David A. Matthews
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University of Bristol, Bristol, United Kingdom
- * E-mail: (DAM); (RF)
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Cantú-Flores K, Rivera-Alfaro G, Muñoz-Escalante JC, Noyola DE. Global distribution of respiratory syncytial virus A and B infections: a systematic review. Pathog Glob Health 2022; 116:398-409. [PMID: 35156555 PMCID: PMC9518599 DOI: 10.1080/20477724.2022.2038053] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
Respiratory syncytial virus (RSV) is the main cause of severe respiratory infections in young children. The need for global epidemiologic data regarding RSV has been increasingly recognized. RSV A infections are reported more frequently than RSV B. Nonetheless, the temporal distribution of infections caused by both RSV groups has not been investigated globally. A systematic review was carried out regarding published studies on RSV A and B epidemiology, as well as RSV G gene ectodomain sequence data available at GenBank. A total of 76,668 [45,990 (60%) RSV A and 30,678 (40%) RSV B] positive samples from 83 countries were identified and included in the analysis. Genotype assignment was obtained in 5,340 RSV A and 2,518 RSV B sequences. Two patterns of RSV circulation were observed: continuous seasons with RSV A predominance and alternate predominance of RSV A and B. These patterns were observed in all regions, but the predominant RSV group seldom coincided in all continents during a given year or season. The most frequently identified RSV A genotype was NA1 (including ON1 viruses) (76.30%), and the most frequently identified RSV B genotype was BA (70.65%). Multiple genotypes circulated simultaneously throughout the evolutionary history of RSV, but genotype diversity decreased after the year 2000. The classification of RSV group and genotype is important for the development of vaccines, as well as to understand viral dynamics. This study displays the global and continental RSV circulation patterns from the first report of human RSV infection until the end of 2020.
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Affiliation(s)
- Karla Cantú-Flores
- Microbiology Department, Facultad de Medicina, Universidad Autónoma de San Luis Potosí, San Luis Potosí, Mexico
| | - Gerardo Rivera-Alfaro
- Microbiology Department, Facultad de Medicina, Universidad Autónoma de San Luis Potosí, San Luis Potosí, Mexico
| | - Juan Carlos Muñoz-Escalante
- Microbiology Department, Facultad de Medicina, Universidad Autónoma de San Luis Potosí, San Luis Potosí, Mexico
| | - Daniel E. Noyola
- Microbiology Department, Facultad de Medicina, Universidad Autónoma de San Luis Potosí, San Luis Potosí, Mexico,CONTACT Daniel E. Noyola Microbiology Department, Facultad de Medicina, Universidad Autónoma de San Luis Potosí, Avenida Venustiano Carranza 2405, San Luis Potosí78210, México
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Chen G, Lan M, Lin S, Zhang Y, Zhang D, Weng Y, Zheng K. Genome analysis of human respiratory syncytial virus in Fujian Province, Southeast China. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 103:105329. [PMID: 35788050 DOI: 10.1016/j.meegid.2022.105329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 06/12/2022] [Accepted: 06/20/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Respiratory syncytial virus (RSV) is one of the main causes of acute respiratory infections (ARI) leading to a heavy disease burden. Reports on RSV in China are limited, especially in Fujian Province, and RSV whole-genome sequences in Fujian Province are not reported. This study aimed to explore the genomic characteristics of RSV to provide evidence for the development of vaccines and medicines. METHODS Reverse transcription-polymerase chain reaction (RT-PCR) was used to amplify and obtain the attachment (G) gene and whole-genome fragments from the positive samples. Genetic evolution as well as nucleotide and amino acid homology analyses of the virus sequences were conducted to identify any amino acid mutations. RESULTS A total of 72 RSV-positive cases were collected, and 53 G gene sequences were obtained using polymerase chain reaction (PCR) amplification. The ON1 and BA11 genotypes were found to be dominant using the Basic Local Alignment Search Tool (BLAST) on the NCBI website. The 40 genotype ON1 sequences had high nucleotide identity (95.3%-99.8%) and amino acid similarity (92.5%-100%), whereas the 13 BA11 genotype sequenceshad 97.3% - 99.6% nucleotide identity and 94.8% - 99.7% amino acid similarity. Compared to the ON1 prototype (JN257693) and BA11 prototype (AY333364), the obtained sequences had no nucleotide insertions or deletions, indicating high similarity among the samples. A total of 17 RSV whole genome sequences were obtained, 10 of which were genotype ON1 and seven were genotype BA11. Certain amino acid mutations were found in the antigen site and epitope of the fusion (F) protein but not in the G protein. Glycosylation analyses of specific RSV genes revealed high positive selection rates for the gene, and the N- and O-linked glycosylation sequences in the F gene were relatively conserved. CONCLUSIONS From July 2018 to January 2020, ON1 and BA11 were the most prevalent RSV genotypes in Fujian Province. A high nucleotide identity and amino acid similarity were observed between the reference strain and the obtained strains, as well as among the sequences of the obtained isotypes. Certain amino acid mutations occur at the antigen site and the epitope of the F protein.
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Affiliation(s)
- Guangmin Chen
- The Practice Base on the School of Public Health, Fujian Medical University, Fuzhou 350001, China; Fujian Provincial Center for Disease Control & Prevention, Fuzhou 350001, China; Fujian Provincial Key Laboratory of Zoonosis Research, Fuzhou 350001, China
| | - Meifang Lan
- The Practice Base on the School of Public Health, Fujian Medical University, Fuzhou 350001, China; Fujian Provincial Center for Disease Control & Prevention, Fuzhou 350001, China; Fujian Provincial Key Laboratory of Zoonosis Research, Fuzhou 350001, China
| | - Sixian Lin
- The Practice Base on the School of Public Health, Fujian Medical University, Fuzhou 350001, China; Fujian Provincial Center for Disease Control & Prevention, Fuzhou 350001, China; Fujian Provincial Key Laboratory of Zoonosis Research, Fuzhou 350001, China
| | - Yanhua Zhang
- The Practice Base on the School of Public Health, Fujian Medical University, Fuzhou 350001, China; Fujian Provincial Center for Disease Control & Prevention, Fuzhou 350001, China; Fujian Provincial Key Laboratory of Zoonosis Research, Fuzhou 350001, China
| | - Dongjuan Zhang
- The Practice Base on the School of Public Health, Fujian Medical University, Fuzhou 350001, China; Fujian Provincial Center for Disease Control & Prevention, Fuzhou 350001, China; Fujian Provincial Key Laboratory of Zoonosis Research, Fuzhou 350001, China
| | - Yuwei Weng
- The Practice Base on the School of Public Health, Fujian Medical University, Fuzhou 350001, China; Fujian Provincial Center for Disease Control & Prevention, Fuzhou 350001, China; Fujian Provincial Key Laboratory of Zoonosis Research, Fuzhou 350001, China
| | - Kuicheng Zheng
- The Practice Base on the School of Public Health, Fujian Medical University, Fuzhou 350001, China; Fujian Provincial Center for Disease Control & Prevention, Fuzhou 350001, China; Fujian Provincial Key Laboratory of Zoonosis Research, Fuzhou 350001, China.
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Zhao X, Wang C, Jiang H, Zhang H, Fang F, Chen M, Yuan Z, Teng Z, Liu J, Zhang X. Analysis of circulating respiratory syncytial virus A strains in Shanghai, China identified a new and increasingly prevalent lineage within the dominant ON1 genotype. Front Microbiol 2022; 13:966235. [PMID: 36033866 PMCID: PMC9403419 DOI: 10.3389/fmicb.2022.966235] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 07/14/2022] [Indexed: 11/13/2022] Open
Abstract
Respiratory syncytial virus A (RSV-A) is one of the commonest pathogens causing acute respiratory tract infections in infants and children globally. The currently dominant circulating genotype of RSV-A, ON1, was first detected in Shanghai, China in 2011, but little data are available regarding its subsequent circulation and clinical impact here. In this work, we analyzed RSV-A infection in a cohort of patients hospitalized for acute respiratory infections in Shanghai Children’s Hospital, and RSV-A was detected in ~10% of these cases. RSV-A G gene sequencing revealed that all successfully sequenced strains belonged to ON1 genotype, but in phylogenetic analysis, the majority of these sequences formed a clade separate from the four previously established lineages within ON1. The new lineage, denoted ON1-5, was supported by phylogenetic analyses using additional G gene sequences from RSV-A strains isolated in Shanghai and elsewhere. ON1-5 first appeared in 2015 in China and the Netherlands, and has since spread to multiple continents and gained dominance in Asia. In our cohort, ON1-5 was not associated with markedly different clinical presentations compared to other ON1 lineages. ON1-5 strains are characterized by four amino acid variations in the two mucin-like regions of G protein, and one variation (N178G) within the highly conserved CCD domain that is involved in receptor binding. These data highlight the continuous evolution of RSV-A, and suggest the possibility of the virus acquiring variations in domains traditionally considered to be conserved for fitness gain.
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Affiliation(s)
- Xue Zhao
- Virus Testing Laboratory, Pathogen Testing Center, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Chun Wang
- Department of Clinical Laboratory, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Hui Jiang
- Virus Testing Laboratory, Pathogen Testing Center, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Hong Zhang
- Department of Clinical Laboratory, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Fanghao Fang
- Virus Testing Laboratory, Pathogen Testing Center, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Min Chen
- Virus Testing Laboratory, Pathogen Testing Center, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Zhengan Yuan
- Virus Testing Laboratory, Pathogen Testing Center, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Zheng Teng
- Virus Testing Laboratory, Pathogen Testing Center, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
- *Correspondence: Zheng Teng,
| | - Jing Liu
- Key Laboratory of Medical Molecular Virology (MOE/MOH/CAMS) and Shanghai Key Laboratory of Medical Epigenetics, Department of Microbiology and Parasitology and Institutes of Biomedical Sciences, School of Basic Medical Sciences and Shanghai Institute of Infectious Diseases and Biosecurity, Shanghai Medical College, Fudan University, Shanghai, China
- Jing Liu,
| | - Xi Zhang
- Virus Testing Laboratory, Pathogen Testing Center, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
- Xi Zhang,
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Beach SS, Hull MA, Ytreberg FM, Patel JS, Miura TA. Molecular Modeling Predicts Novel Antibody Escape Mutations in the Respiratory Syncytial Virus Fusion Glycoprotein. J Virol 2022; 96:e0035322. [PMID: 35678603 PMCID: PMC9278155 DOI: 10.1128/jvi.00353-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Monoclonal antibodies are increasingly used for the prevention and/or treatment of viral infections. One caveat of their use is the ability of viruses to evolve resistance to antibody binding and neutralization. Computational strategies to identify viral mutations that may disrupt antibody binding would leverage the wealth of viral genomic sequence data to monitor for potential antibody-resistant mutations. The respiratory syncytial virus is an important pathogen for which monoclonal antibodies against the fusion (F) protein are used to prevent severe disease in high-risk infants. In this study, we used an approach that combines molecular dynamics simulations with FoldX to estimate changes in free energy in F protein folding and binding to the motavizumab antibody upon each possible amino acid change. We systematically selected 8 predicted escape mutations and tested them in an infectious clone. Consistent with our F protein stability predictions, replication-effective viruses were observed for each selected mutation. Six of the eight variants showed increased resistance to neutralization by motavizumab. Flow cytometry was used to validate the estimated (model-predicted) effects on antibody binding to F. Using surface plasmon resonance, we determined that changes in the on-rate of motavizumab binding were associated with the reduced affinity for two novel escape mutations. Our study empirically validated the accuracy of our molecular modeling approach and emphasized the role of biophysical protein modeling in predicting viral resistance to antibody-based therapeutics that can be used to monitor the emergence of resistant viruses and to design improved therapeutic antibodies. IMPORTANCE Respiratory syncytial virus (RSV) causes severe disease in young infants, particularly those with heart or lung diseases or born prematurely. Because no vaccine is currently available, monoclonal antibodies are used to prevent severe RSV disease in high-risk infants. While it is known that RSV evolves to avoid recognition by antibodies, screening tools that can predict which changes to the virus may lead to antibody resistance are greatly needed.
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Affiliation(s)
- Sierra S. Beach
- Department of Biological Sciences, University of Idahogrid.266456.5, Moscow, Idaho, USA
| | - McKenna A. Hull
- Department of Biological Sciences, University of Idahogrid.266456.5, Moscow, Idaho, USA
| | - F. Marty Ytreberg
- Department of Physics, University of Idahogrid.266456.5, Moscow, Idaho, USA
- Institute for Modeling Collaboration and Innovation, University of Idahogrid.266456.5, Moscow, Idaho, USA
| | - Jagdish Suresh Patel
- Department of Biological Sciences, University of Idahogrid.266456.5, Moscow, Idaho, USA
- Institute for Modeling Collaboration and Innovation, University of Idahogrid.266456.5, Moscow, Idaho, USA
| | - Tanya A. Miura
- Department of Biological Sciences, University of Idahogrid.266456.5, Moscow, Idaho, USA
- Institute for Modeling Collaboration and Innovation, University of Idahogrid.266456.5, Moscow, Idaho, USA
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Jia R, Lu L, Su L, Lin Z, Gao D, Lv H, Xu M, Liu P, Cao L, Xu J. Resurgence of Respiratory Syncytial Virus Infection During COVID-19 Pandemic Among Children in Shanghai, China. Front Microbiol 2022; 13:938372. [PMID: 35875547 PMCID: PMC9298468 DOI: 10.3389/fmicb.2022.938372] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 06/15/2022] [Indexed: 11/24/2022] Open
Abstract
Respiratory syncytial virus (RSV) is the most common pathogen causing acute lower respiratory tract infection (LRTI) in children. RSV usually peaks in winter and declines by early spring in China. The outbreak of coronavirus disease 2019 (COVID-19) was reported to bring changes to the transmission pattern of respiratory pathogens including RSV. Here in this paper, we analyzed RSV-positive nasopharyngeal aspirates from inpatients in the Children’s Hospital of Fudan University from October 2019 to October 2021 and compared the clinical features of the RSV-positive patients before and during COVID-19. We found an atypical upsurge of RSV infection in the late summer of 2021 after a major suppression in 2020. RSV B was the main subtype spreading among children throughout the study. Phylogenetic analysis revealed that all RSV A strains belonged to ON1 genotype and all RSV B strains were BA9 genotype. Deduced amino acid analysis displayed different substitutions in the RSV strains observed before and during COVID-19. Demographic analysis suggested that males and infants aged under 5 months were the main populations infected with RSV by gender and age, respectively. Less severe clinical outcomes were observed in patients during COVID-19 than before the pandemic, especially in RSV B-positive patients. Our findings described the epidemiological changes in RSV infection brought by COVID-19, which further underscored the importance of continuous surveillance of RSV in the shadow of COVID-19 at both local and global scales.
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Affiliation(s)
- Ran Jia
- Department of Clinical Laboratory, Children’s Hospital of Fudan University, Shanghai, China
| | - Lijuan Lu
- Department of Clinical Laboratory, Children’s Hospital of Fudan University, Shanghai, China
| | - Liyun Su
- Department of Clinical Laboratory, Children’s Hospital of Fudan University, Shanghai, China
| | - Ziyan Lin
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Da Gao
- School of Laboratory Medicine, Bengbu Medical College, Bengbu, China
| | - Haiyan Lv
- School of Laboratory Medicine, Bengbu Medical College, Bengbu, China
| | - Menghua Xu
- Department of Clinical Laboratory, Children’s Hospital of Fudan University, Shanghai, China
| | - Pengcheng Liu
- Department of Clinical Laboratory, Children’s Hospital of Fudan University, Shanghai, China
| | - Lingfeng Cao
- Department of Clinical Laboratory, Children’s Hospital of Fudan University, Shanghai, China
| | - Jin Xu
- Department of Clinical Laboratory, Children’s Hospital of Fudan University, Shanghai, China
- Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
- *Correspondence: Jin Xu,
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46
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Nunes DBSM, Vieira C, Sá JM, Araújo GC, Caruso IP, Souza FP. M2-2 gene as a new alternative molecular marker for phylogenetic, phylodynamic, and evolutionary studies of hRSV. Virus Res 2022; 318:198850. [PMID: 35750131 DOI: 10.1016/j.virusres.2022.198850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 06/11/2022] [Accepted: 06/17/2022] [Indexed: 10/18/2022]
Abstract
The human Respiratory Syncytial Virus (hRSV) is the main causative agent of acute respiratory infections (ARI), such as pneumonia and bronchiolitis. One of the factors that lead to success in viral replication is the interaction of the M2-2 protein with the ribosomal complex. This interaction is responsible for the phase change of viral activity, acting as an inhibitor or inducer of viral replication, according to the concentration of mRNA. Based on the importance of M2-2 gene and protein have to viral physiology, we performed here evaluations of genetic diversity, phylogenetic reconstructions, phylodynamics, and selection test. Our results suggested an alternative way of classifying this virus in clades A and B, based on a new phylogenetic marker, the M2-2 gene. Therefore, our study is the first one to investigate the dynamics of the evolutionary diversification process of hRSV from the perspective of the M2-2 viral gene. In our study was also identified that the M2-2 gene is under the effect of purifying selection originated by population genetic bottlenecks. Therefore, the M2-2 gene demonstrated an interesting potential to be applied in evolutionary studies involving hRSV, recovering phylogenetic signals and traits of natural selection under the evolution of this virus.
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Affiliation(s)
- Denis Bruno S M Nunes
- Institute of Biological and Health Sciences, Federal University of Alagoas (UFAL), Campus A.C. Simões, AL, Brazil
| | - Camila Vieira
- Department of Basic Sciences, Faculty of Animal Science and Food Engineering, University of São Paulo (USP), Pirassununga, SP, Brazil
| | - Jéssica M Sá
- Multiuser Biomolecular Innovation Laboratory, Department of Physics Letters and Exact Sciences, Institute of Biosciences, São Paulo State University "Júlio de Mesquita Filho" (UNESP), São José do Rio Preto, SP, Brazil
| | - Gabriela C Araújo
- Multiuser Biomolecular Innovation Laboratory, Department of Physics Letters and Exact Sciences, Institute of Biosciences, São Paulo State University "Júlio de Mesquita Filho" (UNESP), São José do Rio Preto, SP, Brazil
| | - Icaro P Caruso
- Multiuser Biomolecular Innovation Laboratory, Department of Physics Letters and Exact Sciences, Institute of Biosciences, São Paulo State University "Júlio de Mesquita Filho" (UNESP), São José do Rio Preto, SP, Brazil; Institute of Medical Biochemistry Leopoldo de Meis and National Center for Structural Biology and Bioimaging, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil.
| | - Fátima P Souza
- Multiuser Biomolecular Innovation Laboratory, Department of Physics Letters and Exact Sciences, Institute of Biosciences, São Paulo State University "Júlio de Mesquita Filho" (UNESP), São José do Rio Preto, SP, Brazil.
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47
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Off-season RSV epidemics in Australia after easing of COVID-19 restrictions. Nat Commun 2022; 13:2884. [PMID: 35610217 PMCID: PMC9130497 DOI: 10.1038/s41467-022-30485-3] [Citation(s) in RCA: 147] [Impact Index Per Article: 73.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 04/27/2022] [Indexed: 11/10/2022] Open
Abstract
Human respiratory syncytial virus (RSV) is an important cause of acute respiratory infection with the most severe disease in the young and elderly. Non-pharmaceutical interventions and travel restrictions for controlling COVID-19 have impacted the circulation of most respiratory viruses including RSV globally, particularly in Australia, where during 2020 the normal winter epidemics were notably absent. However, in late 2020, unprecedented widespread RSV outbreaks occurred, beginning in spring, and extending into summer across two widely separated regions of the Australian continent, New South Wales (NSW) and Australian Capital Territory (ACT) in the east, and Western Australia. Through genomic sequencing we reveal a major reduction in RSV genetic diversity following COVID-19 emergence with two genetically distinct RSV-A clades circulating cryptically, likely localised for several months prior to an epidemic surge in cases upon relaxation of COVID-19 control measures. The NSW/ACT clade subsequently spread to the neighbouring state of Victoria and to cause extensive outbreaks and hospitalisations in early 2021. These findings highlight the need for continued surveillance and sequencing of RSV and other respiratory viruses during and after the COVID-19 pandemic, as mitigation measures may disrupt seasonal patterns, causing larger or more severe outbreaks. Non-pharmaceutical interventions for COVID-19 also reduced incidence of respiratory pathogens such as respiratory syncytial virus (RSV). Here, the authors report the resurgence of RSV in Australia following lifting of some of the restrictions and describe reduction in genetic diversity in circulating clades.
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48
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Calaor-Morin J, Arguelles VL, Foronda JL, Tan A, Lagamayo E, Dapat C, Lupisan S. Genotyping of respiratory syncytial virus among influenza-like illness and severe acute respiratory infection cases of children in the Philippines from 2006 to 2016. Influenza Other Respir Viruses 2022; 16:942-951. [PMID: 35582932 PMCID: PMC9343341 DOI: 10.1111/irv.12986] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 03/14/2022] [Accepted: 03/15/2022] [Indexed: 11/29/2022] Open
Abstract
Objective Respiratory syncytial virus (RSV) is a leading cause of severe lower respiratory infection, and therefore, a major threat to global health. This study determined the epidemiological and molecular characteristics of RSV among cases of influenza‐like illness (ILI) and severe acute respiratory infection (SARI) among children in the Philippines. Method The study included archived nasopharyngeal swab and oropharyngeal swab samples collected from patients under the age of five who are presented with ILI or SARI for the period of 2006–2016. Swabs were examined for RSV subgroup by multiplex real‐time qRT‐PCR. Partial genome sequencing and phylogenetic analyses of the second hypervariable region (HVR) of the G gene were used to determine the genotype of RSV isolates. Results A total of 1036 representative samples from all sites were selected and tested. Of these samples, 122 were RSV‐positive at 11.8% prevalence rate, and 58.2% (71/122) were classified as RSV‐A. Six genotypes were identified, which include NA1 (27/122, 22.1%), ON1 (5/122, 4.1%), GA2 (1/122, 0.8%), and GA5 (1/122, 0.8%) for RSV‐A; and BA2 (13/122, 10.7%) and BA9 (1/122, 0.8%) for RSV‐B. Most RSV‐related cases were significantly associated with clinical characteristics such as runny nose (88.1% RSV vs. 11.9% non‐RSV: p value = 0.021), pneumonia (80.6% RSV vs. 19.4% non‐RSV; p value = 0.015), and bronchitis (71.7% RSV vs. 28.3% non‐RSV; p value < 0.001). Increased RSV‐related cases were observed among children below 24 months old. Conclusion The RSV trend and genetic variability in the Philippines resembles a similar pattern of transmission globally.
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Affiliation(s)
- Jonjee Calaor-Morin
- Department of Virology, Research Institute for Tropical Medicine, Muntinlupa, Philippines.,Graduate School, University of Santo Tomas, Manila, Philippines
| | - Vina Lea Arguelles
- Department of Virology, Research Institute for Tropical Medicine, Muntinlupa, Philippines
| | - Janiza Lianne Foronda
- Department of Virology, Research Institute for Tropical Medicine, Muntinlupa, Philippines
| | - Alvin Tan
- Department of Epidemiology and Biostatistics, Research Institute for Tropical Medicine, Philippines
| | - Evelina Lagamayo
- Department of Medicine, University of Santo Tomas, Manila, Philippines
| | - Clyde Dapat
- RITM-Tohoku Collaborating Research Center on Emerging and Re-emerging Infectious Diseases, Muntinlupa, Philippines
| | - Socorro Lupisan
- Department of Virology, Research Institute for Tropical Medicine, Muntinlupa, Philippines
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Global Extension and Predominance of Human Metapneumovirus A2 Genotype with Partial G Gene Duplication. Viruses 2022; 14:v14051058. [PMID: 35632799 PMCID: PMC9146545 DOI: 10.3390/v14051058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 04/29/2022] [Accepted: 05/12/2022] [Indexed: 12/10/2022] Open
Abstract
Human metapneumovirus (HMPV) is an important respiratory pathogen and is divided in two main groups (A and B). HMPV strains with partial duplications (111-nt and 180-nt duplication) of the G gene have been reported in recent years. Since the initial reports, viruses with these characteristics have been reported in several countries. We analyzed all complete HMPV G gene ectodomain sequences available at GenBank to determine if viruses with 111-nt or 180-nt duplication have become the leading HMPV strains worldwide, and to describe their temporal and geographic distribution. We identified 1462 sequences that fulfilled study criteria (764 HMPV A and 698 HMPV B) reported from 37 countries. The most frequent HMPV A genotype was A2b2 (n = 366), and the most frequent B genotype was B2 (n = 374). A total of 84 sequences contained the 111-nt duplication, and 90 sequences contained the 180-nt duplication. Since 2016, viruses with a partial duplication comprise the most frequent HMPV A sequences globally and have displaced other HMPV A viruses in Asia, Europe, and South America; no sequences of viruses with partial duplication have been reported in North America or Africa so far. Continued surveillance of HMPV is required to identify the emergence and spread of epidemiologically relevant variants.
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50
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Genetic Diversity and Epidemiological Features of Respiratory Syncytial Virus, Beijing, 2015–2019: A Multicenter and All-Age Groups Study. J Infect 2022; 85:75-85. [DOI: 10.1016/j.jinf.2022.04.046] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 04/26/2022] [Accepted: 04/30/2022] [Indexed: 11/19/2022]
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