1
|
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.
Collapse
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.
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
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.
Collapse
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)
| | | |
Collapse
|
4
|
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: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] [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.
Collapse
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
| |
Collapse
|
5
|
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.
Collapse
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.
| |
Collapse
|
6
|
Hönemann M, Maier M, Frille A, Thiem S, Bergs S, Williams TC, Mas V, Lübbert C, Pietsch C. Respiratory Syncytial Virus in Adult Patients at a Tertiary Care Hospital in Germany: Clinical Features and Molecular Epidemiology of the Fusion Protein in the Severe Respiratory Season of 2022/2023. Viruses 2024; 16:943. [PMID: 38932235 PMCID: PMC11209376 DOI: 10.3390/v16060943] [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: 05/10/2024] [Revised: 05/31/2024] [Accepted: 06/02/2024] [Indexed: 06/28/2024] Open
Abstract
Following an interseasonal rise in mainly pediatric respiratory syncytial virus (RSV) cases in Germany in 2021, an exceptionally high number of adult cases was observed in the subsequent respiratory season of 2022/2023. The aim of this study was to compare the clinical presentation of RSV infections in the pre- and post-SARS-CoV-2 pandemic periods. Additionally, the local epidemiology of the RSV fusion protein was analyzed at a molecular genetic and amino acid level. RSV detections in adults peaked in calendar week 1 of 2023, 8 weeks earlier than the earliest peak observed in the three pre-pandemic seasons. Although the median age of the adult patients was not different (66.5 vs. 65 years), subtle differences between both periods regarding comorbidities and the clinical presentation of RSV cases were noted. High rates of comorbidities prevailed; however, significantly lower numbers of patients with a history of lung transplantation (p = 0.009), chronic kidney disease (p = 0.013), and immunosuppression (p = 0.038) were observed in the 2022/2023 season. In contrast, significantly more lower respiratory tract infections (p < 0.001), in particular in the form of pneumonia (p = 0.015) and exacerbations of obstructive lung diseases (p = 0.008), were detected. An ICU admission was noted for 23.7% of all patients throughout the study period. Sequence analysis of the fusion protein gene revealed a close phylogenetic relatedness, regardless of the season of origin. However, especially for RSV-B, an accumulation of amino acid point substitutions was noted, including in antigenic site Ø. The SARS-CoV-2 pandemic had a tremendous impact on the seasonality of RSV, and the introduction of new vaccination and immunization strategies against RSV warrants further epidemiologic studies of this important pathogen.
Collapse
Affiliation(s)
- Mario Hönemann
- Virology Department, Institute of Medical Microbiology and Virology, Leipzig University Hospital, Johannisalle 30, 04103 Leipzig, Germany
- Interdisciplinary Center for Infectious Diseases, Leipzig University Hospital, Liebigstrasse 20, 04103 Leipzig, Germany
| | - Melanie Maier
- Virology Department, Institute of Medical Microbiology and Virology, Leipzig University Hospital, Johannisalle 30, 04103 Leipzig, Germany
- Interdisciplinary Center for Infectious Diseases, Leipzig University Hospital, Liebigstrasse 20, 04103 Leipzig, Germany
| | - Armin Frille
- Department of Respiratory Medicine, Leipzig University Hospital, Liebigstrasse 20, 04103 Leipzig, Germany
| | - Stephanie Thiem
- Virology Department, Institute of Medical Microbiology and Virology, Leipzig University Hospital, Johannisalle 30, 04103 Leipzig, Germany
| | - Sandra Bergs
- Virology Department, Institute of Medical Microbiology and Virology, Leipzig University Hospital, Johannisalle 30, 04103 Leipzig, Germany
| | - Thomas C. Williams
- Child Life and Health, University of Edinburgh, Royal Hospital for Children and Young People, 50 Little France Crescent, Edinburgh EH16 4TJ, UK
| | - Vicente Mas
- Centro Nacional de Microbiología and CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, C/ Sinesio Delgado, 4, 28029 Madrid, Spain
| | - Christoph Lübbert
- Interdisciplinary Center for Infectious Diseases, Leipzig University Hospital, Liebigstrasse 20, 04103 Leipzig, Germany
- Division of Infectious Diseases and Tropical Medicine, Department of Medicine I, Leipzig University Hospital, Liebigstrasse 20, 04103 Leipzig, Germany
| | - Corinna Pietsch
- Virology Department, Institute of Medical Microbiology and Virology, Leipzig University Hospital, Johannisalle 30, 04103 Leipzig, Germany
- Interdisciplinary Center for Infectious Diseases, Leipzig University Hospital, Liebigstrasse 20, 04103 Leipzig, Germany
| |
Collapse
|
7
|
Sanz-Muñoz I, Sánchez-de Prada L, Castrodeza-Sanz J, Eiros JM. Microbiological and epidemiological features of respiratory syncytial virus. REVISTA ESPANOLA DE QUIMIOTERAPIA : PUBLICACION OFICIAL DE LA SOCIEDAD ESPANOLA DE QUIMIOTERAPIA 2024; 37:209-220. [PMID: 38515332 PMCID: PMC11094634 DOI: 10.37201/req/006.2024] [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: 01/10/2024] [Revised: 02/09/2024] [Accepted: 02/23/2024] [Indexed: 03/23/2024]
Abstract
The properties of the main surface proteins and the viral cycle of the respiratory syncytial virus (RSV) make it an attractive pathogen from the perspective of microbiology. The virus gets its name from the manner it infects cells, which enables it to produce syncytia, which allow the virus' genetic material to move across cells without having to release viral offspring to the cellular exterior, reducing immune system identification. This causes a disease with a high impact in both children and adults over 60, which has sparked the development of several preventive interventions based on vaccines and monoclonal antibodies for both age groups. The epidemiological characteristics of this virus, which circulates in epidemics throughout the coldest months of the year and exhibits a marked genetic and antigenic drift due to its high mutation capability, must be taken into consideration while using these preventive methods. The most important microbiological and epidemiological elements of RSV are covered in this study, along with how they have affected the creation of preventive medications and their use in the future.
Collapse
Affiliation(s)
- I Sanz-Muñoz
- Dr. Iván Sanz-Muñoz, National Influenza Centre, Valladolid, Calle Rondilla de Santa Teresa s/n, Edificio Rondilla, Hospital Clínico Universitario de Valladolid, Valladolid, Spain.
| | | | | | | |
Collapse
|
8
|
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.
Collapse
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
| |
Collapse
|
9
|
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.
Collapse
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.)
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
10
|
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.
Collapse
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
| |
Collapse
|
11
|
Chorlton SD. Ten common issues with reference sequence databases and how to mitigate them. FRONTIERS IN BIOINFORMATICS 2024; 4:1278228. [PMID: 38560517 PMCID: PMC10978663 DOI: 10.3389/fbinf.2024.1278228] [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: 08/15/2023] [Accepted: 03/05/2024] [Indexed: 04/04/2024] Open
Abstract
Metagenomic sequencing has revolutionized our understanding of microbiology. While metagenomic tools and approaches have been extensively evaluated and benchmarked, far less attention has been given to the reference sequence database used in metagenomic classification. Issues with reference sequence databases are pervasive. Database contamination is the most recognized issue in the literature; however, it remains relatively unmitigated in most analyses. Other common issues with reference sequence databases include taxonomic errors, inappropriate inclusion and exclusion criteria, and sequence content errors. This review covers ten common issues with reference sequence databases and the potential downstream consequences of these issues. Mitigation measures are discussed for each issue, including bioinformatic tools and database curation strategies. Together, these strategies present a path towards more accurate, reproducible and translatable metagenomic sequencing.
Collapse
|
12
|
Cai W, Köndgen S, Tolksdorf K, Dürrwald R, Schuler E, Biere B, Schweiger B, Goerlitz L, Haas W, Wolff T, Buda S, Reiche J. Atypical age distribution and high disease severity in children with RSV infections during two irregular epidemic seasons throughout the COVID-19 pandemic, Germany, 2021 to 2023. Euro Surveill 2024; 29:2300465. [PMID: 38551098 PMCID: PMC10979527 DOI: 10.2807/1560-7917.es.2024.29.13.2300465] [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: 08/28/2023] [Accepted: 02/01/2024] [Indexed: 04/01/2024] Open
Abstract
BackgroundNon-pharmaceutical interventions (NPIs) during the COVID-19 pandemic affected respiratory syncytial virus (RSV) circulation worldwide.AimTo describe, for children aged < 5 years, the 2021 and 2022/23 RSV seasons in Germany.MethodsThrough data and 16,754 specimens from outpatient sentinel surveillance, we investigated RSV seasonality, circulating lineages, and affected children's age distributions in 2021 and 2022/23. Available information about disease severity from hospital surveillance was analysed for patients with RSV-specific diagnosis codes (n = 13,104). Differences between RSV seasons were assessed by chi-squared test and age distributions trends by Mann-Kendall test.ResultsRSV seasonality was irregular in 2021 (weeks 35-50) and 2022/23 (weeks 41-3) compared to pre-COVID-19 2011/12-2019/20 seasons (median weeks 51-12). RSV positivity rates (RSV-PR) were higher in 2021 (40% (522/1,291); p < 0.001) and 2022/23 (30% (299/990); p = 0.005) than in prior seasons (26% (1,430/5,511)). Known globally circulating RSV-A (lineages GA2.3.5 and GA2.3.6b) and RSV-B (lineage GB5.0.5a) strains, respectively, dominated in 2021 and 2022/23. In 2021, RSV-PRs were similar in 1 - < 2, 2 - < 3, 3 - < 4, and 4 - < 5-year-olds. RSV hospitalisation incidence in 2021 (1,114/100,000, p < 0.001) and in 2022/23 (1,034/100,000, p < 0.001) was approximately double that of previous seasons' average (2014/15-2019/20: 584/100,000). In 2022/23, proportions of RSV patients admitted to intensive care units rose (8.5% (206/2,413)) relative to pre-COVID-19 seasons (6.8% (551/8,114); p = 0.004), as did those needing ventilator support (6.1% (146/2,413) vs 3.8% (310/8,114); p < 0.001).ConclusionsHigh RSV-infection risk in 2-4-year-olds in 2021 and increased disease severity in 2022/23 possibly result from lower baseline population immunity, after NPIs diminished exposure to RSV.
Collapse
Affiliation(s)
- Wei Cai
- Unit 36, Respiratory Infections, Department of Infectious Disease Epidemiology, Robert Koch Institute, Berlin, Germany
| | - Sophie Köndgen
- Unit 17, Influenza and Other Respiratory Viruses, Department of Infectious Diseases, National Influenza Centre, Robert Koch Institute, Berlin, Germany
- Unit 17, Influenza and Other Respiratory Viruses, Department of Infectious Diseases, Consultant Laboratory for RSV, PIV and HMPV, Robert Koch Institute, Berlin, Germany
| | - Kristin Tolksdorf
- Unit 36, Respiratory Infections, Department of Infectious Disease Epidemiology, Robert Koch Institute, Berlin, Germany
| | - Ralf Dürrwald
- Unit 17, Influenza and Other Respiratory Viruses, Department of Infectious Diseases, National Influenza Centre, Robert Koch Institute, Berlin, Germany
- Unit 17, Influenza and Other Respiratory Viruses, Department of Infectious Diseases, Consultant Laboratory for RSV, PIV and HMPV, Robert Koch Institute, Berlin, Germany
| | | | - Barbara Biere
- Unit 17, Influenza and Other Respiratory Viruses, Department of Infectious Diseases, National Influenza Centre, Robert Koch Institute, Berlin, Germany
| | - Brunhilde Schweiger
- Unit 17, Influenza and Other Respiratory Viruses, Department of Infectious Diseases, National Influenza Centre, Robert Koch Institute, Berlin, Germany
| | - Luise Goerlitz
- Unit 36, Respiratory Infections, Department of Infectious Disease Epidemiology, Robert Koch Institute, Berlin, Germany
| | - Walter Haas
- Unit 36, Respiratory Infections, Department of Infectious Disease Epidemiology, Robert Koch Institute, Berlin, Germany
| | - Thorsten Wolff
- Unit 17, Influenza and Other Respiratory Viruses, Department of Infectious Diseases, National Influenza Centre, Robert Koch Institute, Berlin, Germany
- Unit 17, Influenza and Other Respiratory Viruses, Department of Infectious Diseases, Consultant Laboratory for RSV, PIV and HMPV, Robert Koch Institute, Berlin, Germany
| | - Silke Buda
- Unit 36, Respiratory Infections, Department of Infectious Disease Epidemiology, Robert Koch Institute, Berlin, Germany
| | - Janine Reiche
- Unit 17, Influenza and Other Respiratory Viruses, Department of Infectious Diseases, National Influenza Centre, Robert Koch Institute, Berlin, Germany
- Unit 17, Influenza and Other Respiratory Viruses, Department of Infectious Diseases, Consultant Laboratory for RSV, PIV and HMPV, Robert Koch Institute, Berlin, Germany
| |
Collapse
|
13
|
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.
Collapse
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
| |
Collapse
|
14
|
Presser LD, van den Akker WMR, Meijer A. Respiratory Syncytial Virus European Laboratory Network 2022 Survey: Need for Harmonization and Enhanced Molecular Surveillance. J Infect Dis 2024; 229:S34-S39. [PMID: 37578049 DOI: 10.1093/infdis/jiad341] [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: 06/30/2023] [Revised: 08/01/2023] [Accepted: 08/10/2023] [Indexed: 08/15/2023] Open
Abstract
Respiratory syncytial virus (RSV) is a common pathogen causing mostly cold-like symptoms, but in very young infants and elderly individuals it can lead to severe disease and even death. There are currently promising developments both in vaccine development and in therapeutics that are expected to be approved soon. To get an impression within European countries of the laboratory diagnostics and surveillance activities, in anticipation of these developments, we queried the members of the European Respiratory Syncytial Virus Laboratory Network (RSV-LabNet, under the umbrella of the PROMISE project) via an online survey. The answers from the consortium members showed scattered monitoring and the application of a broad array of techniques in the laboratories. A majority of the members expressed strong interest in harmonization and collaboration for setting up surveillance programs and the need for sharing laboratory protocols. The additional value of RSV whole-genome sequencing is broadly appreciated, but implementation requires further development and closer collaboration. The RSV-LabNet can have an important responsibility in establishing contacts and exchange of expertise and providing a platform for communication to advance diagnostics, preparedness, and surveillance.
Collapse
Affiliation(s)
- Lance D Presser
- Centre for Infectious Diseases Research, Diagnostics and Laboratory Surveillance, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Willem M R van den Akker
- Centre for Infectious Diseases Research, Diagnostics and Laboratory Surveillance, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Adam Meijer
- Centre for Infectious Diseases Research, Diagnostics and Laboratory Surveillance, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| |
Collapse
|
15
|
Vazquez-Pérez JA, Martínez-Alvarado E, Venancio-Landeros AA, Santiago-Olivares C, Mejía-Nepomuceno F, Mendoza-Ramírez E, Rivera-Toledo E. An amplicon-based protocol for whole-genome sequencing of human respiratory syncytial virus subgroup A. Biol Methods Protoc 2024; 9:bpae007. [PMID: 38371356 PMCID: PMC10873904 DOI: 10.1093/biomethods/bpae007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 02/16/2024] [Accepted: 02/16/2024] [Indexed: 02/20/2024] Open
Abstract
It is convenient to study complete genome sequences of human respiratory syncytial virus (hRSV) for ongoing genomic characterization and identification of highly transmissible or pathogenic variants. Whole genome sequencing of hRSV has been challenging from respiratory tract specimens with low viral loads. Herein, we describe an amplicon-based protocol for whole genome sequencing of hRSV subgroup A validated with 24 isolates from nasopharyngeal swabs and infected cell cultures, which showed cycle threshold (Ct) values ranging from 10 to 31, as determined by quantitative reverse-transcription polymerase chain reaction. MinION nanopore generated 3200 to 5400 reads per sample to sequence over 93% of the hRSV-A genome. Coverage of each contig ranged from 130× to 200×. Samples with Ct values of 20.9, 25.2, 27.1, 27.7, 28.2, 28.8, and 29.6 led to the sequencing of over 99.0% of the virus genome, indicating high genome coverage even at high Ct values. This protocol enables the identification of hRSV subgroup A genotypes, as primers were designed to target highly conserved regions. Consequently, it holds potential for application in molecular epidemiology and surveillance of this hRSV subgroup.
Collapse
Affiliation(s)
| | - Eber Martínez-Alvarado
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad Universitaria, Coyoacán, 04510, Mexico City, Mexico
| | | | - Carlos Santiago-Olivares
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad Universitaria, Coyoacán, 04510, Mexico City, Mexico
| | | | | | - Evelyn Rivera-Toledo
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad Universitaria, Coyoacán, 04510, Mexico City, Mexico
| |
Collapse
|
16
|
Meier K, Riepl A, Voitl P, Lischka L, Voitl JJM, Langer K, Kuzio U, Redlberger-Fritz M, Diesner-Treiber SC. Characterisation of RSV infections in children without chronic diseases aged 0-36 months during the post-COVID-19 winter season 2022/2023. Front Pediatr 2024; 12:1342399. [PMID: 38379907 PMCID: PMC10876782 DOI: 10.3389/fped.2024.1342399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 01/25/2024] [Indexed: 02/22/2024] Open
Abstract
Background Respiratory syncytial virus (RSV) is one of the leading causes of hospitalisation, morbidity, and mortality due to respiratory infection in the first years of life. This longitudinal prospective study outlines the 2022/23 season's viral patterns in Austria after the epidemiological changes determined by public health measures. We aimed to highlight differences within the RSV subtypes and genotypes in 0-36-month-old children without chronic diseases in the outpatient setting. Methods From November 2022 to March 2023 children younger than 36 months admitted to Vienna's largest paediatric primary healthcare centre with an acute respiratory infection were enrolled in this study. Nasal swabs and multiplex PCR panels detected 20 viruses including RSV subtypes and genotypes. Clinical presentation, features, and treatment of the participants were documented and analysed using the Modified Tal Score (MTS). Patients were scheduled for a telemedical follow-up one week after the initial appointment. Analysis was done using descriptive statistics, including Cramér V and binominal logarithmic regression. Results Among the 345 samples from 329 children, RSV was the most common virus (31.9%), followed by influenza (17.5%) and rhinovirus infections (20.58%). Of the RSV positive samples, only 13 cases were RSV subtype A (11.8%), whereas 97 were of subtype B (87.3%); ON1 and BA9 were the only detectable RSV genotypes (ON1: BA9 = 1:9.25). RSV was the main predictor of hospitalisation (OR: 7.5, 95% CI: (1.46-38.40), and age had a significant but smaller effect (OR: 0.89, 95% CI: (0.81-0.99). Almost all patients' clinical status improved within the first days. Conclusion RSV cases showed a rapid onset in late November 2022, and subtype B was predominant throughout the season. RSV infection was associated with higher hospitalisation rates, even after excluding high-risk patients (preterm and severe chronic diseases population).Further testing in the upcoming winter seasons will improve our knowledge of the dominant subtype and its association with disease severity, especially with the development of novel RSV vaccine candidates.
Collapse
Affiliation(s)
| | - Angela Riepl
- First Vienna Pediatric Medical Center, Vienna, Austria
| | - Peter Voitl
- First Vienna Pediatric Medical Center, Vienna, Austria
- Sigmund Freud University Vienna, Vienna, Austria
| | - Lena Lischka
- First Vienna Pediatric Medical Center, Vienna, Austria
| | | | - Klara Langer
- First Vienna Pediatric Medical Center, Vienna, Austria
| | - Ulrike Kuzio
- First Vienna Pediatric Medical Center, Vienna, Austria
| | | | | |
Collapse
|
17
|
Simbulan AM, Banico EC, Sira EMJS, Odchimar NMO, Orosco FL. Immunoinformatics-guided approach for designing a pan-proteome multi-epitope subunit vaccine against African swine fever virus. Sci Rep 2024; 14:1354. [PMID: 38228670 DOI: 10.1038/s41598-023-51005-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 12/29/2023] [Indexed: 01/18/2024] Open
Abstract
Despite being identified over a hundred years ago, there is still no commercially available vaccine for the highly contagious and deadly African swine fever virus (ASFV). This study used immunoinformatics for the rapid and inexpensive designing of a safe and effective multi-epitope subunit vaccine for ASFV. A total of 18,858 proteins from 100 well-annotated ASFV proteomes were screened using various computational tools to identify potential epitopes, or peptides capable of triggering an immune response in swine. Proteins from genotypes I and II were prioritized for their involvement in the recent global ASFV outbreaks. The screened epitopes exhibited promising qualities that positioned them as effective components of the ASFV vaccine. They demonstrated antigenicity, immunogenicity, and cytokine-inducing properties indicating their ability to induce potent immune responses. They have strong binding affinities to multiple swine allele receptors suggesting a high likelihood of yielding more amplified responses. Moreover, they were non-allergenic and non-toxic, a crucial prerequisite for ensuring safety and minimizing any potential adverse effects when the vaccine is processed within the host. Integrated with an immunogenic 50S ribosomal protein adjuvant and linkers, the epitopes formed a 364-amino acid multi-epitope subunit vaccine. The ASFV vaccine construct exhibited notable immunogenicity in immune simulation and molecular docking analyses, and stable profiles in secondary and tertiary structure assessments. Moreover, this study designed an optimized codon for efficient translation of the ASFV vaccine construct into the Escherichia coli K-12 expression system using the pET28a(+) vector. Overall, both sequence and structural evaluations suggested the potential of the ASFV vaccine construct as a candidate for controlling and eradicating outbreaks caused by the pathogen.
Collapse
Affiliation(s)
- Alea Maurice Simbulan
- Department of Science and Technology, Virology and Vaccine Research and Development Program, Industrial Technology Development Institute, Bicutan, 1634, Taguig, Metro Manila, Philippines
| | - Edward C Banico
- Department of Science and Technology, Virology and Vaccine Research and Development Program, Industrial Technology Development Institute, Bicutan, 1634, Taguig, Metro Manila, Philippines
| | - Ella Mae Joy S Sira
- Department of Science and Technology, Virology and Vaccine Research and Development Program, Industrial Technology Development Institute, Bicutan, 1634, Taguig, Metro Manila, Philippines
| | - Nyzar Mabeth O Odchimar
- Department of Science and Technology, Virology and Vaccine Research and Development Program, Industrial Technology Development Institute, Bicutan, 1634, Taguig, Metro Manila, Philippines
| | - Fredmoore L Orosco
- Department of Science and Technology, Virology and Vaccine Research and Development Program, Industrial Technology Development Institute, Bicutan, 1634, Taguig, Metro Manila, Philippines.
- Department of Science and Technology, S&T Fellows Program, Bicutan, 1634, Taguig, Metro Manila, Philippines.
- Department of Biology, University of the Philippines Manila, 1000, Manila, Philippines.
| |
Collapse
|
18
|
Guo CY, Zhang Y, Zhang YY, Zhao W, Peng XL, Zheng YP, Fu YH, Yu JM, He JS. Comparative analysis of human respiratory syncytial virus evolutionary patterns during the COVID-19 pandemic and pre-pandemic periods. Front Microbiol 2023; 14:1298026. [PMID: 38111642 PMCID: PMC10725919 DOI: 10.3389/fmicb.2023.1298026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 11/07/2023] [Indexed: 12/20/2023] Open
Abstract
The COVID-19 pandemic has resulted in the implementation of strict mitigation measures that have impacted the transmission dynamics of human respiratory syncytial virus (HRSV). The measures also have the potential to influence the evolutionary patterns of the virus. In this study, we conducted a comprehensive analysis comparing genomic variations and evolving characteristics of its neutralizing antigens, specifically F and G proteins, before and during the COVID-19 pandemic. Our findings showed that both HRSV A and B exhibited an overall chronological evolutionary pattern. For the sequences obtained during the pandemic period (2019-2022), we observed that the HRSV A distributed in A23 genotype, but formed into three subclusters; whereas the HRSV B sequences were relatively concentrated within genotype B6. Additionally, multiple positively selected sites were detected on F and G proteins but none were located at neutralizing antigenic sites of the F protein. Notably, amino acids within antigenic site III, IV, and V of F protein remained strictly conserved, while some substitutions occurred over time on antigenic site Ø, I, II and VIII; substitution S389P on antigenic site I of HRSV B occurred during the pandemic period with nearly 50% frequency. However, further analysis revealed no substitutions have altered the structural conformations of the antigenic sites, the vial antigenicity has not been changed. We inferred that the intensive public health interventions during the COVID-19 pandemic did not affect the evolutionary mode of HRSV.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Jie-mei Yu
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, China
| | - Jin-sheng He
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, China
| |
Collapse
|
19
|
Fleming JA, Baral R, Higgins D, Khan S, Kochar S, Li Y, Ortiz JR, Cherian T, Feikin D, Jit M, Karron RA, Limaye RJ, Marshall C, Munywoki PK, Nair H, Newhouse LC, Nyawanda BO, Pecenka C, Regan K, Srikantiah P, Wittenauer R, Zar HJ, Sparrow E. Value profile for respiratory syncytial virus vaccines and monoclonal antibodies. Vaccine 2023; 41 Suppl 2:S7-S40. [PMID: 37422378 DOI: 10.1016/j.vaccine.2022.09.081] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 09/26/2022] [Accepted: 09/27/2022] [Indexed: 07/10/2023]
Abstract
Respiratory syncytial virus (RSV) is the predominant cause of acute lower respiratory infection (ALRI) in young children worldwide, yet no licensed RSV vaccine exists to help prevent the millions of illnesses and hospitalizations and tens of thousands of young lives taken each year. Monoclonal antibody (mAb) prophylaxis exists for prevention of RSV in a small subset of very high-risk infants and young children, but the only currently licensed product is impractical, requiring multiple doses and expensive for the low-income settings where the RSV disease burden is greatest. A robust candidate pipeline exists to one day prevent RSV disease in infant and pediatric populations, and it focuses on two promising passive immunization approaches appropriate for low-income contexts: maternal RSV vaccines and long-acting infant mAbs. Licensure of one or more candidates is feasible over the next one to three years and, depending on final product characteristics, current economic models suggest both approaches are likely to be cost-effective. Strong coordination between maternal and child health programs and the Expanded Program on Immunization will be needed for effective, efficient, and equitable delivery of either intervention. This 'Vaccine Value Profile' (VVP) for RSV is intended to provide a high-level, holistic assessment of the information and data that are currently available to inform the potential public health, economic and societal value of pipeline vaccines and vaccine-like products. This VVP was developed by a working group of subject matter experts from academia, non-profit organizations, public private partnerships and multi-lateral organizations, and in collaboration with stakeholders from the WHO headquarters. All contributors have extensive expertise on various elements of the RSV VVP and collectively aimed to identify current research and knowledge gaps. The VVP was developed using only existing and publicly available information.
Collapse
Affiliation(s)
- Jessica A Fleming
- Center for Vaccine Innovation and Access, PATH, 2201 Westlake Ave Suite 200, Seattle, WA 98121, United States.
| | - Ranju Baral
- Center for Vaccine Innovation and Access, PATH, 2201 Westlake Ave Suite 200, Seattle, WA 98121, United States.
| | - Deborah Higgins
- Center for Vaccine Innovation and Access, PATH, 2201 Westlake Ave Suite 200, Seattle, WA 98121, United States.
| | - Sadaf Khan
- Maternal, Newborn, Child Health and Nutrition, PATH, 2201 Westlake Ave Suite 200, Seattle, WA 98121, United States.
| | - Sonali Kochar
- Global Healthcare Consulting and Department of Global Health, University of Washington, Hans Rosling Center, 3980 15th Ave NE, Seattle, WA 98105, United States.
| | - You Li
- School of Public Health, Nanjing Medical University, No. 101 Longmian Avenue, Jiangning District, Nanjing, Jiangsu Province 211166, PR China.
| | - Justin R Ortiz
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, 685 West Baltimore Street, Baltimore, MD 21201-1509, United States.
| | - Thomas Cherian
- MMGH Consulting GmbH, Kuerbergstrasse 1, 8049 Zurich, Switzerland.
| | - Daniel Feikin
- Department of Immunization, Vaccines and Biologicals, World Health Organization, Avenue Appia 20, 1211 Geneva 27, Switzerland.
| | - Mark Jit
- London School of Hygiene & Tropical Medicine, University of London, Keppel St, London WC1E 7HT, United Kingdom.
| | - Ruth A Karron
- Center for Immunization Research, Johns Hopkins University, Department of International Health, 624 N. Broadway, Rm 117, Baltimore, MD 21205, United States.
| | - Rupali J Limaye
- International Health, Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Street, Baltimore, MD 21205, United States.
| | - Caroline Marshall
- Department of Immunization, Vaccines and Biologicals, World Health Organization, Avenue Appia 20, 1211 Geneva 27, Switzerland.
| | - Patrick K Munywoki
- Center for Disease Control and Prevention, KEMRI Complex, Mbagathi Road off Mbagathi Way, PO Box 606-00621, Village Market, Nairobi, Kenya.
| | - Harish Nair
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh EH8 9AG, United Kingdom.
| | - Lauren C Newhouse
- Center for Vaccine Innovation and Access, PATH, 2201 Westlake Ave Suite 200, Seattle, WA 98121, United States.
| | - Bryan O Nyawanda
- Kenya Medical Research Institute, Hospital Road, P.O. Box 1357, Kericho, Kenya.
| | - Clint Pecenka
- Center for Vaccine Innovation and Access, PATH, 2201 Westlake Ave Suite 200, Seattle, WA 98121, United States.
| | - Katie Regan
- Center for Vaccine Innovation and Access, PATH, 2201 Westlake Ave Suite 200, Seattle, WA 98121, United States.
| | - Padmini Srikantiah
- Bill & Melinda Gates Foundation, 500 5th Ave N, Seattle, WA 98109, United States.
| | - Rachel Wittenauer
- Department of Pharmacy, University of Washington, Health Sciences Building, 1956 NE Pacific St H362, Seattle, WA 98195, United States.
| | - Heather J Zar
- Department of Paediatrics & Child Health and SA-MRC Unit on Child & Adolescent Health, Red Cross Children's Hospital, University of Cape Town, Klipfontein Road, Rondebosch, Cape Town 7700, South Africa.
| | - Erin Sparrow
- Department of Immunization, Vaccines and Biologicals, World Health Organization, Avenue Appia 20, 1211 Geneva 27, Switzerland.
| |
Collapse
|
20
|
Holland LA, Holland SC, Smith MF, Leonard VR, Murugan V, Nordstrom L, Mulrow M, Salgado R, White M, Lim ES. Genomic Sequencing Surveillance to Identify Respiratory Syncytial Virus Mutations, Arizona, USA. Emerg Infect Dis 2023; 29:2380-2382. [PMID: 37705075 PMCID: PMC10617361 DOI: 10.3201/eid2911.230836] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/15/2023] Open
Abstract
We conducted surveillance of respiratory syncytial virus (RSV) genomic sequences for 100 RSV-A and 27 RSV-B specimens collected during November 2022-April 2023 in Arizona, USA. We identified mutations within prefusion F-protein antigenic sites in both subtypes. Continued genomic surveillance will be critical to ensure RSV vaccine effectiveness.
Collapse
|
21
|
Trang UTH, Phuong HVM, Hoang NH, Son NV, Thanh LT, Hang NLK, Cuong VD, Huong TTT, Hien NT, Anh NP, Mai LQ. Circulation of human respiratory syncytial virus and new ON1 genotype in northern Viet Nam, 2017-2020. Western Pac Surveill Response J 2023; 14:1-9. [PMID: 38021214 PMCID: PMC10646430 DOI: 10.5365/wpsar.2023.14.4.990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2023] Open
Abstract
Objective Human respiratory syncytial virus (RSV) is a primary cause of paediatric severe acute respiratory infection (SARI) worldwide, especially in developing countries. We investigated the genetic characteristics of RSV in northern Viet Nam to determine the prevalence and distribution of subtypes as well as the diversity and transmission patterns of genotypes. Methods In two facilities, from January 2017 to December 2020, 1563 clinical specimens were collected from paediatric patients hospitalized with SARI and tested for RSV. Selected positive samples underwent sequencing analysis targeting the second hypervariable region of the G gene using next-generation sequencing. Results The RSV positivity rate was 28.02% (438/1563 samples), and prevalence was highest in children aged < 1 year (43.84%; 192/438). Subtype RSV-A accounted for 53.42% (234/438) of cases, RSV-B for 45.89% (201/438), and there was coinfection in 0.68% (3/438). Both subtypes cocirculated and peaked during August-September in each year of the study. Phylogenetic analysis showed that RSV-A samples belonged to the ON1 genotype, which has three subgenotypes: ON1.1, ON1.2 and ON1.3. However, we did not find the 72-nucleotide duplication in the second hypervariable region of the G gene, a characteristic of genotype ON1, in any RSV-A samples. RSV-B samples belonged to genotype BA9. Discussion Our results provide additional molecular characterization of RSV infections in Viet Nam. Specially, our study is the first to report the absence of the 72-nucleotide duplication in the G gene of RSV-A genotype ON1 in Viet Nam, which may help in understanding the genetic evolution of RSV and be useful for vaccine development in the future.
Collapse
Affiliation(s)
- Ung Thi Hong Trang
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Viet Nam
- National Institute of Hygiene and Epidemiology, Hanoi, Viet Nam
| | | | - Nguyen Huy Hoang
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Viet Nam
- Institute of Genome Research, Vietnam Academy of Science and Technology, Hanoi, Viet Nam
| | - Nguyen Vu Son
- National Institute of Hygiene and Epidemiology, Hanoi, Viet Nam
| | - Le Thi Thanh
- National Institute of Hygiene and Epidemiology, Hanoi, Viet Nam
| | | | - Vuong Duc Cuong
- National Institute of Hygiene and Epidemiology, Hanoi, Viet Nam
| | | | - Nguyen Thi Hien
- National Institute of Hygiene and Epidemiology, Hanoi, Viet Nam
| | | | - Le Quynh Mai
- National Institute of Hygiene and Epidemiology, Hanoi, Viet Nam
| |
Collapse
|
22
|
Tramuto F, Maida CM, Mazzucco W, Costantino C, Amodio E, Sferlazza G, Previti A, Immordino P, Vitale F. Molecular Epidemiology and Genetic Diversity of Human Respiratory Syncytial Virus in Sicily during Pre- and Post-COVID-19 Surveillance Seasons. Pathogens 2023; 12:1099. [PMID: 37764907 PMCID: PMC10534943 DOI: 10.3390/pathogens12091099] [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: 07/21/2023] [Revised: 08/23/2023] [Accepted: 08/26/2023] [Indexed: 09/29/2023] Open
Abstract
Human respiratory syncytial virus (hRSV) is an important pathogen of acute respiratory tract infection of global significance. In this study, we investigated the molecular epidemiology and the genetic variability of hRSV over seven surveillance seasons between 2015 and 2023 in Sicily, Italy. hRSV subgroups co-circulated through every season, although hRSV-B mostly prevailed. After the considerable reduction in the circulation of hRSV due to the widespread implementation of non-pharmaceutical preventive measures during the COVID-19 pandemic, hRSV rapidly re-emerged at a high intensity in 2022-2023. The G gene was sequenced for genotyping and analysis of deduced amino acids. A total of 128 hRSV-A and 179 hRSV-B G gene sequences were obtained. The phylogenetic analysis revealed that the GA2.3.5a (ON1) and GB5.0.5a (BA9) genotypes were responsible for the hRSV epidemics in Sicily.; only one strain belonged to the genotype GB5.0.4a. No differences were observed in the circulating genotypes during pre- and post-pandemic years. Amino acid sequence alignment revealed the continuous evolution of the G gene, with a combination of amino acid changes specifically appearing in 2022-2023. The predicted N-glycosylation sites were relatively conserved in ON1 and BA9 genotype strains. Our findings augment the understanding and prediction of the seasonal evolution of hRSV at the local level and its implication in the monitoring of novel variants worth considering in better design of candidate vaccines.
Collapse
Affiliation(s)
- Fabio Tramuto
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties “G. D’Alessandro”—Hygiene Section, University of Palermo, 90134 Palermo, Italy; (C.M.M.); (W.M.); (C.C.); (E.A.); (P.I.); (F.V.)
- Regional Reference Laboratory for Molecular Surveillance of Influenza, Clinical Epidemiology Unit, University Hospital “Paolo Giaccone”, 90127 Palermo, Italy; (G.S.); (A.P.)
| | - Carmelo Massimo Maida
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties “G. D’Alessandro”—Hygiene Section, University of Palermo, 90134 Palermo, Italy; (C.M.M.); (W.M.); (C.C.); (E.A.); (P.I.); (F.V.)
- Regional Reference Laboratory for Molecular Surveillance of Influenza, Clinical Epidemiology Unit, University Hospital “Paolo Giaccone”, 90127 Palermo, Italy; (G.S.); (A.P.)
| | - Walter Mazzucco
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties “G. D’Alessandro”—Hygiene Section, University of Palermo, 90134 Palermo, Italy; (C.M.M.); (W.M.); (C.C.); (E.A.); (P.I.); (F.V.)
- Regional Reference Laboratory for Molecular Surveillance of Influenza, Clinical Epidemiology Unit, University Hospital “Paolo Giaccone”, 90127 Palermo, Italy; (G.S.); (A.P.)
| | - Claudio Costantino
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties “G. D’Alessandro”—Hygiene Section, University of Palermo, 90134 Palermo, Italy; (C.M.M.); (W.M.); (C.C.); (E.A.); (P.I.); (F.V.)
- Regional Reference Laboratory for Molecular Surveillance of Influenza, Clinical Epidemiology Unit, University Hospital “Paolo Giaccone”, 90127 Palermo, Italy; (G.S.); (A.P.)
| | - Emanuele Amodio
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties “G. D’Alessandro”—Hygiene Section, University of Palermo, 90134 Palermo, Italy; (C.M.M.); (W.M.); (C.C.); (E.A.); (P.I.); (F.V.)
| | - Giuseppe Sferlazza
- Regional Reference Laboratory for Molecular Surveillance of Influenza, Clinical Epidemiology Unit, University Hospital “Paolo Giaccone”, 90127 Palermo, Italy; (G.S.); (A.P.)
| | - Adriana Previti
- Regional Reference Laboratory for Molecular Surveillance of Influenza, Clinical Epidemiology Unit, University Hospital “Paolo Giaccone”, 90127 Palermo, Italy; (G.S.); (A.P.)
| | - Palmira Immordino
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties “G. D’Alessandro”—Hygiene Section, University of Palermo, 90134 Palermo, Italy; (C.M.M.); (W.M.); (C.C.); (E.A.); (P.I.); (F.V.)
| | - Francesco Vitale
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties “G. D’Alessandro”—Hygiene Section, University of Palermo, 90134 Palermo, Italy; (C.M.M.); (W.M.); (C.C.); (E.A.); (P.I.); (F.V.)
- Regional Reference Laboratory for Molecular Surveillance of Influenza, Clinical Epidemiology Unit, University Hospital “Paolo Giaccone”, 90127 Palermo, Italy; (G.S.); (A.P.)
| |
Collapse
|
23
|
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.
Collapse
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
| |
Collapse
|
24
|
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.
Collapse
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
| |
Collapse
|
25
|
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.
Collapse
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
| |
Collapse
|
26
|
Influence of Sex on Respiratory Syncytial Virus Genotype Infection Frequency and Nasopharyngeal Microbiome. J Virol 2023; 97:e0147222. [PMID: 36815771 PMCID: PMC10062153 DOI: 10.1128/jvi.01472-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023] Open
Abstract
Respiratory syncytial virus (RSV) has a significant health burden in children, older adults, and the immunocompromised. However, limited effort has been made to identify emergence of new RSV genotypes' frequency of infection and how the combination of nasopharyngeal microbiome and viral genotypes impact RSV disease outcomes. In an observational cohort designed to capture the first infant RSV infection, we employed multi-omics approaches to sequence 349 RSV complete genomes and matched nasopharyngeal microbiomes, during which the 2012/2013 season was dominated by RSV-A, whereas 2013 and 2014 was dominated by RSV-B. We found non-G-72nt-duplicated RSV-A strains were more frequent in male infants (P = 0.02), whereas G-72nt-duplicated genotypes (which is ON1 lineage) were seen equally in both males and females. DESeq2 testing of the nasal microbiome showed Haemophilus was significantly more abundant in infants with RSV-A infection compared to infants with RSV-B infection (adjusted P = 0.002). In addition, the broad microbial clustering of the abundant genera was significantly associated with infant sex (P = 0.03). Overall, we show sex differences in infection by RSV genotype and host nasopharyngeal microbiome, suggesting an interaction between host genetics, virus genotype, and associated nasopharyngeal microbiome. IMPORTANCE Respiratory syncytial virus (RSV) is one of the leading causes of lower respiratory tract infections in young children and is responsible for high hospitalization rates and morbidity in infants and the elderly. To understand how the emergence of RSV viral genotypes and viral-respiratory microbiome interactions contribute to infection frequency and severity, we utilized an observational cohort designed to capture the first infant RSV infection we employed multi-omics approaches to sequence 349 RSV complete genomes and matched nasopharyngeal microbiomes. We found non-G-72nt-duplicated RSV-A genotypes were more frequent in male infants, whereas G-72nt-duplicated RSV-A strains (ON1 lineage) were seen equally in both males and females. Microbiome analysis show Haemophilus was significantly more abundant in infants with RSV-A compared to infants with RSV-B infection and the microbial clustering of the abundant genera was associated with infant sex. Overall, we show sex differences in RSV genotype-nasopharyngeal microbiome, suggesting an interaction host genetics-virus-microbiome interaction.
Collapse
|
27
|
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.
Collapse
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
| |
Collapse
|
28
|
Rios Guzman E, Hultquist JF. Clinical and biological consequences of respiratory syncytial virus genetic diversity. Ther Adv Infect Dis 2022; 9:20499361221128091. [PMID: 36225856 PMCID: PMC9549189 DOI: 10.1177/20499361221128091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 08/30/2022] [Indexed: 11/17/2022] Open
Abstract
Respiratory syncytial virus (RSV) is one of the most common etiological agents of global acute respiratory tract infections with a disproportionate burden among infants, individuals over the age of 65, and immunocompromised populations. The two major subtypes of RSV (A and B) co-circulate with a predominance of either group during different epidemic seasons, with frequently emerging genotypes due to RSV's high genetic variability. Global surveillance systems have improved our understanding of seasonality, disease burden, and genomic evolution of RSV through genotyping by sequencing of attachment (G) glycoprotein. However, the integration of these systems into international infrastructures is in its infancy, resulting in a relatively low number (~2200) of publicly available RSV genomes. These limitations in surveillance hinder our ability to contextualize RSV evolution past current canonical attachment glycoprotein (G)-oriented understanding, thus resulting in gaps in understanding of how genetic diversity can play a role in clinical outcome, therapeutic efficacy, and the host immune response. Furthermore, utilizing emerging RSV genotype information from surveillance and testing the impact of viral evolution using molecular techniques allows us to establish causation between the clinical and biological consequences of arising genotypes, which subsequently aids in informed vaccine design and future vaccination strategy. In this review, we aim to discuss the findings from current molecular surveillance efforts and the gaps in knowledge surrounding the consequence of RSV genetic diversity on disease severity, therapeutic efficacy, and RSV-host interactions.
Collapse
Affiliation(s)
- Estefany Rios Guzman
- Department of Medicine, Division of Infectious
Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL,
USA
- Center for Pathogen Genomics and Microbial
Evolution, Institute for Global Health, Northwestern University Feinberg
School of Medicine, Chicago, IL, USA
| | - Judd F. Hultquist
- Robert H. Lurie Medical Research Center,
Northwestern University, 9-141, 303 E. Superior St., Chicago, IL 60611,
USA
- Department of Medicine, Division of Infectious
Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL,
USA
- Center for Pathogen Genomics and Microbial
Evolution, Institute for Global Health, Northwestern University Feinberg
School of Medicine, Chicago, IL, USA
| |
Collapse
|
29
|
Saito M, Tsukagoshi H, Sada M, Sunagawa S, Shirai T, Okayama K, Sugai T, Tsugawa T, Hayashi Y, Ryo A, Takeda M, Kawashima H, Saruki N, Kimura H. Detailed Evolutionary Analyses of the F Gene in the Respiratory Syncytial Virus Subgroup A. Viruses 2021; 13:v13122525. [PMID: 34960794 PMCID: PMC8706373 DOI: 10.3390/v13122525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 12/06/2021] [Accepted: 12/13/2021] [Indexed: 11/20/2022] Open
Abstract
We performed evolution, phylodynamics, and reinfection-related antigenicity analyses of respiratory syncytial virus subgroup A (RSV-A) fusion (F) gene in globally collected strains (1465 strains) using authentic bioinformatics methods. The time-scaled evolutionary tree using the Bayesian Markov chain Monte Carlo method estimated that a common ancestor of the RSV-A, RSV-B, and bovine-RSV diverged at around 450 years ago, and RSV-A and RSV-B diverged around 250 years ago. Finally, the RSV-A F gene formed eight genotypes (GA1-GA7 and NA1) over the last 80 years. Phylodynamics of RSV-A F gene, including all genotype strains, increased twice in the 1990s and 2010s, while patterns of each RSV-A genotype were different. Phylogenetic distance analysis suggested that the genetic distances of the strains were relatively short (less than 0.05). No positive selection sites were estimated, while many negative selection sites were found. Moreover, the F protein 3D structure mapping and conformational epitope analysis implied that the conformational epitopes did not correspond to the neutralizing antibody binding sites of the F protein. These results suggested that the RSV-A F gene is relatively conserved, and mismatches between conformational epitopes and neutralizing antibody binding sites of the F protein are responsible for the virus reinfection.
Collapse
Affiliation(s)
- Mariko Saito
- Gunma Prefectural Institute of Public Health and Environmental Sciences, Maebashi-shi 371-0052, Japan; (M.S.); (H.T.); (N.S.)
| | - Hiroyuki Tsukagoshi
- Gunma Prefectural Institute of Public Health and Environmental Sciences, Maebashi-shi 371-0052, Japan; (M.S.); (H.T.); (N.S.)
| | - Mitsuru Sada
- Department of Health Science, Gunma Paz University Graduate School, Takasaki-shi 370-0006, Japan; (M.S.); (S.S.); (K.O.); (Y.H.)
| | - Soyoka Sunagawa
- Department of Health Science, Gunma Paz University Graduate School, Takasaki-shi 370-0006, Japan; (M.S.); (S.S.); (K.O.); (Y.H.)
| | - Tatsuya Shirai
- Department of Respiratory Medicine, Kyorin University School of Medicine, Mitaka-shi 181-8611, Japan;
| | - Kaori Okayama
- Department of Health Science, Gunma Paz University Graduate School, Takasaki-shi 370-0006, Japan; (M.S.); (S.S.); (K.O.); (Y.H.)
| | - Toshiyuki Sugai
- Division of Nursing Science, Hiroshima University, Hiroshima-shi 734-8551, Japan;
| | - Takeshi Tsugawa
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo-shi 060-8543, Japan;
| | - Yuriko Hayashi
- Department of Health Science, Gunma Paz University Graduate School, Takasaki-shi 370-0006, Japan; (M.S.); (S.S.); (K.O.); (Y.H.)
| | - Akihide Ryo
- Department of Microbiology, Yokohama City University School of Medicine, Yokohama-shi 236-0004, Japan;
| | - Makoto Takeda
- Department of Virology, National Institute of Infectious Diseases, Musashimurayama-shi 208-0011, Japan;
| | - Hisashi Kawashima
- Department of Pediatrics, Tokyo Medical University, Shinjuku-ku 160-0023, Japan;
| | - Nobuhiro Saruki
- Gunma Prefectural Institute of Public Health and Environmental Sciences, Maebashi-shi 371-0052, Japan; (M.S.); (H.T.); (N.S.)
| | - Hirokazu Kimura
- Department of Health Science, Gunma Paz University Graduate School, Takasaki-shi 370-0006, Japan; (M.S.); (S.S.); (K.O.); (Y.H.)
- Correspondence: ; Tel.: +81-27-388-0336
| |
Collapse
|
30
|
Chen J, Qiu X, Avadhanula V, Shepard SS, Kim DK, Hixson J, Piedra PA, Bahl J. Novel and extendable genotyping system for human respiratory syncytial virus based on whole-genome sequence analysis. Influenza Other Respir Viruses 2021; 16:492-500. [PMID: 34894077 PMCID: PMC8983899 DOI: 10.1111/irv.12936] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 09/12/2021] [Accepted: 10/17/2021] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Human respiratory syncytial virus (RSV) is one of the leading causes of respiratory infections, especially in infants and young children. Previous RSV sequencing studies have primarily focused on partial sequencing of G gene (200-300 nucleotides) for genotype characterization or diagnostics. However, the genotype assignment with G gene has not recapitulated the phylogenetic signal of other genes, and there is no consensus on RSV genotype definition. METHODS We conducted maximum likelihood phylogenetic analysis with 10 RSV individual genes and whole-genome sequence (WGS) that are published in GenBank. RSV genotypes were determined by using phylogenetic analysis and pair-wise node distances. RESULTS In this study, we first statistically examined the phylogenetic incongruence, rate variation for each RSV gene sequence and WGS. We then proposed a new RSV genotyping system based on a comparative analysis of WGS and the temporal distribution of strains. We also provide an RSV classification tool to perform RSV genotype assignment and a publicly accessible up-to-date instance of Nextstrain where the phylogenetic relationship of all genotypes can be explored. CONCLUSIONS This revised RSV genotyping system will provide important information for disease surveillance, epidemiology, and vaccine development.
Collapse
Affiliation(s)
- Jiani Chen
- Center for Ecology of Infectious Diseases, Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - Xueting Qiu
- Department of Infectious Disease, University of Georgia, Athens, GA, USA.,Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Vasanthi Avadhanula
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Samuel S Shepard
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Do-Kyun Kim
- Department of Epidemiology, Human Genetics & Environmental Sciences, School of Public Health, University of Texas Health Science Center, Houston, TX, USA
| | - James Hixson
- Department of Epidemiology, Human Genetics & Environmental Sciences, School of Public Health, University of Texas Health Science Center, Houston, TX, USA
| | - Pedro A Piedra
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Justin Bahl
- Center for Ecology of Infectious Diseases, Institute of Bioinformatics, University of Georgia, Athens, GA, USA.,Department of Infectious Disease, University of Georgia, Athens, GA, USA.,Department of Epidemiology and Biostatistics, University of Georgia, Athens, GA, USA
| |
Collapse
|
31
|
Barona-Gómez F, Delaye L, Díaz-Valenzuela E, Plisson F, Cruz-Pérez A, Díaz-Sánchez M, García-Sepúlveda CA, Sanchez-Flores A, Pérez-Abreu R, Valencia-Valdespino FJ, Vega-Magaña N, Muñoz-Valle JF, García-González OP, Bernal-Silva S, Comas-García A, Cibrián-Jaramillo A. Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms. Microb Genom 2021; 7. [PMID: 34846283 PMCID: PMC8743546 DOI: 10.1099/mgen.0.000684] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Understanding the evolution of the SARS-CoV-2 virus in various regions of the world during the Covid-19 pandemic is essential to help mitigate the effects of this devastating disease. We describe the phylogenomic and population genetic patterns of the virus in Mexico during the pre-vaccination stage, including asymptomatic carriers. A real-time quantitative PCR screening and phylogenomic reconstructions directed at sequence/structure analysis of the spike glycoprotein revealed mutation of concern E484K in genomes from central Mexico, in addition to the nationwide prevalence of the imported variant 20C/S:452R (B.1.427/9). Overall, the detected variants in Mexico show spike protein mutations in the N-terminal domain (i.e. R190M), in the receptor-binding motif (i.e. T478K, E484K), within the S1-S2 subdomains (i.e. P681R/H, T732A), and at the basis of the protein, V1176F, raising concerns about the lack of phenotypic and clinical data available for the variants of interest we postulate: 20B/478K.V1 (B.1.1.222 or B.1.1.519) and 20B/P.4 (B.1.1.28.4). Moreover, the population patterns of single nucleotide variants from symptomatic and asymptomatic carriers obtained with a self-sampling scheme confirmed the presence of several fixed variants, and differences in allelic frequencies among localities. We identified the mutation N:S194L of the nucleocapsid protein associated with symptomatic patients. Phylogenetically, this mutation is frequent in Mexican sub-clades. Our results highlight the dual and complementary role of spike and nucleocapsid proteins in adaptive evolution of SARS-CoV-2 to their hosts and provide a baseline for specific follow-up of mutations of concern during the vaccination stage.
Collapse
Affiliation(s)
| | - Luis Delaye
- Departamento de Ingeniería Genética, Unidad Irapuato, Cinvestav-IPN, Irapuato, Guanajuato, México
| | - Erik Díaz-Valenzuela
- Unidad de Genómica Avanzada (Langebio), Cinvestav-IPN, Irapuato, Guanajuato, Mexico
| | - Fabien Plisson
- Conacyt - Unidad de Genómica Avanzada (Langebio), Cinvestav-IPN, Irapuato, Guanajuato, México
| | - Arely Cruz-Pérez
- Unidad de Genómica Avanzada (Langebio), Cinvestav-IPN, Irapuato, Guanajuato, Mexico
| | - Mauricio Díaz-Sánchez
- Molecular Biology Research & Development Department, GrupoT, Irapuato, Guanajuato, México
| | | | - Alejandro Sanchez-Flores
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Rafael Pérez-Abreu
- Centro de Investigación en Matemáticas AC (Cimat), Sede Aguascalientes, Aguascalientes, México
| | | | - Natali Vega-Magaña
- Laboratory for the Diagnosis of Emerging and Reemerging Diseases (LaDEER), University Center for Health Sciences, University of Guadalajara, Guadalajara, Jalisco, México
| | - José Francisco Muñoz-Valle
- Institute for Research in Biomedical Sciences, University Center for Health Sciences, University of Guadalajara, Guadalajara, Jalisco, México
| | | | - Sofía Bernal-Silva
- Centro de Investigación en Ciencias de la Salud y Biomedicina, Universidad Autónoma de San Luis Potosí, San Luis, San Luis Potosí, México
| | - Andreu Comas-García
- Centro de Investigación en Ciencias de la Salud y Biomedicina, Universidad Autónoma de San Luis Potosí, San Luis, San Luis Potosí, México
- Facultad de Medicina, Universidad Autónoma de San Luis Potosí, San Luis, San Luis Potosí, México
| | | |
Collapse
|
32
|
Molecular Characterization of the env Gene of Bovine Leukemia Virus in Cattle from Pakistan with NGS-Based Evidence of Virus Heterogeneity. Pathogens 2021; 10:pathogens10070910. [PMID: 34358060 PMCID: PMC8308526 DOI: 10.3390/pathogens10070910] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 07/14/2021] [Accepted: 07/16/2021] [Indexed: 11/17/2022] Open
Abstract
Characterization of the global genetic diversity of the bovine leukemia virus (BLV) is an ongoing international research effort. Up to now BLV sequences have been classified into eleven distinct genotypes. Although BLV genotyping and molecular analysis of field isolates were reported in many countries, there is no report describing BLV genotypes present in cattle from Pakistan. In this study we examined 27 env gene sequences from BLV-infected cattle coming from four farms located in Khyber Pakhtunkwa, Gilgit Baltisan and Punjab provinces. Phylogenetic analyses revealed the classification of Pakistani sequences into genotypes G1 and G6. The alignment with the FLK-BLV sequence revealed the presence of 45 mutations, namely, seven in genotype G1 and 33 in genotype G6. Five mutations were found in both, G1 and G6 genotypes. Twelve amino acid substitutions were found in the analyzed sequences, of which only one P264S was specific for sequences from Pakistan. Furthermore, a certain degree of nucleotide heterogeneity was identified by NGS. These results highlight the need for further study on the importance of genetic variability of BLV, especially in the context of its pathogenicity and potential effect on serological detection.
Collapse
|
33
|
Yu JM, Fu YH, Peng XL, Zheng YP, He JS. Genetic diversity and molecular evolution of human respiratory syncytial virus A and B. Sci Rep 2021; 11:12941. [PMID: 34155268 PMCID: PMC8217232 DOI: 10.1038/s41598-021-92435-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 06/08/2021] [Indexed: 01/10/2023] Open
Abstract
Human respiratory syncytial viruses (RSVs) are classified into two major groups (A and B) based on antigenic differences in the G glycoprotein. To investigate circulating characteristics and phylodynamic history of RSV, we analyzed the genetic variability and evolutionary pattern of RSVs from 1977 to 2019 in this study. The results revealed that there was no recombination event of intergroup. Single nucleotide polymorphisms (SNPs) were observed through the genome with the highest occurrence rate in the G gene. Five and six sites in G protein of RSV-A and RSV-B, respectively, were further identified with a strong positive selection. The mean evolutionary rates for RSV-A and -B were estimated to be 1.48 × 10–3 and 1.92 × 10–3 nucleotide substitutions/site/year, respectively. The Bayesian skyline plot showed a constant population size of RSV-A and a sharp expansion of population size of RSV-B since 2005, and an obvious decrease 5 years later, then became stable again. The total population size of RSVs showed a similar tendency to that of RSV-B. Time-scaled phylogeny suggested a temporal specificity of the RSV-genotypes. Monitoring nucleotide changes and analyzing evolution pattern for RSVs could give valuable insights for vaccine and therapy strategies against RSV infection.
Collapse
Affiliation(s)
- Jie-Mei Yu
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, 100044, China
| | - Yuan-Hui Fu
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, 100044, China
| | - Xiang-Lei Peng
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, 100044, China
| | - Yan-Peng Zheng
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, 100044, China
| | - Jin-Sheng He
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, 100044, China.
| |
Collapse
|
34
|
Komoyo GF, Yambiyo BM, Manirakiza A, Gody JC, Muller CP, Hübschen JM, Nakoune E, Snoeck CJ. Epidemiology and genetic characterization of respiratory syncytial virus in children with acute respiratory infections: Findings from the influenza sentinel surveillance network in Central African Republic, 2015 to 2018. Health Sci Rep 2021; 4:e298. [PMID: 34013070 PMCID: PMC8112815 DOI: 10.1002/hsr2.298] [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: 08/20/2020] [Revised: 03/21/2021] [Accepted: 04/15/2021] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND AND AIMS Respiratory syncytial virus (RSV) is one of the main viral pathogens causing acute respiratory infections in children under 5 years of age but has seldom been studied in Central African Republic (CAF). Taking advantage of the national influenza surveillance network in CAF, this study aimed at providing the first insights into RSV prevalence and seasonality over 4 years of surveillance and the clinical manifestations of RSV in this population in CAF. METHODS A total of 3903 children under 5 years matching the influenza-like illness (ILI, 68.5%) or severe acute respiratory infection (SARI, 31.5%) case definitions were recruited from January 2015 to December 2018. The presence of RSV viral RNA in nasopharyngeal samples was assessed by RT-PCR, followed by RSV-A and RSV-B typing and Sanger sequencing on a subset of samples. Phylogenetic analyses were carried on partial G protein sequences. Associations between RSV and demographic or clinical manifestations were investigated by statistical analyses. RESULTS RSV prevalence was significantly higher in infants <6 months (13.4%), in hospitalized children (13.3% vs 5.5%) and in male patients (9.5% vs 6.4%). An overall prevalence of RSV of 8.0% in the period of 2015 to 2018 was shown, with significant annual (6.4%-10.6%) and seasonal (12.7% in rainy season vs 3.0% in dry season) fluctuations. While RSV seasons in 2015, 2016, and 2018 were relatively similar, 2017 showed deviations from the overall patterns with significantly higher RSV circulation and an outbreak peak 3 to 5 months earlier. Concomitant circulation of RSV-A and RSV-B with an alternating predominance of RSV-A and RSV-B strains and temporal RSV-A genotype replacement from NA1 to ON1 was observed. CONCLUSION This study represents the first in-depth epidemiological analysis of RSV in CAF and provides first insights into RSV genetic diversity and seasonality in the country.
Collapse
Affiliation(s)
- Giscard F. Komoyo
- Laboratoire des arbovirus, des fièvres hémorragiques virales, des virus émergents et des zoonosesInstitut Pasteur de BanguiBanguiCentral African Republic
- Ecole Doctorale d'Infectiologie Tropicale de Franceville, GabonFrancevilleGabon
| | - Brice M. Yambiyo
- Service d'épidémiologieInstitut Pasteur de BanguiBanguiCentral African Republic
| | | | - Jean C. Gody
- Complexe pédiatrique de BanguiCentre National Hospitalier Universitaire de BanguiBanguiCentral African Republic
| | - Claude P. Muller
- Clinical and Applied Virology group, Department of Infection and ImmunityLuxembourg Institute of HealthEsch‐sur‐AlzetteLuxembourg
| | - Judith M. Hübschen
- Clinical and Applied Virology group, Department of Infection and ImmunityLuxembourg Institute of HealthEsch‐sur‐AlzetteLuxembourg
| | - Emmanuel Nakoune
- Laboratoire des arbovirus, des fièvres hémorragiques virales, des virus émergents et des zoonosesInstitut Pasteur de BanguiBanguiCentral African Republic
| | - Chantal J. Snoeck
- Clinical and Applied Virology group, Department of Infection and ImmunityLuxembourg Institute of HealthEsch‐sur‐AlzetteLuxembourg
| |
Collapse
|
35
|
Vianna LA, Siqueira MM, Volpini LPB, Louro ID, Resende PC. Seasonality, molecular epidemiology, and virulence of Respiratory Syncytial Virus (RSV): A perspective into the Brazilian Influenza Surveillance Program. PLoS One 2021; 16:e0251361. [PMID: 34003843 PMCID: PMC8130917 DOI: 10.1371/journal.pone.0251361] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 04/23/2021] [Indexed: 11/18/2022] Open
Abstract
Background Respiratory Syncytial Virus (RSV) is the main cause of pediatric morbidity and mortality. The complex evolution of RSV creates a need for worldwide surveillance, which may assist in the understanding of multiple viral aspects. Objectives This study aimed to investigate RSV features under the Brazilian Influenza Surveillance Program, evaluating the role of viral load and genetic diversity in disease severity and the influence of climatic factors in viral seasonality. Methodology We have investigated the prevalence of RSV in children up to 3 years of age with severe acute respiratory infection (SARI) in the state of Espirito Santo (ES), Brazil, from 2016 to 2018. RT-qPCR allowed for viral detection and viral load quantification, to evaluate association with clinical features and mapping of local viral seasonality. Gene G sequencing and phylogenetic reconstruction demonstrated local genetic diversity. Results Of 632 evaluated cases, 56% were caused by RSV, with both subtypes A and B co-circulating throughout the years. A discrete inverse association between average temperature and viral circulation was observed. No correlation between viral load and disease severity was observed, but children infected with RSV-A presented a higher clinical severity score (CSS), stayed longer in the hospital, and required intensive care, and ventilatory support more frequently than those infected by RSV-B. Regarding RSV diversity, some local genetic groups were observed within the main genotypes circulation RSV-A ON1 and RSV-B BA, with strains showing modifications in the G gene amino acid chain. Conclusion Local RSV studies using the Brazilian Influenza Surveillance Program are relevant as they can bring useful information to the global RSV surveillance. Understanding seasonality, virulence, and genetic diversity can aid in the development and suitability of antiviral drugs, vaccines, and assist in the administration of prophylactic strategies.
Collapse
Affiliation(s)
- Lucas A Vianna
- Central Laboratory of Public Health of the State of Espirito Santo, Vitoria, Espirito Santo, Brazil.,Nucleus of Human and Molecular Genetics/Federal University of Espirito Santo/UFES, Vitoria, Espirito Santo, Brazil
| | - Marilda M Siqueira
- Laboratory of Respiratory Viruses and Measles, WHO NIC, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Lays P B Volpini
- Virology & Infectious Gastroenteritis Laboratory/Federal University of Espirito Santo/ UFES, Vitoria, Espirito Santo, Brazil
| | - Iuri D Louro
- Nucleus of Human and Molecular Genetics/Federal University of Espirito Santo/UFES, Vitoria, Espirito Santo, Brazil
| | - Paola C Resende
- Laboratory of Respiratory Viruses and Measles, WHO NIC, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil
| |
Collapse
|
36
|
Respiratory syncytial virus B sequence analysis reveals a novel early genotype. Sci Rep 2021; 11:3452. [PMID: 33568737 PMCID: PMC7876121 DOI: 10.1038/s41598-021-83079-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 01/22/2021] [Indexed: 02/08/2023] Open
Abstract
Respiratory syncytial virus (RSV) is a major cause of respiratory infections and is classified in two main groups, RSV-A and RSV-B, with multiple genotypes within each of them. For RSV-B, more than 30 genotypes have been described, without consensus on their definition. The lack of genotype assignation criteria has a direct impact on viral evolution understanding, development of viral detection methods as well as vaccines design. Here we analyzed the totality of complete RSV-B G gene ectodomain sequences published in GenBank until September 2018 (n = 2190) including 478 complete genome sequences using maximum likelihood and Bayesian phylogenetic analyses, as well as intergenotypic and intragenotypic distance matrices, in order to generate a systematic genotype assignation. Individual RSV-B genes were also assessed using maximum likelihood phylogenetic analyses and multiple sequence alignments were used to identify molecular markers associated to specific genotypes. Analyses of the complete G gene ectodomain region, sequences clustering patterns, and the presence of molecular markers of each individual gene indicate that the 37 previously described genotypes can be classified into fifteen distinct genotypes: BA, BA-C, BA-CC, CB1-THB, GB1-GB4, GB6, JAB1-NZB2, SAB1, SAB2, SAB4, URU2 and a novel early circulating genotype characterized in the present study and designated GB0.
Collapse
|