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Moin AT, Ullah MA, Patil RB, Faruqui NA, Araf Y, Das S, Uddin KMK, Hossain MS, Miah MF, Moni MA, Chowdhury DUS, Islam S. A computational approach to design a polyvalent vaccine against human respiratory syncytial virus. Sci Rep 2023; 13:9702. [PMID: 37322049 PMCID: PMC10272159 DOI: 10.1038/s41598-023-35309-y] [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: 11/14/2022] [Accepted: 05/16/2023] [Indexed: 06/17/2023] Open
Abstract
Human Respiratory Syncytial Virus (RSV) is one of the leading causes of lower respiratory tract infections (LRTI), responsible for infecting people from all age groups-a majority of which comprises infants and children. Primarily, severe RSV infections are accountable for multitudes of deaths worldwide, predominantly of children, every year. Despite several efforts to develop a vaccine against RSV as a potential countermeasure, there has been no approved or licensed vaccine available yet, to control the RSV infection effectively. Therefore, through the utilization of immunoinformatics tools, a computational approach was taken in this study, to design a multi-epitope polyvalent vaccine against two major antigenic subtypes of RSV, RSV-A and RSV-B. Potential predictions of the T-cell and B-cell epitopes were followed by extensive tests of antigenicity, allergenicity, toxicity, conservancy, homology to human proteome, transmembrane topology, and cytokine-inducing ability. The peptide vaccine was modeled, refined, and validated. Molecular docking analysis with specific Toll-like receptors (TLRs) revealed excellent interactions with suitable global binding energies. Additionally, molecular dynamics (MD) simulation ensured the stability of the docking interactions between the vaccine and TLRs. Mechanistic approaches to imitate and predict the potential immune response generated by the administration of vaccines were determined through immune simulations. Subsequent mass production of the vaccine peptide was evaluated; however, there remains a necessity for further in vitro and in vivo experiments to validate its efficacy against RSV infections.
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Affiliation(s)
- Abu Tayab Moin
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram, Bangladesh.
| | - Md Asad Ullah
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Jahangirnagar University, Savar, Dhaka, Bangladesh
| | - Rajesh B Patil
- Department of Pharmaceutical Chemistry, Sinhgad Technical Education Society's, Sinhgad College of Pharmacy, Pune, Maharashtra, India
| | - Nairita Ahsan Faruqui
- Biotechnology Program, Department of Mathematics and Natural Sciences, School of Data and Sciences, BRAC University, Dhaka, Bangladesh
| | - Yusha Araf
- Department of Genetic Engineering and Biotechnology, School of Life Sciences, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Sowmen Das
- Department of Computer Science and Engineering, School of Physical Sciences, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Khaza Md Kapil Uddin
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram, Bangladesh
| | - Md Shakhawat Hossain
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram, Bangladesh
| | - Md Faruque Miah
- Department of Genetic Engineering and Biotechnology, School of Life Sciences, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Mohammad Ali Moni
- Bone Biology Division, The Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
- WHO Collaborating Centre on eHealth, UNSW Digital Health, School of Public Health and Community Medicine, Faculty of Medicine, UNSW Sydney, Sydney, Australia
- Artificial Intelligence and Data Science, Faculty of Health and Behavioural Sciences, School of Health and Rehabilitation Sciences, The University of Queensland, Brisbane, Australia
| | - Dil Umme Salma Chowdhury
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram, Bangladesh.
| | - Saiful Islam
- Bangladesh Council of Scientific and Industrial Research (BCSIR), Chattogram Laboratories, Chattogram, Bangladesh.
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2
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Patrono LV, Röthemeier C, Kouadio L, Couacy-Hymann E, Wittig RM, Calvignac-Spencer S, Leendertz FH. Non-invasive genomics of respiratory pathogens infecting wild great apes using hybridisation capture. Influenza Other Respir Viruses 2022; 16:858-861. [PMID: 35388591 PMCID: PMC9343332 DOI: 10.1111/irv.12984] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 03/03/2022] [Accepted: 03/15/2022] [Indexed: 11/29/2022] Open
Abstract
Human respiratory pathogens have repeatedly caused lethal outbreaks in wild great apes across Africa, leading to population declines. Nonetheless, our knowledge of potential genomic changes associated with pathogen introduction and spread at the human‐great ape interface remains sparse. Here, we made use of target enrichment coupled with next generation sequencing to non‐invasively investigate five outbreaks of human‐introduced respiratory disease in wild chimpanzees living in Taï National Park, Ivory Coast. By retrieving 34 complete viral genomes and three distinct constellations of pneumococcal virulence factors, we provide genomic insights into these spillover events and describe a framework for non‐invasive genomic surveillance in wildlife.
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Affiliation(s)
- Livia V Patrono
- Project Group Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute, Berlin, Germany.,Department of Ecology and Emergence of Zoonotic Diseases, Helmholtz Institute for One Health, Greifswald, Germany
| | - Caroline Röthemeier
- Project Group Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute, Berlin, Germany
| | - Leonce Kouadio
- Laboratoire National d'Appui au Développement Agricole/Laboratoire Central de Pathologie Animale, Bingerville, Côte d'Ivoire
| | - Emmanuel Couacy-Hymann
- Laboratoire National d'Appui au Développement Agricole/Laboratoire Central de Pathologie Animale, Bingerville, Côte d'Ivoire
| | - Roman M Wittig
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,Taï Chimpanzee Project, Centre Suisse de Recherches Scientifiques, Abidjan, Côte d'Ivoire
| | | | - Fabian H Leendertz
- Project Group Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute, Berlin, Germany.,Department of Ecology and Emergence of Zoonotic Diseases, Helmholtz Institute for One Health, Greifswald, Germany.,Taï Chimpanzee Project, Centre Suisse de Recherches Scientifiques, Abidjan, Côte d'Ivoire
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3
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Dolores A, Stephanie G, Mercedes S NJ, Érica G, Mistchenko AS, Mariana V. RSV reemergence in Argentina since the SARS-CoV-2 pandemic. J Clin Virol 2022; 149:105126. [PMID: 35299101 PMCID: PMC8906024 DOI: 10.1016/j.jcv.2022.105126] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 03/03/2022] [Accepted: 03/07/2022] [Indexed: 11/28/2022]
Affiliation(s)
- Acuña Dolores
- Virology Laboratory, Ricardo Gutierrez Children's Hospital, Buenos Aires City, Argentina; National Scientific and Technical Research Council, Argentina
| | - Goya Stephanie
- Virology Laboratory, Ricardo Gutierrez Children's Hospital, Buenos Aires City, Argentina
| | | | - Grandis Érica
- Virology Laboratory, Ricardo Gutierrez Children's Hospital, Buenos Aires City, Argentina
| | - Alicia S Mistchenko
- Virology Laboratory, Ricardo Gutierrez Children's Hospital, Buenos Aires City, Argentina; Scientific Research Commission, Buenos Aires province, Argentina
| | - Viegas Mariana
- Virology Laboratory, Ricardo Gutierrez Children's Hospital, Buenos Aires City, Argentina; National Scientific and Technical Research Council, Argentina.
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4
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Korsten K, Adriaenssens N, Coenen S, Butler CC, Pirçon JY, Verheij TJM, Bont LJ, Wildenbeest JG. Contact With Young Children Increases the Risk of Respiratory Infection in Older Adults in Europe-the RESCEU Study. J Infect Dis 2021; 226:S79-S86. [PMID: 34908153 PMCID: PMC9374513 DOI: 10.1093/infdis/jiab519] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Background Knowledge about how older adults get a respiratory infection is crucial for planning preventive strategies. We aimed to determine how contact with young children living outside of the household affects the risk of acute respiratory tract infections (ARTI) in community-dwelling older adults. Methods This study is part of the European RESCEU older adult study. Weekly surveillance was performed to detect ARTI throughout 2 winter seasons (2017-2018, 2018-2019). Child exposure, defined as having regular contact with children under 5 living outside of the subject’s household, was assessed at baseline. The average attributable fraction was calculated to determine the fraction of ARTI explained by exposure to these children. Results We prospectively established that 597/1006 (59%) participants experienced at least 1 ARTI. Child exposure increased the risk of all-cause ARTI (adjusted odds ratio [aOR], 1.58; 95% confidence interval [CI], 1.21 -2.08; P = .001). This risk was highest in those with the most frequent contact (aOR, 1.80; 95% CI, 1.23-2.63; P = .003). The average attributable fraction of child exposure explaining ARTI was 10% (95% CI, 5%-15%). Conclusions One of 10 ARTI in community-dwelling older adults is attributable to exposure to preschool children living outside of the household. Clinical Trials Registration NCT03621930.
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Affiliation(s)
- Koos Korsten
- Department of Pediatric Infectious Diseases and Immunology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Niels Adriaenssens
- Vaccine and Infectious Disease Institute, Laboratory of Medical Microbiology, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium.,Department of Primary and Interdisciplinary Care-Centre for General Practice, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - Samuel Coenen
- Vaccine and Infectious Disease Institute, Laboratory of Medical Microbiology, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium.,Department of Primary and Interdisciplinary Care-Centre for General Practice, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium.,Department of Epidemiology and Social Medicine, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - Chris C Butler
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom
| | | | - Theo J M Verheij
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Louis J Bont
- Department of Pediatric Infectious Diseases and Immunology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Joanne G Wildenbeest
- Department of Pediatric Infectious Diseases and Immunology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, the Netherlands
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5
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Luka MM, Kamau E, de Laurent ZR, Morobe JM, Alii LK, Nokes DJ, Agoti CN. Whole genome sequencing of two human rhinovirus A types (A101 and A15) detected in Kenya, 2016-2018. Wellcome Open Res 2021; 6:178. [PMID: 34522789 PMCID: PMC8408540 DOI: 10.12688/wellcomeopenres.16911.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/21/2021] [Indexed: 11/20/2022] Open
Abstract
Background: Virus genome sequencing is increasingly utilized in epidemiological surveillance. Genomic data allows comprehensive evaluation of underlying viral diversity and epidemiology to inform control. For human rhinovirus (HRV), genomic amplification and sequencing is challenging due to numerous types, high genetic diversity and inadequate reference sequences. Methods: We developed a tiled amplicon type-specific protocol for genome amplification and sequencing on the Illumina MiSeq platform of two HRV types, A15 and A101. We then assessed added value in analyzing whole genomes relative to the VP4/2 region only in the investigation of HRV molecular epidemiology within the community in Kilifi, coastal Kenya. Results: We processed 73 nasopharyngeal swabs collected between 2016-2018, and 48 yielded at least 70% HRV genome coverage. These included all A101 samples (n=10) and 38 (60.3%) A15 samples. Phylogenetic analysis revealed that the Kilifi A101 sequences interspersed with global A101 genomes available in GenBank collected between 1999-2016. On the other hand, our A15 sequences formed a monophyletic group separate from the global genomes collected in 2008 and 2019. An improved phylogenetic resolution was observed with the genome phylogenies compared to the VP4/2 phylogenies. Conclusions: We present a type-specific full genome sequencing approach for obtaining HRV genomic data and characterizing infections.
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Affiliation(s)
- Martha M Luka
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya.,Department of Biochemistry and Biotechnology, Pwani University, Kilifi, Kenya
| | - Everlyn Kamau
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya
| | - Zaydah R de Laurent
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya
| | - John Mwita Morobe
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya
| | - Leonard K Alii
- Department of Mathematics and Computer Science, Pwani University, Kilifi, Kenya
| | - D James Nokes
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya.,School of Life Sciences and Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, Coventry, UK
| | - Charles N Agoti
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya.,Department of Public Health, Pwani University, Kilifi, Kenya
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6
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Luka MM, Kamau E, de Laurent ZR, Morobe JM, Alii LK, Nokes DJ, Agoti CN. Whole genome sequencing of two human rhinovirus A types (A101 and A15) detected in Kenya, 2016-2018. Wellcome Open Res 2021; 6:178. [DOI: 10.12688/wellcomeopenres.16911.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/29/2021] [Indexed: 01/10/2023] Open
Abstract
Background: Virus genome sequencing is increasingly utilized in epidemiological surveillance. Genomic data allows comprehensive evaluation of underlying viral diversity and epidemiology to inform control. For human rhinovirus (HRV), genomic amplification and sequencing is challenging due to numerous types, high genetic diversity and inadequate reference sequences. Methods: We developed a tiled amplicon type-specific protocol for genome amplification and sequencing on the Illumina MiSeq platform of two HRV types, A15 and A101. We then assessed added value in analyzing whole genomes relative to the VP4/2 region only in the investigation of HRV molecular epidemiology within the community in Kilifi, coastal Kenya. Results: We processed 73 samples collected between 2016-2018, and 48 yielded at least 70% HRV genome coverage. These included all A101 samples (n=10) and 38 (60.3%) A15 samples. Phylogenetic analysis revealed that the Kilifi A101 sequences interspersed with global A101 genomes available in GenBank collected between 1999-2016. On the other hand, our A15 sequences formed a monophyletic group separate from the global genomes collected in 2008 and 2019. Improved phylogenetic resolution was observed with the genome phylogenies compared to the VP4/2 phylogenies. Conclusions: We present a type-specific full genome sequencing approach for obtaining HRV genomic data and characterizing infections.
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7
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Salimi V, Viegas M, Trento A, Agoti CN, Anderson LJ, Avadhanula V, Bahl J, Bont L, Brister JR, Cane PA, Galiano M, Graham BS, Hatcher EL, Hellferscee O, Henke DM, Hirve S, Jackson S, Keyaerts E, Kragten-Tabatabaie L, Lindstrom S, Nauwelaers I, Nokes DJ, Openshaw PJ, Peret TC, Piedra PA, Ramaekers K, Rector A, Trovão NS, von Gottberg A, Zambon M, Zhang W, Williams TC, Barr IG, Buchholz UJ. Proposal for Human Respiratory Syncytial Virus Nomenclature below the Species Level. Emerg Infect Dis 2021; 27:1-9. [PMID: 34013862 PMCID: PMC8153853 DOI: 10.3201/eid2706.204608] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Human respiratory syncytial virus (HRSV) is the leading viral cause of serious pediatric respiratory disease, and lifelong reinfections are common. Its 2 major subgroups, A and B, exhibit some antigenic variability, enabling HRSV to circulate annually. Globally, research has increased the number of HRSV genomic sequences available. To ensure accurate molecular epidemiology analyses, we propose a uniform nomenclature for HRSV-positive samples and isolates, and HRSV sequences, namely: HRSV/subgroup identifier/geographic identifier/unique sequence identifier/year of sampling. We also propose a template for submitting associated metadata. Universal nomenclature would help researchers retrieve and analyze sequence data to better understand the evolution of this virus.
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8
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Yeoh DK, Foley DA, Minney-Smith CA, Martin AC, Mace AO, Sikazwe CT, Le H, Levy A, Blyth CC, Moore HC. Impact of Coronavirus Disease 2019 Public Health Measures on Detections of Influenza and Respiratory Syncytial Virus in Children During the 2020 Australian Winter. Clin Infect Dis 2021; 72:2199-2202. [PMID: 32986804 PMCID: PMC7543326 DOI: 10.1093/cid/ciaa1475] [Citation(s) in RCA: 277] [Impact Index Per Article: 92.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Indexed: 11/14/2022] Open
Abstract
Public health measures targeting coronavirus disease 2019 have potential to impact transmission of other respiratory viruses. We found 98.0% and 99.4% reductions in respiratory syncytial virus and influenza detections, respectively, in Western Australian children through winter 2020 despite schools reopening. Border closures have likely been important in limiting external introductions.
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Affiliation(s)
- Daniel K Yeoh
- Infectious Diseases Department, Perth Children's Hospital, Perth, Australia.,National Centre for Infections in Cancer, Peter MacCallum Cancer Centre, Melbourne, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia
| | - David A Foley
- Infectious Diseases Department, Perth Children's Hospital, Perth, Australia
| | - Cara A Minney-Smith
- Department of Microbiology, PathWest Laboratory Medicine WA, Perth, Australia
| | - Andrew C Martin
- Department of General Paediatrics, Perth Children's Hospital, Perth, Australia
| | - Ariel O Mace
- Department of General Paediatrics, Perth Children's Hospital, Perth, Australia.,Department of General Paediatrics, Fiona Stanley Hospital, Perth, Australia.,Wesfarmers Centre for Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, Perth, Australia
| | - Chisha T Sikazwe
- Department of Microbiology, PathWest Laboratory Medicine WA, Perth, Australia.,Department of General Paediatrics, Fiona Stanley Hospital, Perth, Australia
| | - Huong Le
- Wesfarmers Centre for Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, Perth, Australia
| | - Avram Levy
- Department of Microbiology, PathWest Laboratory Medicine WA, Perth, Australia.,Faculty of Health and Medical Sciences, University of Western Australia, Perth, Australia
| | - Christopher C Blyth
- Infectious Diseases Department, Perth Children's Hospital, Perth, Australia.,Department of Microbiology, PathWest Laboratory Medicine WA, Perth, Australia.,Wesfarmers Centre for Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, Perth, Australia.,School of Medicine, University of Western Australia, Perth, Australia
| | - Hannah C Moore
- Wesfarmers Centre for Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, Perth, Australia
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Edwards KM. The Impact of Social Distancing for Severe Acute Respiratory Syndrome Coronavirus 2 on Respiratory Syncytial Virus and Influenza Burden. Clin Infect Dis 2021; 72:2076-2078. [PMID: 33038221 PMCID: PMC7665345 DOI: 10.1093/cid/ciaa1543] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Indexed: 01/15/2023] Open
Affiliation(s)
- Kathryn M Edwards
- Department of Pediatrics, Division of Pediatric Infectious Diseases, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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10
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Zheng Z, Pitzer VE, Warren JL, Weinberger DM. Community factors associated with local epidemic timing of respiratory syncytial virus: A spatiotemporal modeling study. SCIENCE ADVANCES 2021; 7:7/26/eabd6421. [PMID: 34162556 PMCID: PMC8221622 DOI: 10.1126/sciadv.abd6421] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 05/10/2021] [Indexed: 05/29/2023]
Abstract
Respiratory syncytial virus (RSV) causes a large burden of morbidity in young children and the elderly. Spatial variability in the timing of RSV epidemics provides an opportunity to probe the factors driving its transmission, including factors that influence epidemic seeding and growth rates. Using hospitalization data from Connecticut, New Jersey, and New York, we estimated epidemic timing at the ZIP code level using harmonic regression and then used a Bayesian meta-regression model to evaluate correlates of epidemic timing. Earlier epidemics were associated with larger household size and greater population density. Nearby localities had similar epidemic timing. Our results suggest that RSV epidemics grow faster in areas with more local contact opportunities, and that epidemic spread follows a spatial diffusion process based on geographic proximity. Our findings can inform the timing of delivery of RSV extended half-life prophylaxis and maternal vaccines and guide future studies on the transmission dynamics of RSV.
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Affiliation(s)
- Zhe Zheng
- Department of Epidemiology of Microbial Diseases and the Public Health Modeling Unit, Yale School of Public Health, New Haven, CT 06520, USA.
| | - Virginia E Pitzer
- Department of Epidemiology of Microbial Diseases and the Public Health Modeling Unit, Yale School of Public Health, New Haven, CT 06520, USA
| | - Joshua L Warren
- Department of Biostatistics and the Public Health Modeling Unit, Yale School of Public Health, New Haven, CT 06520, USA
| | - Daniel M Weinberger
- Department of Epidemiology of Microbial Diseases and the Public Health Modeling Unit, Yale School of Public Health, New Haven, CT 06520, USA
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11
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Suryadevara M, Domachowske JB. Epidemiology and Seasonality of Childhood Respiratory Syncytial Virus Infections in the Tropics. Viruses 2021; 13:696. [PMID: 33923823 PMCID: PMC8074094 DOI: 10.3390/v13040696] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 02/03/2021] [Accepted: 02/19/2021] [Indexed: 12/19/2022] Open
Abstract
Infections caused by respiratory syncytial virus (RSV) are a major cause of morbidity and mortality in young children worldwide. Understanding seasonal patterns of region-specific RSV activity is important to guide resource allocation for existing and future treatment and prevention strategies. The decades of excellent RSV surveillance data that are available from the developed countries of the world are incredibly instructive in advancing public health initiatives in those regions. With few exceptions, these developed nations are positioned geographically across temperate regions of the world. RSV surveillance across tropical regions of the world has improved in recent years, but remains spotty, and where available, still lacks the necessary longitudinal data to determine the amount of seasonal variation expected over time. However, existing and emerging data collected across tropical regions of the world do indicate that patterns of infection are often quite different from those so well described in temperate areas. Here, we provide a brief summary regarding what is known about general patterns of RSV disease activity across tropical Asia, Africa and South America, then offer additional country-specific details using examples where multiple reports and/or more robust surveillance data have become available.
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12
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Kombe IK, Agoti CN, Munywoki PK, Baguelin M, Nokes DJ, Medley GF. Integrating epidemiological and genetic data with different sampling intensities into a dynamic model of respiratory syncytial virus transmission. Sci Rep 2021; 11:1463. [PMID: 33446831 PMCID: PMC7809427 DOI: 10.1038/s41598-021-81078-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Accepted: 01/04/2021] [Indexed: 01/06/2023] Open
Abstract
Respiratory syncytial virus (RSV) is responsible for a significant burden of severe acute lower respiratory tract illness in children under 5 years old; particularly infants. Prior to rolling out any vaccination program, identification of the source of infant infections could further guide vaccination strategies. We extended a dynamic model calibrated at the individual host level initially fit to social-temporal data on shedding patterns to include whole genome sequencing data available at a lower sampling intensity. The study population was 493 individuals (55 aged < 1 year) distributed across 47 households, observed through one RSV season in coastal Kenya. We found that 58/97 (60%) of RSV-A and 65/125 (52%) of RSV-B cases arose from infection probably occurring within the household. Nineteen (45%) infant infections appeared to be the result of infection by other household members, of which 13 (68%) were a result of transmission from a household co-occupant aged between 2 and 13 years. The applicability of genomic data in studies of transmission dynamics is highly context specific; influenced by the question, data collection protocols and pathogen under investigation. The results further highlight the importance of pre-school and school-aged children in RSV transmission, particularly the role they play in directly infecting the household infant. These age groups are a potential RSV vaccination target group.
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Affiliation(s)
- Ivy K Kombe
- KEMRI-Wellcome Trust Research Programme, KEMRI Centre for Geographical Medical Research-Coast, P.O. Box 230-80108, Kilifi, Kenya.
| | - Charles N Agoti
- KEMRI-Wellcome Trust Research Programme, KEMRI Centre for Geographical Medical Research-Coast, P.O. Box 230-80108, Kilifi, Kenya
| | - Patrick K Munywoki
- KEMRI-Wellcome Trust Research Programme, KEMRI Centre for Geographical Medical Research-Coast, P.O. Box 230-80108, Kilifi, Kenya
| | - Marc Baguelin
- Centre for Mathematical Modelling of Infectious Disease and Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, WC1H 9SH, UK
| | - D James Nokes
- KEMRI-Wellcome Trust Research Programme, KEMRI Centre for Geographical Medical Research-Coast, P.O. Box 230-80108, Kilifi, Kenya.,School of Life Sciences and Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, Coventry, CV4 7AL, UK
| | - Graham F Medley
- Centre for Mathematical Modelling of Infectious Disease and Department of Global Health and Development, London School of Hygiene and Tropical Medicine, London, WC1H 9SH, UK
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13
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Finelli L, Choi Y, Goldstein E. Number needed to immunize to prevent RSV with extended half-life monoclonal antibody. Vaccine 2020; 38:5474-5479. [PMID: 32600912 PMCID: PMC8684408 DOI: 10.1016/j.vaccine.2020.06.034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 06/09/2020] [Accepted: 06/11/2020] [Indexed: 01/16/2023]
Abstract
BACKGROUND Respiratory syncytial virus (RSV) is one of the most important respiratory pathogens in young children. Infants <6 months of age and infants and young children with extreme pre-term birth, and cardiac and pulmonary co-morbidities experience the highest incidence of severe RSV disease. There are no licensed vaccines; immunoprophylaxis is recommended for the highest risk children. Extended half-life RSV monoclonal antibodies (EHL-mAbs) are under development intended for immunization of all infants and high-risk children <2 years of age. We modeled the anticipated public health benefits of RSV EHL-mAb immunization using the number needed to immunize (NNI). METHODS We combined RSV hospitalization, outpatient and outpatient lower respiratory tract infection (LRI) incidence estimates and a range of immunization efficacies to estimate the annual NNI. We calculated the absolute incidence rate reduction (ARR) by multiplying the incidence rates by immunization efficacy. NNI was calculated as the reciprocal of the ARR. RESULTS For an RSV EHL-mAb with 70% efficacy, 6-18 infants would need to be immunized to prevent one RSV-associated outpatient visit, and 13-33 infants would need to be immunized to prevent one RSV-associated LRI outpatient visit. To prevent one RSV-associated hospitalization, 37-85 infants 0-5 months of age, and 107-280 infants 6-11 months of age would need to be immunized. CONCLUSIONS Public health benefits, such as disease cases averted due to immunization, are essential elements in consideration of candidate vaccines for a national immunization program. An RSV EHL-mAb of moderate efficacy could have high impact. These data provide an additional perspective for public health decision making.
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Affiliation(s)
- Lyn Finelli
- Center for Observational and Real-World Evidence, Merck & Co., Inc., Kenilworth, NJ 07033, USA.
| | - Yoonyoung Choi
- Center for Observational and Real-World Evidence, Merck & Co., Inc., Kenilworth, NJ 07033, USA
| | - Edward Goldstein
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, MA 02115, USA
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14
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Kamau E, Otieno JR, Murunga N, Oketch JW, Ngoi JM, de Laurent ZR, Mwema A, Nyiro JU, Agoti CN, Nokes DJ. Genomic epidemiology and evolutionary dynamics of respiratory syncytial virus group B in Kilifi, Kenya, 2015-17. Virus Evol 2020; 6:veaa050. [PMID: 32913665 PMCID: PMC7474930 DOI: 10.1093/ve/veaa050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Respiratory syncytial virus (RSV) circulates worldwide, occurring seasonally in communities, and is a leading cause of acute respiratory illness in young children. There is paucity of genomic data from purposively sampled populations by which to investigate evolutionary dynamics and transmission patterns of RSV. Here we present an analysis of 295 RSV group B (RSVB) genomes from Kilifi, coastal Kenya, sampled from individuals seeking outpatient care in nine health facilities across a defined geographical area (∼890 km2), over two RSV epidemics between 2015 and 2017. RSVB diversity was characterized by multiple virus introductions into the area and co-circulation of distinct genetic clusters, which transmitted and diversified locally with varying frequency. Increase in relative genetic diversity paralleled seasonal virus incidence. Importantly, we identified a cluster of viruses that emerged in the 2016/17 epidemic, carrying distinct amino-acid signatures including a novel nonsynonymous change (K68Q) in antigenic site ∅ in the Fusion protein. RSVB diversity was additionally marked by signature nonsynonymous substitutions that were unique to particular genomic clusters, some under diversifying selection. Our findings provide insights into recent evolutionary and epidemiological behaviors of RSVB, and highlight possible emergence of a novel antigenic variant, which has implications on current prophylactic strategies in development.
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Affiliation(s)
- Everlyn Kamau
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - James R Otieno
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Nickson Murunga
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - John W Oketch
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Joyce M Ngoi
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Zaydah R de Laurent
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Anthony Mwema
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Joyce U Nyiro
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Charles N Agoti
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya.,School of Health and Human Sciences, Pwani University, Kilifi, Kenya
| | - D James Nokes
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya.,School of Life Sciences and Zeeman Institute (SBIDER), University of Warwick, Coventry, UK
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15
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Pérez-Losada M, Arenas M, Galán JC, Bracho MA, Hillung J, García-González N, González-Candelas F. High-throughput sequencing (HTS) for the analysis of viral populations. INFECTION GENETICS AND EVOLUTION 2020; 80:104208. [PMID: 32001386 DOI: 10.1016/j.meegid.2020.104208] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 01/21/2020] [Accepted: 01/24/2020] [Indexed: 12/12/2022]
Abstract
The development of High-Throughput Sequencing (HTS) technologies is having a major impact on the genomic analysis of viral populations. Current HTS platforms can capture nucleic acid variation across millions of genes for both selected amplicons and full viral genomes. HTS has already facilitated the discovery of new viruses, hinted new taxonomic classifications and provided a deeper and broader understanding of their diversity, population and genetic structure. Hence, HTS has already replaced standard Sanger sequencing in basic and applied research fields, but the next step is its implementation as a routine technology for the analysis of viruses in clinical settings. The most likely application of this implementation will be the analysis of viral genomics, because the huge population sizes, high mutation rates and very fast replacement of viral populations have demonstrated the limited information obtained with Sanger technology. In this review, we describe new technologies and provide guidelines for the high-throughput sequencing and genetic and evolutionary analyses of viral populations and metaviromes, including software applications. With the development of new HTS technologies, new and refurbished molecular and bioinformatic tools are also constantly being developed to process and integrate HTS data. These allow assembling viral genomes and inferring viral population diversity and dynamics. Finally, we also present several applications of these approaches to the analysis of viral clinical samples including transmission clusters and outbreak characterization.
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Affiliation(s)
- Marcos Pérez-Losada
- Computational Biology Institute, Milken Institute School of Public Health, George Washington University, Washington, DC, USA; CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão 4485-661, Portugal
| | - Miguel Arenas
- Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310 Vigo, Spain; Biomedical Research Center (CINBIO), University of Vigo, 36310 Vigo, Spain.
| | - Juan Carlos Galán
- Microbiology Service, Hospital Ramón y Cajal, Madrid, Spain; CIBER in Epidemiology and Public Health, Spain.
| | - Mª Alma Bracho
- CIBER in Epidemiology and Public Health, Spain; Joint Research Unit "Infection and Public Health" FISABIO-University of Valencia, Valencia, Spain.
| | - Julia Hillung
- Joint Research Unit "Infection and Public Health" FISABIO-University of Valencia, Valencia, Spain; Institute for Integrative Systems Biology (I2SysBio), CSIC-University of Valencia, Valencia, Spain.
| | - Neris García-González
- Joint Research Unit "Infection and Public Health" FISABIO-University of Valencia, Valencia, Spain; Institute for Integrative Systems Biology (I2SysBio), CSIC-University of Valencia, Valencia, Spain.
| | - Fernando González-Candelas
- CIBER in Epidemiology and Public Health, Spain; Joint Research Unit "Infection and Public Health" FISABIO-University of Valencia, Valencia, Spain; Institute for Integrative Systems Biology (I2SysBio), CSIC-University of Valencia, Valencia, Spain.
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