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Feng Y, He T, Zhang B, Yuan H, Zhou Y. Epidemiology and diagnosis technologies of human metapneumovirus in China: a mini review. Virol J 2024; 21:59. [PMID: 38454484 PMCID: PMC10921660 DOI: 10.1186/s12985-024-02327-9] [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: 12/12/2023] [Accepted: 02/26/2024] [Indexed: 03/09/2024] Open
Abstract
Human metapneumovirus (HMPV) is a newly identified pathogen causing acute respiratory tract infections in young infants worldwide. Since the initial document of HMPV infection in China in 2003, Chinese scientists have made lots of efforts to prevent and control this disease, including developing diagnosis methods, vaccines and antiviral agents against HMPV, as well as conducting epidemiological investigations. However, effective vaccines or special antiviral agents against HMPV are currently not approved, thus developing early diagnosis methods and knowing its epidemiological characteristics will be beneficial for HMPV control. Here, we summarized current research focused on the epidemiological characteristics of HMPV in China and its available detection methods, which will be beneficial to increase the public awareness and disease control in the future.
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Affiliation(s)
- Yuan Feng
- Xiangtan Central Hospital, Xiangtan, 411100, Hunan, China
| | - Tao He
- Xiangtan Maternal and Child Health Hospital, Xiangtan, 411100, China
| | - Bo Zhang
- Xiangtan Central Hospital, Xiangtan, 411100, Hunan, China
| | - Haibin Yuan
- Xiangtan Central Hospital, Xiangtan, 411100, Hunan, China
| | - Yinfei Zhou
- Xiangtan Central Hospital, Xiangtan, 411100, Hunan, China.
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Zhang Y, Xu J, Miranda-Katz M, Sojati J, Tollefson SJ, Manni ML, Alcorn JF, Sarkar SN, Williams JV. Distinct roles for type I and type III interferons in virulent human metapneumovirus pathogenesis. PLoS Pathog 2024; 20:e1011840. [PMID: 38315735 PMCID: PMC10868789 DOI: 10.1371/journal.ppat.1011840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 02/15/2024] [Accepted: 11/17/2023] [Indexed: 02/07/2024] Open
Abstract
Human metapneumovirus (HMPV) is an important cause of acute lower respiratory infection in children and adults worldwide. There are four genetic subgroups of HMPV and both neutralizing antibodies and T cells contribute to protection. However, little is known about mechanisms of pathogenesis and most published work is based on a few extensively passaged, laboratory-adapted strains of HMPV. In this study, we isolated and characterized a panel of low passage HMPV clinical isolates representing all four genetic subgroups. The clinical isolates exhibited lower levels of in vitro replication compared to a lab-adapted strain. We compared disease phenotypes using a well-established mouse model. Several virulent isolates caused severe weight loss, lung pathology, airway dysfunction, and fatal disease in mice, which was confirmed in three inbred mouse strains. Disease severity did not correlate with lung viral titer, as virulent strains exhibited restricted replication in the lower airway. Virulent HMPV isolates were associated with markedly increased proinflammatory cytokine production and neutrophil influx; however, depletion of neutrophils or genetic ablation of inflammasome components did not reverse disease. Virulent clinical isolates induced markedly increased type I and type III interferon (IFN) secretion in vitro and in vivo. STAT1/2-deficient mice lacking both type I and type III IFN signaling showed reduced disease severity and increased lung viral replication. Inhibition of type I IFN signaling using a blocking antibody or genetic ablation of the type I IFN receptor reduced pathology with minimal effect on viral replication. Conversely, blockade of type III IFN signaling with a neutralizing antibody or genetic ablation of the IFN-lambda receptor had no effect on pathogenesis but restored viral replication. Collectively, these results demonstrate distinct roles for type I and type III IFN in HMPV pathogenesis and immunity.
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Affiliation(s)
- Yu Zhang
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Jiuyang Xu
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- Tsinghua University School of Medicine, Beijing, China
| | - Margot Miranda-Katz
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Jorna Sojati
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Sharon J. Tollefson
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Michelle L. Manni
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - John F. Alcorn
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Saumendra N. Sarkar
- Department of Microbiology & Molecular Genetics, University of Pittsburgh School of Medicine, Pennsylvania, United States of America
| | - John V. Williams
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- Department of Microbiology & Molecular Genetics, University of Pittsburgh School of Medicine, Pennsylvania, United States of America
- Institute for Infection, Inflammation, and Immunity in Children, University of Pittsburgh, Pennsylvania, United States of America
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Cho SJ, Kim SH, Lee H, Lee YU, Mun J, Park S, Park J, Park JS, Lee K, Lee CM, Seo J, Kim Y, Chung YS. Re-Emergence of HMPV in Gwangju, South Korea, after the COVID-19 Pandemic. Pathogens 2023; 12:1218. [PMID: 37887734 PMCID: PMC10609798 DOI: 10.3390/pathogens12101218] [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: 07/29/2023] [Revised: 09/30/2023] [Accepted: 10/02/2023] [Indexed: 10/28/2023] Open
Abstract
The non-pharmaceutical interventions implemented to prevent the spread of COVID-19 have affected the epidemiology of other respiratory viruses. In South Korea, Human metapneumovirus (HMPV) typically occurs from winter to the following spring; however, it was not detected for two years during the COVID-19 pandemic and re-emerged in the fall of 2022, which is a non-epidemic season. To examine the molecular genetic characteristics of HMPV before and after the COVID-19 pandemic, we analyzed 427 HMPV-positive samples collected in the Gwangju area from 2018 to 2022. Among these, 24 samples were subjected to whole-genome sequencing. Compared to the period before the COVID-19 pandemic, the incidence rate of HMPV in 2022 increased by 2.5-fold. Especially in the age group of 6-10 years, the incidence rate increased by more than 4.5-fold. In the phylogenetic analysis results, before the COVID-19 pandemic, the A2.2.2 lineage was predominant, while in 2022, the A2.2.1 and B2 lineage were observed. The non-pharmaceutical interventions implemented after COVID-19, such as social distancing, have reduced opportunities for exposure to HMPV, subsequently leading to decreased acquisition of immunity. As a result, HMPV occurred during non-epidemic seasons, influencing the age distribution of its occurrences.
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Affiliation(s)
- Sun-Ju Cho
- Division of Emerging Infectious Disease, Department of Infectious Disease Research, Health and Environment Research Institute of Gwangju, Gwangju 61954, Republic of Korea; (S.-J.C.); (H.L.); (Y.-U.L.); (J.M.); (S.P.); (J.P.); (J.-S.P.); (K.L.); (C.-m.L.); (J.S.); (Y.K.)
| | - Sun-Hee Kim
- Division of Emerging Infectious Disease, Department of Infectious Disease Research, Health and Environment Research Institute of Gwangju, Gwangju 61954, Republic of Korea; (S.-J.C.); (H.L.); (Y.-U.L.); (J.M.); (S.P.); (J.P.); (J.-S.P.); (K.L.); (C.-m.L.); (J.S.); (Y.K.)
| | - Hongsu Lee
- Division of Emerging Infectious Disease, Department of Infectious Disease Research, Health and Environment Research Institute of Gwangju, Gwangju 61954, Republic of Korea; (S.-J.C.); (H.L.); (Y.-U.L.); (J.M.); (S.P.); (J.P.); (J.-S.P.); (K.L.); (C.-m.L.); (J.S.); (Y.K.)
| | - Yeong-Un Lee
- Division of Emerging Infectious Disease, Department of Infectious Disease Research, Health and Environment Research Institute of Gwangju, Gwangju 61954, Republic of Korea; (S.-J.C.); (H.L.); (Y.-U.L.); (J.M.); (S.P.); (J.P.); (J.-S.P.); (K.L.); (C.-m.L.); (J.S.); (Y.K.)
| | - Jeongeun Mun
- Division of Emerging Infectious Disease, Department of Infectious Disease Research, Health and Environment Research Institute of Gwangju, Gwangju 61954, Republic of Korea; (S.-J.C.); (H.L.); (Y.-U.L.); (J.M.); (S.P.); (J.P.); (J.-S.P.); (K.L.); (C.-m.L.); (J.S.); (Y.K.)
| | - Sujung Park
- Division of Emerging Infectious Disease, Department of Infectious Disease Research, Health and Environment Research Institute of Gwangju, Gwangju 61954, Republic of Korea; (S.-J.C.); (H.L.); (Y.-U.L.); (J.M.); (S.P.); (J.P.); (J.-S.P.); (K.L.); (C.-m.L.); (J.S.); (Y.K.)
| | - Jungwook Park
- Division of Emerging Infectious Disease, Department of Infectious Disease Research, Health and Environment Research Institute of Gwangju, Gwangju 61954, Republic of Korea; (S.-J.C.); (H.L.); (Y.-U.L.); (J.M.); (S.P.); (J.P.); (J.-S.P.); (K.L.); (C.-m.L.); (J.S.); (Y.K.)
| | - Ji-Su Park
- Division of Emerging Infectious Disease, Department of Infectious Disease Research, Health and Environment Research Institute of Gwangju, Gwangju 61954, Republic of Korea; (S.-J.C.); (H.L.); (Y.-U.L.); (J.M.); (S.P.); (J.P.); (J.-S.P.); (K.L.); (C.-m.L.); (J.S.); (Y.K.)
| | - Kwangho Lee
- Division of Emerging Infectious Disease, Department of Infectious Disease Research, Health and Environment Research Institute of Gwangju, Gwangju 61954, Republic of Korea; (S.-J.C.); (H.L.); (Y.-U.L.); (J.M.); (S.P.); (J.P.); (J.-S.P.); (K.L.); (C.-m.L.); (J.S.); (Y.K.)
| | - Cheong-mi Lee
- Division of Emerging Infectious Disease, Department of Infectious Disease Research, Health and Environment Research Institute of Gwangju, Gwangju 61954, Republic of Korea; (S.-J.C.); (H.L.); (Y.-U.L.); (J.M.); (S.P.); (J.P.); (J.-S.P.); (K.L.); (C.-m.L.); (J.S.); (Y.K.)
| | - Jinjong Seo
- Division of Emerging Infectious Disease, Department of Infectious Disease Research, Health and Environment Research Institute of Gwangju, Gwangju 61954, Republic of Korea; (S.-J.C.); (H.L.); (Y.-U.L.); (J.M.); (S.P.); (J.P.); (J.-S.P.); (K.L.); (C.-m.L.); (J.S.); (Y.K.)
| | - Yonghwan Kim
- Division of Emerging Infectious Disease, Department of Infectious Disease Research, Health and Environment Research Institute of Gwangju, Gwangju 61954, Republic of Korea; (S.-J.C.); (H.L.); (Y.-U.L.); (J.M.); (S.P.); (J.P.); (J.-S.P.); (K.L.); (C.-m.L.); (J.S.); (Y.K.)
| | - Yoon-Seok Chung
- Division of High-Risk Pathogen, Bureau of Infectious Diseases Diagnosis Control, Korea Disease Control and Prevention Agency (KDCA), Cheongju 28159, Republic of Korea
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Lee K, Seok JH, Kim H, Park S, Lee S, Bae JY, Jeon K, Kang JG, Yoo JR, Heo ST, Cho NH, Lee KH, Kim K, Park MS, Kim JI. Genome-informed investigation of the molecular evolution and genetic reassortment of severe fever with thrombocytopenia syndrome virus. PLoS Negl Trop Dis 2023; 17:e0011630. [PMID: 37713429 PMCID: PMC10529592 DOI: 10.1371/journal.pntd.0011630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 09/27/2023] [Accepted: 08/30/2023] [Indexed: 09/17/2023] Open
Abstract
BACKGROUND Severe fever with thrombocytopenia syndrome virus (SFTSV) is a viral pathogen causing significant clinical signs from mild fever with thrombocytopenia to severe hemorrhages. World Health Organization has paid special attention to the dramatic increase in human SFTS cases in China, Japan, and South Korea since the 2010s. The present study investigated the molecular evolution and genetic reassortment of SFTSVs using complete genomic sequences. METHODS/PRINCIPAL FINDING We collected the complete genome sequences of SFTSVs globally isolated until 2019 (L segment, n = 307; M segment, n = 326; and S segment, n = 564) and evaluated the evolutionary profiles of SFTSVs based on phylogenetic and molecular selection pressure analyses. By employing a time-scaled Bayesian inference method, we found the geographical heterogeneity of dominant SFTSV genotypes in China, Japan, and South Korea around several centuries before and locally spread by tick-born spillover with infrequent long-distance transmission. Purifying selection predominated the molecular evolution of SFTSVs with limited gene reassortment and fixed substitution, but almost all three gene segments appeared to harbor at least one amino acid residue under positive selection. Specifically, the nonstructural protein and glycoprotein (Gn/Gc) genes were preferential selective targets, and the Gn region retained the highest number of positively selected residues. CONCLUSION/SIGNIFICANCE Here, the large-scale genomic analyses of SFTSVs improved prior knowledge of how this virus emerged and evolved in China, Japan, and South Korea. Our results highlight the importance of SFTSV surveillance in both human and non-human reservoirs at the molecular level to fight against fatal human infection with the virus.
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Affiliation(s)
- Kyuyoung Lee
- Department of Microbiology, Institute for Viral Diseases, College of Medicine, Korea University, Seoul, Republic of Korea
| | - Jong Hyeon Seok
- Department of Microbiology, Institute for Viral Diseases, College of Medicine, Korea University, Seoul, Republic of Korea
| | - Hyunbeen Kim
- Department of Microbiology, Institute for Viral Diseases, College of Medicine, Korea University, Seoul, Republic of Korea
| | - Sejik Park
- Department of Microbiology, Institute for Viral Diseases, College of Medicine, Korea University, Seoul, Republic of Korea
| | - Sohyun Lee
- Department of Microbiology, Institute for Viral Diseases, College of Medicine, Korea University, Seoul, Republic of Korea
| | - Joon-Yong Bae
- Department of Microbiology, Institute for Viral Diseases, College of Medicine, Korea University, Seoul, Republic of Korea
| | - Kyeongseok Jeon
- Department of Microbiology and Immunology, College of Medicine, Seoul National University, Seoul, Republic of Korea
| | - Jun-Gu Kang
- Laboratory for Vector Borne Disease, Korea Zoonosis Research Institute, Jeonbuk National University, Iksan, Republic of Korea
| | - Jeong Rae Yoo
- Department of Internal Medicine, College of Medicine, Jeju National University, Jeju, Republic of Korea
| | - Sang Taek Heo
- Department of Internal Medicine, College of Medicine, Jeju National University, Jeju, Republic of Korea
| | - Nam-Hyuk Cho
- Department of Microbiology and Immunology, College of Medicine, Seoul National University, Seoul, Republic of Korea
| | - Keun Hwa Lee
- Department of Microbiology, College of Medicine, Hanyang University, Seoul, Republic of Korea
| | - Kisoon Kim
- Department of Microbiology, Institute for Viral Diseases, College of Medicine, Korea University, Seoul, Republic of Korea
- Vaccine Innovation Center, College of Medicine, Korea University, Seoul, Republic of Korea
| | - Man-Seong Park
- Department of Microbiology, Institute for Viral Diseases, College of Medicine, Korea University, Seoul, Republic of Korea
- Vaccine Innovation Center, College of Medicine, Korea University, Seoul, Republic of Korea
- Biosafety Center, College of Medicine, Korea University, Seoul, Republic of Korea
| | - Jin Il Kim
- Department of Microbiology, Institute for Viral Diseases, College of Medicine, Korea University, Seoul, Republic of Korea
- Vaccine Innovation Center, College of Medicine, Korea University, Seoul, Republic of Korea
- Biosafety Center, College of Medicine, Korea University, Seoul, Republic of Korea
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Piñana M, González-Sánchez A, Andrés C, Abanto M, Vila J, Esperalba J, Moral N, Espartosa E, Saubi N, Creus A, Codina MG, Folgueira D, Martinez-Urtaza J, Pumarola T, Antón A. The emergence, impact, and evolution of human metapneumovirus variants from 2014 to 2021 in Spain. J Infect 2023:S0163-4453(23)00262-1. [PMID: 37178807 DOI: 10.1016/j.jinf.2023.05.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 05/02/2023] [Accepted: 05/03/2023] [Indexed: 05/15/2023]
Abstract
BACKGROUND Human metapneumovirus (HMPV) is an important aetiologic agent of respiratory tract infection (RTI). This study aimed to describe the prevalence, genetic diversity, and evolutionary dynamics of HMPV. METHODS Laboratory-confirmed HMPV were characterised based on partial-coding G gene sequences with MEGA.v6.0. WGS was performed with Illumina, and evolutionary analyses with Datamonkey and Nextstrain. RESULTS HMPV prevalence was 2.5%, peaking in February-April and with an alternation in the predominance of HMPV-A and -B until the emergence of SARS-CoV-2, not circulating until summer and autumn-winter 2021, with a higher prevalence and with the almost only circulation of A2c111dup. G and SH proteins were the most variable, and 70% of F protein was under negative selection. Mutation rate of HMPV genome was 6.95 ×10-4 substitutions/site/year. CONCLUSION HMPV showed a significant morbidity until the emergence of SARS-CoV-2 pandemic in 2020, not circulating again until summer and autumn 2021, with a higher prevalence and with almost the only circulation of A2c111dup, probably due to a more efficient immune evasion mechanism. The F protein showed a very conserved nature, supporting the need for steric shielding. The tMRCA showed a recent emergence of the A2c variants carrying duplications, supporting the importance of virological surveillance.
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Affiliation(s)
- Maria Piñana
- Respiratory Viruses Unit, Microbiology Department, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Alejandra González-Sánchez
- Respiratory Viruses Unit, Microbiology Department, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Cristina Andrés
- Respiratory Viruses Unit, Microbiology Department, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Michel Abanto
- Genomics and Bioinformatics Unit, Scientific and Technological Bioresource Nucleus (BIOREN). Universidad de La Frontera, Temuco, Chile
| | - Jorgina Vila
- Paediatric Hospitalization Unit, Paediatrics Department, Hospital Universitari Maternoinfantil Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Juliana Esperalba
- Respiratory Viruses Unit, Microbiology Department, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Noelia Moral
- Department of Clinical Microbiology, Hospital Universitario 12 de Octubre, Instituto de Investigación Hospital 12 de Octubre (imas12), Universidad Complutense de Madrid, Madrid, Spain
| | - Elena Espartosa
- Department of Clinical Microbiology, Hospital Universitario 12 de Octubre, Instituto de Investigación Hospital 12 de Octubre (imas12), Universidad Complutense de Madrid, Madrid, Spain
| | - Narcís Saubi
- Respiratory Viruses Unit, Microbiology Department, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Anna Creus
- Paediatric Hospitalization Unit, Paediatrics Department, Hospital Universitari Maternoinfantil Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Maria Gema Codina
- Respiratory Viruses Unit, Microbiology Department, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Dolores Folgueira
- Department of Clinical Microbiology, Hospital Universitario 12 de Octubre, Instituto de Investigación Hospital 12 de Octubre (imas12), Universidad Complutense de Madrid, Madrid, Spain
| | - Jaime Martinez-Urtaza
- Department of Genetics and Microbiology, School of Biosciences, Universitat Autonoma de Barcelona, 08193 Bellaterra, Spain
| | - Tomàs Pumarola
- Respiratory Viruses Unit, Microbiology Department, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona, Barcelona, Spain.
| | - Andrés Antón
- Respiratory Viruses Unit, Microbiology Department, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Universitat Autònoma de Barcelona, Barcelona, Spain
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Nigar K, Kakakhel S, Khan A, Khan H, Zaib K, Wen S. Population genetic analyses unveiled genetic stratification and differential natural selection signatures across the G-gene of viral hemorrhagic septicemia virus. Front Genet 2022; 13:982527. [PMID: 36579328 PMCID: PMC9790968 DOI: 10.3389/fgene.2022.982527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 11/28/2022] [Indexed: 12/14/2022] Open
Abstract
Introduction: Viral hemorrhagic septicemia virus (VHSV) is the most lethal pathogen in aquaculture, infecting more than 140 fish species in marine, estuarine, and freshwater environments. Viral hemorrhagic septicemia virus is an enveloped RNA virus that belongs to the family Rhabdoviridae and the genus Novirhabdovirus. The current study is designed to infer the worldwide Viral hemorrhagic septicemia virus isolates' genetic diversity and evolutionary dynamics based on G-gene sequences. Methods: The complete G-gene sequences of viral hemorrhagic septicemia virus were retrieved from the public repositories with known timing and geography details. Pairwise statistical analysis was performed using Arlequin. The Bayesian model-based approach implemented in STRUCTURE software was used to investigate the population genetic structure, and the phylogenetic tree was constructed using MEGA X and IQ-TREE. The natural selection analysis was assessed using different statistical approaches, including IFEL, MEME, and SLAC. Results and Discussion: The global Viral hemorrhagic septicemia virus samples are stratified into five genetically distinct subpopulations. The STRUCTURE analysis unveiled spatial clustering of genotype Ia into two distinct clusters at K = 3. However, at K = 5, the genotype Ia samples, deposited from Denmark, showed temporal distribution into two groups. The analyses unveiled that the genotype Ia samples stratified into subpopulations possibly based on spatiotemporal distribution. Several viral hemorrhagic septicemia virus samples are characterized as genetically admixed or recombinant. In addition, differential or subpopulation cluster-specific natural selection signatures were identified across the G-gene codon sites among the viral hemorrhagic septicemia virus isolates. Evidence of low recombination events elucidates that genetic mutations and positive selection events have possibly driven the observed genetic stratification of viral hemorrhagic septicemia virus samples.
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Affiliation(s)
- Kiran Nigar
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Sehrish Kakakhel
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Asifullah Khan
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Pakistan,*Correspondence: Asifullah Khan, ; Shaoqing Wen,
| | - Hizbullah Khan
- CAS Key Laboratory of Molecular Virology and Immunology, The Center for Microbes, Development and Health, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China,University of Chinese Academy of Sciences, Beijing, China
| | - Komal Zaib
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Shaoqing Wen
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China,Institute of Archaeological Science, Fudan University, Shanghai, China,*Correspondence: Asifullah Khan, ; Shaoqing Wen,
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Gandhi L, Maisnam D, Rathore D, Chauhan P, Bonagiri A, Venkataramana M. Respiratory illness virus infections with special emphasis on COVID-19. Eur J Med Res 2022; 27:236. [PMID: 36348452 PMCID: PMC9641310 DOI: 10.1186/s40001-022-00874-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 10/26/2022] [Indexed: 11/10/2022] Open
Abstract
Viruses that emerge pose challenges for treatment options as their uniqueness would not know completely. Hence, many viruses are causing high morbidity and mortality for a long time. Despite large diversity, viruses share common characteristics for infection. At least 12 different respiratory-borne viruses are reported belonging to various virus taxonomic families. Many of these viruses multiply and cause damage to the upper and lower respiratory tracts. The description of these viruses in comparison with each other concerning their epidemiology, molecular characteristics, disease manifestations, diagnosis and treatment is lacking. Such information helps diagnose, differentiate, and formulate the control measures faster. The leading cause of acute illness worldwide is acute respiratory infections (ARIs) and are responsible for nearly 4 million deaths every year, mostly in young children and infants. Lower respiratory tract infections are the fourth most common cause of death globally, after non-infectious chronic conditions. This review aims to present the characteristics of different viruses causing respiratory infections, highlighting the uniqueness of SARS-CoV-2. We expect this review to help understand the similarities and differences among the closely related viruses causing respiratory infections and formulate specific preventive or control measures.
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Affiliation(s)
- Lekha Gandhi
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, 500046, Telangana, India
| | - Deepti Maisnam
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, 500046, Telangana, India
| | - Deepika Rathore
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, 500046, Telangana, India
| | - Preeti Chauhan
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, 500046, Telangana, India
| | - Anvesh Bonagiri
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, 500046, Telangana, India
| | - Musturi Venkataramana
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, 500046, Telangana, India.
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A Candidate Therapeutic Monoclonal Antibody Inhibits Both HRSV and HMPV Replication in Mice. Biomedicines 2022; 10:biomedicines10102516. [PMID: 36289776 PMCID: PMC9599547 DOI: 10.3390/biomedicines10102516] [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: 09/12/2022] [Revised: 10/05/2022] [Accepted: 10/06/2022] [Indexed: 11/16/2022] Open
Abstract
Human metapneumovirus (HMPV) and human respiratory virus (HRSV) are two leading causes of acute respiratory tract infection in young children. While there is no licensed drug against HMPV, the monoclonal antibody (mAb) Palivizumab is approved against HRSV for prophylaxis use only. Novel therapeutics against both viruses are therefore needed. Here, we describe the identification of human mAbs targeting these viruses by using flow cytometry-based cell sorting. One hundred and two antibodies were initially identified from flow cytometry-based cell sorting as binding to the fusion protein from HRSV, HMPV or both. Of those, 95 were successfully produced in plants, purified and characterized for binding activity by ELISA and neutralization assays as well as by inhibition of virus replication in mice. Twenty-two highly reactive mAbs targeting either HRSV or HMPV were isolated. Of these, three mAbs inhibited replication in vivo of a single virus while one mAb could reduce both HRSV and HMPV titers in the lung. Overall, this study identifies several human mAbs with virus-specific therapeutic potential and a unique mAb with inhibitory activities against both HRSV and HMPV.
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Calvignac-Spencer S, Düx A, Gogarten JF, Patrono LV. Molecular archeology of human viruses. Adv Virus Res 2021; 111:31-61. [PMID: 34663498 DOI: 10.1016/bs.aivir.2021.07.002] [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: 02/07/2023]
Abstract
The evolution of human-virus associations is usually reconstructed from contemporary patterns of genomic diversity. An intriguing, though still rarely implemented, alternative is to search for the genetic material of viruses in archeological and medical archive specimens to document evolution as it happened. In this chapter, we present lessons from ancient DNA research and incorporate insights from virology to explore the potential range of applications and likely limitations of archeovirological approaches. We also highlight the numerous questions archeovirology will hopefully allow us to tackle in the near future, and the main expected roadblocks to these avenues of research.
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Affiliation(s)
- Sébastien Calvignac-Spencer
- Epidemiology of Highly Pathogenic Microorganisms, Robert Koch-Institute, Berlin, Germany; Viral Evolution, Robert Koch-Institute, Berlin, Germany.
| | - Ariane Düx
- Epidemiology of Highly Pathogenic Microorganisms, Robert Koch-Institute, Berlin, Germany; Viral Evolution, Robert Koch-Institute, Berlin, Germany
| | - Jan F Gogarten
- Epidemiology of Highly Pathogenic Microorganisms, Robert Koch-Institute, Berlin, Germany; Viral Evolution, Robert Koch-Institute, Berlin, Germany
| | - Livia V Patrono
- Epidemiology of Highly Pathogenic Microorganisms, Robert Koch-Institute, Berlin, Germany
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10
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Qian W, Huang J, Wang T, He X, Xu G, Li Y. Visual detection of human metapneumovirus using CRISPR-Cas12a diagnostics. Virus Res 2021; 305:198568. [PMID: 34555442 DOI: 10.1016/j.virusres.2021.198568] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 09/04/2021] [Accepted: 09/09/2021] [Indexed: 10/20/2022]
Abstract
Human metapneumovirus (HmPV) is a common and serious virus that causes respiratory tract infection. This study aimed to develop a detection technique by combining reverse transcription recombinase polymerase amplification (RT-RPA) with CRISPR-Cas12a (RT-RPA-Cas12a) for clinical diagnosis of HmPV. Herein, four primer pairs targeting partial nucleoprotein (N) gene of HmPV were designed and evaluated. Then, the products amplified by RT-RPA were detected using CRISPR-Cas12a combined with fluorescence or lateral flow (LF). RT-RPA-Cas12a-based fluorescence or LF assay can be completed within 35 min or 45 min, and the detection limit was up to 6.97 × 102 copies/mL. And there was no cross reaction with human bocavirus, respiratory syncytial virus, adenovirus and parainfluenza virus. By combining with LF, the detection results were evaluated by naked eyes. Furthermore, 28 clinical samples were applied to examine the performance of RT-RPA-Cas12a system. The detection coincidence rates of RT-RPA-Cas12a-fluorescence and RT-RPA-Cas12a-LF with quantitative RT-PCR were 96.4% and 92.9%, respectively. Together, the new method for detecting HmPV with high sensitivity and specificity based on RT-RPA-Cas12a-fluorescence or LF shows promising potential for clinical diagnosis of HmPV without professional skills or ancillary equipment.
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Affiliation(s)
- Weidong Qian
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, PR China.
| | - Jie Huang
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, PR China
| | - Ting Wang
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, PR China
| | - Xiaoxian He
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, PR China
| | - Guozhang Xu
- Ningbo Municipal Center for Disease Control and Prevention, Ningbo, 315010, PR China
| | - Yongdong Li
- Ningbo Municipal Center for Disease Control and Prevention, Ningbo, 315010, PR China.
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11
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Lim YK, Kweon OJ, Kim HR, Kim TH, Lee MK. Clinical Features, Epidemiology, and Climatic Impact of Genotype-specific Human Metapneumovirus Infections: Long-term Surveillance of Hospitalized Patients in South Korea. Clin Infect Dis 2021; 70:2683-2694. [PMID: 31353397 PMCID: PMC7108157 DOI: 10.1093/cid/ciz697] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Accepted: 07/22/2019] [Indexed: 11/14/2022] Open
Abstract
Background Human metapneumovirus (hMPV) commonly causes upper and lower respiratory tract infections. Here, we performed long-term retrospective surveillance of hMPV infection among patients hospitalized in South Korea between 2007 and 2016 and investigated seasonal dynamics and clinical characteristics associated with each virus subtype/genotype. Methods Patient specimens were tested for hMPV and other respiratory viruses by commercial molecular assays. Medical records of hMPV-positive patients were reviewed, and hMPV subtype/genotype analysis was performed. We also collected meteorological data and analyzed relationships with hMPV activity. Results Of 23 694 specimens, 1275 (5.4%) were positive; among them, 94.0% were classified into 5 subtypes (A1, A2a, A2b, B1, and B2). Some clinical manifestations differed according to hMPV genotype; however, there was no correlation between hMPV subtype and clinical outcome. Viral activity peaked at 13–20 weeks (April and May) and was associated with climate-specific factors, including temperature, relative humidity, diurnal temperature variation, wind speed, and sunshine duration. Conclusions This large-scale, 10-year study provides valuable information about the clinical characteristics associated with hMPV subtypes and climate factors contributing to virus transmission.
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Affiliation(s)
- Yong Kwan Lim
- Department of Laboratory Medicine, Armed Forces Capital Hospital, Gyeonggi-do.,Department of Laboratory Medicine, Chung-Ang University College of Medicine, Seoul, Republic of Korea
| | - Oh Joo Kweon
- Department of Laboratory Medicine, Chung-Ang University College of Medicine, Seoul, Republic of Korea
| | - Hye Ryoun Kim
- Department of Laboratory Medicine, Chung-Ang University College of Medicine, Seoul, Republic of Korea
| | - Tae-Hyoung Kim
- Department of Urology, Chung-Ang University College of Medicine, Seoul, Republic of Korea
| | - Mi-Kyung Lee
- Department of Laboratory Medicine, Chung-Ang University College of Medicine, Seoul, Republic of Korea
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12
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Nao N, Saikusa M, Sato K, Sekizuka T, Usuku S, Tanaka N, Nishimura H, Takeda M. Recent Molecular Evolution of Human Metapneumovirus (HMPV): Subdivision of HMPV A2b Strains. Microorganisms 2020; 8:microorganisms8091280. [PMID: 32839394 PMCID: PMC7564156 DOI: 10.3390/microorganisms8091280] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 08/14/2020] [Accepted: 08/19/2020] [Indexed: 01/15/2023] Open
Abstract
Human metapneumovirus (HMPV) is a major etiological agent of acute respiratory infections in humans. HMPV has been circulating worldwide for more than six decades and is currently divided into five agreed-upon subtypes: A1, A2a, A2b, B1, and B2. Recently, the novel HMPV subtypes A2c, A2b1, and A2b2 have been proposed. However, the phylogenetic and evolutionary relationships between these recently proposed HMPV subtypes are unclear. Here, we report a genome-wide phylogenetic and evolutionary analysis of 161 HMPV strains, including unique HMPV subtype A2b strains with a 180- or 111-nucleotide duplication in the G gene (nt-dup). Our data demonstrate that the HMPV A2b subtype contains two distinct subtypes, A2b1 and A2b2, and that the HMPV subtypes A2c and A2b2 may be different names for the same subtype. HMPV A2b strains with a nt-dup also belong to subtype A2b2. Molecular evolutionary analyses indicate that subtypes A2b1 and A2b2 diverged from subtype A2b around a decade after the subtype A2 was divided into the subtypes A2a and A2b. These data support the A2b1 and A2b2 subtypes proposed in 2012 and are essential for the unified classification of HMPV subtype A2 strains, which is important for future HMPV surveillance and epidemiological studies.
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Affiliation(s)
- Naganori Nao
- Department of Virology III, National Institute of Infectious Diseases, Musashimurayama 208-0011, Japan;
- Correspondence: ; Tel.: +81-11-706-9492
| | - Miwako Saikusa
- Yokohama City Institute of Public Health, Yokohama 236-0051, Japan; (M.S.); (S.U.); (N.T.)
| | - Ko Sato
- Virus Research Center, Clinical Research Division, Sendai Medical Center, Sendai 983-8520, Japan; (K.S.); (H.N.)
| | - Tsuyoshi Sekizuka
- Pathogen Genomics Center, National Institute of Infectious Diseases, Shinjuku 162-8640, Japan;
| | - Shuzo Usuku
- Yokohama City Institute of Public Health, Yokohama 236-0051, Japan; (M.S.); (S.U.); (N.T.)
| | - Nobuko Tanaka
- Yokohama City Institute of Public Health, Yokohama 236-0051, Japan; (M.S.); (S.U.); (N.T.)
| | - Hidekazu Nishimura
- Virus Research Center, Clinical Research Division, Sendai Medical Center, Sendai 983-8520, Japan; (K.S.); (H.N.)
| | - Makoto Takeda
- Department of Virology III, National Institute of Infectious Diseases, Musashimurayama 208-0011, Japan;
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13
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Quan FS, Basak S, Chu KB, Kim SS, Kang SM. Progress in the development of virus-like particle vaccines against respiratory viruses. Expert Rev Vaccines 2020; 19:11-24. [PMID: 31903811 PMCID: PMC7103727 DOI: 10.1080/14760584.2020.1711053] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Introduction: Influenza virus, human respiratory syncytial virus (RSV), and human metapneumovirus (HMPV) are important human respiratory pathogens. Recombinant virus-like particle (VLP) vaccines are suggested to be potential promising platforms to protect against these respiratory viruses. This review updates important progress in the development of VLP vaccines against respiratory viruses.Areas Covered: This review summarizes progress in developing VLP and nanoparticle-based vaccines against influenza virus, RSV, and HMPV. The PubMed was mainly used to search for important research articles published since 2010 although earlier key articles were also referenced. The research area covered includes VLP and nanoparticle platform vaccines against seasonal, pandemic, and avian influenza viruses as well as RSV and HMPV respiratory viruses. The production methods, immunogenic properties, and vaccine efficacy of respiratory VLP vaccines in preclinical animal models and clinical studies were reviewed in this article.Expert opinion: Previous and current preclinical and clinical studies suggest that recombinant VLP and nanoparticle vaccines are expected to be developed as promising alternative platforms against respiratory viruses in future. Therefore, continued research efforts are warranted.
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Affiliation(s)
- Fu-Shi Quan
- Department of Medical Zoology, Kyung Hee University School of Medicine, Seoul, Republic of Korea.,Medical Research Center for Bioreaction to Reactive Oxygen Species and Biomedical Science Institute, School of Medicine, Graduate school, Kyung Hee University, Seoul, Republic of Korea
| | - Swarnendu Basak
- Department of Biomedical Science, Graduate School, Kyung Hee University, Seoul, Republic of Korea
| | - Ki-Back Chu
- Department of Biomedical Science, Graduate School, Kyung Hee University, Seoul, Republic of Korea
| | - Sung Soo Kim
- Medical Research Center for Bioreaction to Reactive Oxygen Species and Biomedical Science Institute, School of Medicine, Graduate school, Kyung Hee University, Seoul, Republic of Korea.,Department of Biochemistry and Molecular Biology, Kyung Hee University School of Medicine, Seoul, Republic of Korea
| | - Sang-Moo Kang
- Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA
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14
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Kamau E, Oketch JW, de Laurent ZR, Phan MVT, Agoti CN, Nokes DJ, Cotten M. Whole genome sequencing and phylogenetic analysis of human metapneumovirus strains from Kenya and Zambia. BMC Genomics 2020; 21:5. [PMID: 31898474 PMCID: PMC6941262 DOI: 10.1186/s12864-019-6400-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 12/15/2019] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Human metapneumovirus (HMPV) is an important cause of acute respiratory illness in young children. Whole genome sequencing enables better identification of transmission events and outbreaks, which is not always possible with sub-genomic sequences. RESULTS We report a 2-reaction amplicon-based next generation sequencing method to determine the complete genome sequences of five HMPV strains, representing three subgroups (A2, B1 and B2), directly from clinical samples. In addition to reporting five novel HMPV genomes from Africa we examined genetic diversity and sequence patterns of publicly available HMPV genomes. We found that the overall nucleotide sequence identity was 71.3 and 80% for HMPV group A and B, respectively, the diversity between HMPV groups was greater at amino acid level for SH and G surface protein genes, and multiple subgroups co-circulated in various countries. Comparison of sequences between HMPV groups revealed variability in G protein length (219 to 241 amino acids) due to changes in the stop codon position. Genome-wide phylogenetic analysis showed congruence with the individual gene sequence sets except for F and M2 genes. CONCLUSION This is the first genomic characterization of HMPV genomes from African patients.
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Affiliation(s)
- Everlyn Kamau
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya.
| | - John W Oketch
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - My V T Phan
- Department of Viroscience, Erasmus MC, Rotterdam, The Netherlands
| | | | - D James Nokes
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- School of Life Sciences and Zeeman Institute, University of Warwick, Coventry, UK
| | - Matthew Cotten
- MRC/UVRI & LSHTM Uganda Research Unit, Entebbe, Uganda
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
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15
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Evolutionary timescale and geographical movement of cucumber mosaic virus, with focus on Iranian strains. Arch Virol 2019; 165:185-192. [PMID: 31637514 DOI: 10.1007/s00705-019-04439-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 09/16/2019] [Indexed: 10/25/2022]
Abstract
Cucumber mosaic virus (CMV) is a geographically widespread plant virus with a very broad host range. The virus has been detected in diverse crops all over Iran. In this study, we estimated the timescale of the evolution of CMV subgroup I and the geographical movement of the virus with a focus on Iranian strains. Analyses using the MP and CP genes and their concatenation revealed that the CMV population within subgroup I had a single ancestor dating back to about 450-550 years ago. The Iranian strains formed three clusters in a maximum-clade-credibility phylogenetic tree. It was found that the most recent common ancestor of the Iranian strains within each cluster dates back to less than 100 years ago. Our results also suggest that both short- and long-distance migration of Iranian CMV strains has occurred in the last 100 years.
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16
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Oketch JW, Kamau E, Otieno GP, Otieno JR, Agoti CN, Nokes DJ. Human metapneumovirus prevalence and patterns of subgroup persistence identified through surveillance of pediatric pneumonia hospital admissions in coastal Kenya, 2007-2016. BMC Infect Dis 2019; 19:757. [PMID: 31470805 PMCID: PMC6716807 DOI: 10.1186/s12879-019-4381-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 08/15/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Human metapneumovirus (HMPV) is an important respiratory pathogen that causes seasonal epidemics of acute respiratory illness and contributes significantly to childhood pneumonia. Current knowledge and understanding on its patterns of spread, prevalence and persistence in communities in low resource settings is limited. METHODS We present findings of a molecular-epidemiological analysis of nasal samples from children < 5 years of age admitted with syndromic pneumonia between 2007 and 2016 to Kilifi County Hospital, coastal Kenya. HMPV infection was detected using real-time RT-PCR and positives sequenced in the fusion (F) and attachment (G) genes followed by phylogenetic analysis. The association between disease severity and HMPV subgroup was assessed using Fisher's exact test. RESULTS Over 10 years, 274/6756 (4.1%) samples screened were HMPV positive. Annual prevalence fluctuated between years ranging 1.2 to 8.7% and lowest in the recent years (2014-2016). HMPV detections were most frequent between October of one year to April of the following year. Genotyping was successful for 205/274 (74.8%) positives revealing clades A2b (41.0%) and A2c (10.7%), and subgroups B1 (23.4%) and B2 (24.9%). The dominance patterns were: clade A2b between 2007 and 11, subgroup B1 between 2012 and 14, and clade A2c in more recent epidemics. Subgroup B2 viruses were present in all the years. Temporal phylogenetic clustering within the subgroups for both local and global sequence data was seen. Subgroups occurring in each epidemic season were comprised of multiple variants. Pneumonia severity did not vary by subgroup (p = 0.264). In both the F and G gene, the sequenced regions were found to be predominantly under purifying selection. CONCLUSION Subgroup patterns from this rural African setting temporally map with global strain distribution, suggesting a well-mixed global virus transmission pool of HMPV. Persistence in the local community is characterized by repeated introductions of HMPV variants from the global pool. The factors underlying the declining prevalence of HMPV in this population should be investigated.
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Affiliation(s)
- John W. Oketch
- Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme, Kilifi, KEMRI Centre for Geographic Medicine Research – Coast, Kilifi, Kenya
| | - Everlyn Kamau
- Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme, Kilifi, KEMRI Centre for Geographic Medicine Research – Coast, Kilifi, Kenya
| | - Grieven P. Otieno
- Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme, Kilifi, KEMRI Centre for Geographic Medicine Research – Coast, Kilifi, Kenya
| | - James R. Otieno
- Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme, Kilifi, KEMRI Centre for Geographic Medicine Research – Coast, Kilifi, Kenya
| | - Charles N. Agoti
- Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme, Kilifi, KEMRI Centre for Geographic Medicine Research – Coast, Kilifi, Kenya
- School of Health and Human Sciences, Pwani University, Kilifi, Kenya
| | - D. James Nokes
- Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme, Kilifi, KEMRI Centre for Geographic Medicine Research – Coast, Kilifi, Kenya
- School of Health and Human Sciences, Pwani University, Kilifi, Kenya
- School of Life Sciences, and Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, Coventry, UK
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Phylogenetic evidence of a novel lineage of canine pneumovirus and a naturally recombinant strain isolated from dogs with respiratory illness in Thailand. BMC Vet Res 2019; 15:300. [PMID: 31426794 PMCID: PMC6700830 DOI: 10.1186/s12917-019-2035-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 07/31/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Canine pneumovirus (CPV) is a pathogen that causes respiratory disease in dogs, and recent outbreaks in shelters in America and Europe have been reported. However, based on published data and documents, the identification of CPV and its variant in clinically symptomatic individual dogs in Thailand through Asia is limited. Therefore, the aims of this study were to determine the emergence of CPV and to consequently establish the genetic characterization and phylogenetic analysis of the CPV strains from 209 dogs showing respiratory distress in Thailand. RESULTS This study identified and described the full-length CPV genome from three strains, designated herein as CPV_CP13 TH/2015, CPV_CP82 TH/2016 and CPV_SR1 TH/2016, that were isolated from six dogs out of 209 dogs (2.9%) with respiratory illness in Thailand. Phylogenetic analysis suggested that these three Thai CPV strains (CPV TH strains) belong to the CPV subgroup A and form a novel lineage; proposed as the Asian prototype. Specific mutations in the deduced amino acids of these CPV TH strains were found in the G/glycoprotein sequence, suggesting potential substitution sites for subtype classification. Results of intragenic recombination analysis revealed that CPV_CP82 TH/2016 is a recombinant strain, where the recombination event occurred in the L gene with the Italian prototype CPV Bari/100-12 as the putative major parent. Selective pressure analysis demonstrated that the majority of the nucleotides in the G/glycoprotein were under purifying selection with evidence of positive selection sites. CONCLUSIONS This collective information on the CPV TH strains is the first evidence of CPV emergence with genetic characterization in Thailand and as first report in Asia, where homologous recombination acts as a potential force driving the genetic diversity and shaping the evolution of canine pneumovirus.
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Kumar P, Srivastava M. Prophylactic and therapeutic approaches for human metapneumovirus. Virusdisease 2018; 29:434-444. [PMID: 30539045 PMCID: PMC6261883 DOI: 10.1007/s13337-018-0498-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 10/01/2018] [Indexed: 12/24/2022] Open
Abstract
Human metapneumovirus (HMPV) is an important pneumovirus which causes acute respiratory disease in human beings. The viral infection leads to mild to severe respiratory symptoms depending on the age and immune status of the infected individual. Several groups across the world are working on the development of immunogens and therapy to manage HMPV infection with promising results under laboratory conditions but till date any virus specific vaccine or therapy has not been approved for clinical use. This minireview gives an overview of the prophylactic and therapeutic approaches to manage HMPV infections.
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Affiliation(s)
- Prashant Kumar
- Amity Institute of Virology and Immunology, Amity University Uttar Pradesh, Sector-125, Noida, U.P. 201301 India
| | - Mansi Srivastava
- Amity Institute of Virology and Immunology, Amity University Uttar Pradesh, Sector-125, Noida, U.P. 201301 India
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19
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Abstract
Human metapneumovirus (HMPV) is a leading cause of acute respiratory infection, particularly in children, immunocompromised patients, and the elderly. HMPV, which is closely related to avian metapneumovirus subtype C, has circulated for at least 65 years, and nearly every child will be infected with HMPV by the age of 5. However, immunity is incomplete, and re-infections occur throughout adult life. Symptoms are similar to those of other respiratory viral infections, ranging from mild (cough, rhinorrhea, and fever) to more severe (bronchiolitis and pneumonia). The preferred method for diagnosis is reverse transcription-polymerase chain reaction as HMPV is difficult to culture. Although there have been many advances made in the past 16 years since its discovery, there are still no US Food and Drug Administration-approved antivirals or vaccines available to treat HMPV. Both small animal and non-human primate models have been established for the study of HMPV. This review will focus on the epidemiology, transmission, and clinical manifestations in humans as well as the animal models of HMPV pathogenesis and host immune response.
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Affiliation(s)
- Nazly Shafagati
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - John Williams
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
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