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Liblau RS, Latorre D, Kornum BR, Dauvilliers Y, Mignot EJ. The immunopathogenesis of narcolepsy type 1. Nat Rev Immunol 2024; 24:33-48. [PMID: 37400646 DOI: 10.1038/s41577-023-00902-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/01/2023] [Indexed: 07/05/2023]
Abstract
Narcolepsy type 1 (NT1) is a chronic sleep disorder resulting from the loss of a small population of hypothalamic neurons that produce wake-promoting hypocretin (HCRT; also known as orexin) peptides. An immune-mediated pathology for NT1 has long been suspected given its exceptionally tight association with the MHC class II allele HLA-DQB1*06:02, as well as recent genetic evidence showing associations with polymorphisms of T cell receptor genes and other immune-relevant loci and the increased incidence of NT1 that has been observed after vaccination with the influenza vaccine Pandemrix. The search for both self-antigens and foreign antigens recognized by the pathogenic T cell response in NT1 is ongoing. Increased T cell reactivity against HCRT has been consistently reported in patients with NT1, but data demonstrating a primary role for T cells in neuronal destruction are currently lacking. Animal models are providing clues regarding the roles of autoreactive CD4+ and CD8+ T cells in the disease. Elucidation of the pathogenesis of NT1 will allow for the development of targeted immunotherapies at disease onset and could serve as a model for other immune-mediated neurological diseases.
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Affiliation(s)
- Roland S Liblau
- Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), University of Toulouse, CNRS, INSERM, Toulouse, France.
- Department of Immunology, Toulouse University Hospitals, Toulouse, France.
| | | | - Birgitte R Kornum
- Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Yves Dauvilliers
- National Reference Center for Orphan Diseases, Narcolepsy, Idiopathic Hypersomnia and Kleine-Levin Syndrome, Department of Neurology, Gui-de-Chauliac Hospital, CHU de Montpellier, Montpellier, France
- INSERM Institute for Neurosciences of Montpellier, Montpellier, France
| | - Emmanuel J Mignot
- Stanford University, Center for Narcolepsy, Department of Psychiatry and Behavioral Sciences, Palo Alto, CA, USA.
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2
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Liu Y, Wang Y, Wang Y, Mai H, Chen Y, Zhang Y, Ji Y, Cong X, Gao Y. Phylogenetic analysis of HA and NA genes of influenza A viruses in immunosuppressed inpatients in Beijing during the 2018-2020 influenza seasons. Virol J 2023; 20:101. [PMID: 37237356 DOI: 10.1186/s12985-023-02067-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Accepted: 05/09/2023] [Indexed: 05/28/2023] Open
Abstract
BACKGROUND Influenza A viruses have undergone rapid evolution with virulent; however, complete and comprehensive data on gene evolution and amino acid variation of HA and NA in immunosuppressed patients was few. In this study, we analysed molecular epidemiology and evolution of influenza A viruses in immunosuppressed population, and immunocompetent population were used as controls. METHODS Full sequences of HA and NA of A(H1N1)pdm09 and A(H3N2) were acquired through reverse transcription-polymerase chain reaction (RT-PCR). HA and NA genes were sequenced using the Sanger method and phylogenetically analysed using ClustalW 2.10 and MEGA software version 11.0. RESULTS During the 2018-2020 influenza seasons, 54 immunosuppressed and 46 immunocompetent inpatients screened positive for influenza A viruses by using the quantitative real-time PCR (qRT-PCR) were enrolled. 27 immunosuppressed and 23 immunocompetent nasal swab or bronchoalveolar lavage fluid samples were randomly selected and sequenced using the Sanger method. A(H1N1)pdm09 were detected in 15 samples and the remaining 35 samples were A(H3N2) positive. By analyzing the HA and NA gene sequences of these virus strains, we found that all A(H1N1)pdm09 viruses shared high similarities to each other and the HA and NA genes of these viruses exclusively belonged to subclade 6B.1A.1. Some NA genes of A(H3N2) viruses were not in the same clade as those of A/Singapore/INFIMH-16-0019/2016 and A/Kansas/14/2017, which may have led to A(H3N2) being the dominant strain in the 2019-2020 influenza season. Both A(H1N1)pdm09 and A(H3N2) viruses showed similar evolutionary lineages patterns of HA and NA between immunosuppressed and immunocompetent patients. Compared with the vaccine strains, there were no statistically significant of HA and NA genes and amino acid sequences of influenza A viruses in immunosuppressed and immunocompetent patients. However, the oseltamivir resistance substitution of NA-H275Y and R292K have been observed in immunosuppressed patients. CONCLUSIONS A(H1N1)pdm09 and A(H3N2) viruses showed similar evolutionary lineages patterns of HA and NA between immunosuppressed and immunocompetent patients. Both immunocompetent and immunosuppressed patients have some key substitutions, which should be of note monitored, especially those with potential to affect the viral antigen.
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Affiliation(s)
- Yafen Liu
- Department of Infectious Diseases, Peking University Hepatology Institute, Peking University People's Hospital, No. 11, Xizhimen South Street, Xicheng District, Beijing, 100044, People's Republic of China
| | - Yue Wang
- Department of Infectious Diseases, Peking University Hepatology Institute, Peking University People's Hospital, No. 11, Xizhimen South Street, Xicheng District, Beijing, 100044, People's Republic of China
| | - Yanxin Wang
- Department of Infectious Diseases, Peking University Hepatology Institute, Peking University People's Hospital, No. 11, Xizhimen South Street, Xicheng District, Beijing, 100044, People's Republic of China
| | - Huan Mai
- Department of Infectious Diseases, Peking University Hepatology Institute, Peking University People's Hospital, No. 11, Xizhimen South Street, Xicheng District, Beijing, 100044, People's Republic of China
| | - YuanYuan Chen
- Department of Infectious Diseases, Peking University Hepatology Institute, Peking University People's Hospital, No. 11, Xizhimen South Street, Xicheng District, Beijing, 100044, People's Republic of China
| | - Yifan Zhang
- Department of Infectious Diseases, Peking University Hepatology Institute, Peking University People's Hospital, No. 11, Xizhimen South Street, Xicheng District, Beijing, 100044, People's Republic of China
| | - Ying Ji
- Peking University Hepatology Institute, Peking University People's Hospital, No. 11, Xizhimen South Street, Xicheng District, Beijing, 100044, People's Republic of China
| | - Xu Cong
- Peking University Hepatology Institute, Peking University People's Hospital, No. 11, Xizhimen South Street, Xicheng District, Beijing, 100044, People's Republic of China
| | - Yan Gao
- Department of Infectious Diseases, Peking University Hepatology Institute, Peking University People's Hospital, No. 11, Xizhimen South Street, Xicheng District, Beijing, 100044, People's Republic of China.
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3
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Gauthier NPG, Chorlton SD, Krajden M, Manges AR. Agnostic Sequencing for Detection of Viral Pathogens. Clin Microbiol Rev 2023; 36:e0011922. [PMID: 36847515 PMCID: PMC10035330 DOI: 10.1128/cmr.00119-22] [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] [Indexed: 03/01/2023] Open
Abstract
The advent of next-generation sequencing (NGS) technologies has expanded our ability to detect and analyze microbial genomes and has yielded novel molecular approaches for infectious disease diagnostics. While several targeted multiplex PCR and NGS-based assays have been widely used in public health settings in recent years, these targeted approaches are limited in that they still rely on a priori knowledge of a pathogen's genome, and an untargeted or unknown pathogen will not be detected. Recent public health crises have emphasized the need to prepare for a wide and rapid deployment of an agnostic diagnostic assay at the start of an outbreak to ensure an effective response to emerging viral pathogens. Metagenomic techniques can nonspecifically sequence all detectable nucleic acids in a sample and therefore do not rely on prior knowledge of a pathogen's genome. While this technology has been reviewed for bacterial diagnostics and adopted in research settings for the detection and characterization of viruses, viral metagenomics has yet to be widely deployed as a diagnostic tool in clinical laboratories. In this review, we highlight recent improvements to the performance of metagenomic viral sequencing, the current applications of metagenomic sequencing in clinical laboratories, as well as the challenges that impede the widespread adoption of this technology.
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Affiliation(s)
- Nick P. G. Gauthier
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Mel Krajden
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada
| | - Amee R. Manges
- British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada
- School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada
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4
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Liu X, Chen D, Su J, Zheng R, Ning Z, Zhao M, Zhu B, Li Y. Selenium nanoparticles inhibited H1N1 influenza virus-induced apoptosis by ROS-mediated signaling pathways. RSC Adv 2022; 12:3862-3870. [PMID: 35425430 PMCID: PMC8981154 DOI: 10.1039/d1ra08658h] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 01/11/2022] [Indexed: 12/24/2022] Open
Abstract
Influenza A (H1N1) viruses are distributed around the world and pose a threat to public health. Vaccination is the main treatment strategy to prevent influenza infection, but antiviral drugs also play an important role in controlling seasonal and pandemic influenza. Currently, as influenza viruses may be developing antiviral resistance, new agents with different modes of action are being investigated. Recently, selenium nanoparticles (SeNPs), which have antiviral effects, have attracted increasing attention in biomedical interventions. The appearance of nanotechnology has attracted great attention in the field of nanomedicine. SeNPs constitute an attractive vector platform for delivering a variety of drugs to action targets. SeNPs are being explored for potential therapeutic efficacy in a variety of oxidative stress and inflammation-mediated diseases, such as cancer, arthritis, diabetes, and kidney disease. SeNPs could inhibit infection of Madin–Darby canine kidney (MDCK) cells with H1N1 and prevent chromatin condensation and DNA fragmentation. ROS play a key role in physiological processes for apoptosis. SeNPs significantly inhibited the production of reactive oxygen species (ROS) in MDCK cells. Mechanistic investigation revealed that SeNPs inhibited the apoptosis induced by H1N1 virus infection in MDCK cells by improving the level of GPx1. Our results suggest that SeNPs are an effective selenium source and a promising H1N1 influenza antiviral candidate. SeNPs inhibited the apoptosis induced by H1N1 virus infection in MDCK cells by improving the level of GPx1. Our results suggest that SeNPs are an effective selenium source and a promising H1N1 influenza antiviral candidate.![]()
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Affiliation(s)
- Xia Liu
- Center Laboratory, Guangzhou Women and Children's Medical Center, Guangzhou Medical University No. 318 Renminzhong Road, Yuexiu District Guangzhou 510120 People's Republic of China
| | - Danyang Chen
- Center Laboratory, Guangzhou Women and Children's Medical Center, Guangzhou Medical University No. 318 Renminzhong Road, Yuexiu District Guangzhou 510120 People's Republic of China
| | - Jingyao Su
- Center Laboratory, Guangzhou Women and Children's Medical Center, Guangzhou Medical University No. 318 Renminzhong Road, Yuexiu District Guangzhou 510120 People's Republic of China
| | - Ruilin Zheng
- Center Laboratory, Guangzhou Women and Children's Medical Center, Guangzhou Medical University No. 318 Renminzhong Road, Yuexiu District Guangzhou 510120 People's Republic of China
| | - Zhihui Ning
- Center Laboratory, Guangzhou Women and Children's Medical Center, Guangzhou Medical University No. 318 Renminzhong Road, Yuexiu District Guangzhou 510120 People's Republic of China
| | - Mingqi Zhao
- Center Laboratory, Guangzhou Women and Children's Medical Center, Guangzhou Medical University No. 318 Renminzhong Road, Yuexiu District Guangzhou 510120 People's Republic of China
| | - Bing Zhu
- Center Laboratory, Guangzhou Women and Children's Medical Center, Guangzhou Medical University No. 318 Renminzhong Road, Yuexiu District Guangzhou 510120 People's Republic of China
| | - Yinghua Li
- Center Laboratory, Guangzhou Women and Children's Medical Center, Guangzhou Medical University No. 318 Renminzhong Road, Yuexiu District Guangzhou 510120 People's Republic of China
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5
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Korsun N, Trifonova I, Voleva S, Grigorova I, Angelova S. Genetic characterisation of the influenza viruses circulating in Bulgaria during the 2019-2020 winter season. Virus Genes 2021; 57:401-412. [PMID: 34156583 PMCID: PMC8217981 DOI: 10.1007/s11262-021-01853-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 06/04/2021] [Indexed: 11/24/2022]
Abstract
Influenza viruses have a high potential for genetic changes. The objectives of this study were to analyse influenza virus circulation in Bulgaria during the 2019/2020 season, to perform a phylogenetic and molecular analyses of the haemagglutinin (HA) and neuraminidase (NA) sequences of representative influenza strains, and to identify amino acid substitutions compared to the current vaccine strains. Seasonal influenza viruses A(H3N2), A(H1N1)pdm09 and B/Victoria-lineage were detected using a real-time RT-PCR in 323 (23.3%), 149 (10.7%) and 138 (9.9%) out of 1387 patient samples studied, respectively. The HA genes of A(H3N2) viruses analysed belonged to clades 3C.3a (21 strains) and 3C.2a (5 strains): subclades 3C.2a1b + T131K, 3C.2a1b + T135K-B and 3C.2a1b + T135K-A. The clade 3C.3a and subclade 3C.2a1b viruses carried 5 and 14-17 substitutions in HA, as well as 3 and 9 substitutions in NA, respectively, in comparison with the A/Kansas/14/2017 vaccine virus, including some substitutions in the HA antigenic sites A, B, C and E. All 21 A(H1N1)pdm09 viruses sequenced fell into 6B.1A5A subclade. Amino acid sequence analysis revealed the presence of 7-11 substitutions in HA, compared to the A/Brisbane/02/2018 vaccine virus, three of which occurred in antigenic site Sb, along with 6-9 changes at positions in NA. All 10 B/Victoria-lineage viruses sequenced belonged to clade 1A with a triple deletion in HA1 (genetic group 1A(Δ3)B) and carried 7 and 3 substitutions in HA and NA, respectively, with respect to the B/Colorado/06/2017 vaccine virus. The results of this study confirm the rapid evolution of influenza viruses and the need for continuous antigenic and genetic surveillance.
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Affiliation(s)
- Neli Korsun
- Department of Virology, National Laboratory "Influenza and ARI", National Centre of Infectious and Parasitic Diseases, Sofia, Bulgaria.
| | - Ivelina Trifonova
- Department of Virology, National Laboratory "Influenza and ARI", National Centre of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Silvia Voleva
- Department of Virology, National Laboratory "Influenza and ARI", National Centre of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Iliyana Grigorova
- Department of Virology, National Laboratory "Influenza and ARI", National Centre of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Svetla Angelova
- Department of Virology, National Laboratory "Influenza and ARI", National Centre of Infectious and Parasitic Diseases, Sofia, Bulgaria
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6
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Yu JL, Hou S, Feng YT, Bu G, Chen QQ, Meng ZQ, Ding ZT, Guo LZ, Zhou X, Wang M, Huang XE, Li WW, He L, Gong L, Sun Y, Xu Z, Pan HF, He J, Wu JB. Emergence of a young case infected with avian influenza A (H5N6) in Anhui Province, East China during the COVID-19 pandemic. J Med Virol 2021; 93:5998-6007. [PMID: 34232513 PMCID: PMC8426836 DOI: 10.1002/jmv.27179] [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] [Received: 06/22/2021] [Accepted: 07/02/2021] [Indexed: 12/14/2022]
Abstract
In the context of the coronavirus disease 2019 pandemic, we investigated the epidemiological and clinical characteristics of a young patient infected by avian influenza A (H5N6) virus in Anhui Province, East China, and analyzed genomic features of the pathogen in 2020. Through the cross‐sectional investigation of external environment monitoring (December 29–31, 2020), 1909 samples were collected from Fuyang City. It was found that the positive rate of H5N6 was higher than other areas obviously in Tianma poultry market, where the case appeared. In addition, dual coinfections were detected with a 0.057% polymerase chain reaction positive rate the surveillance years. The virus was the clade 2.3.4.4, which was most likely formed by genetic reassortment between H5N6 and H9N2 viruses. This study found that the evolution rates of the hemagglutinin and neuraminidase genes of the virus were higher than those of common seasonal influenza viruses. The virus was still highly pathogenic to poultry and had a preference for avian receptor binding. Various avian influenza virus (AIV) subtypes naturally have caused zoonotic infections, but the subtypes H5N1 and H7N9 have caused a prominent impact. At present, the outbreak of novel coronavirus pneumonia (coronavirus disease 2019 [COVID‐19]) has caused a worldwide pandemic. To our knowledge, this is the youngest child infected with H5N6 subtype avian influenza in Anhui Province. Herein, we analyzed the epidemiology of the case and the characteristics of the pathogen genome, to find out the possible evolution of the virus.
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Affiliation(s)
- Jun-Ling Yu
- Microbiological Laboratory, Anhui Provincial Center for Disease Control and Prevention, Hefei, Anhui, China.,Microbiological Laboratory, Public Health Research Institute of Anhui Province, Hefei, Anhui, China
| | - Sai Hou
- Microbiological Laboratory, Anhui Provincial Center for Disease Control and Prevention, Hefei, Anhui, China.,Microbiological Laboratory, Public Health Research Institute of Anhui Province, Hefei, Anhui, China
| | - Ya-Ting Feng
- Department of Epidemiolgy and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China.,Inflammation and Immune Mediated Diseases Laboratory, Anhui Medical University, Hefei, Anhui, China
| | - Ge Bu
- Microbiological Laboratory, Fuyang City Center for Disease Control and Prevention, Fuyang, Anhui, China
| | - Qing-Qing Chen
- Microbiological Laboratory, Anhui Provincial Center for Disease Control and Prevention, Hefei, Anhui, China.,Microbiological Laboratory, Public Health Research Institute of Anhui Province, Hefei, Anhui, China
| | - Zhao-Qian Meng
- Microbiological Laboratory, Fuyang City Center for Disease Control and Prevention, Fuyang, Anhui, China
| | - Zhen-Tao Ding
- Microbiological Laboratory, Fuyang City Center for Disease Control and Prevention, Fuyang, Anhui, China
| | - Liang-Zi Guo
- Microbiological Laboratory, Fuyang City Center for Disease Control and Prevention, Fuyang, Anhui, China
| | - Xue Zhou
- Microbiological Laboratory, Anhui Provincial Center for Disease Control and Prevention, Hefei, Anhui, China.,Microbiological Laboratory, Public Health Research Institute of Anhui Province, Hefei, Anhui, China
| | - Meng Wang
- Microbiological Laboratory, Anhui Provincial Center for Disease Control and Prevention, Hefei, Anhui, China.,Microbiological Laboratory, Public Health Research Institute of Anhui Province, Hefei, Anhui, China
| | - Xin-Er Huang
- Department of Epidemiolgy and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China.,Inflammation and Immune Mediated Diseases Laboratory, Anhui Medical University, Hefei, Anhui, China
| | - Wei-Wei Li
- Microbiological Laboratory, Anhui Provincial Center for Disease Control and Prevention, Hefei, Anhui, China.,Microbiological Laboratory, Public Health Research Institute of Anhui Province, Hefei, Anhui, China
| | - Lan He
- Microbiological Laboratory, Anhui Provincial Center for Disease Control and Prevention, Hefei, Anhui, China.,Microbiological Laboratory, Public Health Research Institute of Anhui Province, Hefei, Anhui, China
| | - Lei Gong
- Microbiological Laboratory, Anhui Provincial Center for Disease Control and Prevention, Hefei, Anhui, China.,Microbiological Laboratory, Public Health Research Institute of Anhui Province, Hefei, Anhui, China
| | - Yong Sun
- Microbiological Laboratory, Anhui Provincial Center for Disease Control and Prevention, Hefei, Anhui, China.,Microbiological Laboratory, Public Health Research Institute of Anhui Province, Hefei, Anhui, China
| | - Zhiwei Xu
- School of Public Health, Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
| | - Hai-Feng Pan
- Department of Epidemiolgy and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China.,Inflammation and Immune Mediated Diseases Laboratory, Anhui Medical University, Hefei, Anhui, China
| | - Jun He
- Microbiological Laboratory, Anhui Provincial Center for Disease Control and Prevention, Hefei, Anhui, China.,Microbiological Laboratory, Public Health Research Institute of Anhui Province, Hefei, Anhui, China
| | - Jia-Bing Wu
- Microbiological Laboratory, Anhui Provincial Center for Disease Control and Prevention, Hefei, Anhui, China.,Microbiological Laboratory, Public Health Research Institute of Anhui Province, Hefei, Anhui, China
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7
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Liu Y, Wang Y, Liu B, Cong X, Ji Y, Guo X, Gao Y. Phylogenetic analysis and clinical characteristics of the co-occurring mutations in HA and NA genes of influenza A(H1N1)pdm09 viruses during 2015-2017 in Beijing, China. Virol J 2020; 17:182. [PMID: 33213486 PMCID: PMC7678287 DOI: 10.1186/s12985-020-01446-3] [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: 04/21/2020] [Accepted: 11/05/2020] [Indexed: 11/25/2022] Open
Abstract
Background Influenza A(H1N1)pdm09 viruses have undergone rapid evolution, and in recent years the complementary and antagonistic effects of HA and NA have gathered more attentions; however, the effects of co-occurring mutations in HA and NA on the patients’ clinical characteristics are still poorly understood. In this study, we analyzed molecular epidemiology and evolution of A(H1N1) pdm09, explored co-occurring mutations of HA and NA, and investigated effect of co-occurring mutations on patients’ clinical features. Methods A(H1N1)pdm09 was confirmed by reverse transcription-polymerase chain reaction. HA and NA genes were sequenced and phylogenetically analyzed. Clinical characteristics of the co-occurring mutations were analyzed statistically. Results By analyzing the HA and NA gene sequences of 33 A(H1N1)pdm09 viruses during the 2015–2017 influenza season, we found that all the viruses shared high similarities to each other and the HA genes of these viruses exclusively belonged to subclade 6B.1A. Several unreported substitutions in HA and NA proteins were observed, furthermore, co-occurring mutations of HA-V169T, A278S, E508G, D518E and NA-V67I were detected in 30.3% (10/33) A(H1N1)pdm09 virus strains when comparing with vaccine strains A/California/07/2009 and A/Michigan/45/2015 (H1N1). Sore throat was significantly associated with co-occurring mutations in HA and NA of A(H1N1)pdm09 (χ2, P < 0.05). Conclusions Co-occurring mutations in HA and NA were detected in A(H1N1)pdm09 isolated during 2015–2017 in Beijing. Symptomatically, sore throat was associated with co-occurring mutations in HA and NA of A(H1N1)pdm09. Therefore, studying the effect and mechanism of co-occurring mutations in HA and NA on patients’ clinical features is of note needed.
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Affiliation(s)
- Yafen Liu
- Department of Infectious Diseases, Peking University Hepatology Institute, Peking University People's Hospital, No. 11, Xizhimen South Street, Xicheng District, Beijing, 100044, People's Republic of China
| | - Yue Wang
- Department of Infectious Diseases, Peking University Hepatology Institute, Peking University People's Hospital, No. 11, Xizhimen South Street, Xicheng District, Beijing, 100044, People's Republic of China
| | - Baiyi Liu
- Department of Infectious Diseases, Peking University Hepatology Institute, Peking University People's Hospital, No. 11, Xizhimen South Street, Xicheng District, Beijing, 100044, People's Republic of China
| | - Xu Cong
- Peking University Hepatology Institute, Peking University People's Hospital, No. 11, Xizhimen South Street, Xicheng District, Beijing, 100044, People's Republic of China
| | - Ying Ji
- Peking University Hepatology Institute, Peking University People's Hospital, No. 11, Xizhimen South Street, Xicheng District, Beijing, 100044, People's Republic of China
| | - Xiaolin Guo
- Department of Infectious Diseases, Peking University Hepatology Institute, Peking University People's Hospital, No. 11, Xizhimen South Street, Xicheng District, Beijing, 100044, People's Republic of China
| | - Yan Gao
- Department of Infectious Diseases, Peking University Hepatology Institute, Peking University People's Hospital, No. 11, Xizhimen South Street, Xicheng District, Beijing, 100044, People's Republic of China.
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8
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Korsun N, Daniels R, Angelova S, Ermetal B, Grigorova I, Voleva S, Trifonova I, Kurchatova A, McCauley J. Genetic diversity of influenza A viruses circulating in Bulgaria during the 2018-2019 winter season. J Med Microbiol 2020; 69:986-998. [PMID: 32459617 PMCID: PMC7481746 DOI: 10.1099/jmm.0.001198] [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] [Indexed: 01/30/2023] Open
Abstract
Introduction Influenza viruses evolve rapidly and change their antigenic characteristics, necessitating biannual updates of flu vaccines. Aim The aim of this study was to characterize influenza viruses circulating in Bulgaria during the 2018/2019 season and to identify amino acid substitutions in them that might impact vaccine effectiveness. Methodology Typing/subtyping of influenza viruses were performed using real-time Reverse Transcription-PCR (RT-PCR) and results of phylogenetic and amino acid sequence analyses of influenza strains are presented. Results A(H1N1)pdm09 (66 %) predominated over A(H3N2) (34 %) viruses, with undetected circulation of B viruses in the 2018/2019 season. All A(H1N1)pdm09 viruses studied fell into the recently designated 6B.1A subclade with over 50 % falling in four subgroups: 6B.1A2, 6B.1A5, 6B.1A6 and 6B.1A7. Analysed A(H3N2) viruses belonged to subclades 3C.2a1b and 3C.2a2. Amino acid sequence analysis of 36 A(H1N1)pdm09 isolates revealed the presence of six–ten substitutions in haemagglutinin (HA), compared to the A/Michigan/45/2015 vaccine virus, three of which occurred in antigenic sites Sa and Cb, together with four–nine changes at positions in neuraminidase (NA), and a number of substitutions in internal proteins. HA1 D222N substitution, associated with increased virulence, was identified in two A(H1N1)pdm09 viruses. Despite the presence of several amino acid substitutions, A(H1N1)pdm09 viruses remained antigenically similar to the vaccine virus. The 28 A(H3N2) viruses characterized carried substitutions in HA, including some in antigenic sites A, B, C and E, in NA and internal protein sequences. Conclusion The results of this study showed the genetic diversity of circulating influenza viruses and the need for continuous antigenic and molecular surveillance.
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Affiliation(s)
- Neli Korsun
- National Laboratory "Influenza and ARI", Department of Virology, National Centre of Infectious and Parasitic Diseases, 44A Stoletov Blvd, 1233 Sofia, Bulgaria
| | - Rodney Daniels
- WHO Collaborating Centre for Reference and Research on Influenza, Worldwide Influenza Centre, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Svetla Angelova
- National Laboratory "Influenza and ARI", Department of Virology, National Centre of Infectious and Parasitic Diseases, 44A Stoletov Blvd, 1233 Sofia, Bulgaria
| | - Burcu Ermetal
- WHO Collaborating Centre for Reference and Research on Influenza, Worldwide Influenza Centre, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Iliyana Grigorova
- National Laboratory "Influenza and ARI", Department of Virology, National Centre of Infectious and Parasitic Diseases, 44A Stoletov Blvd, 1233 Sofia, Bulgaria
| | - Silvia Voleva
- National Laboratory "Influenza and ARI", Department of Virology, National Centre of Infectious and Parasitic Diseases, 44A Stoletov Blvd, 1233 Sofia, Bulgaria
| | - Ivelina Trifonova
- National Laboratory "Influenza and ARI", Department of Virology, National Centre of Infectious and Parasitic Diseases, 44A Stoletov Blvd, 1233 Sofia, Bulgaria
| | - Anna Kurchatova
- Department of Epidemiology, National Centre of Infectious and Parasitic Diseases, 26 Yanko Sakazov Blvd, 1504 Sofia, Bulgaria
| | - John McCauley
- WHO Collaborating Centre for Reference and Research on Influenza, Worldwide Influenza Centre, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
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9
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Kyaw Win SM, Saito R, Win NC, Lasham DJ, Kyaw Y, Lin N, Thein KN, Chon I, Odagiri T, Thein W, Kyaw LL, Tin OS, Saitoh A, Tamura T, Hirokawa C, Uchida Y, Saito T, Watanabe S, Odagiri T, Kamata K, Osada H, Dapat C, Watanabe H, Tin HH. Epidemic of influenza A(H1N1)pdm09 analyzed by full genome sequences and the first case of oseltamivir-resistant strain in Myanmar 2017. PLoS One 2020; 15:e0229601. [PMID: 32130243 PMCID: PMC7055873 DOI: 10.1371/journal.pone.0229601] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 02/10/2020] [Indexed: 12/16/2022] Open
Abstract
A community outbreak of human influenza A(H1N1)pdm09 virus strains was observed in Myanmar in 2017. We investigated the circulation patterns, antigenicity, and drug resistance of 2017 influenza A(H1N1)pdm09 viruses from Myanmar and characterized the full genome of influenza virus strains in Myanmar from in-patients and out-patients to assess the pathogenicity of the viruses. Nasopharyngeal swabs were collected from out-patients and in-patients with acute respiratory tract infections in Yangon and Pyinmana City in Myanmar during January-December 2017. A total of 215 out-patients and 18 in-patients infected with A(H1N1)pdm09 were detected by virus isolation and real-time RT-PCR. Among the positive patients, 90.6% were less than 14 years old. Hemagglutination inhibition (HI) antibody titers against A(H1N1)pdm09 viruses in Myanmar were similar to the recommended Japanese influenza vaccine strain for 2017–2018 seasons (A/Singapore/GP1908/2015) and WHO recommended 2017 southern hemisphere vaccine component (A/Michigan/45/2015). Phylogenetic analysis of the hemagglutinin sequence showed that the Myanmar strains belonged to the genetic subclade 6B.1, possessing mutations of S162N and S164T at potential antigenic sites. However, the amino acid mutation at position 222, which may enhance the severity of disease and mortality, was not found. One case with no prior history of oseltamivir treatment possessed H275Y mutated virus in neuraminidase (NA), which confers resistance to oseltamivir and peramivir with elevated IC50 values. The full genome sequence of Myanmar strains showed no difference between samples from in-patients and out-patients, suggesting no additional viral mutations associated with patient severity. Several amino acid changes were observed in PB2, PB1, and M2 of Myanmar strains when compared to the vaccine strain and other Asian strains. However, no mutations associated with pathogenicity were found in the Myanmar strains, suggesting that viral factors cannot explain the underlying reasons of the massive outbreak in Myanmar. This study reported the first detection of an oseltamivir-resistant influenza virus in Myanmar, highlighting the importance of continuous antiviral monitoring and genetic characterization of the influenza virus in Myanmar.
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Affiliation(s)
- Su Mon Kyaw Win
- Infectious Diseases Research Center of Niigata University in Myanmar (IDRC), Yangon, Yangon Region, Myanmar
| | - Reiko Saito
- Infectious Diseases Research Center of Niigata University in Myanmar (IDRC), Yangon, Yangon Region, Myanmar.,Division of International Health, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Niigata, Japan
| | - Nay Chi Win
- Infectious Diseases Research Center of Niigata University in Myanmar (IDRC), Yangon, Yangon Region, Myanmar
| | - Di Ja Lasham
- Infectious Diseases Research Center of Niigata University in Myanmar (IDRC), Yangon, Yangon Region, Myanmar
| | - Yadanar Kyaw
- Respiratory Medicine Department, Thingangyun Sanpya General Hospital, Yangon, Yangon Region, Myanmar
| | - Nay Lin
- Clinical Laboratory, Microbiology Section, Pyinmana General Hospital, Pyinmana Township, Nay Pyi Taw, Myanmar
| | - Khin Nyo Thein
- Pediatric Ward 1, Yankin Children Hospital, Yangon, Yangon Region, Myanmar
| | - Irina Chon
- Division of International Health, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Niigata, Japan
| | - Takashi Odagiri
- Department of Microbiology, Infectious diseases and Immunology, Iwate Medical University, Morioka, Iwate, Japan
| | - Win Thein
- National Health Laboratory, Department of Medical Services, Ministry of Health and Sports, Yangon, Yangon Region, Myanmar
| | - Latt Latt Kyaw
- National Health Laboratory, Department of Medical Services, Ministry of Health and Sports, Yangon, Yangon Region, Myanmar
| | - Ommar Swe Tin
- National Health Laboratory, Department of Medical Services, Ministry of Health and Sports, Yangon, Yangon Region, Myanmar
| | - Akihiko Saitoh
- Department of Pediatrics, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Niigata, Japan
| | - Tsutomu Tamura
- Division of Virology, Niigata Prefectural Institute of Public Health and Environmental Sciences, Niigata, Niigata, Japan
| | - Chika Hirokawa
- Division of Virology, Niigata Prefectural Institute of Public Health and Environmental Sciences, Niigata, Niigata, Japan
| | - Yuko Uchida
- Division of Transboundary Animal Disease, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
| | - Takehiko Saito
- Division of Transboundary Animal Disease, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
| | - Shinji Watanabe
- Laboratory of Influenza Virus Surveillance, Influenza Research Center, National Institute of Infectious Diseases, Sinjuku-ku, Tokyo, Japan
| | - Takato Odagiri
- Laboratory of Influenza Virus Surveillance, Influenza Research Center, National Institute of Infectious Diseases, Sinjuku-ku, Tokyo, Japan
| | - Kazuhiro Kamata
- Infectious Diseases Research Center of Niigata University in Myanmar (IDRC), Yangon, Yangon Region, Myanmar.,Institute of Medicine and Dentistry, Niigata University, Niigata, Japan
| | - Hidekazu Osada
- Infectious Diseases Research Center of Niigata University in Myanmar (IDRC), Yangon, Yangon Region, Myanmar.,Institute of Medicine and Dentistry, Niigata University, Niigata, Japan
| | - Clyde Dapat
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
| | - Hisami Watanabe
- Infectious Diseases Research Center of Niigata University in Myanmar (IDRC), Yangon, Yangon Region, Myanmar.,Institute of Medicine and Dentistry, Niigata University, Niigata, Japan
| | - Htay Htay Tin
- National Health Laboratory, Department of Medical Services, Ministry of Health and Sports, Yangon, Yangon Region, Myanmar
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10
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Saha P, Biswas M, Gupta R, Majumdar A, Mitra S, Banerjee A, Mukherjee A, Dutta S, Chawla-Sarkar M. Molecular characterization of Influenza A pandemic H1N1 viruses circulating in eastern India during 2017-19: Antigenic diversity in comparison to the vaccine strains. INFECTION GENETICS AND EVOLUTION 2020; 81:104270. [PMID: 32142936 DOI: 10.1016/j.meegid.2020.104270] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 02/08/2020] [Accepted: 03/02/2020] [Indexed: 11/27/2022]
Abstract
In the endemic settings of India, high CFR (3.6-7.02%) was observed in the consecutive 2009, 2015 and 2017 A/H1N1pdm09 outbreaks, though in eastern India CFR varied between 0 and 5.5% during same period. Recurrent outbreaks of pandemic Influenza A/H1N1pdm09, fragmented nationwide incidence data, lack of national policy for Influenza vaccination in India underscores the necessity for generating regional level data. Thus, during 2017-19, 4106 referred samples from patients hospitalized with severe acute respiratory illness (SARI) in eastern India were tested for A/H1N1pdm09 infection. Among which 16.5% (n = 677/4106) were found A/H1N1pdm09 positive. Individuals <20 years and middle-aged persons (40-60 years) were most susceptible to A/H1N1pdm09 infection. The vaccine strain (A/human/California/07/2009) which was globally used before 2017, clustered in a different lineage away from the representative eastern Indian strains in the phylogenetic dendrogram. The vaccine strain (A/human/Michigan/45/2015) used in India during the study period and the WHO recommended strain (A/human/Brisbane/02/2018) for 2019-20 flu season for the northern hemisphere, clustered with the circulating isolates in the same lineage-6b. Dissimilarities in the amino acids encompassing the antigenic epitopes were seen to be highest with the vaccine strain- A/human/California/07/2009. The significant amino acid variations in the circulating strains with the current WHO recommended vaccine strain, implies the exigency of continuous pandemic A/H1N1pdm09 surveillance studies in this epidemiological setting. The absence of any Oseltamivir resistant mutation (H275Y) in the neuraminidase gene of the current isolates suggests continuing use of Tamiflu® as an antiviral therapy in suspected subjects in this region.
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Affiliation(s)
- Priyanka Saha
- Division of Virology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Madhumonti Biswas
- Regional Virus Research and Diagnostic Lab, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Rudrak Gupta
- Regional Virus Research and Diagnostic Lab, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Agniva Majumdar
- Regional Virus Research and Diagnostic Lab, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Suvrotoa Mitra
- Division of Virology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Anindita Banerjee
- Division of Virology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | | | - Shanta Dutta
- Regional Virus Research and Diagnostic Lab, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Mamta Chawla-Sarkar
- Division of Virology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India.
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11
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Li X, Guo L, Liu C, Cheng Y, Kong M, Yang L, Zhuang Z, Liu J, Zou M, Dong X, Su X, Gu Q. Human infection with a novel reassortant Eurasian-avian lineage swine H1N1 virus in northern China. Emerg Microbes Infect 2020; 8:1535-1545. [PMID: 31661383 PMCID: PMC6830285 DOI: 10.1080/22221751.2019.1679611] [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] [Indexed: 11/30/2022]
Abstract
Influenza A virus infections occur in different species, causing mild to severe respiratory symptoms that lead to a heavy disease burden. Eurasian avian-like swine influenza A(H1N1) viruses (EAS-H1N1) are predominant in pigs and occasionally infect humans. An influenza A(H1N1) virus was isolated from a boy who was suffering from fever and headache and designated as A/Tianjin-baodi/1606/2018(H1N1). Full-genome sequencing and phylogenetic analysis revealed that A/Tianjin-baodi/1606/2018(H1N1) is a novel reassortant EAS-H1N1 containing gene segments from EAS-H1N1 (HA and NA), classical swine H1N1(NS) and A(H1N1)pdm09(PB2, PB2, PA, NP and M) viruses. The isolation and analysis of A/Tianjin-baodi/1606/2018(H1) provide further evidence that EAS-H1N1 poses a threat to human health and greater attention should be paid to surveillance of influenza virus infection in pigs and humans.
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Affiliation(s)
- Xiaoyan Li
- Tianjin Centers for Disease Control and Prevention, Tianjin, People's Republic of China
| | - Liru Guo
- Tianjin Centers for Disease Control and Prevention, Tianjin, People's Republic of China
| | - Caixia Liu
- Jizhou District Center for Disease Control and Prevention, Tianjin, People's Republic of China
| | - Yanhui Cheng
- Chinese National Influenza Center, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Mei Kong
- Tianjin Centers for Disease Control and Prevention, Tianjin, People's Republic of China
| | - Lei Yang
- Chinese National Influenza Center, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Zhichao Zhuang
- Tianjin Centers for Disease Control and Prevention, Tianjin, People's Republic of China
| | - Jia Liu
- Chinese National Influenza Center, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Ming Zou
- Tianjin Centers for Disease Control and Prevention, Tianjin, People's Republic of China
| | - Xiaochun Dong
- Tianjin Centers for Disease Control and Prevention, Tianjin, People's Republic of China
| | - Xu Su
- Tianjin Centers for Disease Control and Prevention, Tianjin, People's Republic of China
| | - Qing Gu
- Tianjin Centers for Disease Control and Prevention, Tianjin, People's Republic of China
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12
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Al Khatib HA, Al Thani AA, Gallouzi I, Yassine HM. Epidemiological and genetic characterization of pH1N1 and H3N2 influenza viruses circulated in MENA region during 2009-2017. BMC Infect Dis 2019; 19:314. [PMID: 30971204 PMCID: PMC6458790 DOI: 10.1186/s12879-019-3930-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 03/20/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Influenza surveillance is necessary for detection of emerging variants of epidemiologic and clinical significance. This study describes the epidemiology of influenza types A and B, and molecular characteristics of surface glycoproteins (hemagglutinin [HA] and neuraminidase [NA]) of influenza A subtypes: pH1N1 and H3N2 circulated in Arabian Gulf, Levant and North Africa regions during 2009-2017. METHODS Analysis of phylogenetics and evolution of HA and NA genes was done using full HA and NA sequences (n = 1229) downloaded from Influenza Research Database (IRD). RESULTS In total, 130,354 influenza positive cases were reported to WHO during study period. Of these, 50.8% were pH1N1 positive, 15.9% were H3N2 positives and 17.2% were influenza B positive. With few exceptions, all three regions were showing the typical seasonal influenza peak similar to that reported in Northern hemisphere (December-March). However, influenza activity started earlier (October) in both Gulf and North Africa while commenced later during November in Levant countries. The molecular analysis of the HA genes (influenza A subtypes) revealed similar mutations to those reported worldwide. Generally, amino acid substitutions were most frequently found in head domain in H1N1 pandemic viruses, while localized mainly in the stem region in H3N2 viruses. Expectedly, seasons with high pH1N1 influenza activity was associated with a relatively higher number of substitutions in the head domain of the HA in pH1N1 subtype. Furthermore, nucleotide variations were lower at the antigenic sites of pH1N1 viruses compared to H3N2 viruses, which experienced higher variability at the antigenic sites, reflecting the increased immunological pressure because of longer circulation and continuous vaccine changes. Analysis of NA gene of pH1N1 viruses revealed sporadic detections of oseltamivir-resistance mutation, H275Y, in 4% of reported sequences, however, none of NAI resistance mutations were found in the NA of H3N2 viruses. CONCLUSIONS Molecular characterization of H1N1 and H3N2 viruses over 9 years revealed significant differences with regard to position and function of characterized substitutions. While pH1N1 virus substitutions were mainly found in HA head domain, H3N2 virus substitutions were mostly found in HA stem domain. Additionally, more fixed substitutions were encountered in H3N2 virus compared to larger number of non-fixed substitutions in pH1N1.
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Affiliation(s)
- Hebah A Al Khatib
- Life Science division, College of Science and Engineering, Hamad Ben Khalifah University, Doha, 34110, Qatar
| | | | - Imed Gallouzi
- Life Science division, College of Science and Engineering, Hamad Ben Khalifah University, Doha, 34110, Qatar.,Biochemistry Department and Goodman Cancer Center, 3655 Promenade Sir William Osler, McGill University, Montreal, Quebec, H3G1Y6, Canada
| | - Hadi M Yassine
- Biomedical Research Center, Qatar University, Doha, 2713, Qatar.
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13
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Khan A, AlBalwi MA, AlAbdulkareem I, AlMasoud A, AlAsiri A, AlHarbi W, AlSehile F, El-Saed A, Balkhy HH. Atypical influenza A(H1N1)pdm09 strains caused an influenza virus outbreak in Saudi Arabia during the 2009-2011 pandemic season. J Infect Public Health 2019; 12:557-567. [PMID: 30799182 DOI: 10.1016/j.jiph.2019.01.067] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 01/22/2019] [Accepted: 01/30/2019] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND The triple assortment influenza A(H1N1) virus emerged in spring 2009 and disseminated worldwide, including Saudi Arabia. This study was carried out to characterize Saudi influenza isolates in relation to the global strains and to evaluate the potential role of mutated residues in transmission, adaptation, and the pathogenicity of the virus. METHODS Nasopharyngeal samples (n = 6492) collected between September 2009 to March 2011 from patients with influenza-like illness were screened by PCR for influenza A(H1N1). Phylogenetic and Molecular evolutionary analysis were carried out to place the Saudi strains in relation to the global strains followed by Mutation analysis of surface and internal proteins. RESULTS Concatenated whole-genome phylogenetic analysis along with hemagglutinin (HA) signature changes, that is, Aspartic Acid (D) at position 187, P83S, S203T, and R223Q confirmed that the Saudi strains belong to the antigenic category of A/California/07/2009. However, phylogenetic analysis revealed unusual strains of A(H1N1) circulating in Saudi Arabia, not belonging to any of known clades, appearing in five distinct groups well supported by group-specific mutations and novel mutation complexes. These cases had characteristic inter- and intragroup substitution patterns while few of their closest matches showed up as sporadic cases the world over. Specific mutation patterns were detected within the functional domains of internal proteins PB2, PB1, PA, NP, NS1, and M2 having a putative role in viral fitness and virulence. Bayesian coalescent MCMC analysis revealed that Saudi strains belonged to cluster 2 of A(H1N1)pdm09 and spread a month later as compared to other strains of this cluster. CONCLUSION Influenza outbreak in Saudi Arabia during 2009-2011 was caused by atypical strains of influenza A(H1N1)pdm09, probably introduced in this community on multiple occasions. To understand the antigenic significance of these novel point mutations and mutation complexes require functional studies, which will be crucial for risk assessment of emergent strains and defining infection control measures.
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Affiliation(s)
- Anis Khan
- Department of Medical Genomics Research, King Abdullah International Medical Research Center, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Mohammed A AlBalwi
- Department of Medical Genomics Research, King Abdullah International Medical Research Center, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia; Department of Pathology & Laboratory Medicine, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia; King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia.
| | - Ibraheem AlAbdulkareem
- Intramural health sciences research, Princess Nourah Bint Abdulrahman university, Riyadh, Saudi Arabia
| | - Abdulrahman AlMasoud
- Department of Medical Genomics Research, King Abdullah International Medical Research Center, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Abdulrahman AlAsiri
- Department of Medical Genomics Research, King Abdullah International Medical Research Center, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Wardah AlHarbi
- Department of Medical Genomics Research, King Abdullah International Medical Research Center, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Faisal AlSehile
- King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Aiman El-Saed
- Department of Infection Prevention & Control Department, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Hanan H Balkhy
- King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia; Department of Infection Prevention & Control Department, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
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14
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Genetic variations of the Hemagglutinin gene of Pandemic Influenza A (H1N1) viruses in Assam, India during 2016. 3 Biotech 2018; 8:408. [PMID: 30237955 DOI: 10.1007/s13205-018-1427-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 09/10/2018] [Indexed: 10/28/2022] Open
Abstract
Since its emergence in 2009, Influenza A/H1N1pdm09 virus has evolved continuously. Marked genetic variations have occurred in the HA1 domain of the hemagglutinin gene causing the emergence of new variants. The present study genetically characterized the hemagglutinin (HA) gene of Influenza A/H1N1pdm09 strains from Assam circulating in 2016 that caused a mild outbreak without any reported mortality. Sequence analysis of the HA gene of 20 positive Assam/H1N1pdm09 strains revealed 3 mutations (K180Q, S202T, S220T) at the antigenic sites along with several other reported mutations which are in close proximity to the antigenic sites and therefore might affect the viral antigenicity. Phylogenetically, the Assam/H1N1pdm09 strains clustered into genogroup 6B. These genetic variations highlight the importance of continuous surveillance and characterization of Influenza A/H1N1pdm09 virus activity to track the genetic makeup and diversification that may affect the behavior of the virus.
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15
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Molecular Evidence of Transmission of Influenza A/H1N1 2009 on a University Campus. PLoS One 2017; 12:e0168596. [PMID: 28060851 PMCID: PMC5218485 DOI: 10.1371/journal.pone.0168596] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2016] [Accepted: 12/03/2016] [Indexed: 01/10/2023] Open
Abstract
Background In the recent years, the data on the molecular epidemiology of influenza viruses have expanded enormously because of the availability of cutting-edge sequencing technologies. However, much of the information is from the temperate regions with few studies from tropical regions such as South-east Asia. Despite the fact that influenza has been known to transmit rapidly within semi-closed communities, such as military camps and educational institutions, data are limited from these communities. Objectives To determine the phylogeography of influenza viruses on a university campus, we examined the spatial distribution of influenza virus on the National University of Singapore (NUS) campus. Methods Consenting students from the NUS who sought medical attention at the UHC provided two nasopharyngeal swabs and demographic data. PCR was used for detection of influenza viruses. 34 full-genomes of pH1N1/09 viruses were successfully sequenced by Sanger method and concatenated using Geneious R7. Phylogenetic analysis was conducted using these 34 sequences and 1518 global sequences. Phylogeographic analysis was done using BaTS software and Association index and Fitch parsimony scores were determined. Results Integrating whole genome sequencing data with epidemiological data, we found strong evidence of influenza transmission on campus as isolates from students residing on-campus were highly similar to each other (AI, P value = 0.009; PS, P value = 0.04). There was also evidence of multiple introductions from the community. Conclusions Such data are useful in formulating pandemic preparedness plans which can use these communities as sentinel sites for detection and monitoring of emerging respiratory viral infections.
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16
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Cao P, Wong CM, Chan KH, Wang X, Chan KP, Peiris JSM, Poon LLM, Yang L. Age-specific genetic and antigenic variations of influenza A viruses in Hong Kong, 2013-2014. Sci Rep 2016; 6:30260. [PMID: 27453320 PMCID: PMC4958999 DOI: 10.1038/srep30260] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 07/04/2016] [Indexed: 11/18/2022] Open
Abstract
Age-specific genetic and antigenic variations of influenza viruses have not been documented in tropical and subtropical regions. We implemented a systematic surveillance program in two tertiary hospitals in Hong Kong Island, to collect 112 A(H1N1)pdm09 and 254 A(H3N2) positive specimens from 2013 to 2014. Of these, 56 and 72 were identified as genetic variants of the WHO recommended vaccine composition strains, respectively. A subset of these genetic variants was selected for hemagglutination-inhibition (HI) tests, but none appeared to be antigenic variants of the vaccine composition strains. We also found that genetic and antigenicity variations were similar across sex and age groups of ≤18 yrs, 18 to 65 yrs, and ≥65 yrs. Our findings suggest that none of the age groups led other age groups in genetic evolution of influenza virus A strains. Future studies from different regions and longer study periods are needed to further investigate the age and sex heterogeneity of influenza viruses.
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Affiliation(s)
- Peihua Cao
- Division of Epidemiology and Biostatistics, School of Public Health, The University of Hong Kong, Hong Kong SAR, China
| | - Chit-Ming Wong
- Division of Epidemiology and Biostatistics, School of Public Health, The University of Hong Kong, Hong Kong SAR, China
| | - Kwok-Hung Chan
- Department of Microbiology, The University of Hong Kong, Hong Kong SAR, China
| | - Xiling Wang
- Department of Biostatistics, School of Public Health and Key Laboratory of Public Health Safety, Fudan University, Shanghai, China
| | - King-Pan Chan
- Division of Epidemiology and Biostatistics, School of Public Health, The University of Hong Kong, Hong Kong SAR, China
| | - Joseph Sriyal Malik Peiris
- Division of Public Health Laboratory Sciences, School of Public Health, The University of Hong Kong, Hong Kong SAR, China
| | - Leo Lit-Man Poon
- Division of Public Health Laboratory Sciences, School of Public Health, The University of Hong Kong, Hong Kong SAR, China
| | - Lin Yang
- School of Nursing, The Hong Kong Polytechnic University, Hong Kong SAR, China
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17
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Resende PC, Motta FC, Born PS, Machado D, Caetano BC, Brown D, Siqueira MM. Phylogenetic analyses of influenza A (H1N1)pdm09 hemagglutinin gene during and after the pandemic event in Brazil. INFECTION GENETICS AND EVOLUTION 2015; 36:147-155. [PMID: 26371065 DOI: 10.1016/j.meegid.2015.09.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 08/20/2015] [Accepted: 09/04/2015] [Indexed: 12/17/2022]
Abstract
Pandemic influenza A H1N1 [A(H1N1)pdm09] was first detected in Brazil in May 2009, and spread extensively throughout the country causing a peak of infection during June to August 2009. Since then, it has continued to circulate with a seasonal pattern, causing high rates of morbidity and mortality. Over this period, the virus has continually evolved with the accumulation of new mutations. In this study we analyze the phylogenetic relationship in a collection of 220 A(H1N1)pdm09 hemagglutinin (HA) gene sequences collected during and after the pandemic period (2009 to 2014) in Brazil. In addition, we have looked for evidence of viral polymorphisms associated with severe disease and compared the range of viral variants with the vaccine strain (A/California/7/2009) used throughout this period. The phylogenetic analyses in this study revealed the circulation of at least eight genetic groups in Brazil. Two (G6-pdm and G7-pdm) co-circulated during the pandemic period, showing an early pattern of viral diversification with a low genetic distance from vaccine strain. Other phylogenetic groups, G5, G6 (including 6B, 6C and 6D subgroups), and G7 were found in the subsequent epidemic seasons from 2011 to 2014. These viruses exhibited more amino acid differences from the vaccine strain with several substitutions at the antigenic sites. This is associated with a theoretical decrease in the vaccine efficacy. Furthermore, we observed that the presence of any polymorphism at residue 222 of the HA gene was significantly associated with severe/fatal cases, reinforcing previous reports that described this residue as a potential virulence marker. This study provides new information about the circulation of some viral variants in Brazil, follows up potential genetic markers associated with virulence and allows infer if the efficacy of the current vaccine against more recent A(H1N1)pdm09 strains may be reduced.
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Affiliation(s)
- Paola Cristina Resende
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil.
| | - Fernando Couto Motta
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil
| | - Priscila Silva Born
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil
| | - Daniela Machado
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil; Fondation Mérieux, Emerging Pathogens Laboratory, Centre International de Recherche en Infectologie (CIRI), Lyon, France
| | - Braulia Costa Caetano
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil
| | - David Brown
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil
| | - Marilda Mendonça Siqueira
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil
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New genetic variants of influenza A(H1N1)pdm09 detected in Cuba during 2011-2013. INFECTION GENETICS AND EVOLUTION 2015; 32:322-6. [PMID: 25839842 DOI: 10.1016/j.meegid.2015.03.028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Revised: 03/23/2015] [Accepted: 03/24/2015] [Indexed: 11/20/2022]
Abstract
Influenza A(H1N1)pdm09 virus has evolved continually since its emergence in 2009. For influenza virus strains, genetic changes occurring in HA1 domain of the hemagglutinin cause the emergence of new variants. The aim of our study is to establish genetic associations between 35 A(H1N1)pdm09 viruses circulating in Cuba in 2011-2012 and 2012-2013 seasons, and A/California/07/2009 strain recommended by WHO as the H1N1 component of the influenza vaccine. The phylogenetic analysis revealed the circulation of clades 3, 6A, 6B, 6C and 7. Mutations were detected in the antigenic site or in the receptor-binding domains of HA1 segment, including S174P, S179N, K180Q, S202T, S220T and R222K. Substitutions S174P, S179N, K180Q and R222K were detected in Cuban strains for the first time.
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Pérez LJ, Perera CL, Coronado L, Rios L, Vega A, Frías MT, Ganges L, Núñez JI, Díaz de Arce H. Molecular epidemiology study of swine influenza virus revealing a reassorted virus H1N1 in swine farms in Cuba. Prev Vet Med 2015; 119:172-8. [PMID: 25745869 DOI: 10.1016/j.prevetmed.2015.02.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Revised: 02/09/2015] [Accepted: 02/16/2015] [Indexed: 10/23/2022]
Abstract
In this report, we describe the emergence of reassorted H1N1 swine influenza virus, originated from a reassortment event between the H1N1 pandemic influenza virus (H1N1p/2009) and endemic swine influenza virus in Cuban swine population. In November 2010, a clinical respiratory outbreak was reported on a pig fattening farm in Cuba. Phylogenetic analysis showed that all the genes of one of the isolate obtained, with the exception of neuraminidase, belonged to the H1N1p/2009 cluster. This finding suggests that H1N1pdm has been established in swine and has become a reservoir of reassortment that may produce new viruses with both animal and public health risks.
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Affiliation(s)
- Lester J Pérez
- Centro Nacional de Sanidad Agropecuaria (CENSA), La Habana, Cuba.
| | | | - Liani Coronado
- Centro Nacional de Sanidad Agropecuaria (CENSA), La Habana, Cuba
| | - Liliam Rios
- Centro Nacional de Sanidad Agropecuaria (CENSA), La Habana, Cuba
| | - Armando Vega
- Centro Nacional de Sanidad Agropecuaria (CENSA), La Habana, Cuba
| | - Maria T Frías
- Centro Nacional de Sanidad Agropecuaria (CENSA), La Habana, Cuba
| | - Llilianne Ganges
- Centre de Recerca en Sanitat Animal (CReSA), UAB-IRTA, Campus de la Universitat Autònoma de Barcelona, Bellaterra, Cerdanyola del Vallès, Spain
| | - José Ignacio Núñez
- Centre de Recerca en Sanitat Animal (CReSA), UAB-IRTA, Campus de la Universitat Autònoma de Barcelona, Bellaterra, Cerdanyola del Vallès, Spain
| | - Heidy Díaz de Arce
- Centro Nacional de Sanidad Agropecuaria (CENSA), La Habana, Cuba; Hospital Italiano de Buenos Aires, Juan D. Perón 4190, C1181ACH Buenos Aires, Argentina
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20
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Fang Q, Gao Y, Chen M, Guo X, Yang X, Wei L. Molecular epidemiology and evolution of influenza A and B viruses during winter 2013-2014 in Beijing, China. Arch Virol 2015; 160:1083-95. [PMID: 25676826 DOI: 10.1007/s00705-015-2362-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 01/31/2015] [Indexed: 11/25/2022]
Abstract
In this study, we investigated the molecular epidemiology and evolution of influenza viruses from patients infected during the 2013-2014 influenza season in Beijing. A phylogenetic analysis of the hemagglutinin (HA) and neuraminidase (NA) sequences of influenza A and B viruses from 18 patients (6 A(H1N1)pdm09, 4 H3N2, and 8 influenza B virus) was performed. Among the influenza A viruses, A(H1N1)pdm09 was the dominant subtype, whereas the B/Yamagata lineage was predominant for influenza B. The influenza B HA and NA strains in Beijing were dominated by reassortants derived from the Yamagata lineage and the Victoria lineage, respectively. All six A(H1N1)pdm09 strains fell into the 6B genetic group with amino acid substitutions D97N, S185T, K163Q, and A256T; the four H3N2 strains fell into genetic group 3C.3 with substitutions T128A, R142G, N145S, and V186G, and the eight influenza B strains were categorized into subgroup 3.1 and harbored an N217S mutation. Two new mutations (K180Q and G187E at the Sa and Ca antigenic sites of the H1 segment, respectively), which were not detected during the preceding influenza season, were identified. Mutations N131K, S165I, N181Y, and D212N in HA of influenza B mapped to the 120-loop, 150-loop, 160-loop, and 190-helix, respectively. Our results reveal the molecular epidemiology and phylogenetic characteristics of influenza viruses within a single geographic location and can have implications for vaccination selection in northern China.
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Affiliation(s)
- Qiongxuan Fang
- Department of Infectious Disease, Peking University Hepatology Institute, Peking University People's Hospital, Xizhimen South Street, Xicheng District, No. 11, Beijing, 100044, China
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21
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Phylogenetic analysis of the neuraminidase gene of pandemic H1N1 influenza A virus circulating in the South American region. Virus Res 2015; 197:1-7. [PMID: 25479596 DOI: 10.1016/j.virusres.2014.11.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Revised: 09/30/2014] [Accepted: 11/08/2014] [Indexed: 11/22/2022]
Abstract
Molecular characterization of circulating influenza A viruses (IAV) in all regions of the world is essential to detect mutations potentially involved in increased virulence, anti-viral resistance and immune escape. In order to gain insight into these matters, a phylogenetic analysis of the neuraminidase (NA) gene of 146 pandemic H1N1 (H1N1pdm) influenza A virus strains isolated in Argentina, Brazil, Chile, Paraguay, Peru and Uruguay from 2009 to 2013 was performed. Comparison of vaccine strain A/California/7/2009 included in the influenza vaccine recommended for the Southern hemisphere from 2010 through 2013 influenza seasons and strains isolated in South America revealed several amino acid substitutions. Mapping of these substitutions revealed that most of them are located at the surface of the protein and do not interfere with the active site. 3.4% of the strains enrolled in these studies carried the H275Y substitution that confers resistance to oseltamivir. Strains isolated in South America differ from vaccine in two predicted B-cell epitope regions present at positions 102-103 and 351-352 of the NA protein. Moreover, vaccine and strains isolated in Paraguay differ also in an epitope present at position 229. These differences among strains isolated in South America and vaccine strain suggests that these epitopes may not be present in strains isolated in this region. A potential new N-linked glycosylation site was observed in the NA protein of an H1N1pdm IAV strain isolated in Brazil. The results of these studies revealed several genetic and antigenic differences in the NA of H1N1pdm IAV among vaccine and strains circulating in South America. All these findings contribute to our understanding of the course of genetic and antigenic evolution of H1N1pdm IAV populations circulating in the South American region and, consequently, contribute to the study and selection of future and more appropriate vaccines and anti-viral drugs.
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22
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Goka EA, Vallely PJ, Mutton KJ, Klapper PE. Mutations associated with severity of the pandemic influenza A(H1N1)pdm09 in humans: a systematic review and meta-analysis of epidemiological evidence. Arch Virol 2014; 159:3167-83. [PMID: 25078388 DOI: 10.1007/s00705-014-2179-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Accepted: 07/12/2014] [Indexed: 10/25/2022]
Abstract
Mutations in the haemagglutinin (HA), non-structural protein 1 (NS1) and polymerase basic protein 2 (PB2) of influenza viruses have been associated with virulence. This study investigated the association between mutations in these genes in influenza A(H1N1)pdm09 virus and the risk of severe or fatal disease. Searches were conducted on the MEDLINE, EMBASE and Web of Science electronic databases and the reference lists of published studies. The PRISMA and STROBE guidelines were followed in assessing the quality of studies and writing-up. Eighteen (18) studies, from all continents, were included in the systematic review (recruiting patients 0 - 77 years old). The mutation D222G was associated with a significant increase in severe disease (pooled RD: 11 %, 95 % CI: 3.0 % - 18.0 %, p = 0.004) and the risk of fatality (RD: 23 %, 95 % CI: 14.0 %-31.0 %, p = < 0.0001). No association was observed between the mutations HA-D222N, D222E, PB2-E627K and NS1-T123V and severe/fatal disease. The results suggest that no virus quasispecies bearing virulence-conferring mutations in the HA, PB2 and NS1 predominated. However issues of sampling bias, and bias due to uncontrolled confounders such as comorbidities, and viral and bacterial coinfection, should be born in mind. Influenza A viruses should continue to be monitored for the occurrence of virulence-conferring mutations in HA, PB2 and NS1. There are suggestions that respiratory virus coinfections also affect virus virulence. Studies investigating the role of genetic mutations on disease outcome should make efforts to also investigate the role of respiratory virus coinfections.
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Affiliation(s)
- E A Goka
- Institute of Inflammation and Repair, Faculty of Medical and Human Sciences, University of Manchester, 1st Floor Stopford building, Oxford Road, Manchester, M13 9PL, UK,
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23
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Molecular epidemiology and evolution of A(H1N1)pdm09 and H3N2 virus during winter 2012-2013 in Beijing, China. INFECTION GENETICS AND EVOLUTION 2014; 26:228-40. [PMID: 24911284 DOI: 10.1016/j.meegid.2014.05.034] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Revised: 05/12/2014] [Accepted: 05/30/2014] [Indexed: 12/12/2022]
Abstract
In order to evaluate the epidemiology of influenza A and its surface antigens (haemagglutinin [HA] and neuraminidase [NA]) for molecular epidemiology and evolution analysis during winter 2012-2013 in Beijing, China, we worked within the framework of the Chinese National Influenza Center and collected nasal swabs of patients presenting with influenza-like illness. We found that both A(H1N1)pdm09 (46.8%) and H3N2 (53.2%) viruses were the predominant strains during the 2012-2013 influenza epidemic. The peak phase started at the second week of 2013 and lasted about 1month. We obtained HA and NA sequences of viruses from 44 patients by using Sanger sequencing. None of the strains had the oseltamivir resistance site H274Y. Phylogenetic analysis of 29 A(H1N1)pdm09 viruses showed a genetic drift from the vaccine strain A/California/07/2009 with mutations (H155Q/R and L178I) at the antigenic sites Ca and Sa of HA; the strains were classified into genetic groups 6 and 7 because of the presence of D114N, S160G, S202T, and A214T mutations in HA. H3N2 viruses formed seasonal phylogenetic clusters representative for each season from 2000 to 2013; 15 of the 2012-2013 H3N2 strains were assigned to the A/Victoria/361/2011 genetic clade with mutations at the antigenic sites A, B and C of HA, including R158K/G, N161S, Q172H, and N294K; the 2012-2013 strains with V239I, S61N, T64I, and A214S HA mutations were classified into subgroup 3C. The mutation of potential N-linked glycosylation residues at the antigenic sites of HA and around the enzymatic active center of NA may have increased viral pathogenicity by masking antigenic sites from immune recognition. Our data suggest that influenza vaccines are generally effective, but still provide suboptimal protection due to antigenic variation. This study increases the understanding of influenza A viruses in humans and is informative for future vaccine strain selection.
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Dangi T, Jain B, Singh AK, Singh J, Kumar R, Dwivedi M, Verma AK, Chadha MS, Jain A. Molecular characterization of circulating pandemic strains of influenza A virus during 2012 to 2013 in Lucknow (India). J Med Virol 2014; 86:2134-41. [DOI: 10.1002/jmv.23946] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/25/2014] [Indexed: 01/24/2023]
Affiliation(s)
- Tanushree Dangi
- Department of Microbiology; King George's Medical University; Lucknow India
| | - Bhawana Jain
- Department of Microbiology; King George's Medical University; Lucknow India
| | - Ajay Kumar Singh
- Department of Microbiology; King George's Medical University; Lucknow India
| | - J.V. Singh
- Department of Community Medicine; King George's Medical University; Lucknow India
| | - Rashmi Kumar
- Department of Paediatrics; King George's Medical University; Lucknow India
| | - Mukesh Dwivedi
- Department of Microbiology; King George's Medical University; Lucknow India
| | - Anil Kumar Verma
- Department of Microbiology; King George's Medical University; Lucknow India
| | | | - Amita Jain
- Department of Microbiology; King George's Medical University; Lucknow India
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25
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Mesquita M, Resende P, Marttorelli A, Machado V, Sacramento CQ, Fintelman-Rodrigues N, Abrantes JL, Tavares R, Schirmer M, Siqueira MM, Souza TML. Detection of the influenza A(H1N1)pdm09 virus carrying the K-15E, P83S and Q293H mutations in patients who have undergone bone marrow transplant. PLoS One 2014; 9:e94822. [PMID: 24740088 PMCID: PMC3989246 DOI: 10.1371/journal.pone.0094822] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Accepted: 03/20/2014] [Indexed: 12/17/2022] Open
Abstract
The 2009 pandemic influenza A(H1N1)pdm09 virus emerged and caused considerable morbidity and mortality in the third world, especially in Brazil. Although circulating strains of A(H1N1)pdm09 are A/California/04/2009-like (CA-04-like) viruses, various studies have suggested that some mutations in the viral hemagglutinin (HA) may be associated with enhanced severity and fatality. This phenomenon is particularly challenging for immunocompromised individuals, such as those who have undergone bone marrow transplant (BMT), because they are more likely to display worse clinical outcomes to influenza infection than non-immunocompromised individuals. We studied the clinical and viral aspects of post-BMT patients with confirmed A(H1N1)pdm09 diagnosis in the largest cancer hospital in Brazil. We found a viral strain with K-15E, P83S and Q293H polymorphisms in the HA, which is presumably more virulent, in these individuals. Despite that, these patients showed only mild symptoms of infection. Our findings complement the discovery of mild cases of infection with the A(H1N1)pdm09 virus with the K-15E, P83S and Q293H mutations in Brazil and oppose other studies that have linked these changes with increased disease severity. These results could be important for a better comprehension of the impact of the pandemic influenza in the context of BMT.
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Affiliation(s)
- Milene Mesquita
- Measles and Respiratory viruses Laboratory, WHO/NIC, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Paola Resende
- Measles and Respiratory viruses Laboratory, WHO/NIC, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Andressa Marttorelli
- Measles and Respiratory viruses Laboratory, WHO/NIC, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Viviane Machado
- Measles and Respiratory viruses Laboratory, WHO/NIC, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Carolina Q. Sacramento
- Measles and Respiratory viruses Laboratory, WHO/NIC, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Natalia Fintelman-Rodrigues
- Measles and Respiratory viruses Laboratory, WHO/NIC, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Juliana L. Abrantes
- Measles and Respiratory viruses Laboratory, WHO/NIC, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Rita Tavares
- Center for Bone Marrow Transplantation (CEMO), National Cancer Institute (INCa), Rio de Janeiro, RJ, Brazil
| | - Marcelo Schirmer
- Center for Bone Marrow Transplantation (CEMO), National Cancer Institute (INCa), Rio de Janeiro, RJ, Brazil
| | - Marilda M. Siqueira
- Measles and Respiratory viruses Laboratory, WHO/NIC, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Thiago Moreno L. Souza
- Measles and Respiratory viruses Laboratory, WHO/NIC, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, RJ, Brazil
- * E-mail:
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26
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Sitaras I, Kalthoff D, Beer M, Peeters B, de Jong MCM. Immune escape mutants of Highly Pathogenic Avian Influenza H5N1 selected using polyclonal sera: identification of key amino acids in the HA protein. PLoS One 2014; 9:e84628. [PMID: 24586231 PMCID: PMC3934824 DOI: 10.1371/journal.pone.0084628] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Accepted: 11/16/2013] [Indexed: 11/19/2022] Open
Abstract
Evolution of Avian Influenza (AI) viruses--especially of the Highly Pathogenic Avian Influenza (HPAI) H5N1 subtype--is a major issue for the poultry industry. HPAI H5N1 epidemics are associated with huge economic losses and are sometimes connected to human morbidity and mortality. Vaccination (either as a preventive measure or as a means to control outbreaks) is an approach that splits the scientific community, due to the risk of it being a potential driving force in HPAI evolution through the selection of mutants able to escape vaccination-induced immunity. It is therefore essential to study how mutations are selected due to immune pressure. To this effect, we performed an in vitro selection of mutants from HPAI A/turkey/Turkey/1/05 (H5N1), using immune pressure from homologous polyclonal sera. After 42 rounds of selection, we identified 5 amino acid substitutions in the Haemagglutinin (HA) protein, most of which were located in areas of antigenic importance and suspected to be prone to selection pressure. We report that most of the mutations took place early in the selection process. Finally, our antigenic cartography studies showed that the antigenic distance between the selected isolates and their parent strain increased with passage number.
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Affiliation(s)
- Ioannis Sitaras
- Quantitative Veterinary Epidemiology, Department of Animal Sciences, Wageningen University, Wageningen, The Netherlands
- Department of Virology, Central Veterinary Institute of Wageningen University and Research Centre, Lelystad, The Netherlands
| | - Donata Kalthoff
- Institute of Diagnostic Virology, Friedrich-Loeffler Institut, Greifswald-Insel Riems, Germany
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler Institut, Greifswald-Insel Riems, Germany
| | - Ben Peeters
- Department of Virology, Central Veterinary Institute of Wageningen University and Research Centre, Lelystad, The Netherlands
| | - Mart C. M. de Jong
- Quantitative Veterinary Epidemiology, Department of Animal Sciences, Wageningen University, Wageningen, The Netherlands
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Radomski JP, Płoński P, Zagórski-Ostoja W. The hemagglutinin mutation E391K of pandemic 2009 influenza revisited. Mol Phylogenet Evol 2014; 70:29-36. [DOI: 10.1016/j.ympev.2013.08.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Revised: 08/25/2013] [Accepted: 08/26/2013] [Indexed: 10/26/2022]
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28
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Genomic analysis of pandemic and post-pandemic influenza A pH1N1 viruses isolated in Rio Grande do Sul, Brazil. Arch Virol 2013; 159:621-30. [PMID: 24114147 DOI: 10.1007/s00705-013-1855-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Accepted: 09/14/2013] [Indexed: 01/23/2023]
Abstract
During the 2009 influenza A pH1N1 pandemics in Brazil, the state that was most affected was Rio Grande do Sul (RS), with over 3,000 confirmed cases, including 298 deaths. While no cases were confirmed in 2010, 103 infections with 14 deaths by pH1N1 were reported in 2011. Genomic analysis of the circulating viruses is fundamental for understanding viral evolution and supporting vaccine development against these pathogens. This study investigated whole genomes of six pH1N1 virus isolates from pandemic and post-pandemic periods in RS, Brazil. Phylogenetic analysis using the concatenated genome segments demonstrated that at least two lineages of the virus co-circulated in RS during the 2009 pandemic period. Moreover, our analysis showed that the post-pandemic pH1N1 virus from 2011 constitutes a distinct clade whose ancestor belongs to clade 7. All six isolates contained amino acid substitutions in their proteins when compared to the archetype strains California/04/2009 and California/07/2009. The 2011 isolates contained more amino acid substitutions, and most of their genes were under purifying selection. Based on the amino acid substitutions in HA epitopes from strains isolated in RS, Brazil, in silico analysis predicted a decrease in vaccine efficacy against post-pandemic strains (median 31.562 %) in relation to pandemic ones (median 39.735 %).
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29
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Khandaker I, Suzuki A, Kamigaki T, Tohma K, Odagiri T, Okada T, Ohno A, Otani K, Sawayama R, Kawamura K, Okamoto M, Oshitani H. Molecular evolution of the hemagglutinin and neuraminidase genes of pandemic (H1N1) 2009 influenza viruses in Sendai, Japan, during 2009-2011. Virus Genes 2013; 47:456-466. [PMID: 24078044 PMCID: PMC3834170 DOI: 10.1007/s11262-013-0980-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Accepted: 09/07/2013] [Indexed: 01/17/2023]
Abstract
Analyzing the evolutionary pattern of the influenza A(H1N1)pdm09 strain in different regions is important for understanding its diversification. We therefore conducted this study to elucidate the genetic variability and molecular evolution of the influenza A(H1N1)pdm09 strains that circulated during the 2009-2010 and 2010-2011 influenza seasons in Sendai, Japan. Nasopharyngeal swab specimens were collected from patients with influenza-like illnesses who visited outpatient clinics in Sendai City, Japan, from September 2009 to April 2011. A total of 75 isolates were selected from September 2009 to April 2011 to analyze the genetic changes in the entire hemagglutinin 1 (HA1) segment of the HA gene and the neuraminidase (NA) gene based on sequence analysis. Bayesian coalescent Markov chain Monte Carlo analyses of HA1 and NA gene sequences were performed for further analysis. High sequence identities were observed for HA1 and NA in influenza A(H1N1)pdm09, displaying 99.06 and 99.33 % nucleotide identities, respectively, with the A(H1N1)pdm09 vaccine strain A/California/07/2009. The substitution rates of nucleotides for HA1 in the 2009-2010 and 2010-2011 were 1.5 × 10-3 and 1.6 × 10-3 substitutions per site per year, respectively. Phylogenetic tree analysis demonstrated that Sendai isolates were clustered into global clade 7, which is characterized by an S203T mutation in the HA1 gene. Moreover, two distinct circulation clusters were present in the 2010-2011 season. Mutations were present in antigenic or receptor-binding domains of the HA1 segment, including A141V, S143G, S183P, S185T, and S203T. The Bayesian skyline plot model illustrated a steady rate for the maintenance of genetic diversity, followed by a slight increase in the later part of the 2010-2011 season. Selection analysis revealed that the HA1 (position 197) and NA (position 46) sites were under positive selection; however, no known mutation conferring resistance to NA inhibitors such as H275Y was observed. The effect on control of the influenza A(H1N1)pdm09 virus, including vaccine strain selection, requires continuous monitoring of the strain by genetic surveillance.
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Affiliation(s)
- Irona Khandaker
- Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryomachi, Aoba, Sendai, Miyagi 9807585 Japan
| | - Akira Suzuki
- Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryomachi, Aoba, Sendai, Miyagi 9807585 Japan
| | - Taro Kamigaki
- Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryomachi, Aoba, Sendai, Miyagi 9807585 Japan
| | - Kentaro Tohma
- Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryomachi, Aoba, Sendai, Miyagi 9807585 Japan
| | - Takashi Odagiri
- Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryomachi, Aoba, Sendai, Miyagi 9807585 Japan
| | - Takashi Okada
- Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryomachi, Aoba, Sendai, Miyagi 9807585 Japan
| | - Ayumu Ohno
- Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryomachi, Aoba, Sendai, Miyagi 9807585 Japan
| | - Kanako Otani
- Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryomachi, Aoba, Sendai, Miyagi 9807585 Japan
| | - Rumi Sawayama
- Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryomachi, Aoba, Sendai, Miyagi 9807585 Japan
| | - Kazuhisa Kawamura
- Kawamura Pediatric Clinic, 2-22-27, Saiwaicho, Miyagino-Ku, Sendai, Miyagi 983-0836 Japan
| | - Michiko Okamoto
- Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryomachi, Aoba, Sendai, Miyagi 9807585 Japan
| | - Hitoshi Oshitani
- Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryomachi, Aoba, Sendai, Miyagi 9807585 Japan
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30
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Li X, Kong M, Chen J, Su X, Zou M, Guo L, Li L, Ding J. Epidemiology and full genome sequence analysis of H1N1pdm09 from Northeast China. Virus Genes 2013; 47:199-209. [PMID: 23771788 DOI: 10.1007/s11262-013-0931-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2013] [Accepted: 05/31/2013] [Indexed: 12/30/2022]
Abstract
Pandemic influenza A (H1N1) 2009 virus (H1N1pdm09) was a novel tri-assortment virus that emerged in Mexico and North America in 2009 and caused the first influenza pandemic in the 21st century. This study investigated the prevalence pattern and molecular characteristics of H1N1pdm09 in three continuous years from April 2009 to March 2012 in populations of Tianjin, Northeast China. Totally, 3,068 influenza viruses (25.4 %) were detected from 12,089 respiratory specimens. Among them, 41.4 % (1,269/3,068) were H1N1pdm09 positive. 15.1 % (192/1,269) severe respiratory infection cases were H1N1pdm09 positive. H1N1pdm09 was the predominant prevalence subtype in October 2009-March 2010 (69.1 %, 930/1,346) and October 2010-March 2011 (42.1 %, 220/523). Eight isolated H1N1pdm09 viruses from severe infection/death cases in three different years were selected to sequence the whole genome through splicing the sequences following 46 PCRs. HA sequences of seven H1N1pdm09 isolates from mild infection cases were detected. Phylogenetic analysis showed that HA, NA, M, NP and NS genes of H1N1pdm09 viruses gathered together with swine influenza A (H1N1), whereas PB2 and PA genes originated from avian influenza virus, and PB1 gene originated from human seasonal influenza virus. Identity analysis indicated that all the genes were highly conserved. Compared with vaccine strain A/California/07/2009(H1N1), the maximal mutation gene was HA (0.7-2.6 %), then NA (0.6-1.7 %), last one was M (mutation rate 0-0.6 %). More site substitutions were observed in 2011 isolates than in 2009 and 2010 isolates of HA (p = 0.002), NA (p = 0.003) and PA (p = 0.001) proteins. The amino acid substitution rates were varied among eight gene segments, ranging from 7.39 × 10(-4) for PB2 to 7.40 × 10(-3) for NA. The higher d N / d S rates were observed in HA, PA and NS segments in H1N1pdm09 in Tianjin. Three HA amino acid site substitutions occurred at the HA receptor-binding sites and antigenic determinant, including S179N and K180T (located at antigenic site Sa) in A/Tianjinhedong/SWL44/2011(H1) and A/Tianjinjinnan/SWL41/2011(H1), and D239N (located at antigenic site Ca) in A/Tianjinninghe/SWL49/2009(H1). Antigenic drift may have occurred in H1N1pdm09 with time. No oseltamivir-resistance site substitution was observed at 275 and 295 sites. Amino acid residue site at 31 in M2 protein was N in all 8 isolates, which suggested that H1N1pdm09 was resistant to amantadine.
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Affiliation(s)
- Xiaoyan Li
- School of Basic Medicine, Tianjin Medical University, No.22 Qixiangtai Road, Heping District, Tianjin, 300070, People's Republic of China,
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31
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Piralla A, Pariani E, Campanini G, Rovida F, Ranghiero A, Fiorina L, Amendola A, Zanetti A, Baldanti F. Multiple clusters of A(H1N1)pdm09 virus circulating in severe cases of influenza during the 2010-2011 season: a phylogenetic and molecular analysis of the neuraminidase gene. J Med Virol 2013; 85:944-52. [PMID: 23588719 DOI: 10.1002/jmv.23569] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/27/2012] [Indexed: 02/04/2023]
Abstract
The molecular characterization of circulating influenza A viruses is crucial to detect mutations potentially involved in increased virulence, drug resistance and immune escape. A molecular and phylogenetic analysis of A(H1N1)pdm09 neuraminidase (NA) gene sequences from different patient categories defined according to the severity of influenza infection were analyzed. A total of 126 influenza A(H1N1)pdm09 positive samples from patients with severe infections in comparison with those with moderate and mild infections was performed in Lombardy (Northern Italy, nearly 10 million inhabitants) during the 2010-2011 season. NA sequences included in this study segregated into five distinct clusters. Nineteen amino acid substitutions were detected exclusively in NA sequences of viruses identified in patients with severe or moderate influenza infection. Three of them (F74S, S79P, E287K) were observed in virus strains with the 222G/N hemagglutinin mutation. None of NA sequences under study had mutations related to the resistance to the NA inhibitors. Four out of 126 (3.2%) NA sequences from patients with severe infection lost a N-linked glycosylation site due to the change from N to K at residue 386. Two additional N-linked glycosylation sites in the NA stalk region (residues 42 and 44) were found in 12 (9.5%) NA sequences. Sporadic NA mutations were detected in NA viral sequences from critically ill patients, and no variants with reduced sensitivity to NA inhibitors were observed either in treated or untreated patients.
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Affiliation(s)
- Antonio Piralla
- Molecular Virology Unit, Virology and Microbiology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
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Kiyota N, Kushibuchi I, Kobayashi M, Tsukagoshi H, Ryo A, Nishimura K, Hirata-Saito A, Harada S, Arakawa M, Kozawa K, Noda M, Kimura H. Genetic analysis of the VP4/VP2 coding region in human rhinovirus species C in patients with acute respiratory infection in Japan. J Med Microbiol 2013; 62:610-617. [DOI: 10.1099/jmm.0.049072-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Affiliation(s)
- Naoko Kiyota
- Kumamoto Prefectural Institute of Public Health and Environmental Sciences, Uto-shi, Kumamoto 869-0425, Japan
| | - Izumi Kushibuchi
- Tochigi Prefectural Institute of Public Health, Utsunomiya-shi, Tochigi 329-1196, Japan
| | - Miho Kobayashi
- Gunma Prefectural Institute of Public Health and Environmental Sciences, Maebashi-shi, Gunma 371-0052, Japan
| | - Hiroyuki Tsukagoshi
- Gunma Prefectural Institute of Public Health and Environmental Sciences, Maebashi-shi, Gunma 371-0052, Japan
| | - Akihide Ryo
- Department of Molecular Biodefence Research, Yokohama City University Graduate School of Medicine, Yokohama-shi, Kanagawa 236-0004, Japan
| | - Koichi Nishimura
- Kumamoto Prefectural Institute of Public Health and Environmental Sciences, Uto-shi, Kumamoto 869-0425, Japan
| | - Asumi Hirata-Saito
- Tochigi Prefectural Institute of Public Health, Utsunomiya-shi, Tochigi 329-1196, Japan
| | - Seiya Harada
- Kumamoto Prefectural Institute of Public Health and Environmental Sciences, Uto-shi, Kumamoto 869-0425, Japan
| | - Mika Arakawa
- Tochigi Prefectural Institute of Public Health, Utsunomiya-shi, Tochigi 329-1196, Japan
| | - Kunihisa Kozawa
- Gunma Prefectural Institute of Public Health and Environmental Sciences, Maebashi-shi, Gunma 371-0052, Japan
| | - Masahiro Noda
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Musashimurayama-shi, Tokyo 208-0011, Japan
| | - Hirokazu Kimura
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Musashimurayama-shi, Tokyo 208-0011, Japan
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Viboud C, Nelson MI, Tan Y, Holmes EC. Contrasting the epidemiological and evolutionary dynamics of influenza spatial transmission. Philos Trans R Soc Lond B Biol Sci 2013; 368:20120199. [PMID: 23382422 DOI: 10.1098/rstb.2012.0199] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In the past decade, rapid increases in the availability of high-resolution molecular and epidemiological data, combined with developments in statistical and computational methods to simulate and infer migration patterns, have provided key insights into the spatial dynamics of influenza A viruses in humans. In this review, we contrast findings from epidemiological and molecular studies of influenza virus transmission at different spatial scales. We show that findings are broadly consistent in large-scale studies of inter-regional or inter-hemispheric spread in temperate regions, revealing intense epidemics associated with multiple viral introductions, followed by deep troughs driven by seasonal bottlenecks. However, aspects of the global transmission dynamics of influenza viruses are still debated, especially with respect to the existence of tropical source populations experiencing high levels of genetic diversity and the extent of prolonged viral persistence between epidemics. At the scale of a country or community, epidemiological studies have revealed spatially structured diffusion patterns in seasonal and pandemic outbreaks, which were not identified in molecular studies. We discuss the role of sampling issues in generating these conflicting results, and suggest strategies for future research that may help to fully integrate the epidemiological and evolutionary dynamics of influenza virus over space and time.
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Affiliation(s)
- Cécile Viboud
- Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA.
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Pérez LJ, Perera CL, Vega A, Frías MT, Rouseaux D, Ganges L, Nuñez JI, Díaz de Arce H. Isolation and complete genomic characterization of pandemic H1N1/2009 influenza viruses from Cuban swine herds. Res Vet Sci 2013; 94:781-8. [PMID: 23318219 DOI: 10.1016/j.rvsc.2012.11.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2012] [Revised: 11/23/2012] [Accepted: 11/26/2012] [Indexed: 11/19/2022]
Abstract
The emergence of the pandemic H1N1/2009 influenza virus poses a potential global threat for human and animal health. In this study, we carried out pandemic H1N1/2009 influenza virus surveillance in swine herds in Cuba intending to determine whether the virus was circulating among pig populations. As a result we describe, for the first time, the detection of pandemic H1N1/2009 influenza virus in swine herds in Cuba. In addition, phylogenetic analysis and molecular characterization of three viral isolates were performed. Phylogenetic relationships confirmed that all of the eight genes of the three isolates were derived from the pandemic H1N1/2009 virus. The Cuban isolates, formed an independent cluster within the pandemic H1N1/2009 influenza strains. Different molecular markers, previously described in pandemic H1N1/2009 influenza viruses, related with adaptive evolution, viral evasion from the host-immune response, virulence and dissemination were also present in Cuban pandemic H1N1/2009 isolates.
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35
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Influenza A(H1N1)pdm09 virus: viral characteristics and genetic evolution. Enferm Infecc Microbiol Clin 2012; 30 Suppl 4:10-7. [DOI: 10.1016/s0213-005x(12)70099-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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36
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Chen GW, Tsao KC, Huang CG, Gong YN, Chang SC, Liu YC, Wu HH, Yang SL, Lin TY, Huang YC, Shih SR. Amino acids transitioning of 2009 H1N1pdm in Taiwan from 2009 to 2011. PLoS One 2012; 7:e45946. [PMID: 23029335 PMCID: PMC3454337 DOI: 10.1371/journal.pone.0045946] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Accepted: 08/23/2012] [Indexed: 11/19/2022] Open
Abstract
A swine-origin influenza A was detected in April 2009 and soon became the 2009 H1N1 pandemic strain (H1N1pdm). The current study revealed the genetic diversity of H1N1pdm, based on 77 and 70 isolates which we collected, respectively, during the 2009/2010 and 2010/2011 influenza seasons in Taiwan. We focused on tracking the amino acid transitioning of hemagglutinin (HA) and neuraminidase (NA) genes in the early diversification of the virus and compared them with H1N1pdm strains reported worldwide. We identified newly emerged mutation markers based on A/California/04/2009, described how these markers shifted from the first H1N1pdm season to the one that immediately followed, and discussed how these observations may relate to antigenicity, receptor-binding, and drug susceptibility. It was found that the amino acid mutation rates of H1N1pdm were elevated, from 9.29×10−3 substitutions per site in the first season to 1.46×10−2 in the second season in HA, and from 5.23×10−3 to 1.10×10−2 in NA. Many mutation markers were newly detected in the second season, including 11 in HA and 8 in NA, and some were found having statistical correlation to disease severity. There were five noticeable HA mutations made to antigenic sites. No significant titer changes, however, were detected based on hemagglutination inhibition tests. Only one isolate with H275Y mutation known to reduce susceptibility to NA inhibitors was detected. As limited Taiwanese H1N1pdm viruses were isolated after our sampling period, we gathered 8,876 HA and 6,017 NA H1N1pdm sequences up to April 2012 from NCBI to follow up the dynamics of mentioned HA mutations. While some mutations described in this study seemed to either settle in or die out in the 2011–2012 season, a number of them still showed signs of transitioning, prompting the importance of continuous monitoring of this virus for more seasons to come.
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Affiliation(s)
- Guang-Wu Chen
- Department of Computer Science and Information Engineering, Chang Gung University, Taoyuan, Taiwan, Republic of China
- Research Center for Emerging Viral Infections, Chang Gung University, Taoyuan, Taiwan, Republic of China
| | - Kuo-Chien Tsao
- Research Center for Emerging Viral Infections, Chang Gung University, Taoyuan, Taiwan, Republic of China
- Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Taoyuan, Taiwan, Republic of China
- Department of Laboratory Medicine, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan, Republic of China
- * E-mail:
| | - Chung-Guei Huang
- Research Center for Emerging Viral Infections, Chang Gung University, Taoyuan, Taiwan, Republic of China
- Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Taoyuan, Taiwan, Republic of China
- Department of Laboratory Medicine, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan, Republic of China
| | - Yu-Nong Gong
- Graduate Institute of Electrical Engineering, Chang Gung University, Taoyuan, Taiwan, Republic of China
| | - Shih-Cheng Chang
- Research Center for Emerging Viral Infections, Chang Gung University, Taoyuan, Taiwan, Republic of China
- Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Taoyuan, Taiwan, Republic of China
| | - Yi-Chun Liu
- Department of Laboratory Medicine, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan, Republic of China
| | - Hsiao-Han Wu
- Department of Laboratory Medicine, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan, Republic of China
| | - Shu-Li Yang
- Department of Laboratory Medicine, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan, Republic of China
| | - Tzou-Yien Lin
- Research Center for Emerging Viral Infections, Chang Gung University, Taoyuan, Taiwan, Republic of China
- College of Medicine, Chang Gung University, Taoyuan, Taiwan, Republic of China
- Department of Pediatrics, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan, Republic of China
| | - Yhu-Chering Huang
- College of Medicine, Chang Gung University, Taoyuan, Taiwan, Republic of China
- Department of Pediatrics, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan, Republic of China
| | - Shin-Ru Shih
- Research Center for Emerging Viral Infections, Chang Gung University, Taoyuan, Taiwan, Republic of China
- Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Taoyuan, Taiwan, Republic of China
- Department of Laboratory Medicine, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan, Republic of China
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Pascalis H, Temmam S, Wilkinson DA, Dsouli N, Turpin M, de Lamballerie X, Dellagi K. Molecular evolutionary analysis of pH1N1 2009 influenza virus in Reunion Island, South West Indian Ocean region: a cohort study. PLoS One 2012; 7:e43742. [PMID: 22952752 PMCID: PMC3428279 DOI: 10.1371/journal.pone.0043742] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Accepted: 07/23/2012] [Indexed: 01/08/2023] Open
Abstract
Background/Objectives Molecular epidemiology is a powerful tool to decipher the dynamics of viral transmission, quasispecies temporal evolution and origins. Little is known about the pH1N1 molecular dynamics in general population. A prospective study (CoPanFlu-RUN) was carried out in Reunion Island to characterize pH1N1 genetic variability and molecular evolution occurring in population during the pH1N1 Influenza pandemic in 2009. Methodology We directly amplified pH1N1 genomes from 28 different nasal swabs (26 individuals from 21 households). Fifteen strains were fully sequenced and 13 partially. This includes pairs of sequences from different members of 5 separate households; and two pairs from individuals, collected at different times. We assessed the molecular evolution of pH1N1 by genetic variability and phylogenetic analyses. Principal Findings We found that i) Reunion pH1N1 sequences stemmed from global “clade 7” but shaped two phylogenetic sub-clades; ii) D239E mutation was identified in the hemagglutinin protein of all Reunion sequences, a mutation which has been associated elsewhere with mild-, upper-respiratory tract pH1N1 infecting strains; iii) Date estimates from molecular phylogenies predicted clade emergence some time before the first detection of pH1N1 by the epidemiological surveillance system; iv) Phylogenetic relatedness was observed between Reunion pH1N1 viruses and those from other countries in South-western Indian Ocean area; v) Quasispecies populations were observed within households and individuals of the cohort-study. Conclusions Surveillance and/or prevention systems presently based on Influenza virus sequence variation should take into account that the majority of studies of pH1N1 Influenza generate genetic data for the HA/NA viral segments obtained from hospitalized-patients, which is potentially non-representative of the overall viral diversity within whole populations. Our observations highlight the importance of collecting unbiased data at the community level and conducting whole genome analysis to accurately understand viral dynamics.
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Affiliation(s)
- Hervé Pascalis
- GIS CRVOI, Centre de Recherche et de Veille sur maladies émergentes dans l'Océan Indien, Plateforme technologique CYROI, Saint-Denis, La Réunion, France.
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Dugan VG, Saira K, Ghedin E. Large-scale sequencing and the natural history of model human RNA viruses. Future Virol 2012; 7:563-573. [PMID: 23682295 DOI: 10.2217/fvl.12.45] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
RNA virus exploration within the field of medical virology has greatly benefited from technological developments in genomics, deepening our understanding of viral dynamics and emergence. Large-scale first-generation technology sequencing projects have expedited molecular epidemiology studies at an unprecedented scale for two pathogenic RNA viruses chosen as models: influenza A virus and dengue. Next-generation sequencing approaches are now leading to a more in-depth analysis of virus genetic diversity, which is greater for RNA than DNA viruses because of high replication rates and the absence of proofreading activity of the RNA-dependent RNA polymerase. In the field of virus discovery, technological advancements and metagenomic approaches are expanding the catalogs of novel viruses by facilitating our probing into the RNA virus world.
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Affiliation(s)
- Vivien G Dugan
- Viral Genomics, J Craig Venter Institute, Rockville, MD, USA
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39
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Yoshida A, Kiyota N, Kobayashi M, Nishimura K, Tsutsui R, Tsukagoshi H, Hirano E, Yamamoto N, Ryo A, Saitoh M, Harada S, Inoue O, Kozawa K, Tanaka R, Noda M, Okabe N, Tashiro M, Mizuta K, Kimura H. Molecular epidemiology of the attachment glycoprotein (G) gene in respiratory syncytial virus in children with acute respiratory infection in Japan in 2009/2010. J Med Microbiol 2012; 61:820-829. [PMID: 22383445 DOI: 10.1099/jmm.0.041137-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
This study performed a detailed genetic analysis of the glycoprotein (G) gene of respiratory syncytial virus (RSV) detected in 50 Japanese children with acute respiratory infection (ARI) in the 2009/2010 season. A phylogenetic tree constructed by the neighbour-joining method showed that 34 and 16 of the RSV strains could be classified into subgroups A and B, respectively. Strains belonging to subgroups A and B were further subdivided into GA2 and BA, respectively. The nucleotide and deduced amino acid sequence identities were relatively high among these strains (>90%). The deduced amino acid sequences implied that a relatively high frequency of amino acid substitutions occurred in the C-terminal 3rd hypervariable region of the G protein in these strains. In addition, some positively selected sites were estimated. The results suggest that RSV with genotypes GA2 and BA was associated with ARI in Japanese children in 2009/2010.
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Affiliation(s)
- Ayako Yoshida
- Aomori Prefectural Institute of Public Health and Environment, 1-1-1 Higashitsukurimichi, Aomori-shi, Aomori 030-8566, Japan
| | - Naoko Kiyota
- Kumamoto Prefectural Institute of Public Health and Environmental Sciences, 1240-1 Kurisaki-machi, Uto-shi, Kumamoto 869-0425, Japan
| | - Miho Kobayashi
- Gunma Prefectural Institute of Public Health and Environmental Sciences, 378 Kamioki-machi, Maebashi-shi, Gunma 371-0052, Japan
| | - Koichi Nishimura
- Kumamoto Prefectural Institute of Public Health and Environmental Sciences, 1240-1 Kurisaki-machi, Uto-shi, Kumamoto 869-0425, Japan
| | - Rika Tsutsui
- Aomori Prefectural Institute of Public Health and Environment, 1-1-1 Higashitsukurimichi, Aomori-shi, Aomori 030-8566, Japan
| | - Hiroyuki Tsukagoshi
- Gunma Prefectural Institute of Public Health and Environmental Sciences, 378 Kamioki-machi, Maebashi-shi, Gunma 371-0052, Japan
| | - Eiko Hirano
- Fukui Prefectural Institute of Public Health and Environmental Science, 39-4 Harame-cho, Fukui-shi, Fukui 910-8551, Japan
| | - Norio Yamamoto
- Influenza Virus Research Center and Infectious Disease Surveillance Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama-shi, Tokyo 208-0011, Japan
| | - Akihide Ryo
- Department of Molecular Biodefence Research, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama-shi, Kanagawa 236-0004, Japan
| | - Mika Saitoh
- Gunma Prefectural Institute of Public Health and Environmental Sciences, 378 Kamioki-machi, Maebashi-shi, Gunma 371-0052, Japan
| | - Seiya Harada
- Kumamoto Prefectural Institute of Public Health and Environmental Sciences, 1240-1 Kurisaki-machi, Uto-shi, Kumamoto 869-0425, Japan
| | - Osamu Inoue
- Aomori Prefectural Institute of Public Health and Environment, 1-1-1 Higashitsukurimichi, Aomori-shi, Aomori 030-8566, Japan
| | - Kunihisa Kozawa
- Gunma Prefectural Institute of Public Health and Environmental Sciences, 378 Kamioki-machi, Maebashi-shi, Gunma 371-0052, Japan
| | - Ryota Tanaka
- Department of Surgery, Institute of Medical Sciences, Kyorin University, 6-20-2 Shinkawa, Mitaka-shi, Tokyo 181-8611, Japan
| | - Masahiro Noda
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama-shi, Tokyo 208-0011, Japan
| | - Nobuhiko Okabe
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama-shi, Tokyo 208-0011, Japan
| | - Masato Tashiro
- Influenza Virus Research Center and Infectious Disease Surveillance Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama-shi, Tokyo 208-0011, Japan
| | - Katsumi Mizuta
- Yamagata Prefectural Institute of Public Health, 1-6-6 Toka-machi, Yamagata-shi, Yamagata 990-0031, Japan
| | - Hirokazu Kimura
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama-shi, Tokyo 208-0011, Japan.,Gunma Prefectural Institute of Public Health and Environmental Sciences, 378 Kamioki-machi, Maebashi-shi, Gunma 371-0052, Japan
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Kao CL, Chan TC, Tsai CH, Chu KY, Chuang SF, Lee CC, Li ZRT, Wu KW, Chang LY, Shen YH, Huang LM, Lee PI, Yang C, Compans R, Rouse BT, King CC. Emerged HA and NA mutants of the pandemic influenza H1N1 viruses with increasing epidemiological significance in Taipei and Kaohsiung, Taiwan, 2009-10. PLoS One 2012; 7:e31162. [PMID: 22328930 PMCID: PMC3273476 DOI: 10.1371/journal.pone.0031162] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2011] [Accepted: 01/03/2012] [Indexed: 11/22/2022] Open
Abstract
The 2009 influenza pandemic provided an opportunity to observe dynamic changes of the hemagglutinin (HA) and neuraminidase (NA) of pH1N1 strains that spread in two metropolitan areas -Taipei and Kaohsiung. We observed cumulative increases of amino acid substitutions of both HA and NA that were higher in the post–peak than in the pre-peak period of the epidemic. About 14.94% and 3.44% of 174 isolates had one and two amino acids changes, respective, in the four antigenic sites. One unique adaptive mutation of HA2 (E374K) was first detected three weeks before the epidemic peak. This mutation evolved through the epidemic, and finally emerged as the major circulated strain, with significantly higher frequency in the post-peak period than in the pre-peak (64.65% vs 9.28%, p<0.0001). E374K persisted until ten months post-nationwide vaccination without further antigenic changes (e.g. prior to the highest selective pressure). In public health measures, the epidemic peaked at seven weeks after oseltamivir treatment was initiated. The emerging E374K mutants spread before the first peak of school class suspension, extended their survival in high-density population areas before vaccination, dominated in the second wave of class suspension, and were fixed as herd immunity developed. The tempo-spatial spreading of E374K mutants was more concentrated during the post–peak (p = 0.000004) in seven districts with higher spatial clusters (p<0.001). This is the first study examining viral changes during the naïve phase of a pandemic of influenza through integrated virological/serological/clinical surveillance, tempo-spatial analysis, and intervention policies. The vaccination increased the percentage of E374K mutants (22.86% vs 72.34%, p<0.001) and significantly elevated the frequency of mutations in Sa antigenic site (2.36% vs 23.40%, p<0.001). Future pre-vaccination public health efforts should monitor amino acids of HA and NA of pandemic influenza viruses isolated at exponential and peak phases in areas with high cluster cases.
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Affiliation(s)
- Chuan-Liang Kao
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University (NTU), Taipei, Taiwan, Republic of China (ROC)
- Department of Clinical Laboratory Sciences & Medical Biotechnology, College of Medicine, NTU, Taipei, Taiwan, Republic of China (ROC)
- Department of Laboratory Medicine, NTU Hospital, Taipei, Taiwan, Republic of China (ROC)
| | - Ta-Chien Chan
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University (NTU), Taipei, Taiwan, Republic of China (ROC)
| | - Chu-Han Tsai
- Department of Clinical Laboratory Sciences & Medical Biotechnology, College of Medicine, NTU, Taipei, Taiwan, Republic of China (ROC)
| | - Kuan-Ying Chu
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University (NTU), Taipei, Taiwan, Republic of China (ROC)
| | - Shu-Fang Chuang
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University (NTU), Taipei, Taiwan, Republic of China (ROC)
- Department of Clinical Laboratory Sciences & Medical Biotechnology, College of Medicine, NTU, Taipei, Taiwan, Republic of China (ROC)
| | - Chang-Chun Lee
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University (NTU), Taipei, Taiwan, Republic of China (ROC)
| | - Zheng-Rong Tiger Li
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University (NTU), Taipei, Taiwan, Republic of China (ROC)
| | - Ko-Wen Wu
- Institute of Biomedical Informatics, School of Life Sciences, National Yang-Ming University, Taipei, Taiwan, Republic of China (ROC)
| | - Luan-Yin Chang
- Department of Pediatrics, NTU Hospital, Taipei, Taiwan, Republic of China (ROC)
| | - Yea-Huei Shen
- Department of Internal Medicine, Yuan's General Hospital, Kaohsiung, Taiwan, Republic of China (ROC)
| | - Li-Min Huang
- Department of Pediatrics, NTU Hospital, Taipei, Taiwan, Republic of China (ROC)
| | - Ping-Ing Lee
- Department of Pediatrics, NTU Hospital, Taipei, Taiwan, Republic of China (ROC)
| | - ChingLai Yang
- Department of Microbiology and Immunology and Emory Vaccine Center, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Richard Compans
- Department of Microbiology and Immunology and Emory Vaccine Center, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Barry T. Rouse
- Department of Pathobiology, College of Veterinary Medicine, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Chwan-Chuen King
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University (NTU), Taipei, Taiwan, Republic of China (ROC)
- * E-mail:
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Ferraris O, Escuret V, Bouscambert M, Casalegno JS, Jacquot F, Raoul H, Caro V, Valette M, Lina B, Ottmann M. H1N1 influenza A virus neuraminidase modulates infectivity in mice. Antiviral Res 2012; 93:374-80. [PMID: 22321413 DOI: 10.1016/j.antiviral.2012.01.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Revised: 01/18/2012] [Accepted: 01/24/2012] [Indexed: 11/25/2022]
Abstract
In the 2years since the onset of the H1N1 2009 pandemic virus (H1N1pdm09), sporadic cases of oseltamivir-resistant viruses have been reported. We investigated the impact of oseltamivir-resistant neuraminidase from H1N1 Brisbane-like (seasonal) and H1N1pdm09 viruses on viral pathogenicity in mice. Reassortant viruses with the neuraminidase from seasonal H1N1 virus were obtained by co-infection of a H1N1pdm09 virus and an oseltamivir-resistant H1N1 Brisbane-like virus. Oseltamivir-resistant H1N1pdm09 viruses were also isolated from patients. After biochemical characterization, the pathogenicity of these viruses was assessed in a murine model. We confirmed a higher infectivity, in mice, of the H1N1pdm09 virus compared to seasonal viruses. Surprisingly, the oseltamivir-resistant H1N1pdm09 virus was more infectious than its sensitive counterpart. Moreover, the association of H1N1pdm09 hemagglutinin and an oseltamivir-resistant neuraminidase improved the infectivity of reassortant viruses in mice, regardless of the NA origin: seasonal (Brisbane-like) or pandemic strain. This study highlights the need to closely monitor the emergence of oseltamivir-resistant viruses.
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Mir MA, Lal RB, Sullender W, Singh Y, Garten R, Krishnan A, Broor S. Genetic diversity of HA1 domain of hemagglutinin gene of pandemic influenza H1N1pdm09 viruses in New Delhi, India. J Med Virol 2012; 84:386-93. [DOI: 10.1002/jmv.23205] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Piralla A, Pariani E, Rovida F, Campanini G, Muzzi A, Emmi V, Iotti GA, Pesenti A, Conaldi PG, Zanetti A, Baldanti F. Segregation of virulent influenza A(H1N1) variants in the lower respiratory tract of critically ill patients during the 2010-2011 seasonal epidemic. PLoS One 2011; 6:e28332. [PMID: 22194826 PMCID: PMC3237448 DOI: 10.1371/journal.pone.0028332] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2011] [Accepted: 11/06/2011] [Indexed: 12/23/2022] Open
Abstract
Background Since its appearance in 2009, the pandemic influenza A(H1N1) virus circulated worldwide causing several severe infections. Methods Respiratory samples from patients with 2009 influenza A(H1N1) and acute respiratory distress attending 24 intensive care units (ICUs) as well as from patients with lower respiratory tract infections not requiring ICU admission and community upper respiratory tract infections in the Lombardy region (10 million inhabitants) of Italy during the 2010–2011 winter-spring season, were analyzed. Results In patients with severe ILI, the viral load was higher in bronchoalveolar lavage (BAL) with respect to nasal swab (NS), (p<0.001) suggesting a higher virus replication in the lower respiratory tract. Four distinct virus clusters (referred to as cluster A to D) circulated simultaneously. Most (72.7%, n = 48) of the 66 patients infected with viruses belonging to cluster A had a severe (n = 26) or moderate ILI (n = 22). Amino acid mutations (V26I, I116M, A186T, D187Y, D222G/N, M257I, S263F, I286L/M, and N473D) were observed only in patients with severe ILI. D222G/N variants were detected exclusively in BAL samples. Conclusions Multiple virus clusters co-circulated during the 2010–2011 winter-spring season. Severe or moderate ILI were associated with specific 2009 influenza A(H1N1) variants, which replicated preferentially in the lower respiratory tract.
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MESH Headings
- Adolescent
- Adult
- Aged
- Aged, 80 and over
- Amino Acid Sequence
- Child
- Child, Preschool
- Critical Illness/epidemiology
- Epidemics
- Female
- Humans
- Infant
- Infant, Newborn
- Influenza A Virus, H1N1 Subtype/genetics
- Influenza A Virus, H1N1 Subtype/immunology
- Influenza A Virus, H1N1 Subtype/pathogenicity
- Influenza, Human/epidemiology
- Influenza, Human/virology
- Italy/epidemiology
- Male
- Middle Aged
- Molecular Sequence Data
- Mutation/genetics
- Phylogeny
- Receptors, Virus/chemistry
- Receptors, Virus/metabolism
- Respiratory System/virology
- Seasons
- Virulence
- Young Adult
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Affiliation(s)
- Antonio Piralla
- Struttura Semplice Virologia Molecolare, Struttura Complessa Virologia e Microbiologia, Fondazione Istituto Ricovero e Cura a Carattere Scientifico Policlinico San Matteo, Pavia, Italy
| | - Elena Pariani
- Dipartimento di Sanità Pubblica-Microbiologia-Virologia, Università degli Studi di Milano, Milan, Italy
| | - Francesca Rovida
- Struttura Semplice Virologia Molecolare, Struttura Complessa Virologia e Microbiologia, Fondazione Istituto Ricovero e Cura a Carattere Scientifico Policlinico San Matteo, Pavia, Italy
| | - Giulia Campanini
- Struttura Semplice Virologia Molecolare, Struttura Complessa Virologia e Microbiologia, Fondazione Istituto Ricovero e Cura a Carattere Scientifico Policlinico San Matteo, Pavia, Italy
| | - Alba Muzzi
- Struttura Complessa Direzione Medica di Presidio, Fondazione Istituto Ricovero e Cura a Carattere Scientifico Policlinico San Matteo, Pavia, Italy
| | - Vincenzo Emmi
- Struttura Complessa Anestesia e Rianimazione I, Fondazione Istituto Ricovero e Cura a Carattere Scientifico Policlinico San Matteo, Pavia, Italy
| | - Giorgio A. Iotti
- Struttura Complessa Anestesia e Rianimazione II, Fondazione Istituto Ricovero e Cura a Carattere Scientifico Policlinico San Matteo, Pavia, Italy
| | - Antonio Pesenti
- Struttura Complessa Anestesia e Rianimazione, Azienda Ospedaliera San Gerardo, Monza, Italy
| | - Pier Giulio Conaldi
- Laboratorio di Patologia Clinica, Microbiologia e Virologia Istituto Mediterraneo per i Trapianti e Terapie ad Alta Specializzazione, Palermo, Italy
| | - Alessandro Zanetti
- Dipartimento di Sanità Pubblica-Microbiologia-Virologia, Università degli Studi di Milano, Milan, Italy
| | - Fausto Baldanti
- Struttura Semplice Virologia Molecolare, Struttura Complessa Virologia e Microbiologia, Fondazione Istituto Ricovero e Cura a Carattere Scientifico Policlinico San Matteo, Pavia, Italy
- * E-mail:
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Pabbaraju K, Wong S, Drews SJ. Rethinking approaches to improve the utilization of nucleic acid amplification tests for detection and characterization of influenza A in diagnostic and reference laboratories. Future Microbiol 2011; 6:1443-60. [PMID: 22122441 DOI: 10.2217/fmb.11.126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Influenza A virus (IFVA) is a significant cause of respiratory infections worldwide and was also responsible for a recent pandemic in 2009. Laboratory identification of IFVA can guide antiviral therapy, assist in cohorting of patients and prevent antibiotic use. Characterization of the virus can track the emergence of novel strains, identify resistance and determine how circulating strains match with vaccine components. The gold standard for detection and characterization of IFVA is nucleic acid amplification technology (e.g., reverse transcriptase PCR [RT-PCR]), which must contend with a constantly evolving viral genome. Although molecular technology has been available for over two decades, there is still an operational gap between assay design and utilization of these tests for the diagnosis and characterization of IFVA. This review will discuss issues surrounding the implementation and use of RT-PCR for the identification and characterization of IFVA, and speculate on why RT-PCR has not been used more widely in clinical laboratories or moved closer to the patient. Newer, less widely used technologies that may change our laboratory practices will be identified and the authors will close with an attempt to identify some future applications of RT-PCR-based technologies for the detection and characterization of IFVA.
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Affiliation(s)
- Kanti Pabbaraju
- Provincial Laboratory for Public Health, Microbiology, 3030 Hospital Drive NW, Calgary, Alberta T2N 4W4, Canada
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Meslin EM, Garba I. Biobanking and public health: is a human rights approach the tie that binds? Hum Genet 2011; 130:451-63. [PMID: 21761137 PMCID: PMC7088251 DOI: 10.1007/s00439-011-1061-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2011] [Accepted: 06/30/2011] [Indexed: 10/29/2022]
Abstract
Ethical principles guiding public health and genomic medicine are often at odds: whereas public health practice adopts collectivist principles that emphasize population-based benefits, recent advances in genomic and personalized medicine are grounded in an individualist ethic that privileges informed consent, and the balancing of individual risk and benefit. Indeed, the attraction of personalized medicine is the promise it holds out to help individuals get the "right medicine for the right problem at the right time." Research biobanks are an effective tool in the genomic medicine toolbox. Biobanking in public health presents a unique case study to unpack some of these issues in more detail. For example, there is a long history of using banked tissue obtained under clinical diagnostic conditions for later public health uses. But despite the collectivist approach of public health, the principles applied to the ethical challenges of biobanking (e.g. informed consent, autonomy, privacy) remain individualist. We demonstrate the value of using human rights as a public health ethics framework to address this tension in biobanking by applying it to two illustrative cases.
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Affiliation(s)
- Eric M Meslin
- Indiana University Center for Bioethics, 410 W 10th Street, Suite 3100, Indianapolis, IN 46202, USA.
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Extensive geographical mixing of 2009 human H1N1 influenza A virus in a single university community. J Virol 2011; 85:6923-9. [PMID: 21593168 DOI: 10.1128/jvi.00438-11] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Despite growing interest in the molecular epidemiology of influenza virus, the pattern of viral spread within individual communities remains poorly understood. To determine the phylogeography of influenza virus in a single population, we examined the spatial diffusion of H1N1/09 influenza A virus within the student body of the University of California, San Diego (UCSD), sampling for a 1-month period between October and November 2009. Despite the highly focused nature of our study, an analysis of complete viral genome sequences revealed between 24 and 33 independent introductions of H1N1/09 into the UCSD community, comprising much of the global genetic diversity in this virus. These data were also characterized by a relatively low level of on-campus transmission as well as extensive spatial mixing, such that there was little geographical clustering by either student residence or city ZIP code. Most notably, students experiencing illness on the same day and residing in the same dorm possessed phylogenetically distinct lineages. H1N1/09 influenza A virus is therefore characterized by a remarkable spatial fluidity, which is likely to impede community-based methods for its control, including class cancellations, quarantine, and chemoprophylaxis.
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