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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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2
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Wang MH, Lou J, Cao L, Zhao S, Chan RW, Chan PK, Chan MCW, Chong MK, Wu WK, Wei Y, Zhang H, Zee BC, Yeoh EK. Characterization of key amino acid substitutions and dynamics of the influenza virus H3N2 hemagglutinin. J Infect 2021; 83:671-677. [PMID: 34627840 DOI: 10.1016/j.jinf.2021.09.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 06/10/2021] [Accepted: 09/30/2021] [Indexed: 10/20/2022]
Abstract
The annual epidemics of seasonal influenza is partly attributed to the continued virus evolution. It is challenging to evaluate the effect of influenza virus mutations on evading population immunity. In this study, we introduce a novel statistical and computational approach to measure the dynamic molecular determinants underlying epidemics using effective mutations (EMs), and account for the time of waning mutation advantage against herd immunity by measuring the effective mutation periods (EMPs). Extensive analysis is performed on the sequencing and epidemiology data of H3N2 epidemics in ten regions from season to season. We systematically identified 46 EMs in the hemagglutinin (HA) gene, in which the majority were antigenic sites. Eight EMs were located in immunosubdominant stalk domain, an important target for developing broadly reactive antibodies. The EMs might provide timely information on key substitutions for influenza vaccines antigen design. The EMP suggested that major genetic variants of H3N2 circulated in Southeast Asia for an average duration of 4.5 years (SD 2.4) compared to a significantly shorter 2.0 years (SD 1.0) in temperate regions. The proposed method bridges population epidemics and molecular characteristics of infectious diseases, and would find broad applications in various pathogens mutation estimations.
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Affiliation(s)
- Maggie Haitian Wang
- JC School of Public Health and Primary Care, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China; CUHK Shenzhen Research Institute, Shenzhen, China.
| | - Jingzhi Lou
- JC School of Public Health and Primary Care, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China; CUHK Shenzhen Research Institute, Shenzhen, China
| | - Lirong Cao
- JC School of Public Health and Primary Care, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China; CUHK Shenzhen Research Institute, Shenzhen, China
| | - Shi Zhao
- JC School of Public Health and Primary Care, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China; CUHK Shenzhen Research Institute, Shenzhen, China
| | - Renee Wy Chan
- CUHK-UMCU Joint Research Laboratory of Respiratory Virus & Immunobiology, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China; Department of Paediatrics, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
| | - Paul Ks Chan
- Department of Microbiology, Stanley Ho Center for Emerging Infectious Diseases, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
| | - Martin Chi-Wai Chan
- Department of Microbiology, Stanley Ho Center for Emerging Infectious Diseases, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
| | - Marc Kc Chong
- JC School of Public Health and Primary Care, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China; CUHK Shenzhen Research Institute, Shenzhen, China
| | - William Kk Wu
- Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
| | - Yuchen Wei
- Department of Microbiology, Stanley Ho Center for Emerging Infectious Diseases, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
| | - Haoyang Zhang
- JC School of Public Health and Primary Care, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
| | - Benny Cy Zee
- JC School of Public Health and Primary Care, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China; CUHK Shenzhen Research Institute, Shenzhen, China
| | - Eng-Kiong Yeoh
- JC School of Public Health and Primary Care, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China.
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3
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Stadtmueller MN, Bhatia S, Kiran P, Hilsch M, Reiter-Scherer V, Adam L, Parshad B, Budt M, Klenk S, Sellrie K, Lauster D, Seeberger PH, Hackenberger CPR, Herrmann A, Haag R, Wolff T. Evaluation of Multivalent Sialylated Polyglycerols for Resistance Induction in and Broad Antiviral Activity against Influenza A Viruses. J Med Chem 2021; 64:12774-12789. [PMID: 34432457 DOI: 10.1021/acs.jmedchem.1c00794] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The development of multivalent sialic acid-based inhibitors active against a variety of influenza A virus (IAV) strains has been hampered by high genetic and structural variability of the targeted viral hemagglutinin (HA). Here, we addressed this challenge by employing sialylated polyglycerols (PGs). Efficacy of prototypic PGs was restricted to a narrow spectrum of IAV strains. To understand this restriction, we selected IAV mutants resistant to a prototypic multivalent sialylated PG by serial passaging. Resistance mutations mapped to the receptor binding site of HA, which was accompanied by altered receptor binding profiles of mutant viruses as detected by glycan array analysis. Specifying the inhibitor functionalization to 2,6-α-sialyllactose (SL) and adjusting the linker yielded a rationally designed inhibitor covering an extended spectrum of inhibited IAV strains. These results highlight the importance of integrating virological data with chemical synthesis and structural data for the development of sialylated PGs toward broad anti-influenza compounds.
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Affiliation(s)
- Marlena N Stadtmueller
- Unit 17, Influenza and Other Respiratory Viruses, Robert Koch-Institut, Seestraße 10, 13353 Berlin, Germany
| | - Sumati Bhatia
- Institut für Chemie und Biochemie, Freie Universität Berlin, Takustr. 3, 14195 Berlin, Germany
| | - Pallavi Kiran
- Institut für Chemie und Biochemie, Freie Universität Berlin, Takustr. 3, 14195 Berlin, Germany
| | - Malte Hilsch
- Institut für Biologie, Molekulare Biophysik, IRI Life Sciences, Humboldt-Universität zu Berlin, Invalidenstr. 42, 10115 Berlin, Germany
| | - Valentin Reiter-Scherer
- Institut für Biologie, Molekulare Biophysik, IRI Life Sciences, Humboldt-Universität zu Berlin, Invalidenstr. 42, 10115 Berlin, Germany
| | - Lutz Adam
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle Strasse 10, 13125 Berlin, Germany.,Institut für Chemie, Humboldt Universität zu Berlin, Brook-Taylor Str. 2, 12489 Berlin, Germany
| | - Badri Parshad
- Institut für Chemie und Biochemie, Freie Universität Berlin, Takustr. 3, 14195 Berlin, Germany
| | - Matthias Budt
- Unit 17, Influenza and Other Respiratory Viruses, Robert Koch-Institut, Seestraße 10, 13353 Berlin, Germany
| | - Simon Klenk
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle Strasse 10, 13125 Berlin, Germany.,Institut für Chemie, Humboldt Universität zu Berlin, Brook-Taylor Str. 2, 12489 Berlin, Germany
| | - Katrin Sellrie
- Department for Biomolecular Systems, Max Planck Institute for Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Daniel Lauster
- Institut für Chemie und Biochemie, Freie Universität Berlin, Takustr. 3, 14195 Berlin, Germany.,Institut für Biologie, Molekulare Biophysik, IRI Life Sciences, Humboldt-Universität zu Berlin, Invalidenstr. 42, 10115 Berlin, Germany
| | - Peter H Seeberger
- Department for Biomolecular Systems, Max Planck Institute for Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Christian P R Hackenberger
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle Strasse 10, 13125 Berlin, Germany
| | - Andreas Herrmann
- Institut für Biologie, Molekulare Biophysik, IRI Life Sciences, Humboldt-Universität zu Berlin, Invalidenstr. 42, 10115 Berlin, Germany
| | - Rainer Haag
- Institut für Chemie und Biochemie, Freie Universität Berlin, Takustr. 3, 14195 Berlin, Germany
| | - Thorsten Wolff
- Unit 17, Influenza and Other Respiratory Viruses, Robert Koch-Institut, Seestraße 10, 13353 Berlin, Germany
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4
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Naeem A, Elbakkouri K, Alfaiz A, Hamed ME, Alsaran H, AlOtaiby S, Enani M, Alosaimi B. Antigenic drift of hemagglutinin and neuraminidase in seasonal H1N1 influenza viruses from Saudi Arabia in 2014 to 2015. J Med Virol 2020; 92:3016-3027. [PMID: 32159230 PMCID: PMC7228267 DOI: 10.1002/jmv.25759] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Accepted: 03/04/2020] [Indexed: 01/19/2023]
Abstract
Antigenic drift of the hemagglutinin (HA) and neuraminidase (NA) proteins of the influenza virus cause a decrease in vaccine efficacy. Since the information about the evolution of these viruses in Saudi is deficient so we investigated the genetic diversity of circulating H1N1 viruses. Nasopharyngeal aspirates/swabs collected from 149 patients hospitalized with flu-like symptoms during 2014 and 2015 were analyzed. Viral RNA extraction was followed by a reverse transcription-polymerase chain reaction and genetic sequencing. We analyzed complete gene sequences of HA and NA from 80 positive isolates. Phylogenetic analysis of HA and NA genes of 80 isolates showed similar topologies and co-circulation of clades 6b. Genetic diversity was observed among circulating viruses belonging to clade 6B.1A. The amino acid residues in the HA epitope domain were under purifying selection. Amino acid changes at key antigenic sites, such as position S101N, S179N (antigenic site-Sa), I233T (antigenic site-Sb) in the head domain might have resulted in antigenic drift and emergence of variant viruses. For NA protein, 36% isolates showed the presence of amino acid changes such as V13I (n = 29), I314M (n = 29) and 12% had I34V (n = 10). However, H257Y mutation responsible for resistance to neuraminidase inhibitors was missing. The presence of amino acid changes at key antigenic sites and their topologies with structural mapping of residues under purifying selection highlights the importance of antigenic drift and warrants further characterization of recently circulating viruses in view of vaccine effectiveness. The co-circulation of several clades and the predominance of clade 6B.1 suggest multiple introductions in Saudi.
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MESH Headings
- Humans
- Neuraminidase/genetics
- Saudi Arabia/epidemiology
- Influenza, Human/virology
- Influenza, Human/epidemiology
- Phylogeny
- Influenza A Virus, H1N1 Subtype/genetics
- Influenza A Virus, H1N1 Subtype/immunology
- Influenza A Virus, H1N1 Subtype/enzymology
- Influenza A Virus, H1N1 Subtype/isolation & purification
- Hemagglutinin Glycoproteins, Influenza Virus/genetics
- Adult
- Male
- Female
- Young Adult
- Genetic Variation
- Middle Aged
- Adolescent
- Genetic Drift
- Child
- Child, Preschool
- Amino Acid Substitution
- Viral Proteins/genetics
- Nasopharynx/virology
- Antigens, Viral/genetics
- Antigens, Viral/immunology
- RNA, Viral/genetics
- Antigenic Variation
- Aged
- Sequence Analysis, DNA
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Affiliation(s)
- Asif Naeem
- Research CenterKing Fahad Medical CityRiyadhSaudi Arabia
| | | | - Ali Alfaiz
- Research CenterKing Fahad Medical CityRiyadhSaudi Arabia
| | | | - Hadel Alsaran
- Research CenterKing Fahad Medical CityRiyadhSaudi Arabia
| | | | - Mushira Enani
- Medical Specialties Department, Section of Infectious DiseasesKing Fahad Medical CityRiyadhSaudi Arabia
| | - Bandar Alosaimi
- Research CenterKing Fahad Medical CityRiyadhSaudi Arabia
- College of MedicineKing Fahad Medical CityRiyadhSaudi Arabia
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5
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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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Kiseleva I, Rekstin A, Al Farroukh M, Bazhenova E, Katelnikova A, Puchkova L, Rudenko L. Non-Mouse-Adapted H1N1pdm09 Virus as a Model for Influenza Research. Viruses 2020; 12:v12060590. [PMID: 32485821 PMCID: PMC7354452 DOI: 10.3390/v12060590] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 05/21/2020] [Accepted: 05/27/2020] [Indexed: 12/26/2022] Open
Abstract
The number of lung-adapted influenza viruses is limited. Most of them are not antigenically related to current circulating viruses. Viruses similar to recent strains are required for screening modern antiviral compounds and studying new vaccine candidates against novel influenza viruses. The process by which an influenza virus adapts to a new host is rather difficult. The aim of this study was to select a non-adapted current virus whose major biological properties correspond to those of classical lab-adapted viruses. Mice were inoculated intranasally with non-lung-adapted influenza viruses of subtype H1N1pdm09. They were monitored closely for body weight loss, mortality outcomes and gross pathology for 14 days following inoculation, as well as viral replication in lung tissue. Lung-adapted PR8 virus was used as a control. The tested viruses multiplied equally well in the lower respiratory tract of mice without prior adaptation but dramatically differed in lethality; the differences in their toxicity and pathogenicity in mice were established. A/South Africa/3626/2013 (H1N1)pdm09 virus was found to be an appropriate candidate to replace PR8 as a model virus for influenza research. No prior adaptation to the animal model is needed to reach the pathogenicity level of the classical mouse-adapted PR8 virus.
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Affiliation(s)
- Irina Kiseleva
- Department of Virology, Federal State Budgetary Scientific Institution “Institute of Experimental Medicine”, 197376 St Petersburg, Russia; (A.R.); (M.A.F.); (E.B.); (L.P.); (L.R.)
- Correspondence:
| | - Andrey Rekstin
- Department of Virology, Federal State Budgetary Scientific Institution “Institute of Experimental Medicine”, 197376 St Petersburg, Russia; (A.R.); (M.A.F.); (E.B.); (L.P.); (L.R.)
| | - Mohammad Al Farroukh
- Department of Virology, Federal State Budgetary Scientific Institution “Institute of Experimental Medicine”, 197376 St Petersburg, Russia; (A.R.); (M.A.F.); (E.B.); (L.P.); (L.R.)
| | - Ekaterina Bazhenova
- Department of Virology, Federal State Budgetary Scientific Institution “Institute of Experimental Medicine”, 197376 St Petersburg, Russia; (A.R.); (M.A.F.); (E.B.); (L.P.); (L.R.)
| | - Anastasia Katelnikova
- Department of Toxicology and Microbiology, Institute of Preclinical Research Ltd., 188663 St Petersburg, Russia;
| | - Ludmila Puchkova
- Department of Virology, Federal State Budgetary Scientific Institution “Institute of Experimental Medicine”, 197376 St Petersburg, Russia; (A.R.); (M.A.F.); (E.B.); (L.P.); (L.R.)
| | - Larisa Rudenko
- Department of Virology, Federal State Budgetary Scientific Institution “Institute of Experimental Medicine”, 197376 St Petersburg, Russia; (A.R.); (M.A.F.); (E.B.); (L.P.); (L.R.)
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7
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Glatman-Freedman A, Pando R, Sefty H, Omer I, Rosenberg A, Drori Y, Nemet I, Mendelson E, Keinan-Boker L, Mandelboim M. Predominance of a Drifted Influenza A (H3N2) Clade and its Association with Age-specific Influenza Vaccine Effectiveness Variations, Influenza Season 2018-2019. Vaccines (Basel) 2020; 8:vaccines8010078. [PMID: 32050460 PMCID: PMC7157661 DOI: 10.3390/vaccines8010078] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 01/24/2020] [Accepted: 01/29/2020] [Indexed: 12/20/2022] Open
Abstract
Background: Influenza A (H3N2) clade 3C.3a was the predominant influenza virus in Israel throughout the 2018-2019 season, constituting a drift from the influenza A (H3N2) vaccine. We estimated the end-of season vaccine effectiveness (VE) by age, among community patients with influenza-like illness (ILI), considering the hemagglutinin (HA) gene mutations and amino acid substitutions of influenza A (H3N2) viruses detected. Methods: Nose-throat samples were analyzed for the presence of influenza virus, type/subtype, and HA gene sequence. HA gene sequences and amino acid substitutions were compared to the influenza A/Singapore/INFIMH-16-0019/2016 (H3N2)-like 2018-2019 vaccine virus, and a phylogenetic tree was generated. Influenza VE against influenza A (H3N2) was estimated using the test-negative design. VE was estimated by age group and by 15 year moving age intervals. Results: In total, 90% of the influenza A (H3N2) viruses belonged to the 3C.3a clade, constituting a unique situation in the northern hemisphere. Adjusted all-age influenza A (H3N2) VE was −3.5% (95% CI: −51.2 to 29.1). Although adjusted VEs were very low among infants, children, and young adults, a VE of 45% (95% CI: −19.2 to 74.6) was estimated among adults aged ≥45 years old. Conclusions: The higher VE point estimates among older adults may be related to previous exposure to similar influenza viruses.
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Affiliation(s)
- Aharona Glatman-Freedman
- Israel Center for Disease Control, Israel Ministry of Health, Tel Hashomer, Ramat Gan 5265601, Israel
- School of Public Health, Tel Aviv University Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
- Correspondence:
| | - Rakefet Pando
- Israel Center for Disease Control, Israel Ministry of Health, Tel Hashomer, Ramat Gan 5265601, Israel
- Central Virology Laboratory, Sheba Medical Center, Israel Ministry of Health, Tel Hashomer, Ramat Gan 5265601, Israel
| | - Hanna Sefty
- Israel Center for Disease Control, Israel Ministry of Health, Tel Hashomer, Ramat Gan 5265601, Israel
| | - Itay Omer
- School of Public Health, Tel Aviv University Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Alina Rosenberg
- Israel Center for Disease Control, Israel Ministry of Health, Tel Hashomer, Ramat Gan 5265601, Israel
| | - Yaron Drori
- School of Public Health, Tel Aviv University Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
- Central Virology Laboratory, Sheba Medical Center, Israel Ministry of Health, Tel Hashomer, Ramat Gan 5265601, Israel
| | - Ital Nemet
- Central Virology Laboratory, Sheba Medical Center, Israel Ministry of Health, Tel Hashomer, Ramat Gan 5265601, Israel
| | - Ella Mendelson
- School of Public Health, Tel Aviv University Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
- Central Virology Laboratory, Sheba Medical Center, Israel Ministry of Health, Tel Hashomer, Ramat Gan 5265601, Israel
| | - Lital Keinan-Boker
- Israel Center for Disease Control, Israel Ministry of Health, Tel Hashomer, Ramat Gan 5265601, Israel
- School of Public Health, University of Haifa, Haifa 3498838, Israel
| | - Michal Mandelboim
- School of Public Health, Tel Aviv University Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
- Central Virology Laboratory, Sheba Medical Center, Israel Ministry of Health, Tel Hashomer, Ramat Gan 5265601, Israel
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8
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Nearly Complete Genome Sequence of Human Influenza Virus Strain A/Almaty/6327/2014 (H1N1) from Central Asia. Microbiol Resour Announc 2019; 8:8/47/e00527-19. [PMID: 31753934 PMCID: PMC6872876 DOI: 10.1128/mra.00527-19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
An influenza virus strain, A/Almaty/6327/2014 (H1N1), was isolated in Almaty (in southeastern Kazakhstan) during a human population surveillance study in 2014. Here, we present the nearly complete genome sequence of this epidemic strain that was compared to the postpandemic variants of A(H1N1)pdm09. An influenza virus strain, A/Almaty/6327/2014 (H1N1), was isolated in Almaty (in southeastern Kazakhstan) during a human population surveillance study in 2014. Here, we present the nearly complete genome sequence of this epidemic strain that was compared to the postpandemic variants of A(H1N1)pdm09.
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9
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Guldemir D, Coskun-Ari FF, Altas AB, Bakkaloglu Z, Unaldi O, Bayraktar F, Korukluoglu G, Aktas AR, Durmaz R. Molecular characterization of the influenza A(H1N1)pdm09 isolates collected in the 2015-2016 season and comparison of HA mutations detected in Turkey since 2009. J Med Virol 2019; 91:2074-2082. [PMID: 31389035 DOI: 10.1002/jmv.25565] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 08/01/2019] [Indexed: 01/02/2023]
Abstract
Influenza A(H1N1)pdm09 pandemic virus causing the 2009 global outbreak moved into the post-pandemic period, but its variants continued to be the prevailing subtype in the 2015-2016 influenza season in Europe and Asia. To determine the molecular characteristics of influenza A(H1N1)pdm09 isolates circulating during the 2015-2016 season in Turkey, we identified mutations in the hemagglutinin (HA) genes and investigated the presence of H275Y alteration in the neuraminidase genes in the randomly selected isolates. The comparison of the HA nucleotide sequences revealed a very high homology (>99.5%) among the studied influenza A(H1N1)pdm09 isolates, while a relatively low homology (96.6%-97.2%), was observed between Turkish isolates and the A/California/07/2009 vaccine virus. Overall 14 common mutations were detected in HA sequences of all 2015-2016 influenza A(H1N1)pdm09 isolates with respect to the A/California/07/2009 virus, four of which located in three different antigenic sites. Eleven rare mutations in 12 HA sequences were also detected. Phylogenetic analysis revealed that all characterized influenza A(H1N1)pdm09 isolates formed a single genetic cluster, belonging to the genetic subclade 6B.1, defined by HA amino acid substitutions S84N, S162N, and I216T. Furthermore, all isolates showed an oseltamivir-sensitive genotype, suggesting that Tamiflu (Oseltamivir) could still be the drug of choice in Turkey.
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Affiliation(s)
- Dilek Guldemir
- National Molecular Microbiology Reference Laboratory, Public Health General Directorate, Ministry of Health, Ankara, Turkey
| | - Fatma Filiz Coskun-Ari
- National Molecular Microbiology Reference Laboratory, Public Health General Directorate, Ministry of Health, Ankara, Turkey
| | - Ayse Basak Altas
- National Viral Respiratory Pathogens Reference Laboratory, Public Health General Directorate, Ministry of Health, Ankara, Turkey
| | - Zekiye Bakkaloglu
- National Molecular Microbiology Reference Laboratory, Public Health General Directorate, Ministry of Health, Ankara, Turkey
| | - Ozlem Unaldi
- National Molecular Microbiology Reference Laboratory, Public Health General Directorate, Ministry of Health, Ankara, Turkey
| | - Fatma Bayraktar
- National Viral Respiratory Pathogens Reference Laboratory, Public Health General Directorate, Ministry of Health, Ankara, Turkey
| | - Gulay Korukluoglu
- National Viral Respiratory Pathogens Reference Laboratory, Public Health General Directorate, Ministry of Health, Ankara, Turkey
| | - Ali Riza Aktas
- National Molecular Microbiology Reference Laboratory, Public Health General Directorate, Ministry of Health, Ankara, Turkey
| | - Riza Durmaz
- Department of Clinical Microbiology, Faculty of Medicine, Yildirim Beyazit University, Ankara, Turkey
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10
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Haveri A, Ikonen N, Kantele A, Anttila VJ, Ruotsalainen E, Savolainen-Kopra C, Julkunen I. Seasonal influenza vaccines induced high levels of neutralizing cross-reactive antibody responses against different genetic group influenza A(H1N1)pdm09 viruses. Vaccine 2019; 37:2731-2740. [PMID: 30954308 DOI: 10.1016/j.vaccine.2019.03.078] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 03/25/2019] [Accepted: 03/31/2019] [Indexed: 12/27/2022]
Abstract
Influenza A(H1N1)pdm09 viruses have been circulating throughout the world since the 2009 pandemic. A/California/07/2009 (H1N1) virus was included in seasonal influenza vaccines for seven years altogether, providing a great opportunity to analyse vaccine-induced immunity in relation to the postpandemic evolution of the A(H1N1)pdm09 virus. Serum antibodies against various epidemic strains of influenza A(H1N1)pdm09 viruses were measured among health care workers (HCWs) by haemagglutination inhibition and microneutralization tests before and after 2010 and 2012 seasonal influenza vaccinations. We detected high responses of vaccine-induced neutralizing antibodies to six distinct genetic groups. Our results indicate antigenic similarity between vaccine and circulating A(H1N1)pdm09 strains, and substantial vaccine-induced immunity against circulating epidemic viruses.
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MESH Headings
- Antibodies, Neutralizing/immunology
- Antibodies, Viral/immunology
- Hemagglutinin Glycoproteins, Influenza Virus/chemistry
- Hemagglutinin Glycoproteins, Influenza Virus/immunology
- Humans
- Immunity, Humoral
- Influenza A Virus, H1N1 Subtype/classification
- Influenza A Virus, H1N1 Subtype/genetics
- Influenza A Virus, H1N1 Subtype/immunology
- Influenza Vaccines/immunology
- Influenza, Human/immunology
- Influenza, Human/prevention & control
- Neutralization Tests
- Phylogeny
- Seasons
- Serologic Tests
- Structure-Activity Relationship
- Vaccination
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Affiliation(s)
- Anu Haveri
- Expert Microbiology Unit, Department of Health Security, National Institute for Health and Welfare (THL), POB 30, 00271 Helsinki, Finland.
| | - Niina Ikonen
- Expert Microbiology Unit, Department of Health Security, National Institute for Health and Welfare (THL), POB 30, 00271 Helsinki, Finland
| | - Anu Kantele
- Division of Infectious Diseases, Inflammation Center, University of Helsinki and Helsinki University Hospital, POB 348, 00029 HUS Helsinki, Finland
| | - Veli-Jukka Anttila
- Division of Infectious Diseases, Inflammation Center, University of Helsinki and Helsinki University Hospital, POB 348, 00029 HUS Helsinki, Finland
| | - Eeva Ruotsalainen
- Division of Infectious Diseases, Inflammation Center, University of Helsinki and Helsinki University Hospital, POB 348, 00029 HUS Helsinki, Finland
| | - Carita Savolainen-Kopra
- Expert Microbiology Unit, Department of Health Security, National Institute for Health and Welfare (THL), POB 30, 00271 Helsinki, Finland
| | - Ilkka Julkunen
- Expert Microbiology Unit, Department of Health Security, National Institute for Health and Welfare (THL), POB 30, 00271 Helsinki, Finland; Institute of Biomedicine, University of Turku and Turku University Hospital, Kiinamyllynkatu 10, 20520 Turku, Finland
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11
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Molecular characterization of influenza A(H1N1)pdm09 in Cameroon during the 2014-2016 influenza seasons. PLoS One 2019; 14:e0210119. [PMID: 30640922 PMCID: PMC6331099 DOI: 10.1371/journal.pone.0210119] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 12/17/2018] [Indexed: 12/11/2022] Open
Abstract
In 2009, Influenza A(H1N1)pdm09 caused the first influenza pandemic of the 21st century with high mortality rates of about 284 500 deaths. This virus, however, continues to circulate as a seasonal influenza virus and to cause illness and deaths worldwide. In this study, we describe the genetic diversity of A(H1N1)pdm09 viruses collected between 2014 and 2016 in Cameroon. Three gene segments (HA, NA and M) of Cameroon strains were studied. The phylogenetic tree of the coding nucleotide sequences was generated by MEGA version 6.0 using a Maximum Likelihood method. The NA and M protein coding sequences were analyzed for the reported genetic markers of resistance against neuraminidase inhibitors and adamantanes, while predicted vaccine efficacy was estimated using the Pepitope method. Overall 39 strains were obtained. Phylogenetic analysis of the HA gene of influenza A(H1N1)pdm09 showed that Cameroon strains belonged to two major clades. The 2014 Cameroon sequences belonged to clade 6C while all sequences collected between 2015 and 2016 belonged to clade 6B. Majority of the samples had some mutations in the NA gene notably: I117M, N248D, and N369K while the amantadine-resistant M mutant, S31N, was found to be absent only in the two sequences collected in 2014. Overall, A/California/07/2009 vaccine strain showed a predicted vaccine efficacy of 24.55% to 35.77% against Cameroon A(H1N1)pdm09 strains circulating between 2014 and 2016. Our findings confirms the fast evolution of A(H1N1)pdm09 since its first introduction and highlights on the importance of influenza vaccine in reducing the burden caused by influenza in the community.
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12
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Mohebbi A, Fotouhi F, Jamali A, Yaghobi R, Farahmand B, Mohebbi R. Molecular epidemiology of the hemagglutinin gene of prevalent influenza virus A/H1N1/pdm09 among patient in Iran. Virus Res 2018; 259:38-45. [PMID: 30336188 DOI: 10.1016/j.virusres.2018.10.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 10/01/2018] [Accepted: 10/02/2018] [Indexed: 11/17/2022]
Abstract
In 2015, the influenza virus A/H1N1/pdm09 strain outbreak became prevalent throughout the different provinces of Iran. There are relatively limited complete genetic sequences available for this virus from Asian countries. Diagnosis and virological surveillance of influenza is essential for detecting novel genetic variants causing epidemic potential. This study describes the genetic properties of HA genome of influenza A/H1N1 pdm09 viruses circulating in Iran during the 2015/2016 season. In order to investigate the genetic pattern of influenza A/H1N1 pdm09, a total of 1758 nasopharyngeal swabs were screened by real-time RT-PCR. Of those, 510 cases were found to be positive for A/H1N1/pdm09 virus. Evolution of the approximately 100 positive specimens with high virus load was conducted via genomic phylogeny. Phylogenetic analysis of the HA genes of the A/H1N1pdm09 viruses revealed the circulation of clade 6B1, characterized by amino acid substitutions S84N, S162N and I216T, where position 162 became glycosylated. The N-glycosylation of HA protein is post or co-translational modification that affect the evolution of influenza viruses. For influenza A(H1N1) pdm09 viruses, we found more mutations in the antigenic sites than in the stem region. The results of this study confirmed the necessity of constant regular antigenic and molecular surveillance of circulating seasonal influenza viruses.
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Affiliation(s)
- Atefeh Mohebbi
- Department of Microbiology, College of Science Agriculture and Modern Technology, Shiraz Branch, Islamic Azad University, Shiraz, Iran.
| | - Fatemeh Fotouhi
- Department of Influenza and other Respiratory Viruses, Pasteur Institute of Iran, Tehran, Iran.
| | - Abbas Jamali
- Department of Influenza and other Respiratory Viruses, Pasteur Institute of Iran, Tehran, Iran.
| | - Ramin Yaghobi
- Shiraz Transplant Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Behrokh Farahmand
- Department of Influenza and other Respiratory Viruses, Pasteur Institute of Iran, Tehran, Iran.
| | - Reza Mohebbi
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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13
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Hashem AM, Azhar EI, Shalhoub S, Abujamel TS, Othman NA, Al Zahrani AB, Abdullah HM, Al-Alawi MM, Sindi AA. Genetic characterization and diversity of circulating influenza A/H1N1pdm09 viruses isolated in Jeddah, Saudi Arabia between 2014 and 2015. Arch Virol 2018; 163:1219-1230. [PMID: 29396684 DOI: 10.1007/s00705-018-3732-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Accepted: 12/19/2017] [Indexed: 12/28/2022]
Abstract
The emerged influenza A/H1N1pdm09 viruses have replaced the previously circulating seasonal H1N1 viruses. The close antigenic properties of these viruses to the 1918 H1N1 pandemic viruses and their post-pandemic evolution pattern could further enhance their adaptation and pathogenicity in humans representing a major public health threat. Given that data on the dynamics and evolution of these viruses in Saudi Arabia is sparse we investigated the genetic diversity of circulating influenza A/H1N1pdm09 viruses from Jeddah, Saudi Arabia, by analyzing 39 full genomes from isolates obtained between 2014-2015, from patients with varying symptoms. Phylogenetic analysis of all gene segments and concatenated genomes showed similar topologies and co-circulation of clades 6b, 6b.1 and 6b.2, with clade 6b.1 being the most predominate since 2015. Most viruses were more closely related to the vaccine strain (Michigan/45/2015) recommended for the 2017/2018 season, than to the California/07/2009 strain. Low sequence variability was observed in the haemagglutinin protein compared to the neuraminidase protein. Resistance to neuraminidase inhibitors was limited as only one isolate had the H275Y substitution. Interestingly, two isolates had short PA-X proteins of 206 amino acids compared to the 232 amino acid protein found in most influenza A/H1N1pdm09 viruses. Together, the co-circulation of several clades and the predominance of clade 6b.1, despite its low circulation in Asia in 2015, suggests multiple introductions most probably during the mass gathering events of Hajj and Umrah. Jeddah represents the main port of entry to the holy cities of Makkah and Al-Madinah, emphasizing the need for vigilant surveillance in the kingdom.
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MESH Headings
- Amino Acid Substitution
- Female
- Genetic Variation
- Genome, Viral
- Hemagglutinin Glycoproteins, Influenza Virus/genetics
- Humans
- Influenza A Virus, H1N1 Subtype/classification
- Influenza A Virus, H1N1 Subtype/genetics
- Influenza A Virus, H1N1 Subtype/isolation & purification
- Influenza, Human/epidemiology
- Influenza, Human/transmission
- Influenza, Human/virology
- Male
- Nasopharynx/virology
- Neuraminidase/genetics
- Phylogeny
- RNA, Viral/genetics
- Saudi Arabia/epidemiology
- Seasons
- Sequence Analysis, DNA
- Viral Proteins/genetics
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Affiliation(s)
- Anwar M Hashem
- Special Infectious Agent Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia.
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia.
| | - Esam I Azhar
- Special Infectious Agent Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia.
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia.
| | - Sarah Shalhoub
- Division of Infectious Diseases, Department of Medicine, King Fahd Armed Forces Hospital, Jeddah, Kingdom of Saudi Arabia
| | - Turki S Abujamel
- Special Infectious Agent Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Norah A Othman
- Special Infectious Agent Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Abdulwahab B Al Zahrani
- Molecular Diagnostics Laboratory, King Fahd Armed Forces Hospital, Jeddah, Kingdom of Saudi Arabia
| | - Hanan M Abdullah
- Students' Research and Innovation Unit, Faculty of Medicine, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Maha M Al-Alawi
- Special Infectious Agent Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
- Infection Control and Environmental Health Unit, Faculty of Medicine, King Abdulaziz University Hospital, Jeddah, Kingdom of Saudi Arabia
| | - Anees A Sindi
- Department of Anesthesia and Critical Care, Faculty of Medicine, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
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14
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Korsun N, Angelova S, Trifonova I, Tzotcheva I, Mileva S, Voleva S, Georgieva I, Perenovska P. Predominance of influenza A(H3N2) viruses during the 2016/2017 season in Bulgaria. J Med Microbiol 2018; 67:228-239. [PMID: 29297852 DOI: 10.1099/jmm.0.000668] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
PURPOSE Influenza viruses are characterised by high variability, which makes them able to cause annual epidemics. The aim of this study is to determine the antigenic and genetic characteristics of influenza viruses circulating in Bulgaria during the 2016/2017 season. METHODOLOGY The detection and typing/subtyping of influenza viruses were performed using real time RT-PCR. Results of antigenic characterisation, phylogenetic and amino acid sequence analyses of representative influenza strains are presented herein. RESULTS The 2016/2017 season was characterised by an early start, an exclusive dominance of A(H3N2) viruses accounting for 93 % of total influenza virus detections, and a low circulation of A(H1N1)pdm09 (4.2 %) and type B (2.5 %) viruses. The analysed A(H3N2) viruses belonged to subclades 3C.2a (52 %) and 3C.2a1 (48 %); all studied A(H1N1)pdm09 and B/Victoria-lineage viruses belonged to subclades 6B.1 and 1A, respectively. The amino acid sequence analysis of 56 A(H3N2) isolates revealed the presence of substitutions in 18 positions in haemagglutinin (HA) as compared to the A/Hong Kong/4801/2014 vaccine virus, seven of which occurred in four antigenic sites, together with changes in 23 positions in neuraminidase (NA), and a number of substitutions in internal proteins PB2, PB1, PB1-F2, PA, NP and NS1. Despite the many amino acid substitutions, A(H3N2) viruses remained antigenically similar to the vaccine strain. Substitutions in HA and NA sequences of A(H1N1)pdm09 and B/Victoria-lineage strains were also identified, including in antigenic sites. CONCLUSION The results of this study confirm the genetic variability of circulating influenza viruses, particularly A(H3N2), and the need for continued antigenic and molecular surveillance.
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MESH Headings
- Adolescent
- Adult
- Amino Acid Substitution
- Bulgaria/epidemiology
- Child
- Child, Preschool
- Epidemiological Monitoring
- Evolution, Molecular
- Female
- Genetic Variation
- Genome, Viral
- Hemagglutinin Glycoproteins, Influenza Virus/genetics
- Humans
- Influenza A Virus, H1N1 Subtype/classification
- Influenza A Virus, H1N1 Subtype/genetics
- Influenza A Virus, H1N1 Subtype/isolation & purification
- Influenza A Virus, H3N2 Subtype/classification
- Influenza A Virus, H3N2 Subtype/genetics
- Influenza A Virus, H3N2 Subtype/immunology
- Influenza A Virus, H3N2 Subtype/isolation & purification
- Influenza B virus/classification
- Influenza B virus/genetics
- Influenza B virus/isolation & purification
- Influenza, Human/epidemiology
- Influenza, Human/virology
- Male
- Neuraminidase/genetics
- Phylogeny
- RNA, Viral/genetics
- Real-Time Polymerase Chain Reaction
- Seasons
- Sequence Analysis, DNA
- Young Adult
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Affiliation(s)
- Neli Korsun
- National Reference Laboratory "Influenza and ARD", National Centre of Infectious and Parasitic Diseases, 44A Stoletov Blvd, 1233 Sofia, Bulgaria
| | - Svetla Angelova
- National Reference Laboratory "Influenza and ARD", National Centre of Infectious and Parasitic Diseases, 44A Stoletov Blvd, 1233 Sofia, Bulgaria
| | - Ivelina Trifonova
- National Reference Laboratory "Influenza and ARD", National Centre of Infectious and Parasitic Diseases, 44A Stoletov Blvd, 1233 Sofia, Bulgaria
| | - Iren Tzotcheva
- Paediatric Clinic, University Hospital Alexandrovska, Medical University, 1"Sv. Georgi Sofiiski" Str., 1431 Sofia, Bulgaria
| | - Sirma Mileva
- Paediatric Clinic, University Hospital Alexandrovska, Medical University, 1"Sv. Georgi Sofiiski" Str., 1431 Sofia, Bulgaria
| | - Silvia Voleva
- National Reference Laboratory "Influenza and ARD", National Centre of Infectious and Parasitic Diseases, 44A Stoletov Blvd, 1233 Sofia, Bulgaria
| | - Irina Georgieva
- National Reference Laboratory "Influenza and ARD", National Centre of Infectious and Parasitic Diseases, 44A Stoletov Blvd, 1233 Sofia, Bulgaria
| | - Penka Perenovska
- Paediatric Clinic, University Hospital Alexandrovska, Medical University, 1"Sv. Georgi Sofiiski" Str., 1431 Sofia, Bulgaria
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15
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Monamele GC, Vernet MA, Njankouo MR, Victoir K, Akoachere JF, Anong D, Njouom R. Genetic and antigenic characterization of influenza A(H3N2) in Cameroon during the 2014-2016 influenza seasons. PLoS One 2017; 12:e0184411. [PMID: 28877235 PMCID: PMC5587321 DOI: 10.1371/journal.pone.0184411] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 08/23/2017] [Indexed: 12/25/2022] Open
Abstract
The first outbreak of influenza A(H3N2) occurred in 1968 and caused the third flu pandemic of the 20th century. It has affected multiple countries over time. The best strategy to reduce the burden of influenza is through vaccination whose efficacy varies with respect to the circulating strains. This study was performed to better understand the molecular evolution of influenza A(H3N2) and assess vaccine efficacy in Cameroon. Complete sequences of three gene segments were obtained from 2014 to 2016 influenza seasons in Cameroon. Hemagglutinin (HA), Neuraminidase (NA) and matrix (M) genes of 35 A(H3N2) virus strains were amplified and sequenced. Predicted vaccine efficacy was measured using the Pepitope model. Phylogenetic analysis of the HA gene showed that all Cameroonian strains had evolved away from the 3C.1-A/Texas/50/2012-like clade. Globally, 2014 virus strains clustered with the 2015–2016 vaccine strain, 3C.3a-A/Switzerland/9715293/2013, whereas 2015 and 2016 virus strains clustered with the 2016–2017 vaccine strain, 3C.2a-A/HongKong/4801/2014. In order to determine the genotypic drug susceptibility to neuraminidase inhibitors and amantadine, the NA and M2 protein coding sequences were analyzed. There was no strain with characteristic mutation for resistance to neuraminidase inhibitors, per contra; all strains possessed the substitution S31N, peculiar of resistance to adamantanes. There was drift in influenza A(H3N2) dominant epitopes B (2014 and 2015) to epitopes A (2016) with a theoretical efficiency in vaccine ranging from low to moderate. The presence of several antigenic site mutations among H3N2 virus strains between 2014–2016 influenza seasons in Cameroon confirms the progressing evolution of circulating H3N2 strains.
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Affiliation(s)
- Gwladys C. Monamele
- National Influenza Centre, Centre Pasteur du Cameroun, Yaoundé, Cameroon
- Department of Microbiology and Parasitology, University of Buea, Buea, Cameroon
| | | | | | - Kathleen Victoir
- International Director, Institut Pasteur de Paris, Paris, France
| | | | - Damian Anong
- Department of Microbiology and Parasitology, University of Buea, Buea, Cameroon
| | - Richard Njouom
- National Influenza Centre, Centre Pasteur du Cameroun, Yaoundé, Cameroon
- * E-mail:
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16
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Korsun N, Angelova S, Gregory V, Daniels R, Georgieva I, McCauley J. Antigenic and genetic characterization of influenza viruses circulating in Bulgaria during the 2015/2016 season. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2017; 49:241-250. [PMID: 28132927 PMCID: PMC5348111 DOI: 10.1016/j.meegid.2017.01.027] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 01/21/2017] [Accepted: 01/25/2017] [Indexed: 12/13/2022]
Abstract
Influenza virological surveillance is an essential tool for early detection of novel genetic variants of epidemiologic and clinical significance. The aim of this study was to determine the antigenic and molecular characteristics of influenza viruses circulating in Bulgaria during the 2015/2016 season. The season was characterized by dominant circulation of A(H1N1)pdm09 viruses, accounting for 66% of detected influenza viruses, followed by B/Victoria-lineage viruses (24%) and A(H3N2) viruses (10%). All sequenced influenza A(H1N1)pdm09, A(H3N2) and B/Victoria-lineage viruses belonged to the 6B.1, 3C.2a and 1A genetic groups, respectively. Amino acid analysis of 57 A(H1N1)pdm09 isolates revealed the presence of 16 changes in hemagglutinin (HA) compared to the vaccine virus, five of which occurred in four antigenic sites, together with 16 changes in neuraminidase (NA) and a number of substitutions in proteins MP, NP, NS and PB2. Despite the many amino acid substitutions, A(H1N1)pdm09 viruses remained antigenically closely related to A/California/7/2009 vaccine virus. Bulgarian A(H3N2) strains (subclade 3C.2a) showed changes at 11 HA positions four of which were located in antigenic sites A and B, together with 6 positions in NA, compared to the subclade 3C.3a vaccine virus. They contained unique HA1 substitutions N171K, S312R and HA2 substitutions I77V and G155E compared to Bulgarian 3C.2a viruses of the previous season. All 20 B/Victoria-lineage viruses sequenced harboured two substitutions in the antigenic 120-loop region of HA, and 5 changes in NA, compared to the B/Brisbane/60/2008 vaccine virus. The results of this study reaffirm the continuous genetic variability of circulating seasonal influenza viruses and the need for continued systematic antigenic and molecular surveillance.
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MESH Headings
- Adolescent
- Adult
- Aged
- Amino Acid Sequence
- Amino Acid Substitution
- Antigens, Viral/genetics
- Bulgaria/epidemiology
- Child
- Child, Preschool
- Epidemiological Monitoring
- Female
- Hemagglutinin Glycoproteins, Influenza Virus/genetics
- Humans
- Infant
- Infant, Newborn
- Influenza A Virus, H1N1 Subtype/classification
- Influenza A Virus, H1N1 Subtype/genetics
- Influenza A Virus, H3N2 Subtype/classification
- Influenza A Virus, H3N2 Subtype/genetics
- Influenza, Human/epidemiology
- Influenza, Human/transmission
- Influenza, Human/virology
- Male
- Middle Aged
- Neuraminidase/genetics
- Phylogeny
- Seasons
- Sequence Analysis, DNA
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Affiliation(s)
- Neli Korsun
- National Laboratory "Influenza and ARD", National Centre of Infectious and Parasitic Diseases, 44A Stoletov Blvd, 1233 Sofia, Bulgaria.
| | - Svetla Angelova
- National Laboratory "Influenza and ARD", National Centre of Infectious and Parasitic Diseases, 44A Stoletov Blvd, 1233 Sofia, Bulgaria
| | - Viki Gregory
- WHO Collaborating Centre for Reference and Research on Influenza, Crick Worldwide Influenza Centre, The Francis Crick Institute, 1, Midland Road, London NW1 1AT, United Kingdom
| | - Rodney Daniels
- WHO Collaborating Centre for Reference and Research on Influenza, Crick Worldwide Influenza Centre, The Francis Crick Institute, 1, Midland Road, London NW1 1AT, United Kingdom
| | - Irina Georgieva
- National Laboratory "Influenza and ARD", National Centre of Infectious and Parasitic Diseases, 44A Stoletov Blvd, 1233 Sofia, Bulgaria
| | - John McCauley
- WHO Collaborating Centre for Reference and Research on Influenza, Crick Worldwide Influenza Centre, The Francis Crick Institute, 1, Midland Road, London NW1 1AT, United Kingdom
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Vogel U, Beermann S, Gerlich W, Hamouda O, Kempf VAJ, Slack M. Twenty years of National Reference and Consultant laboratories for infectious diseases in Germany. Int J Med Microbiol 2015; 305:591-4. [PMID: 26363622 DOI: 10.1016/j.ijmm.2015.08.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Affiliation(s)
- Ulrich Vogel
- University of Würzburg, Institute for Hygiene and Microbiology, National Reference Centre for Meningococci and Haemophilus influenzae, Josef-Schneider-Str. 2 (E1), 97080 Würzburg, Germany.
| | - Sandra Beermann
- Robert Koch Institute, Department of Infectious Diseases Epidemiology, Berlin, Germany
| | - Wolfram Gerlich
- Justus Liebig University Giessen, Institute for Medical Virology, National Reference Centre for Hepatitis B and D, Giessen, Germany
| | - Osamah Hamouda
- Robert Koch Institute, Department of Infectious Diseases Epidemiology, Berlin, Germany
| | - Volkhard A J Kempf
- University Hospital of Frankfurt am Main, Institute for Medical Microbiology and Infection Control, National Consultant Laboratory for Bartonella spp., Frankfurt am Main, Germany
| | - Mary Slack
- School of Medicine, Griffith University, Gold Coast Campus, Southport, QLD, Australia
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