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Zhang M, Zhou J, Ni R, Zhao X, Chen Y, Sun Y, Liu Z, Han X, Luo C, Fu X, Shao Y. Genomic Analyses Uncover Evolutionary Features of Influenza A/H3N2 Viruses in Yunnan Province, China, from 2017 to 2022. Viruses 2024; 16:138. [PMID: 38257838 PMCID: PMC10820241 DOI: 10.3390/v16010138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 01/13/2024] [Accepted: 01/16/2024] [Indexed: 01/24/2024] Open
Abstract
Influenza A viruses evolve at a high rate of nucleotide substitution, thereby requiring continuous monitoring to determine the efficacy of vaccines and antiviral drugs. In the current study, we performed whole-genome sequencing analyses of 253 influenza A/H3N2 strains from Yunnan Province, China, during 2017-2022. The hemagglutinin (HA) segments of Yunnan A/H3N2 strains isolated during 2017-2018 harbored a high genetic diversity due to heterogeneous distribution across branches. The mutation regularity of the predominant antigenic epitopes of HA segments in Yunnan was inconsistent in different years. Some important functional mutations in gene segments associated with viral adaptation and drug tolerance were revealed. The rapid genomic evolution of Yunnan A/H3N2 strains from 2017 to 2022 mainly concentrated on segments, i.e., matrix protein 2 (M2), non-structural protein 1 (NS1), neuraminidase (NA), NS2, and HA, with a high overall non-synonymous/synonymous substitution ratio (dN/dS). Our results highlighted a decline in vaccine efficacy against the A/H3N2 circulating strains, particularly against the Yunnan 2021-2022 A/H3N2 strains. These findings aid our understanding of evolutionary characteristics and epidemiological monitoring of the A/H3N2 viruses and provide in-depth insights into the protective efficacy of influenza vaccines.
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Affiliation(s)
- Meiling Zhang
- Department of Acute Infectious Diseases Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming 650022, China; (M.Z.); (J.Z.); (R.N.); (X.Z.); (Y.C.); (Y.S.); (Z.L.); (X.H.); (C.L.)
| | - Jienan Zhou
- Department of Acute Infectious Diseases Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming 650022, China; (M.Z.); (J.Z.); (R.N.); (X.Z.); (Y.C.); (Y.S.); (Z.L.); (X.H.); (C.L.)
| | - Ruize Ni
- Department of Acute Infectious Diseases Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming 650022, China; (M.Z.); (J.Z.); (R.N.); (X.Z.); (Y.C.); (Y.S.); (Z.L.); (X.H.); (C.L.)
| | - Xiaonan Zhao
- Department of Acute Infectious Diseases Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming 650022, China; (M.Z.); (J.Z.); (R.N.); (X.Z.); (Y.C.); (Y.S.); (Z.L.); (X.H.); (C.L.)
| | - Yaoyao Chen
- Department of Acute Infectious Diseases Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming 650022, China; (M.Z.); (J.Z.); (R.N.); (X.Z.); (Y.C.); (Y.S.); (Z.L.); (X.H.); (C.L.)
| | - Yanhong Sun
- Department of Acute Infectious Diseases Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming 650022, China; (M.Z.); (J.Z.); (R.N.); (X.Z.); (Y.C.); (Y.S.); (Z.L.); (X.H.); (C.L.)
| | - Zhaosheng Liu
- Department of Acute Infectious Diseases Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming 650022, China; (M.Z.); (J.Z.); (R.N.); (X.Z.); (Y.C.); (Y.S.); (Z.L.); (X.H.); (C.L.)
| | - Xiaoyu Han
- Department of Acute Infectious Diseases Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming 650022, China; (M.Z.); (J.Z.); (R.N.); (X.Z.); (Y.C.); (Y.S.); (Z.L.); (X.H.); (C.L.)
| | - Chunrui Luo
- Department of Acute Infectious Diseases Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming 650022, China; (M.Z.); (J.Z.); (R.N.); (X.Z.); (Y.C.); (Y.S.); (Z.L.); (X.H.); (C.L.)
| | - Xiaoqing Fu
- Department of Acute Infectious Diseases Control and Prevention, Yunnan Center for Disease Control and Prevention, Kunming 650022, China; (M.Z.); (J.Z.); (R.N.); (X.Z.); (Y.C.); (Y.S.); (Z.L.); (X.H.); (C.L.)
| | - Yong Shao
- State Key Laboratory of Genetic Resources and Evolution, Chinese Academy of Sciences, Kunming Institute of Zoology, Kunming 650201, China
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2
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Zhang Z, Li S, Zhu X, Hou J, Zhang H, Zhao B, Tian Z. Increased genetic variation of A(H3N2) virus from influenza surveillance at the end of the 2016/2017 season for Shanghai port, China. Sci Rep 2022; 12:17089. [PMID: 36224196 PMCID: PMC9556717 DOI: 10.1038/s41598-022-19228-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 08/25/2022] [Indexed: 01/04/2023] Open
Abstract
Influenza A(H3N2) virus exhibited complex seasonal patterns to evade pre-existing antibodies, resulting in changes in the antigenicity of the viron surface protein hemagglutinin (HA). To monitor the currently imported influenza viruses as well as to assess the capacity of health emergencies at the Shanghai port, we collected respiratory specimens of passengers from different countries and regions including some of Europe with influenza-like illness at the Shanghai port during 2016/2017, examined amino acid substitutions, and calculated the perfect-match vaccine efficacy using the p epitope model. Phylogenetic analysis of the HA genes revealed that influenza A(H3N2) viruses belonging to eight subclades were detected, and three amino acid substitutions in the subclade 3C.2a.4 were also added. Besides, two epidemic influenza virus strains were found in the 2016/2017 winter and 2016 summer. The results of lower predicted vaccine effectiveness in summer suggest that the imported A(H3N2) strains were not a good match for the A/Hong Kong/4801/2014 vaccine strain since the summer of 2017. Therefore, the Shanghai Port might stop the risk of the international spread of influenza for the first time, and curb the entry of A(H3N2) from overseas at the earliest stage of a probable influenza pandemic.
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Affiliation(s)
- Zilong Zhang
- Shanghai International Travel Healthcare Center, Shanghai, 200335 China ,Shanghai Customs District P.R.China, Shanghai, 200135 China
| | - Shenwei Li
- Shanghai International Travel Healthcare Center, Shanghai, 200335 China ,Shanghai Customs District P.R.China, Shanghai, 200135 China
| | - Xiaolin Zhu
- Shanghai BioGerm Medical Biotechnology Co., Ltd, Shanghai, 201401 China
| | - Jian Hou
- Shanghai Customs District P.R.China, Shanghai, 200135 China
| | - Hong Zhang
- Shanghai International Travel Healthcare Center, Shanghai, 200335 China ,Shanghai Customs District P.R.China, Shanghai, 200135 China
| | - Baihui Zhao
- grid.16821.3c0000 0004 0368 8293Bio-X Life Science Research Center, Shanghai Jiao Tong University, Shanghai, 200030 China ,Shanghai BioGerm Medical Biotechnology Co., Ltd, Shanghai, 201401 China
| | - Zhengan Tian
- Shanghai International Travel Healthcare Center, Shanghai, 200335 China ,Shanghai Customs District P.R.China, Shanghai, 200135 China
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Van Poelvoorde L, Vanneste K, De Keersmaecker SCJ, Thomas I, Van Goethem N, Van Gucht S, Saelens X, Roosens NHC. Whole-Genome Sequence Approach and Phylogenomic Stratification Improve the Association Analysis of Mutations With Patient Data in Influenza Surveillance. Front Microbiol 2022; 13:809887. [PMID: 35516436 PMCID: PMC9063638 DOI: 10.3389/fmicb.2022.809887] [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] [Received: 11/05/2021] [Accepted: 03/28/2022] [Indexed: 12/02/2022] Open
Abstract
Each year, seasonal influenza results in high mortality and morbidity. The current classification of circulating influenza viruses is mainly focused on the hemagglutinin gene. Whole-genome sequencing (WGS) enables tracking mutations across all influenza segments allowing a better understanding of the epidemiological effects of intra- and inter-seasonal evolutionary dynamics, and exploring potential associations between mutations across the viral genome and patient’s clinical data. In this study, mutations were identified in 253 Influenza A (H3N2) clinical isolates from the 2016-2017 influenza season in Belgium. As a proof of concept, available patient data were integrated with this genomic data, resulting in statistically significant associations that could be relevant to improve the vaccine and clinical management of infected patients. Several mutations were significantly associated with the sampling period. A new approach was proposed for exploring mutational effects in highly diverse Influenza A (H3N2) strains through considering the viral genetic background by using phylogenetic classification to stratify the samples. This resulted in several mutations that were significantly associated with patients suffering from renal insufficiency. This study demonstrates the usefulness of using WGS data for tracking mutations across the complete genome and linking these to patient data, and illustrates the importance of accounting for the viral genetic background in association studies. A limitation of this association study, especially when analyzing stratified groups, relates to the number of samples, especially in the context of national surveillance of small countries. Therefore, we investigated if international databases like GISAID may help to verify whether observed associations in the Belgium A (H3N2) samples, could be extrapolated to a global level. This work highlights the need to construct international databases with both information of viral genome sequences and patient data.
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Affiliation(s)
- Laura Van Poelvoorde
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
- National Influenza Centre, Sciensano, Brussels, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
| | - Kevin Vanneste
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
| | | | | | - Nina Van Goethem
- Public Health and Genome, Epidemiology and Public Health, Sciensano, Brussels, Belgium
| | | | - Xavier Saelens
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
| | - Nancy H. C. Roosens
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
- *Correspondence: Nancy H. C. Roosens,
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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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Influenza vaccine effectiveness within prospective cohorts of healthcare personnel in Israel and Peru 2016-2019. Vaccine 2021; 39:6956-6967. [PMID: 34509322 DOI: 10.1016/j.vaccine.2021.07.077] [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: 01/09/2021] [Revised: 06/29/2021] [Accepted: 07/28/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND There are limited data on influenza vaccine effectiveness (IVE) in preventing laboratory-confirmed influenza illness among healthcare personnel (HCP). METHODS HCP with direct patient contact working full-time in hospitals were followed during three influenza seasons in Israel (2016-2017 to 2018-2019) and Peru (2016 to 2018). Trivalent influenza vaccines were available at all sites, except during 2018-2019 when Israel used quadrivalent vaccines; vaccination was documented by electronic medical records, vaccine registries, and/or self-report (for vaccinations outside the hospital). Twice-weekly active surveillance identified acute respiratory symptoms or febrile illness (ARFI); self-collected respiratory specimens were tested by real-time reverse transcription polymerase chain reaction (PCR) assay. IVE was 100 × 1-hazard ratio (adjusted for sex, age, occupation, and hospital). RESULTS Among 5,489 HCP who contributed 10,041 person-seasons, influenza vaccination coverage was 47% in Israel and 32% in Peru. Of 3,056 ARFIs in Israel and 3,538 in Peru, A or B influenza virus infections were identified in 205 (7%) in Israel and 87 (2.5%) in Peru. IVE against all viruses across seasons was 1% (95% confidence interval [CI] = -30%, 25%) in Israel and 12% (95% CI = -61%, 52%) in Peru. CONCLUSION Estimates of IVE were null using person-time models during six study seasons in Israel and Peru.
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Drori Y, Pando R, Sefty H, Rosenberg A, Mendelson E, Keinan-Boker L, Shohat T, Mandelboim M, Glatman-Freedman A. Influenza vaccine effectiveness against laboratory-confirmed influenza in a vaccine-mismatched influenza B-dominant season. Vaccine 2020; 38:8387-8395. [PMID: 33243633 DOI: 10.1016/j.vaccine.2020.10.074] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 10/21/2020] [Accepted: 10/23/2020] [Indexed: 01/08/2023]
Abstract
BACKGROUND The 2017-2018 influenza season in Israel was characterized by the predominance of influenza B Yamagata, with a lesser circulation of influenza A(H1N1)pdm09 and influenza A(H3N2). We estimated vaccine effectiveness (VE) of the inactivated influenza vaccine which was selected for use that season. METHODS End-of-season VE and 95% confidence intervals (CI) against laboratory-confirmed influenza-like illness (ILI) were estimated by means of the test-negative design. Age-specific VE analysis was carried out using a moving age interval. RESULTS Specimen were obtained from 1,453 community ILI patients; 610 (42.0%) were influenza-positive, among which 69.7% were B, 17.2% A(H1N1)pdm09 and 13.4% A(H3N2). A 98.6% of molecularly characterized influenza B belonged to the Yamagata lineage. Of the sampled individuals, 1320 were suitable for VE analysis. Of those vaccinated, 90.6% received the inactivated trivalent influenza vaccine (TIV) containing a Victoria lineage influenza B-like virus. VE against influenza A differed by age, with the highest VE of 72.9% (95%CI 31.9-89.2%) observed in children 0.5-14 years old, while all ages VE was 46.6% (95%CI 10.4-68.2%). All ages VE against influenza B was 23.2% (95%CI -10.1-46.4%) with age-specific analysis showing non-significant VE estimates. Utilizing a moving age interval of 15 years, afforded a detailed age-specific insight into influenza VE against the influenza viruses circulating during the 2017-2018 season. CONCLUSIONS The moderate-high 2017-2018 influenza A VE among children and adolescents, supports seasonal influenza vaccination at a young age. The low VE against influenza B in Israel, is most likely the result of influenza B/TIV-mismatch.
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Affiliation(s)
- Y Drori
- Central Virology Laboratory, Chaim Sheba Medical Center, Israel Ministry of Health, Tel-Hashomer, Ramat Gan, Israel
| | - R Pando
- Central Virology Laboratory, Chaim Sheba Medical Center, Israel Ministry of Health, Tel-Hashomer, Ramat Gan, Israel; Israel Center for Disease Control, Ministry of Health, Tel Hashomer, Ramat Gan, Israel
| | - H Sefty
- Israel Center for Disease Control, Ministry of Health, Tel Hashomer, Ramat Gan, Israel
| | - A Rosenberg
- Israel Center for Disease Control, Ministry of Health, Tel Hashomer, Ramat Gan, Israel
| | - E Mendelson
- Central Virology Laboratory, Chaim Sheba Medical Center, Israel Ministry of Health, Tel-Hashomer, Ramat Gan, Israel; School of Public Health, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - L Keinan-Boker
- Israel Center for Disease Control, Ministry of Health, Tel Hashomer, Ramat Gan, Israel; School of Public Health, University of Haifa, Haifa, Israel
| | - T Shohat
- Israel Center for Disease Control, Ministry of Health, Tel Hashomer, Ramat Gan, Israel; School of Public Health, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - M Mandelboim
- Central Virology Laboratory, Chaim Sheba Medical Center, Israel Ministry of Health, Tel-Hashomer, Ramat Gan, Israel; School of Public Health, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - A Glatman-Freedman
- Israel Center for Disease Control, Ministry of Health, Tel Hashomer, Ramat Gan, Israel; School of Public Health, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.
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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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Shi W, Ke C, Fang S, Li J, Song H, Li X, Hu T, Wu J, Chen T, Yi L, Song Y, Wang X, Xing W, Huang W, Xiao H, Liang L, Peng B, Wu W, Liu H, Liu WJ, Holmes EC, Gao GF, Wang D. Co-circulation and persistence of multiple A/H3N2 influenza variants in China. Emerg Microbes Infect 2019; 8:1157-1167. [PMID: 31373538 PMCID: PMC6713139 DOI: 10.1080/22221751.2019.1648183] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The spread of influenza A/H3N2 variants possessing the hemagglutinin 121 K mutation and the unexpectedly high incidence of influenza in the 2017–2018 northern hemisphere influenza season have raised serious concerns about the next pandemic. We summarized the national surveillance data of seasonal influenza in China and identified marked differences in influenza epidemics between northern and southern China, particularly the predominating subtype and the presence of an additional summer peak in southern China. Notably, a minor spring peak of influenza caused by a different virus subtype was also observed. We also revealed that the 3C.2a lineage was dominant from the summer of 2015 to the end of the 2015–2016 peak season in China, after which the 3C.2a2 lineage predominated despite the importation and co-circulation of the 121 K variants of 3C.2a1 and 3C.2a3 lineages at the global level. Finally, an analysis based on genetic distances revealed a delay in A/H3N2 vaccine strain update. Overall, our results highlight the complicated circulation pattern of seasonal influenza in China and the necessity for a timely vaccine strain update worldwide.
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Affiliation(s)
- Weifeng Shi
- d Key Laboratory of Etiology and Epidemiology of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences , Taian , People's Republic of China
| | - Changwen Ke
- e Guangdong Provincial Center for Disease Control and Prevention , Guangzhou , People's Republic of China
| | - Shisong Fang
- f Division of Microbiology Test, Shenzhen Centre for Disease Control and Prevention , Shenzhen , People's Republic of China
| | - Juan Li
- d Key Laboratory of Etiology and Epidemiology of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences , Taian , People's Republic of China
| | - Hao Song
- g Chinese Academy of Sciences, Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science , Beijing , People's Republic of China
| | - Xiyan Li
- a 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.,b WHO Collaborating Center for Reference and Research on Influenza , Beijing , People's Republic of China.,c Key Laboratory for Medical Virology, National Health Commission , Beijing , People's Republic of China
| | - Tao Hu
- d Key Laboratory of Etiology and Epidemiology of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences , Taian , People's Republic of China
| | - Jie Wu
- e Guangdong Provincial Center for Disease Control and Prevention , Guangzhou , People's Republic of China
| | - Tao Chen
- a 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.,b WHO Collaborating Center for Reference and Research on Influenza , Beijing , People's Republic of China.,c Key Laboratory for Medical Virology, National Health Commission , Beijing , People's Republic of China
| | - Lina Yi
- e Guangdong Provincial Center for Disease Control and Prevention , Guangzhou , People's Republic of China.,h Guangdong Provincial Institution of Public Health, Guangdong Provincial Center for Disease Control and Prevention , Guangzhou , People's Republic of China
| | - Yingchao Song
- e Guangdong Provincial Center for Disease Control and Prevention , Guangzhou , People's Republic of China
| | - Xin Wang
- f Division of Microbiology Test, Shenzhen Centre for Disease Control and Prevention , Shenzhen , People's Republic of China
| | - Weijia Xing
- d Key Laboratory of Etiology and Epidemiology of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences , Taian , People's Republic of China
| | - Weijuan Huang
- a 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.,b WHO Collaborating Center for Reference and Research on Influenza , Beijing , People's Republic of China.,c Key Laboratory for Medical Virology, National Health Commission , Beijing , People's Republic of China
| | - Hong Xiao
- e Guangdong Provincial Center for Disease Control and Prevention , Guangzhou , People's Republic of China
| | - Lijun Liang
- e Guangdong Provincial Center for Disease Control and Prevention , Guangzhou , People's Republic of China
| | - Bo Peng
- f Division of Microbiology Test, Shenzhen Centre for Disease Control and Prevention , Shenzhen , People's Republic of China
| | - Weihua Wu
- f Division of Microbiology Test, Shenzhen Centre for Disease Control and Prevention , Shenzhen , People's Republic of China
| | - Hui Liu
- f Division of Microbiology Test, Shenzhen Centre for Disease Control and Prevention , Shenzhen , People's Republic of China
| | - William J Liu
- a 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.,b WHO Collaborating Center for Reference and Research on Influenza , Beijing , People's Republic of China.,c Key Laboratory for Medical Virology, National Health Commission , Beijing , People's Republic of China
| | - Edward C Holmes
- i Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney , Sydney , Australia
| | - George F Gao
- j Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences , Beijing , People's Republic of China.,k Center for Influenza Research and Early-Warning (CASCIRE), Chinese Academy of Sciences , Beijing , People's Republic of China.,l Chinese Center for Disease Control and Prevention (China CDC) , Beijing , People's Republic of China
| | - Dayan Wang
- a 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.,b WHO Collaborating Center for Reference and Research on Influenza , Beijing , People's Republic of China.,c Key Laboratory for Medical Virology, National Health Commission , Beijing , People's Republic of China
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9
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Njifon HLM, Monamele CG, Vernet MA, Njankouo MR, Deweerdt L, Nono R, Kenmoe S, Mbacham W, Njouom R. Genetic diversity of influenza A(H3N2) viruses in Northern Cameroon during the 2014-2016 influenza seasons. J Med Virol 2019; 91:1400-1407. [PMID: 30866072 DOI: 10.1002/jmv.25456] [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: 09/28/2018] [Revised: 02/05/2019] [Accepted: 02/06/2019] [Indexed: 12/11/2022]
Abstract
In Cameroon, genome characterization of influenza virus has been performed only in the Southern regions meanwhile genetic diversity of this virus varies with respect to locality. The Northern region characterized by a Sudan tropical climate might have distinct genetic characterization. This study aimed to better understand the genetic diversity of influenza A(H3N2) viruses circulating in Northern Cameroon. Sequences of three gene segments (hemagglutinin (HA), neuraminidase (NA) and matrix (M) genes) were obtained from 16 A(H3N2) virus strains collected during the 2014 to 2016 influenza seasons in Garoua. The HA gene segments were analysed with respect to reference strains while the NA and M gene was analysed for reported genetic markers of resistance to antivirals. Analysis of the HA sequences revealed that majority of the virus strains grouped together with the 2016-2017 vaccine strain (3C.2a-A/Hong Kong/4801/2014) while 3/5 (60%) of the 2015 viral strains grouped together with the 2015-2016 vaccine strain 3C.3a-A/Switzerland/9715293/2013. Within clade 3C.2a, Northern Cameroon sequences mostly grouped in sub-clade A3 (10/16). Analysis of the coding regions of the NA and M genes showed that none had genetic markers of resistance to neuraminidase inhibitors but all strains possessed the S31N substitution of resistance to amantadine. Due to some discrepancies observed in this region with respect to the Southern regions of Cameroon, there is necessity of including all regions within a country in the sentinel surveillance of influenza. These data will enable to track changes in influenza viruses in Cameroon.
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Affiliation(s)
- Hermann Landry Munshili Njifon
- National Influenza Centre, Centre Pasteur of Cameroon, Yaoundé, Cameroon, PO Box 1274, Yaoundé, Cameroon.,Centre Pasteur of Cameroon, Annex of Garoua, PO Box 921, Garoua, Cameroon.,Faculty of Science, University of Yaoundé 1, P.O Box 812, Yaoundé, Cameroon
| | - Chavely Gwladys Monamele
- National Influenza Centre, Centre Pasteur of Cameroon, Yaoundé, Cameroon, PO Box 1274, Yaoundé, Cameroon
| | - Marie-Astrid Vernet
- National Influenza Centre, Centre Pasteur of Cameroon, Yaoundé, Cameroon, PO Box 1274, Yaoundé, Cameroon
| | - Mohamadou Ripa Njankouo
- National Influenza Centre, Centre Pasteur of Cameroon, Yaoundé, Cameroon, PO Box 1274, Yaoundé, Cameroon
| | - Louis Deweerdt
- Centre Pasteur of Cameroon, Annex of Garoua, PO Box 921, Garoua, Cameroon
| | - Raphael Nono
- Centre Pasteur of Cameroon, Annex of Garoua, PO Box 921, Garoua, Cameroon
| | - Sebastien Kenmoe
- National Influenza Centre, Centre Pasteur of Cameroon, Yaoundé, Cameroon, PO Box 1274, Yaoundé, Cameroon
| | - Wilfred Mbacham
- Faculty of Science, University of Yaoundé 1, P.O Box 812, Yaoundé, Cameroon
| | - Richard Njouom
- National Influenza Centre, Centre Pasteur of Cameroon, Yaoundé, Cameroon, PO Box 1274, Yaoundé, Cameroon
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10
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Kuypers J, Chu HY, Gaydos CA, Katz J, Khatry SK, LeClerq SC, Tielsch JM, Steinhoff MC, Englund JA. Molecular characterization of influenza viruses from women and infants in Sarlahi, Nepal. Diagn Microbiol Infect Dis 2018; 93:305-310. [PMID: 30528424 DOI: 10.1016/j.diagmicrobio.2018.11.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 10/30/2018] [Accepted: 11/07/2018] [Indexed: 11/30/2022]
Abstract
We used RT-PCR-electrospray ionization-mass spectrometry to identify subtypes and strains of influenza viruses detected during a maternal influenza immunization study in Nepal from May 2011 to April 2014. Hemagglutinin (HA) gene amino acid (aa) sequences of inferred reference strains were compared to those of the vaccines to determine impact of aa relatedness on vaccine efficacy (VE) and disease severity. Three influenza subtypes and many strains were identified. A(H3N2) strains with less than 13 aa differences in HA compared to vaccine strains (matched) showed higher VE than strains with 13 or more differences (mismatched). Yamagata lineage B strains, which were mismatched to the Victoria strain in the vaccine, demonstrated lower VE compared to Victoria strains. Differences in VE were not statistically significant. All A(H1N1pdm) matched the vaccine strain, with 10 or fewer aa differences. Except for women infected with vaccine-matched strains of influenza A, clinical signs and symptoms did not differ between vaccinated and unvaccinated participants.
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Affiliation(s)
- Jane Kuypers
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA.
| | - Helen Y Chu
- Department of Medicine, University of Washington, Seattle, WA, USA
| | | | - Joanne Katz
- Department of International Health, Johns Hopkins University, Baltimore, MD, USA
| | | | - Steven C LeClerq
- Department of International Health, Johns Hopkins University, Baltimore, MD, USA; Nepal Nutrition Intervention Project, Kathmandu, Nepal
| | - James M Tielsch
- Department of Global Health, George Washington University, Washington, DC, USA
| | - Mark C Steinhoff
- Global Health Center, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Janet A Englund
- Seattle Children's Hospital and Research Foundation, University of Washington, Seattle, WA, USA
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11
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Korenkov DA, Laurie KL, Reading PC, Carolan LA, Chan KF, Isakova-Sivak II, Smolonogina TA, Subbarao K, Barr IG, Villanueva J, Shcherbik S, Bousse T, Rudenko LG. Safety, immunogenicity and protection of A(H3N2) live attenuated influenza vaccines containing wild-type nucleoprotein in a ferret model. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2018; 64:95-104. [PMID: 29929009 PMCID: PMC6330673 DOI: 10.1016/j.meegid.2018.06.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 06/14/2018] [Accepted: 06/16/2018] [Indexed: 11/21/2022]
Abstract
Live attenuated influenza vaccines (LAIVs) are promising tools for the induction of broad protection from influenza due to their ability to stimulate cross-reactive T cells against influenza pathogens. One of the major targets for cytotoxic T-cell immunity is viral nucleoprotein (NP), which is relatively conserved among antigenically distant influenza viruses. Nevertheless, a diversity of epitope composition has been found in the NP protein of different lineages of influenza A viruses. The H2N2 master donor virus which is currently used as a backbone for the LAIV and donor of the six genomic segments encoding the internal proteins, A/Leningrad/134/17/57 (MDV Len/17), was isolated 60 years ago. As such, NP-specific T-cell immunity induced upon vaccination with classical LAIVs with a 6:2 genome composition containing this older NP might be suboptimal against currently circulating influenza viruses. In this study, a panel of H3N2 LAIV candidates with wild-type NP genes derived from circulating viruses were generated by reverse genetics (5:3 genome composition). These viruses displayed the cold adaptation and temperature sensitivity phenotypes of MDV Len/17 in vitro. LAIVs with both 6:2 and 5:3 genome compositions were attenuated and replicated to a similar extent in the upper respiratory tract of ferrets. LAIVs were immunogenic as high neutralizing and hemagglutination inhibition serum antibody titers were detected 21 days after infection. All vaccinated animals were protected against infection with heterologous H3N2 influenza A viruses. Thus, LAIV with a 5:3 genome composition is safe, immunogenic and can induce cross-protective immunity.
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MESH Headings
- Animal Diseases/immunology
- Animal Diseases/prevention & control
- Animal Diseases/virology
- Animals
- Antibodies, Neutralizing/blood
- Antibodies, Neutralizing/immunology
- Antibodies, Viral/blood
- Antibodies, Viral/immunology
- Disease Models, Animal
- Female
- Ferrets
- Genome, Viral
- Immunogenicity, Vaccine
- Influenza A Virus, H3N2 Subtype/genetics
- Influenza A Virus, H3N2 Subtype/immunology
- Influenza Vaccines/adverse effects
- Influenza Vaccines/genetics
- Influenza Vaccines/immunology
- Male
- Neutralization Tests
- Nucleoproteins/genetics
- Nucleoproteins/immunology
- Orthomyxoviridae Infections/veterinary
- Vaccination
- Vaccines, Attenuated/adverse effects
- Vaccines, Attenuated/genetics
- Vaccines, Attenuated/immunology
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Affiliation(s)
- Daniil A Korenkov
- Department of Virology, Institute of Experimental Medicine, 12, acad. Pavlova street, Saint Petersburg, Russia.
| | - Karen L Laurie
- WHO Collaborating Centre for Reference and Research on Influenza, Victorian Infectious Diseases Reference Laboratory at The Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
| | - Patrick C Reading
- WHO Collaborating Centre for Reference and Research on Influenza, Victorian Infectious Diseases Reference Laboratory at The Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
| | - Louise A Carolan
- WHO Collaborating Centre for Reference and Research on Influenza, Victorian Infectious Diseases Reference Laboratory at The Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
| | - Kok Fei Chan
- WHO Collaborating Centre for Reference and Research on Influenza, Victorian Infectious Diseases Reference Laboratory at The Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
| | - Irina I Isakova-Sivak
- Department of Virology, Institute of Experimental Medicine, 12, acad. Pavlova street, Saint Petersburg, Russia
| | - Tatiana A Smolonogina
- Department of Virology, Institute of Experimental Medicine, 12, acad. Pavlova street, Saint Petersburg, Russia
| | - Kanta Subbarao
- WHO Collaborating Centre for Reference and Research on Influenza, Victorian Infectious Diseases Reference Laboratory at The Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
| | - Ian G Barr
- WHO Collaborating Centre for Reference and Research on Influenza, Victorian Infectious Diseases Reference Laboratory at The Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
| | | | | | - Tatiana Bousse
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Larisa G Rudenko
- Department of Virology, Institute of Experimental Medicine, 12, acad. Pavlova street, Saint Petersburg, Russia
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12
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Pando R, Sharabi S, Mandelboim M. Exceptional influenza morbidity in summer season of 2017 in Israel may predict the vaccine efficiency in the coming winter. Vaccine 2018; 36:1326-1329. [PMID: 29429813 DOI: 10.1016/j.vaccine.2018.01.085] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 01/17/2018] [Accepted: 01/28/2018] [Indexed: 10/18/2022]
Abstract
Influenza infections are the leading cause of respiratory viral infections worldwide, and are mostly common in the winter season. The seasonal influenza vaccine is currently the most effective preventive modality against influenza infection. Immediately following each winter season the World Health Organization (WHO) announces the vaccine composition for the following winter. Unexpectedly, during the summer of 2017, in Israel, we observed in hospitalized patients, an exceptionally high numbers of Influenza positive cases. The majority of the influenza B infections were caused by influenza B/Yamagata lineage, which did not circulate in Israel in the previous winter, and most of the influenza A infections were caused by influenza A/H3N2, a strain similar to the strain that circulated in Israel in the previous winter. We therefore predict that these two viruses will circulate in the coming winter of 2017/18 and that the trivalent vaccine, which includes antigenically different viruses will be inefficient.
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Affiliation(s)
- Rakefet Pando
- The Israel Center for Disease Control, Israel Ministry of Health, Tel-Hashomer, Israel; Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel
| | - Sivan Sharabi
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel; Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Michal Mandelboim
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel; Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel.
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13
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Humoral immunity to influenza in an at-risk population and severe influenza cases in Russia in 2016-2017. Arch Virol 2018; 163:2675-2685. [PMID: 29872951 DOI: 10.1007/s00705-018-3904-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Accepted: 04/19/2018] [Indexed: 12/19/2022]
Abstract
This work aimed to analyze the herd immunity to influenza among a Russian population living in regions with an increased risk of emergence of viruses with pandemic potential, and to isolate and investigate virus strains from severe influenza cases, including fatal cases, during the 2016-2017 epidemic season. In November 2016 - March 2017 highly pathogenic influenza outbreaks were registered in Russia among wild birds and poultry. No cases of human infection were registered. Analysis of 760 sera from people who had contact with infected or perished birds revealed the presence of antibodies to A(H5N1) virus of clade 2.3.2.1c and A(H5N8) virus of clade 2.3.4.4. The 2016-2017 influenza epidemic season in Russia began in weeks 46-47 of 2016 with predominant circulation of influenza A(H3N2) viruses. Strains isolated from severe influenza cases mainly belonged to 3C.2a.2 and 3C.2a.3 genetic groups. Up to the 8th week of 2017 severe influenza cases were often caused by influenza B viruses which belonged to 1A genetic group with antigenic properties similar to B/Brisbane/60/2008. All influenza A and B virus strains isolated in the 2016-2017 epidemic season were sensitive to oseltamivir and zanamivir.
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14
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Tsou TP, Su CP, Huang WT, Yang JR, Liu MT. Influenza A(H3N2) virus variants and patient characteristics during a summer influenza epidemic in Taiwan, 2017. ACTA ACUST UNITED AC 2018; 22. [PMID: 29258649 PMCID: PMC5743095 DOI: 10.2807/1560-7917.es.2017.22.50.17-00767] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report a summer influenza epidemic caused by co-circulation of multiple influenza A(H3N2) variants in clade 3C.2a. Compared with other clades, a putative clade 3C.2a.3a was more commonly isolated from severely ill patients; 3C.2a.4 was more commonly isolated in outbreak cases. Time from vaccination to illness onset was significantly shorter in severely ill patients infected with clade 3C.2a.3; characteristics and outcomes of patients infected with different clades were similar. No resistance to antiviral medications was found.
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Affiliation(s)
- Tsung-Pei Tsou
- Division of Preparedness and Emerging Infectious Diseases, Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan
| | - Chia-Ping Su
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan.,Office of Preventive Medicine, Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan
| | - Wan-Ting Huang
- Office of Preventive Medicine, Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan
| | - Ji-Rong Yang
- Center for Research, Diagnostics and Vaccine Development, Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan
| | - Ming-Tsan Liu
- Center for Research, Diagnostics and Vaccine Development, Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan
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15
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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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16
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Yang JR, Hsu SZ, Kuo CY, Huang HY, Huang TY, Wang HC, Liu MT. An epidemic surge of influenza A(H3N2) virus at the end of the 2016-2017 season in Taiwan with an increased viral genetic heterogeneity. J Clin Virol 2017; 99-100:15-21. [PMID: 29278832 DOI: 10.1016/j.jcv.2017.12.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 12/04/2017] [Accepted: 12/21/2017] [Indexed: 11/29/2022]
Abstract
BACKGROUND The epidemic of the 2016-2017 influenza season in Taiwan started early with moderate activity and was predominated by the influenza A(H3N2) virus. However, the influenza activity increased dramatically during the late stage of the 2016-2017 season. OBJECTIVES The genetic and antigenic characteristics of the influenza A(H3N2) virus circulating in Taiwan during the 2016-2017 season were investigated. The relationship between virus clades and the patients' 2016-2017 vaccination histories was determined. STUDY DESIGN Respiratory samples from patients with influenza-like illness in the community, clustered outbreaks, and inpatients with severe complications were tested for influenza virus. Influenza gene sequencing, phylogenetic analysis and hemagglutination inhibition assay were performed. RESULTS A total of 1185, 690 and 353 cases of outpatients, inpatients and cluster events were tested positive for the A(H3N2) virus in this report. Multiple clades of the H3N2 virus co-circulated. New genetic variants were detected, including clade 3C.2a.1 with additional N121 K, K92R or T135 K mutations, 3C.2a.3a with T135 K and R150 K mutations and 3C.2a.4. The proportions of N121 K and T135 K mutations were continuously increasing. Most of the viruses (85.4%, 111/130) were antigenically related to the current vaccine strain. Infection by different clade H3N2 viruses did not correlate with immunization with the 2016-2017 vaccine. CONCLUSIONS The data in this study indicate that antigenic drift is not the primary determinant of the epidemic wave at the end of the 2016-2017 season. The fitness changes in new variants, waning immunity and climatic changes are considered as possible contributors to the resurgence of the influenza A(H3N2) virus.
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Affiliation(s)
- Ji-Rong Yang
- Centers for Disease Control, Taipei, Taiwan, ROC
| | - Shu-Zhen Hsu
- Centers for Disease Control, Taipei, Taiwan, ROC
| | - Chuan-Yi Kuo
- Centers for Disease Control, Taipei, Taiwan, ROC
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17
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Genetic and antigenic divergence in the influenza A(H3N2) virus circulating between 2016 and 2017 in Thailand. PLoS One 2017; 12:e0189511. [PMID: 29252990 PMCID: PMC5734729 DOI: 10.1371/journal.pone.0189511] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 11/28/2017] [Indexed: 12/23/2022] Open
Abstract
Influenza virus evolves rapidly due to the accumulated genetic variations on the viral sequence. Unlike in North America and Europe, influenza season in the tropical Southeast Asia spans both the rainy and cool seasons. Thus, influenza epidemiology and viral evolution sometimes differ from other regions, which affect the ever-changing efficacy of the vaccine. To monitor the current circulating influenza viruses in this region, we determined the predominant influenza virus strains circulating in Thailand between January 2016 and June 2017 by screening 7,228 samples from patients with influenza-like illness. During this time, influenza A(H3N2) virus was the predominant influenza virus detected. We then phylogenetically compared the hemagglutinin (HA) gene from a subset of these A(H3N2) strains (n = 62) to the reference sequences and evaluated amino acid changes in the dominant antigenic epitopes on the HA protein structure. The divergence of the circulating A(H3N2) from the A/Hong Kong/4801/2014 vaccine strain formed five genetic groups (designated I to V) within the 3C.2a clade. Our results suggest a marked drift of the current circulating A(H3N2) strains in Thailand, which collectively contributed to the declining predicted vaccine effectiveness (VE) from 74% in 2016 down to 48% in 2017.
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18
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Stein Y, Mandelboim M, Sefty H, Pando R, Mendelson E, Shohat T, Glatman-Freedman A, Muhamed A, Arkadi A, Yoav A, Shlomo A, Galab A, Lev D, Akiva F, Michael G, Ali HD, Kamil H, Yael H, Ella K, Angela K, Yoseph L, Tali L, Alexander L, Nadia MW, Nir M, Oded M, Idit M, Margarita N, Shiri PM, Karen R, Nirit S, Eva S, Rephael S, Paul S, Ronen Y, Ran Z. Seasonal Influenza Vaccine Effectiveness in Preventing Laboratory-Confirmed Influenza in Primary Care in Israel, 2016–2017 Season: Insights Into Novel Age-Specific Analysis. Clin Infect Dis 2017; 66:1383-1391. [DOI: 10.1093/cid/cix1013] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 11/13/2017] [Indexed: 01/24/2023] Open
Affiliation(s)
- Yaniv Stein
- Israel Center for Disease Control, Israel Ministry of Health, Tel-Hashomer, Tel Aviv University, Israel
| | - Michal Mandelboim
- Central Virology Laboratory, Israel Ministry of Health, Chaim Sheba Medical Center, Tel-Hashomer, Tel Aviv University, Israel
- Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel Aviv University, Israel
| | - Hanna Sefty
- Israel Center for Disease Control, Israel Ministry of Health, Tel-Hashomer, Tel Aviv University, Israel
| | - Rakefet Pando
- Central Virology Laboratory, Israel Ministry of Health, Chaim Sheba Medical Center, Tel-Hashomer, Tel Aviv University, Israel
| | - Ella Mendelson
- Central Virology Laboratory, Israel Ministry of Health, Chaim Sheba Medical Center, Tel-Hashomer, Tel Aviv University, Israel
- Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel Aviv University, Israel
| | - Tamy Shohat
- Israel Center for Disease Control, Israel Ministry of Health, Tel-Hashomer, Tel Aviv University, Israel
- Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel Aviv University, Israel
| | - Aharona Glatman-Freedman
- Israel Center for Disease Control, Israel Ministry of Health, Tel-Hashomer, Tel Aviv University, Israel
- Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel Aviv University, Israel
- Departments of Pediatrics and Family and Community Medicine, New York Medical College, Valhalla
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