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Owuor DC, de Laurent ZR, Nyawanda BO, Emukule GO, Kondor R, Barnes JR, Nokes DJ, Agoti CN, Chaves SS. Genetic and potential antigenic evolution of influenza A(H1N1)pdm09 viruses circulating in Kenya during 2009-2018 influenza seasons. Sci Rep 2023; 13:22342. [PMID: 38102198 PMCID: PMC10724140 DOI: 10.1038/s41598-023-49157-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 12/05/2023] [Indexed: 12/17/2023] Open
Abstract
Influenza viruses undergo rapid evolutionary changes, which requires continuous surveillance to monitor for genetic and potential antigenic changes in circulating viruses that can guide control and prevention decision making. We sequenced and phylogenetically analyzed A(H1N1)pdm09 virus genome sequences obtained from specimens collected from hospitalized patients of all ages with or without pneumonia between 2009 and 2018 from seven sentinel surveillance sites across Kenya. We compared these sequences with recommended vaccine strains during the study period to infer genetic and potential antigenic changes in circulating viruses and associations of clinical outcome. We generated and analyzed a total of 383 A(H1N1)pdm09 virus genome sequences. Phylogenetic analyses of HA protein revealed that multiple genetic groups (clades, subclades, and subgroups) of A(H1N1)pdm09 virus circulated in Kenya over the study period; these evolved away from their vaccine strain, forming clades 7 and 6, subclades 6C, 6B, and 6B.1, and subgroups 6B.1A and 6B.1A1 through acquisition of additional substitutions. Several amino acid substitutions among circulating viruses were associated with continued evolution of the viruses, especially in antigenic epitopes and receptor binding sites (RBS) of circulating viruses. Disease severity declined with an increase in age among children aged < 5 years. Our study highlights the necessity of timely genomic surveillance to monitor the evolutionary changes of influenza viruses. Routine influenza surveillance with broad geographic representation and whole genome sequencing capacity to inform on prioritization of antigenic analysis and the severity of circulating strains are critical to improved selection of influenza strains for inclusion in vaccines.
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Affiliation(s)
- D Collins Owuor
- Epidemiology and Demography Department, Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi, Kenya.
| | - Zaydah R de Laurent
- Epidemiology and Demography Department, Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - Gideon O Emukule
- Influenza Division, Centers for Disease Control and Prevention, Nairobi, Kenya
| | - Rebecca Kondor
- Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - John R Barnes
- Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - D James Nokes
- Epidemiology and Demography Department, Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi, Kenya
- School of Life Sciences and Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, Coventry, UK
| | - Charles N Agoti
- Epidemiology and Demography Department, Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi, Kenya
- School of Public Health and Human Sciences, Pwani University, Kilifi, Kenya
| | - Sandra S Chaves
- Influenza Division, Centers for Disease Control and Prevention, Nairobi, Kenya
- Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention, Atlanta, GA, USA
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2
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Nabakooza G, Owuor DC, de Laurent ZR, Galiwango R, Owor N, Kayiwa JT, Jjingo D, Agoti CN, Nokes DJ, Kateete DP, Kitayimbwa JM, Frost SDW, Lutwama JJ. Phylogenomic analysis uncovers a 9-year variation of Uganda influenza type-A strains from the WHO-recommended vaccines and other Africa strains. Sci Rep 2023; 13:5516. [PMID: 37015946 PMCID: PMC10072032 DOI: 10.1038/s41598-023-30667-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 02/28/2023] [Indexed: 04/06/2023] Open
Abstract
Genetic characterisation of circulating influenza viruses directs annual vaccine strain selection and mitigation of infection spread. We used next-generation sequencing to locally generate whole genomes from 116 A(H1N1)pdm09 and 118 A(H3N2) positive patient swabs collected across Uganda between 2010 and 2018. We recovered sequences from 92% (215/234) of the swabs, 90% (193/215) of which were whole genomes. The newly-generated sequences were genetically and phylogenetically compared to the WHO-recommended vaccines and other Africa strains sampled since 1994. Uganda strain hemagglutinin (n = 206), neuraminidase (n = 207), and matrix protein (MP, n = 213) sequences had 95.23-99.65%, 95.31-99.79%, and 95.46-100% amino acid similarity to the 2010-2020 season vaccines, respectively, with several mutated hemagglutinin antigenic, receptor binding, and N-linked glycosylation sites. Uganda influenza type-A virus strains sequenced before 2016 clustered uniquely while later strains mixed with other Africa and global strains. We are the first to report novel A(H1N1)pdm09 subclades 6B.1A.3, 6B.1A.5(a,b), and 6B.1A.6 (± T120A) that circulated in Eastern, Western, and Southern Africa in 2017-2019. Africa forms part of the global influenza ecology with high viral genetic diversity, progressive antigenic drift, and local transmissions. For a continent with inadequate health resources and where social distancing is unsustainable, vaccination is the best option. Hence, African stakeholders should prioritise routine genome sequencing and analysis to direct vaccine selection and virus control.
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Affiliation(s)
- Grace Nabakooza
- Department of Immunology and Molecular Biology, Makerere University, Kampala, Uganda.
- Makerere University/UVRI Centre of Excellence in Infection and Immunity Research and Training (MUII-Plus), Uganda Virus Research Institute (UVRI), Entebbe, Uganda.
- Centre for Computational Biology, Uganda Christian University, Mukono, Uganda.
- Oak Ridge Institute for Science and Education, Bioinformatics Research Fellow to the Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States.
| | - D Collins Owuor
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Zaydah R de Laurent
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Ronald Galiwango
- Makerere University/UVRI Centre of Excellence in Infection and Immunity Research and Training (MUII-Plus), Uganda Virus Research Institute (UVRI), Entebbe, Uganda
- Centre for Computational Biology, Uganda Christian University, Mukono, Uganda
- The African Center of Excellence in Bioinformatics and Data Intensive Sciences (ACE), Infectious Diseases Institute, Makerere University, Kampala, Uganda
| | - Nicholas Owor
- Department of Arbovirology Emerging and Re-Emerging Infectious Diseases, Uganda Virus Research Institute (UVRI), Entebbe, Uganda
| | - John T Kayiwa
- Department of Arbovirology Emerging and Re-Emerging Infectious Diseases, Uganda Virus Research Institute (UVRI), Entebbe, Uganda
| | - Daudi Jjingo
- The African Center of Excellence in Bioinformatics and Data Intensive Sciences (ACE), Infectious Diseases Institute, Makerere University, Kampala, Uganda
- Department of Computer Science, College of Computing, Makerere University, Kampala, Uganda
| | - Charles N Agoti
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - D James Nokes
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- School of Life Sciences and Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, Coventry, United Kingdom
| | - David P Kateete
- Department of Immunology and Molecular Biology, Makerere University, Kampala, Uganda
- Makerere University/UVRI Centre of Excellence in Infection and Immunity Research and Training (MUII-Plus), Uganda Virus Research Institute (UVRI), Entebbe, Uganda
| | - John M Kitayimbwa
- Makerere University/UVRI Centre of Excellence in Infection and Immunity Research and Training (MUII-Plus), Uganda Virus Research Institute (UVRI), Entebbe, Uganda
- Centre for Computational Biology, Uganda Christian University, Mukono, Uganda
| | - Simon D W Frost
- Microsoft Research, Redmond, Washington, 98052, United States
- London School of Hygiene and Tropical Medicine (LSHTM), Keppel St, Bloomsbury, London, United Kingdom
| | - Julius J Lutwama
- Department of Arbovirology Emerging and Re-Emerging Infectious Diseases, Uganda Virus Research Institute (UVRI), Entebbe, Uganda
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Soga T, Duong C, Pattinson D, Sakai-Tagawa Y, Tokita A, Izumida N, Nishino T, Hagiwara H, Wada N, Miyamoto Y, Kuroki H, Hayashi Y, Seki M, Kasuya N, Koga M, Adachi E, Iwatsuki-Horimoto K, Yotsuyanagi H, Yamayoshi S, Kawaoka Y. Characterization of Influenza A(H1N1)pdm09 Viruses Isolated in the 2018-2019 and 2019-2020 Influenza Seasons in Japan. Viruses 2023; 15:v15020535. [PMID: 36851749 PMCID: PMC9968111 DOI: 10.3390/v15020535] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/09/2023] [Accepted: 02/09/2023] [Indexed: 02/17/2023] Open
Abstract
The influenza A(H1N1)pdm09 virus that emerged in 2009 causes seasonal epidemic worldwide. The virus acquired several amino acid substitutions that were responsible for antigenic drift until the 2018-2019 influenza season. Viruses possessing mutations in the NA and PA proteins that cause reduced susceptibility to NA inhibitors and baloxavir marboxil, respectively, have been detected after antiviral treatment, albeit infrequently. Here, we analyzed HA, NA, and PA sequences derived from A(H1N1)pdm09 viruses that were isolated during the 2018-2019 and 2019-2020 influenza seasons in Japan. We found that A(H1N1)pdm09 viruses possessing the D187A and Q189E substitutions in HA emerged and dominated during the 2019-2020 season; these substitutions in the antigenic site Sb, a high potency neutralizing antibody-eliciting site for humans, changed the antigenicity of A(H1N1)pdm09 viruses. Furthermore, we found that isolates possessing the N156K substitution, which was predicted to affect the antigenicity of A(H1N1)pdm09 virus at the laboratory level, were detected at a frequency of 1.0% in the 2018-2019 season but 10.1% in the 2019-2020 season. These findings indicate that two kinds of antigenically drifted viruses-N156K and D187A/Q189E viruses-co-circulated during the 2019-2020 influenza season in Japan.
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Affiliation(s)
- Takuma Soga
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Calvin Duong
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - David Pattinson
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Yuko Sakai-Tagawa
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Akifumi Tokita
- Tokyo Pediatric Association Public Health Committee, Saitama 331-0815, Japan
- Clinic Bambini, Tokyo 108-0071, Japan
| | - Naomi Izumida
- Tokyo Pediatric Association Public Health Committee, Saitama 331-0815, Japan
- Akebonocho Clinic, Tokyo 120-0023, Japan
| | - Tamon Nishino
- Tokyo Pediatric Association Public Health Committee, Saitama 331-0815, Japan
- Alpaca Kids ENT Clinic, Tokyo 171-0052, Japan
| | - Haruhisa Hagiwara
- Tokyo Pediatric Association Public Health Committee, Saitama 331-0815, Japan
- Hagiwara Clinic, Tokyo 173-0016, Japan
| | - Noriyuki Wada
- Tokyo Pediatric Association Public Health Committee, Saitama 331-0815, Japan
- Wada Pediatric Clinic, Tokyo 121-0812, Japan
| | | | | | - Yuka Hayashi
- Saitama Citizens Medical Center, Saitama 331-0054, Japan
| | - Masafumi Seki
- Division of Infectious Diseases and Infection Control, Tohoku Medical and Pharmaceutical University, Sendai 983-8536, Japan
| | | | - Michiko Koga
- Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Eisuke Adachi
- Department of Infectious Diseases and Applied Immunology, IMSUT Hospital of the Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | | | - Hiroshi Yotsuyanagi
- Department of Infectious Diseases and Applied Immunology, IMSUT Hospital of the Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Seiya Yamayoshi
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
- Department of Special Pathogens, International Research Center for Infectious Diseases, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
- Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo 162-8655, Japan
- Correspondence: (S.Y.); (Y.K.)
| | - Yoshihiro Kawaoka
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Special Pathogens, International Research Center for Infectious Diseases, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
- Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo 162-8655, Japan
- The University of Tokyo Pandemic Preparedness, Infection and Advanced Research Center (UTOPIA), Minato-ku, Tokyo 108-8639, Japan
- Correspondence: (S.Y.); (Y.K.)
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Nabakooza G, Galiwango R, Frost SDW, Kateete DP, Kitayimbwa JM. Molecular Epidemiology and Evolutionary Dynamics of Human Influenza Type-A Viruses in Africa: A Systematic Review. Microorganisms 2022; 10:900. [PMID: 35630344 PMCID: PMC9145646 DOI: 10.3390/microorganisms10050900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 03/21/2022] [Accepted: 03/22/2022] [Indexed: 02/01/2023] Open
Abstract
Genomic characterization of circulating influenza type-A viruses (IAVs) directs the selection of appropriate vaccine formulations and early detection of potentially pandemic virus strains. However, longitudinal data on the genomic evolution and transmission of IAVs in Africa are scarce, limiting Africa's benefits from potential influenza control strategies. We searched seven databases: African Journals Online, Embase, Global Health, Google Scholar, PubMed, Scopus, and Web of Science according to the PRISMA guidelines for studies that sequenced and/or genomically characterized Africa IAVs. Our review highlights the emergence and diversification of IAVs in Africa since 1993. Circulating strains continuously acquired new amino acid substitutions at the major antigenic and potential N-linked glycosylation sites in their hemagglutinin proteins, which dramatically affected vaccine protectiveness. Africa IAVs phylogenetically mixed with global strains forming strong temporal and geographical evolution structures. Phylogeographic analyses confirmed that viral migration into Africa from abroad, especially South Asia, Europe, and North America, and extensive local viral mixing sustained the genomic diversity, antigenic drift, and persistence of IAVs in Africa. However, the role of reassortment and zoonosis remains unknown. Interestingly, we observed substitutions and clades and persistent viral lineages unique to Africa. Therefore, Africa's contribution to the global influenza ecology may be understated. Our results were geographically biased, with data from 63% (34/54) of African countries. Thus, there is a need to expand influenza surveillance across Africa and prioritize routine whole-genome sequencing and genomic analysis to detect new strains early for effective viral control.
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Affiliation(s)
- Grace Nabakooza
- Department of Immunology and Molecular Biology, Makerere University, Old Mulago Hill Road, P.O. Box 7072, Kampala 256, Uganda
- UVRI Centre of Excellence in Infection and Immunity Research and Training (MUII-Plus), Makerere University, Plot No: 51-59 Nakiwogo Road, P.O. Box 49, Entebbe 256, Uganda
| | - Ronald Galiwango
- UVRI Centre of Excellence in Infection and Immunity Research and Training (MUII-Plus), Makerere University, Plot No: 51-59 Nakiwogo Road, P.O. Box 49, Entebbe 256, Uganda
- Centre for Computational Biology, Uganda Christian University, Plot 67-173, Bishop Tucker Road, P.O. Box 4, Mukono 256, Uganda
- African Center of Excellence in Bioinformatics and Data Intensive Sciences, Infectious Diseases Institute, Makerere University, Kampala 256, Uganda
| | - Simon D W Frost
- Microsoft Research, Redmond, 14820 NE 36th Street, Washington, DC 98052, USA
- London School of Hygiene & Tropical Medicine (LSHTM), University of London, Keppel Street, Bloomsbury, London WC1E7HT, UK
| | - David P Kateete
- Department of Immunology and Molecular Biology, Makerere University, Old Mulago Hill Road, P.O. Box 7072, Kampala 256, Uganda
- UVRI Centre of Excellence in Infection and Immunity Research and Training (MUII-Plus), Makerere University, Plot No: 51-59 Nakiwogo Road, P.O. Box 49, Entebbe 256, Uganda
| | - John M Kitayimbwa
- UVRI Centre of Excellence in Infection and Immunity Research and Training (MUII-Plus), Makerere University, Plot No: 51-59 Nakiwogo Road, P.O. Box 49, Entebbe 256, Uganda
- Centre for Computational Biology, Uganda Christian University, Plot 67-173, Bishop Tucker Road, P.O. Box 4, Mukono 256, Uganda
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Zolotarova O, Fesenko A, Holubka O, Radchenko L, Bortz E, Budzanivska I, Mironenko A. Genotypic Variants of Pandemic H1N1 Influenza A Viruses Isolated from Severe Acute Respiratory Infections in Ukraine during the 2015/16 Influenza Season. Viruses 2021; 13:2125. [PMID: 34834932 PMCID: PMC8619959 DOI: 10.3390/v13112125] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 10/05/2021] [Accepted: 10/15/2021] [Indexed: 01/15/2023] Open
Abstract
Human type A influenza viruses A(H1N1)pdm09 have caused seasonal epidemics of influenza since the 2009-2010 pandemic. A(H1N1)pdm09 viruses had a leading role in the severe epidemic season of 2015/16 in the Northern Hemisphere and caused a high incidence of acute respiratory infection (ARI) in Ukraine. Serious complications of influenza-associated severe ARI (SARI) were observed in the very young and individuals at increased risk, and 391 fatal cases occurred in the 2015/16 epidemic season. We analyzed the genetic changes in the genomes of A(H1N1)pdm09 influenza viruses isolated from SARI cases in Ukraine during the 2015/16 season. The viral hemagglutinin (HA) fell in H1 group 6B.1 for all but four isolates, with known mutations affecting glycosylation, the Sa antigenic site (S162N in all 6B.1 isolates), or virulence (D222G/N in two isolates). Other mutations occurred in antigenic site Ca (A141P and S236P), and a subgroup of four strains were in group 6B.2, with potential alterations to antigenicity in A(H1N1)pdm09 viruses circulating in 2015/16 in Ukraine. A cluster of Ukrainian isolates exhibited novel D2E and N48S mutations in the RNA binding domain, and E125D in the effector domain, of immune evasion nonstructural protein 1 (NS1). The diverse spectrum of amino-acid substitutions in HA, NS1, and other viral proteins including nucleoprotein (NP) and the polymerase complex suggested the concurrent circulation of multiple lineages of A(H1N1)pdm09 influenza viruses in the human population in Ukraine, a country with low vaccination coverage, complicating public health measures against influenza.
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Affiliation(s)
- Oksana Zolotarova
- Educational Scientific Centre “Institute of Biology and Medicine”, Taras Shevchenko National University of Kyiv, 01601 Kyiv, Ukraine;
| | - Anna Fesenko
- Gromashevsky L.V. Institute of Epidemiology and Infectious Diseases, National Academy of Medical Sciences of Ukraine, 03680 Kyiv, Ukraine; (A.F.); (O.H.); (L.R.); (A.M.)
| | - Olga Holubka
- Gromashevsky L.V. Institute of Epidemiology and Infectious Diseases, National Academy of Medical Sciences of Ukraine, 03680 Kyiv, Ukraine; (A.F.); (O.H.); (L.R.); (A.M.)
| | - Larysa Radchenko
- Gromashevsky L.V. Institute of Epidemiology and Infectious Diseases, National Academy of Medical Sciences of Ukraine, 03680 Kyiv, Ukraine; (A.F.); (O.H.); (L.R.); (A.M.)
| | - Eric Bortz
- Department of Biological Sciences, University of Alaska, 3211 Providence Dr., Anchorage, AK 99508, USA;
| | - Iryna Budzanivska
- Educational Scientific Centre “Institute of Biology and Medicine”, Taras Shevchenko National University of Kyiv, 01601 Kyiv, Ukraine;
| | - Alla Mironenko
- Gromashevsky L.V. Institute of Epidemiology and Infectious Diseases, National Academy of Medical Sciences of Ukraine, 03680 Kyiv, Ukraine; (A.F.); (O.H.); (L.R.); (A.M.)
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Liu V, Walker S. Testing for genetic mutation of seasonal influenza virus. J Appl Stat 2021; 50:1-18. [DOI: 10.1080/02664763.2021.1978955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Vera Liu
- Department of Statistics and Data Science, University of Texas at Austin, Austin, TX, USA
| | - Stephen Walker
- Department of Mathematics, University of Texas at Austin, Austin, TX, USA
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Zhao XN, Zhang HJ, Li D, Zhou JN, Chen YY, Sun YH, Adeola AC, Fu XQ, Shao Y, Zhang ML. Whole-genome sequencing reveals origin and evolution of influenza A(H1N1)pdm09 viruses in Lincang, China, from 2014 to 2018. PLoS One 2020; 15:e0234869. [PMID: 32579578 PMCID: PMC7314029 DOI: 10.1371/journal.pone.0234869] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 06/03/2020] [Indexed: 11/18/2022] Open
Abstract
The continuous variation of the seasonal influenza viruses, particularly A(H1N1)pdm09, persistently threatens human life and health around the world. In local areas of southwest china, the large time-scale genomic research on A(H1N1)pdm09 is still insufficient. Here, we sequenced 45 whole-genome sequences of influenza A(H1N1)pdm09 viruses in Lincang, China, from 2014 to 2018, by next-generation sequencing technology to characterize molecular mechanisms of their origin and evolution. Our phylogenetic analyses suggest that the A(H1N1)pdm09 strains circulating in Lincang belong to clade 6B and the subclade 6B.1A predominates in 2018. Further, the strains in 2018 possess elevated evolutionary rate as compared to strains in other years. Several newly emerged mutations for HA (hemagglutinin) in 2018 are revealed (i.e., S183P and R221K). Intriguingly, the substitution R221K falls into the RBS (receptor binding site) of HA protein, which could affect antigenic properties of influenza A(H1N1)pdm09 viruses, and another substitution S183P near to RBS with a high covering frequency (11/14 strains) in 2018 is exactly located at the epitope B. Notably, the NA (neuraminidase) protein harbors a new mutation I23T, potentially involved in N-glycosylation. Based on the background with a higher evolutionary rate in 2018 strains, we deeply evaluate the potential vaccine efficacy against Lincang strains and discover a substantive decline of the vaccine efficacy in 2018. Our analyses reaffirm that the real-time molecular surveillance and timely updated vaccine strains for prevention and control of influenza A(H1N1)pdm09 are crucial in the future.
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Affiliation(s)
- Xiao-Nan Zhao
- Department of Acute Infectious Diseases Control and Prevention, Yunnan Provincial Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - Han-Ju Zhang
- Lincang Center for Disease Control and Prevention, Lincang, Yunnan, China
| | - Duo Li
- Department of Acute Infectious Diseases Control and Prevention, Yunnan Provincial Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - Jie-Nan Zhou
- Department of Acute Infectious Diseases Control and Prevention, Yunnan Provincial Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - Yao-Yao Chen
- Department of Acute Infectious Diseases Control and Prevention, Yunnan Provincial Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - Yan-Hong Sun
- Department of Acute Infectious Diseases Control and Prevention, Yunnan Provincial Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - Adeniyi C. Adeola
- State Key Laboratory of Genetic Resources and Evolution, Chinese Academy of Sciences, Kunming Institute of Zoology, Kunming, Yunnan, China
| | - Xiao-Qing Fu
- Department of Acute Infectious Diseases Control and Prevention, Yunnan Provincial Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - Yong Shao
- State Key Laboratory of Genetic Resources and Evolution, Chinese Academy of Sciences, Kunming Institute of Zoology, Kunming, Yunnan, China
- * E-mail: (MLZ); (YS)
| | - Mei-Ling Zhang
- Department of Acute Infectious Diseases Control and Prevention, Yunnan Provincial Center for Disease Control and Prevention, Kunming, Yunnan, China
- * E-mail: (MLZ); (YS)
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