Genomics & Informatics

  • 제20권2호
  • /
  • Pages.21.1-21.14
  • /
  • 2022
  • /
  • 1598-866X(pISSN)
  • /
  • 2234-0742(eISSN)
한국유전체학회 (Korea Genome Organization)
권호 표지
DOI QR코드

DOI QR Code

Genome characterization and mutation analysis of human influenza A virus in Thailand

  • Rattanaburi, Somruthai (Interdisciplinary Program of Biomedical Sciences, Graduate School, Chulalongkorn University) ;
  • Sawaswong, Vorthon (Research Unit of Systems Microbiology, Faculty of Medicine, Chulalongkorn University) ;
  • Nimsamer, Pattaraporn (Research Unit of Systems Microbiology, Faculty of Medicine, Chulalongkorn University) ;
  • Mayuramart, Oraphan (Research Unit of Systems Microbiology, Faculty of Medicine, Chulalongkorn University) ;
  • Sivapornnukul, Pavaret (Research Unit of Systems Microbiology, Faculty of Medicine, Chulalongkorn University) ;
  • Khamwut, Ariya (Research Unit of Systems Microbiology, Faculty of Medicine, Chulalongkorn University) ;
  • Chanchaem, Prangwalai (Research Unit of Systems Microbiology, Faculty of Medicine, Chulalongkorn University) ;
  • Kongnomnan, Kritsada (Research Unit of Systems Microbiology, Faculty of Medicine, Chulalongkorn University) ;
  • Suntronwong, Nungruthai (Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University) ;
  • Poovorawan, Yong (Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University) ;
  • Payungporn, Sunchai (Research Unit of Systems Microbiology, Faculty of Medicine, Chulalongkorn University)
  • 투고 : 2022.12.01
  • 심사 : 2022.04.05
  • 발행 : 2022.06.30
PDF 다운로드
⟨ 이전 논문 다음 논문 ⟩

초록

The influenza A viruses have high mutation rates and cause a serious health problem worldwide. Therefore, this study focused on genome characterization of the viruses isolated from Thai patients based on the next-generation sequencing technology. The nasal swabs were collected from patients with influenza-like illness in Thailand during 2017-2018. Then, the influenza A viruses were detected by reverse transcription-quantitative polymerase chain reaction and isolated by MDCK cells. The viral genomes were amplified and sequenced by Illumina MiSeq platform. Whole genome sequences were used for characterization, phylogenetic construction, mutation analysis and nucleotide diversity of the viruses. The result revealed that 90 samples were positive for the viruses including 44 of A/H1N1 and 46 of A/H3N2. Among these, 43 samples were successfully isolated and then the viral genomes of 25 samples were completely amplified. Finally, 17 whole genomes of the viruses (A/H1N1, n=12 and A/H3N2, n=5) were successfully sequenced with an average of 232,578 mapped reads and 1,720 genome coverage per sample. Phylogenetic analysis demonstrated that the A/H1N1 viruses were distinguishable from the recommended vaccine strains. However, the A/H3N2 viruses from this study were closely related to the recommended vaccine strains. The nonsynonymous mutations were found in all genes of both viruses, especially in hemagglutinin (HA) and neuraminidase (NA) genes. The nucleotide diversity analysis revealed negative selection in the PB1, PA, HA, and NA genes of the A/H1N1 viruses. High-throughput data in this study allow for genetic characterization of circulating influenza viruses which would be crucial for preparation against pandemic and epidemic outbreaks in the future.

키워드

과제정보

This work was partly supported by a grant from the National Science and Technology Development Agency (NSTDA) (P-17-51377), the Royal Golden Jubilee (RGJ) Ph.D. Programme scholarship (PHD/0150/2558), National Research Council of Thailand (NRCT)[2564NRCT321520] and Thailand Research Fund (TRF), the Chulalongkorn University Center of Excellence in Systems Biology and Chulalongkorn Academic Advancement into its 2nd Century Project. We would like to express gratitude to all the members of the Center of Excellence in Clinical Virology (Miss Preeyaporn Vichaiwattana and Mr. Sumeth Korkong), Faculty of Medicine, Chulalongkorn University for facilitating the sample collection. Moreover, we would like to thank the Department of Virology, Faculty of Veterinary Medicine Chulalongkorn University for support in influenza virus isolation (Assistant Prof. Aunyaratana Thontiravong, D.V.M., Ph.D.).

참고문헌

  1. Stohr K. Influenza: WHO cares. Lancet Infect Dis 2002;2:517. https://doi.org/10.1016/S1473-3099(02)00366-3
  2. World Health Organization. Up to 650000 people die of respiratory diseases linked to seasonal flu each year. Geneva: World Health Organization, 2017. Accessed 2021 Dec 10. Available from: http://www.who.int/mediacentre/news/releases/2017/seasonal-flu/en/.
  3. Shao W, Li X, Goraya MU, Wang S, Chen JL. Evolution of influenza A virus by mutation and re-assortment. Int J Mol Sci 2017;18:1650. https://doi.org/10.3390/ijms18081650
  4. Cox NJ, Subbarao K. Global epidemiology of influenza: past and present. Annu Rev Med 2000;51:407-421. https://doi.org/10.1146/annurev.med.51.1.407
  5. Boivin S, Cusack S, Ruigrok RW, Hart DJ. Influenza A virus polymerase: structural insights into replication and host adaptation mechanisms. J Biol Chem 2010;285:28411-28417. https://doi.org/10.1074/jbc.R110.117531
  6. Bloom JD. An experimentally determined evolutionary model dramatically improves phylogenetic fit. Mol Biol Evol 2014;31: 1956-1978. https://doi.org/10.1093/molbev/msu173
  7. Nobusawa E, Sato K. Comparison of the mutation rates of human influenza A and B viruses. J Virol 2006;80:3675-3678. https://doi.org/10.1128/JVI.80.7.3675-3678.2006
  8. Pauly MD, Procario MC, Lauring AS. A novel twelve class fluctuation test reveals higher than expected mutation rates for influenza A viruses. Elife 2017;6:e26437. https://doi.org/10.7554/eLife.26437
  9. Suarez DL. Evolution of avian influenza viruses. Vet Microbiol 2000;74:15-27. https://doi.org/10.1016/S0378-1135(00)00161-9
  10. Doyle JD, Chung JR, Kim SS, Gaglani M, Raiyani C, Zimmerman RK, et al. Interim estimates of 2018-19 seasonal influenza vaccine effectiveness - United States, February 2019. MMWR Morb Mortal Wkly Rep 2019;68:135-139. https://doi.org/10.15585/mmwr.mm6806a2
  11. Rose A, Kissling E, Emborg HD, Larrauri A, McMenamin J, Pozo F, et al. Interim 2019/20 influenza vaccine effectiveness: six European studies, September 2019 to January 2020. Euro Surveill 2020;25:2000153.
  12. Chittaganpitch M, Supawat K, Olsen SJ, Waicharoen S, Patthamadilok S, Yingyong T, et al. Influenza viruses in Thailand: 7 years of sentinel surveillance data, 2004-2010. Influenza Other Respir Viruses 2012;6:276-283. https://doi.org/10.1111/j.1750-2659.2011.00302.x
  13. Simmerman JM, Chittaganpitch M, Levy J, Chantra S, Maloney S, Uyeki T, et al. Incidence, seasonality and mortality associated with influenza pneumonia in Thailand: 2005-2008. PLoS One 2009;4:e7776. https://doi.org/10.1371/journal.pone.0007776
  14. Tewawong N, Vichiwattana P, Korkong S, Klinfueng S, Suntronwong N, Thongmee T, et al. Evolution of the neuraminidase gene of seasonal influenza A and B viruses in Thailand between 2010 and 2015. PLoS One 2017;12:e0175655. https://doi.org/10.1371/journal.pone.0175655
  15. Tewawong N, Suntronwong N, Korkong S, Theamboonlers A, Vongpunsawad S, Poovorawan Y. Evidence for influenza B virus lineage shifts and reassortants circulating in Thailand in 2014- 2016. Infect Genet Evol 2017;47:35-40. https://doi.org/10.1016/j.meegid.2016.11.010
  16. Tewawong N, Suntronwong N, Vichiwattana P, Vongpunsawad S, Theamboonlers A, Poovorawan Y. Genetic and antigenic characterization of hemagglutinin of influenza A/H3N2 virus from the 2015 season in Thailand. Virus Genes 2016;52:711-715. https://doi.org/10.1007/s11262-016-1347-5
  17. Suntronwong N, Klinfueng S, Vichiwattana P, Korkong S, Thongmee T, Vongpunsawad S, et al. Genetic and antigenic divergence in the influenza A(H3N2) virus circulating between 2016 and 2017 in Thailand. PLoS One 2017;12:e0189511. https://doi.org/10.1371/journal.pone.0189511
  18. Imai K, Tamura K, Tanigaki T, Takizawa M, Nakayama E, Taniguchi T, et al. Whole genome sequencing of influenza A and B viruses with the MinION sequencer in the clinical setting: a pilot study. Front Microbiol 2018;9:2748. https://doi.org/10.3389/fmicb.2018.02748
  19. Alnaji FG, Holmes JR, Rendon G, Vera JC, Fields CJ, Martin BE, et al. Sequencing framework for the sensitive detection and precise mapping of defective interfering particle-associated deletions across influenza A and B viruses. J Virol 2019;93:e00354-e00319.
  20. Suwannakarn K, Payungporn S, Chieochansin T, Samransamruajkit R, Amonsin A, Songserm T, et al. Typing (A/B) and subtyping (H1/H3/H5) of influenza A viruses by multiplex real-time RT-PCR assays. J Virol Methods 2008;152:25-31. https://doi.org/10.1016/j.jviromet.2008.06.002
  21. Tewawong N, Chansaenroj J, Klinfueng S, Vichiwattana P, Korkong S, Thongmee T, et al. Lineage-specific detection of influenza B virus using real-time polymerase chain reaction with melting curve analysis. Arch Virol 2016;161:1425-1435. https://doi.org/10.1007/s00705-016-2802-2
  22. World Health Organization. WHO manual on animal influenza diagnosis and surveillance. Geneva: World Health Organization, 2002. Accessed 2021 Dec 10. Available from: https://apps.who.int/iris/handle/10665/68026.
  23. Ilyushina NA, Ikizler MR, Kawaoka Y, Rudenko LG, Treanor JJ, Subbarao K, et al. Comparative study of influenza virus replication in MDCK cells and in primary cells derived from adenoids and airway epithelium. J Virol 2012;86:11725-11734. https://doi.org/10.1128/JVI.01477-12
  24. Xue J, Chambers BS, Hensley SE, Lopez CB. Propagation and characterization of influenza virus stocks that lack high levels of defective viral genomes and hemagglutinin mutations. Front Microbiol 2016;7:326.
  25. Zhou B, Donnelly ME, Scholes DT, St George K, Hatta M, Kawaoka Y, et al. Single-reaction genomic amplification accelerates sequencing and vaccine production for classical and Swine origin human influenza a viruses. J Virol 2009;83:10309-10313. https://doi.org/10.1128/JVI.01109-09
  26. Korsun NS, Angelova SG, Trifonova IT, Georgieva IL, Tzotcheva IS, Mileva SD, et al. Predominance of influenza B/Yamagata lineage viruses in Bulgaria during the 2017/2018 season. Epidemiol Infect 2019;147:e76. https://doi.org/10.1017/S0950268818003588
  27. Hall T. BioEdit: an important software for molecular biology. GERF Bull Biosci 2011;2:60-61.
  28. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Mol Biol Evol 2018;35:1547-1549. https://doi.org/10.1093/molbev/msy096
  29. Kofler R, Orozco-terWengel P, De Maio N, Pandey RV, Nolte V, Futschik A, et al. PoPoolation: a toolbox for population genetic analysis of next generation sequencing data from pooled individuals. PLoS One 2011;6:e15925. https://doi.org/10.1371/journal.pone.0015925
  30. Thongpan I, Suntronwong N, Vichaiwattana P, Wanlapakorn N, Vongpunsawad S, Poovorawan Y. Respiratory syncytial virus, human metapneumovirus, and influenza virus infection in Bangkok, 2016-2017. PeerJ 2019;7:e6748. https://doi.org/10.7717/peerj.6748
  31. Hoper D, Hoffmann B, Beer M. A comprehensive deep sequencing strategy for full-length genomes of influenza A. PLoS One 2011;6:e19075. https://doi.org/10.1371/journal.pone.0019075
  32. Zhao J, Liu J, Vemula SV, Lin C, Tan J, Ragupathy V, et al. Sensitive detection and simultaneous discrimination of influenza A and B viruses in nasopharyngeal swabs in a single assay using next-generation sequencing-based diagnostics. PLoS One 2016;11:e0163175. https://doi.org/10.1371/journal.pone.0163175
  33. Kampmann ML, Fordyce SL, Avila-Arcos MC, Rasmussen M, Willerslev E, Nielsen LP, et al. A simple method for the parallel deep sequencing of full influenza A genomes. J Virol Methods 2011;178:243-248. https://doi.org/10.1016/j.jviromet.2011.09.001
  34. Zhao XN, Zhang HJ, Li D, Zhou JN, Chen YY, Sun YH, et al. 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. https://doi.org/10.1371/journal.pone.0234869
  35. Meinel DM, Heinzinger S, Eberle U, Ackermann N, Schonberger K, Sing A. Whole genome sequencing identifies influenza A H3N2 transmission and offers superior resolution to classical typing methods. Infection 2018;46:69-76. https://doi.org/10.1007/s15010-017-1091-3
  36. Xue KS, Moncla LH, Bedford T, Bloom JD. Within-host evolution of human influenza virus. Trends Microbiol 2018;26:781-793. https://doi.org/10.1016/j.tim.2018.02.007
  37. Van Poelvoorde LAE, Saelens X, Thomas I, Roosens NH. Next-generation sequencing: an eye-opener for the surveillance of antiviral resistance in influenza. Trends Biotechnol 2020; 38:360-367. https://doi.org/10.1016/j.tibtech.2019.09.009
  38. Deng YM, Spirason N, Iannello P, Jelley L, Lau H, Barr IG. A simplified Sanger sequencing method for full genome sequencing of multiple subtypes of human influenza A viruses. J Clin Virol 2015;68:43-48. https://doi.org/10.1016/j.jcv.2015.04.019
  39. Cobbin JCA, Alfelali M, Barasheed O, Taylor J, Dwyer DE, Kok J, et al. Multiple sources of genetic diversity of influenza A viruses during the Hajj. J Virol 2017;91:e00096-00017.
  40. Sobel Leonard A, McClain MT, Smith GJ, Wentworth DE, Halpin RA, Lin X, et al. Deep sequencing of influenza A virus from a human challenge study reveals a selective bottleneck and only limited intrahost genetic diversification. J Virol 2016;90:11247-11258. https://doi.org/10.1128/JVI.01657-16
  41. Rondy M, Kissling E, Emborg HD, Gherasim A, Pebody R, Trebbien R, et al. Interim 2017/18 influenza seasonal vaccine effectiveness: combined results from five European studies. Euro Surveill 2018;23:18-00086.
  42. Flannery B, Chung JR, Belongia EA, McLean HQ, Gaglani M, Murthy K, et al. Interim estimates of 2017-18 seasonal influenza vaccine effectiveness - United States, February 2018. MMWR Morb Mortal Wkly Rep 2018;67:180-185. https://doi.org/10.15585/mmwr.mm6706a2
  43. Centers for Disease Control and Prevention. Summary of the 2017-2018 Influenza Season, 2019. Atlanta, GA: Centers for Disease Control and Prevention, 2019. Accessed 2021 Dec 10. Available from: https://www.cdc.gov/flu/about/season/flu-season-2017-2018.htm.
  44. World Health Organization. Recommended composition of influenza virus vaccines for use in the 2018 southern hemisphere influenza season. Geneva: World Health Organization, 2017. Accessed 2021 Dec 10. Available from: https://www.who.int/influenza/vaccines/virus/recommendations/201709_recommendation.pdf?ua=1.
  45. Suntronwong N, Klinfueng S, Korkong S, Vichaiwattana P, Thongmee T, Vongpunsawad S, et al. Characterizing genetic and antigenic divergence from vaccine strain of influenza A and B viruses circulating in Thailand, 2017-2020. Sci Rep 2021;11:735. https://doi.org/10.1038/s41598-020-80895-w
  46. Belanov SS, Bychkov D, Benner C, Ripatti S, Ojala T, Kankainen M, et al. Genome-wide analysis of evolutionary markers of human influenza A(H1N1)pdm09 and A(H3N2) viruses may guide selection of vaccine strain candidates. Genome Biol Evol 2015;7:3472-3483. https://doi.org/10.1093/gbe/evv240
  47. Elderfield RA, Watson SJ, Godlee A, Adamson WE, Thompson CI, Dunning J, et al. Accumulation of human-adapting mutations during circulation of A(H1N1)pdm09 influenza virus in humans in the United Kingdom. J Virol 2014;88:13269-13283. https://doi.org/10.1128/JVI.01636-14
  48. Sarmah K, Borkakoty B, Sarma K, Hazarika R, Das PK, Jakharia A, et al. Genetic variations of the Hemagglutinin gene of Pandemic Influenza A (H1N1) viruses in Assam, India during 2016. 3 Biotech 2018;8:408.
  49. Ramos AP, Herrera BA, Ramirez OV, Garcia AA, Jimenez MM, Valdes CS, et al. Molecular and phylogenetic analysis of influenza A H1N1 pandemic viruses in Cuba, May 2009 to August 2010. Int J Infect Dis 2013;17:e565-e567. https://doi.org/10.1016/j.ijid.2013.01.028
  50. Roubidoux EK, Carreno JM, McMahon M, Jiang K, van Bakel H, Wilson P, et al. Mutations in the hemagglutinin stalk domain do not permit escape from a protective, stalk-based vaccine-induced immune response in the mouse model. mBio 2021;12:e03617-e03620.
  51. Jimenez-Jorge S, Pozo F, de Mateo S, Delgado-Sanz C, Casas I, Garcia-Cenoz M, et al. Influenza vaccine effectiveness in Spain 2013/14: subtype-specific early estimates using the cycEVA study. Euro Surveill 2014;19:20727.
  52. European Centre of Disease Prevention and Control (ECDC). Surveillance report. Influenza virus characterization. Summary Europe. Solna: European Centre of Disease Prevention and Control, 2016. Accessed 2021 Dec 10. Available from: https://www.ecdc.europa.eu/sites/default/files/media/en/publications/Publications/influenza-virus-characterisation-may-2016.pdf.
  53. Cheng AC, Subbarao K. Epidemiological data on the effectiveness of influenza vaccine: another piece of the puzzle. J Infect Dis 2018;218:176-178. https://doi.org/10.1093/infdis/jix635
  54. Jones S, Prasad R, Nair AS, Dharmaseelan S, Usha R, Nair RR, et al. Whole-genome sequences of influenza A(H1N1)pdm09 virus isolates from Kerala, India. Genome Announc 2017;5:e00598-00517.
  55. Al Khatib HA, Al Maslamani MA, Coyle PV, Thompson IR, Farag EA, Al Thani AA, et al. Inter- versus intra-host sequence diversity of pH1N1 and associated clinical outcomes. Microorganisms 2020;8:133. https://doi.org/10.3390/microorganisms8010133
  56. Clark AM, Nogales A, Martinez-Sobrido L, Topham DJ, DeDiego ML. Functional evolution of influenza virus NS1 protein in currently circulating human 2009 pandemic H1N1 viruses. J Virol 2017;91:e00721-00717.
  57. Krug RM. Functions of the influenza A virus NS1 protein in antiviral defense. Curr Opin Virol 2015;12:1-6. https://doi.org/10.1016/j.coviro.2015.01.007
  58. Nemeroff ME, Barabino SM, Li Y, Keller W, Krug RM. Influenza virus NS1 protein interacts with the cellular 30 kDa subunit of CPSF and inhibits 3'end formation of cellular pre-mRNAs. Mol Cell 1998;1:991-1000. https://doi.org/10.1016/S1097-2765(00)80099-4
  59. Komissarov A, Fadeev A, Sergeeva M, Petrov S, Sintsova K, Egorova A, et al. Rapid spread of influenza A(H1N1)pdm09 viruses with a new set of specific mutations in the internal genes in the beginning of 2015/2016 epidemic season in Moscow and Saint Petersburg (Russian Federation). Influenza Other Respir Viruses 2016;10:247-253. https://doi.org/10.1111/irv.12389
  60. Mao H, Sun Y, Chen Y, Lou X, Yu Z, Wang X, et al. Co-circulation of influenza A(H1N1), A(H3N2), B(Yamagata) and B(Victoria) during the 2017-2018 influenza season in Zhejiang Province, China. Epidemiol Infect 2020;148:e296. https://doi.org/10.1017/S0950268820000412
  61. Boonnak K, Mansanguan C, Schuerch D, Boonyuen U, Lerdsamran H, Jiamsomboon K, et al. Molecular characterization of seasonal influenza A and B from hospitalized patients in Thailand in 2018-2019. Viruses 2021;13:977. https://doi.org/10.3390/v13060977
  62. Jagadesh A, Krishnan A, Nair S, Sivadas S, Arunkumar G. Genetic characterization of hemagglutinin (HA) gene of influenza A viruses circulating in Southwest India during 2017 season. Virus Genes 2019;55:458-464. https://doi.org/10.1007/s11262-019-01675-x
  63. Wan H, Gao J, Yang H, Yang S, Harvey R, Chen YQ, et al. The neuraminidase of A(H3N2) influenza viruses circulating since 2016 is antigenically distinct from the A/Hong Kong/4801/ 2014 vaccine strain. Nat Microbiol 2019;4:2216-2225. https://doi.org/10.1038/s41564-019-0522-6
  64. Potter BI, Kondor R, Hadfield J, Huddleston J, Barnes J, Rowe T, et al. Evolution and rapid spread of a reassortant A(H3N2) virus that predominated the 2017-2018 influenza season. Virus Evol 2019;5:vez046. https://doi.org/10.1093/ve/vez046
  65. Takashita E, Daniels RS, Fujisaki S, Gregory V, Gubareva LV, Huang W, et al. Global update on the susceptibilities of human influenza viruses to neuraminidase inhibitors and the cap-dependent endonuclease inhibitor baloxavir, 2017-2018. Antiviral Res 2020;175:104718. https://doi.org/10.1016/j.antiviral.2020.104718