Untranslated region-5' and viral protein 1-based genetic stability analysis of bulk polio in Indonesia 2010-2019

https://doi.org/10.19106/JMedSci005304202106

Andi Yasmon(1), Normasari Normasari(2*), Fithriyah Fithriyah(3), Fadilah Fadilah(4)

(1) Microbiology Department, Faculty of Medicine, Universitas Indonesia, Jakarta
(2) Master Program in Biomedical Science, Faculty of Medicine, Universitas Indonesia, Jakarta/National Quality Control Laboratory of Drug and Food, National Agency of Drug and Food Control
(3) Microbiology Department, Faculty of Medicine, Universitas Indonesia, Jakarta
(4) Chemistry Department, Faculty of Medicine, Universitas Indonesia, Jakarta
(*) Corresponding Author

Abstract


Cases of vaccine-associated paralytic poliomyelitis (VAPP) continued increasingly from 2010-2019 in the world. Oral polio vaccine (OPV) is the live attenuated virus-based vaccine that could genetically revert to neurovirulent during the vaccine production process or when the virus replicates in the human body. The poliovirus neurovirulence is determined by the UTR-5' region and VP1 coding region. UTR-5' played a role in protein translation and VP1 was responsible for the immunogenicity of the virus. Some reported mutations in UTR-5' and VP1 could affect the neurovirulence of poliovirus. In this study, we analyzed the genetic stability of the UTR-5' and VP1 in the bulk of OPV types -1 and -3 produced in 2010 - 2019. The results of the analysis of UTR-5' sequences in Sabin strain types-1 and -3 and VP1 sequences on Sabin virus type 1 did not show any mutations. Meanwhile, the VP1 sequences in Sabin strain type 3 showed nucleotide mutation C2493U that caused the substitution amino acid Thr6Ile amino acid in all samples of the type 3 bulk polio test. Based on the results of in silico analysis, this mutation in VP1 did not contribute significantly to the neurovirulence of the virus.


Keywords


poliovirus; UTR-5’; VP1; Sabin; genetic characterization

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References

  1. 1.Platt LR, Estivariz CF, Sutter RW. Vaccine-associated paralytic poliomyelitis: A review of the epidemiology and estimation of the global burden. J Infect Dis 2014; 210(Suppl 1):S380-9. https://doi.org/10.1093/infdis/jiu184
  2. Macklin G, Diop OM, Humayun A, Shahmahmoodi S, El-Sayed ZA, Triki H, et al. Update on Immunodeficiency-Associated Vaccine-Derived Polioviruses - Worldwide, July 2018 - December 2019. MMWR Morb Mortal Wkly Rep 2020; 69(28):913-7. https://doi.org/10.15585/mmwr.mm6928a4
  3. Deng Y, Cai W, Li J, Li Y, Yang X, Ma Y, et al. Evaluation of the genetic stability of Sabin strains and the consistency of inactivated poliomyelitis vaccine made from Sabin strains using direct deep-sequencing. Vaccine 2019; 37(1):130-6. https://doi.org/10.1016/j.vaccine.2018.11.020
  4. Rezapkin GV, Alexander W, Dragunsky E, Parker M, Pomeroy K, Asher DM, et al. Genetic stability of Sabin 1 strain of poliovirus: Implications for quality control of oral poliovirus vaccine. Virology 1998; 245(2):183-7. https://doi.org/10.1006/viro.1998.9191
  5. Taherkhani R, Farshadpour F, Ravanbod MR. Vaccine-associated paralytic poliomyelitis in a patient with acute lymphocytic leukemia. J Neurovirol 2018; 24(3):372-5. https://doi.org/10.1007/s13365-017-0610-4
  6. Zhang Y, Zhu S, Yan D, Wang D, Li X, Zhu H, et al. Type I vaccine-derived polioviruses in China from 1995 to 2019. Biosaf Healt 2019; 1(3):155-8. http://dx.doi.org/10.1016/j.bsheal.2019.12.002
  7. Gumede N, Muthambi V, Schoub BD. Immunodeficiency-associated vaccine-derived poliovirus type 3 in infant, South Africa, 2011. Emerg Infect Dis 2012; 18(6):992-4. https://doi.org/10.3201/eid1806.120037.
  8. World Health Organization. WHO Expert Committee on Biological Standardization. Sixty-third report. Geneva:WHO Press, 2012.
  9. Pliaka V, Dedepsidis E, Kyriakopoulou Z, Papadopoulou I, Levidiotou S, Markoulatos P. Use of mutational pattern in 5′-NCR and VP1 regions of polioviruses for molecular diagnosis. Mol Cell Probes 2007; 21(4):267-5. https://doi.org/10.1016/j.mcp.2007.01.004
  10. Kilpatrick DR, Iber JC, Chen Q, Ching K, Yang SJ, De L, et al. Poliovirus serotype-specific VP1 sequencing primers. J Virol Methods 2011; 174(1-2):128-30. https://doi.org/10.1016/j.jviromet.2011.03.020
  11. Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser 1999; 41(41):95-8.
  12. Hall T. BioEdit: an important software for molecular biology. GERF Bulletin of Biosciences 2011; 2(1):60-6.
  13. Kim YG, Kim MJ, Lee JS, Lee JA, Songg JY, Cho SI, et al. SnackVar: An Open-Source Software for Sanger Sequencing Analysis Optimized for Clinical Use. J Mol Diagn 2021; 23(2):140-8 https://doi.org/10.1016/j.jmoldx.2020.11.001
  14. Kim DE, Chivian D, Baker D. Protein structure prediction and analysis using the Robetta server. Nucleic Acids Res 2004; 32:W526-31. https://doi.org/10.1093/nar/gkh468
  15. Kolaskar AS, Sawant S. Prediction of conformational states of amino acids using a Ramachandran plot. Int J Pept Protein Res 1996; 47(1-2):110-6. https://doi.org/10.1111/j.1399-3011.1996.tb00817.x
  16. amura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 2011; 28(10):2731-9. https://doi.org/ 10.1093/molbev/msr121
  17. Famulare M, Chang S, Iber J, Zhao K, Adeniji JA, Bukbuk D, et al. Sabin Vaccine Reversion in the Field: a Comprehensive Analysis of Sabin-Like Poliovirus Isolates in Nigeria. J Virol 2016; 90(1):317-31. https://doi.org/10.1128/JVI.01532-15.
  18. Cherkasova EA, Korotkova EA, Yakovenko ML, Ivanova OE, Eremeeva TP, Chumakov KM, et al. Long-term circulation of vaccine-derived poliovirus that causes paralytic disease. J Virol 2002; 76(13):6791-9. https://doi.org/ 10.1128/jvi.76.13.6791-6799.2002
  19. Foiadelli T, Savasta S, Battistone A, Kota M, Passera C, Fiore S, et al. Nucleotide variation in Sabin type 3 poliovirus from an Albanian infant with agammaglobulinemia and vaccine associated poliomyelitis. BMC Infect Dis 2016; 16(1):277. https://doi.org/10.1186/s12879-016-1587-y
  20. Avanzino BC, Jue H, Miller CM, Cheung E, Fuchs G, Fraser CS. Molecular mechanism of poliovirus Sabin vaccine strain attenuation. J Biol Chem 2018; 293(40):15471-82. https://doi.org/10.1074/jbc.RA118.004913.
  21. Gamarnik AV, Andino R. Switch from translation to RNA replication in a positive-stranded RNA virus. Genes Dev 1998; 12(15):2293-304. https://doi.org/10.1101/gad.12.15.2293.
  22. Gamarnik AV, Andino R. Interactions of viral protein 3CD and poly(rC) binding protein with the 5’ untranslated region of the poliovirus genome. J Virol 2000; 74(5):2219-26. https://doi.org/10.1128/jvi.74.5.2219-2226.2000
  23. Thermet SM, Shulman NS, Ahmed A, Shahriar R, Liu T, Wang C, et al. Ultra-deep pyrosequencing of hepatitis B virus quasispecies from nucleoside and nucleotide reverse-transcriptase inhibitor (NRTI)-treated patients and NRTI-naive patients. J Infect Dis 2009; 199(9):1275-85. https://doi.org/10.1086/597808
  24. Liu Y, Ma T, Liu J, Zhao X, Cheng Z, Guo H, et al. Bioinformatics analysis and genetic diversity of the poliovirus. J Med Microbiol 2014; 63(Pt 12):1724-31. https://doi.org/10.1099/jmm.0.081992-0
  25. Neverov A, Chumakov K. Massively parallel sequencing for monitoring genetic consistency and quality control of live viral vaccines. Proc Natl Acad Sci U S A 2010; 107(46):20063-8. https://doi.org/10.1073/pnas.1012537107.
  26. Tatem JM, Weeks-levy C, Georgiu A, Dimichele SJ, Gorgacz EJ, Racaniello VR, et al. A mutation present in the amino terminus of Sabin 3 poliovirus VP1 protein is attenuating. Virology 1992; 66(5):3194-7. https://doi.org/10.1128/JVI.66.5.3194-3197.1992.
  27. World Health Organization. Meeting Report WHO Working Group Meeting to Discuss the Revision of the WHO Recommendations for OPV: TRS No 904 and World Health. Geneva: WHO Press, 2010; (904):1–16.
  28. Yutani K, Ogasahara K, Sugino Y. Effect of amino acid substitutions on conformational stability of a protein. Adv Biophys 1985; 20:13-29. https://doi.org/ 10.1016/0065-227x(85)90028-0
  29. Wien MW, Chow M, Hogle JM. Poliovirus: new insights from an old paradigm. Structure 1996; 4(7):763-7. https://doi.org/10.1016/s0969-2126(96)00082-2
  30. Kirkegaard K. Mutations in VP1 of poliovirus specifically affect both encapsidation and release of viral RNA. J Virol 1990; 64(1):195-206 https://doi.org/10.1128/JVI.64.1.195-206.1990.



DOI: https://doi.org/10.19106/JMedSci005304202106

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