Original Article

A comparative genomic approach to decipher the mutations associated with Nipah viral human isolates from southeast Asia

Abstract

Background and Objectives: Multiple outbreaks over two decades and a high mortality rate have emphasized the Nipah virus (NiV) as a priority research area. The study focuses on identifying the mutational landscape in sequences from NiV human isolates from different geographical regions.
Materials and Methods: Thirty-seven NiV genomes of human samples from Malaysia, Bangladesh, and India were subjected to phylogeny and metagenomic analysis to decipher the genome variability using MEGA11 software and the meta-CATS web server. Using the Single-Likelihood Ancestor Counting method, the synonymous and nonsynonymous mutations among NiV genes were identified. Further, the nonsynonymous variations were used to identify mutations in all the NiV proteins.
Results: The NiV isolates were categorized into NiV-M, NiV-B, and NiV-I clades based on phylogenetic analysis. Metagenomic analysis revealed 1636 variations in the noncoding and coding regions of the genomes of the three clades of NiV. Further analysis of nonsynonymous mutations showed the phosphoprotein to be highly mutating, whereas the matrix protein was stable.
Conclusion: Deciphering the mutation pattern using a comparative genomics approach for human isolates provided valuable insight into the stability of NiV proteins which can be further used for understanding variations in host-pathogen interaction and developing effective therapeutic measures.

1. Epstein JH, Anthony SJ, Islam A, Kilpatrick AM, Ali Khan S, Balkey MD, et al. Nipah virus dynamics in bats and implications for spillover to humans. Proc Natl Acad Sci U S A 2020; 117: 29190-29201.
2. Devnath P, Masud HMAA. Nipah virus: a potential pandemic agent in the context of the current severe acute respiratory syndrome coronavirus 2 pandemic. New Microbes New Infect 2021; 41: 100873.
3. Ang BSP, Lim TCC, Wang L. Nipah virus infection. J Clin Microbiol 2018; 56(6): e01875-17.
4. Aljofan M. Hendra and Nipah infection: emerging paramyxoviruses. Virus Res 2013; 177: 119-126.
5. Soman Pillai V, Krishna G, Valiya Veettil M. Nipah virus: past outbreaks and future containment. Viruses 2020; 12: 465.
6. Looi LM, Chua KB. Lessons from the Nipah virus outbreak in Malaysia. Malays J Pathol 2007; 29: 63-67.
7. Kulkarni DD, Tosh C, Venkatesh G, Senthil Kumar D. Nipah virus infection: current scenario. Indian J Virol 2013; 24: 398-408.
8. Arunkumar G, Chandni R, Mourya DT, Singh SK, Sadanandan R, Sudan P, et al. Outbreak investigation of Nipah virus disease in Kerala, India, 2018. J Infect Dis 2019; 219: 1867-1878.
9. Mire CE, Satterfield BA, Geisbert JB, Agans KN, Borisevich V, Yan L, et al. Pathogenic differences between Nipah virus Bangladesh and Malaysia strains in primates: implications for antibody therapy. Sci Rep 2016; 6: 30916.
10. Harcourt BH, Lowe L, Tamin A, Liu X, Bankamp B, Bowden N, et al. Genetic characterization of Nipah virus, Bangladesh, 2004. Emerg Infect Dis 2005; 11: 1594-1597.
11. Mohandas S, Shete A, Sarkale P, Kumar A, Mote C, Yadav P. Genomic characterization, transcriptome analysis, and pathogenicity of the Nipah virus (Indian isolate). Virulence 2023; 14: 2224642.
12. Singh RK, Dhama K, Chakraborty S, Tiwari R, Natesan S, Khandia R, et al. Nipah virus: epidemiology, pathology, immunobiology and advances in diagnosis, vaccine designing and control strategies - a comprehensive review. Vet Q 2019; 39: 26-55.
13. Li H, Kim JV, Pickering BS. Henipavirus zoonosis: outbreaks, animal hosts and potential new emergence. Front Microbiol 2023; 14: 1167085.
14. Tamura K, Stecher G, Kumar S. MEGA11: molecular evolutionary genetics analysis Version 11. Mol Biol Evol 2021; 38: 3022-3027.
15. Pickett BE, Liu M, Sadat EL, Squires RB, Noronha JM, He S, et al. Metadata-driven comparative analysis tool for sequences (meta-CATS): an automated process for identifying significant sequence variations that correlate with virus attributes. Virology 2013; 447: 45-51.
16. Kosakovsky Pond SL, Frost SD. Not so different after all: a comparison of methods for detecting amino acid sites under selection. Mol Biol Evol 2005; 22: 1208-1222.
17. Rahman SA, Hassan SS, Olival KJ, Mohamed M, Chang LY, Hassan L, et al. Characterization of Nipah virus from naturally infected Pteropus vampyrus bats, Malaysia. Emerg Infect Dis 2010; 16: 1990-1993.
18. Tycowski KT, Guo YE, Lee N, Moss WN, Vallery TK, Xie M, et al. Viral noncoding RNAs: more surprises. Genes Dev 2015; 29: 567-584.
19. Withers JB, Mondol V, Pawlica P, Rosa-Mercado NA, Tycowski KT, Ghasempur S, et al. Idiosyncrasies of viral noncoding RNAs provide insights into host cell biology. Annu Rev Virol 2019; 6: 297-317.
20. Sugai A, Sato H, Yoneda M, Kai C. Gene end-like sequences within the 3' non-coding region of the Nipah virus genome attenuate viral gene transcription. Virology 2017; 508: 36-44.
21. Ma L, Chen Z, Guan W, Chen Q, Liu D. Rapid and specific detection of all known Nipah virus strains' sequences with reverse transcription-loop-mediated isothermal amplification. Front Microbiol 2019; 10: 418.
22. Nguyen TT, Pathirana PN, Nguyen T, Nguyen QVH, Bhatti A, Nguyen DC, et al. Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). Sci Rep 2021; 11: 3487.
23. Gupta AM, Chakrabarti J, Mandal S. Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. Microbes Infect 2020; 22: 598-607.
24. Jensen MR, Yabukarski F, Communie G, Condamine E, Mas C, Volchkova V, et al. Structural description of the Nipah virus phosphoprotein and its interaction with STAT1. Biophys J 2020; 118: 2470-2488.
25. Shi J, Sun J, Hu N, Hu Y. Phylogenetic and genetic analyses of the emerging Nipah virus from bats to humans. Infect Genet Evol 2020; 85: 104442.
Files
IssueVol 16 No 1 (2024) QRcode
SectionOriginal Article(s)
DOI https://doi.org/10.18502/ijm.v16i1.14879
Keywords
Nipah virus; Phylogeny; Synonymous mutations; Mutations; Host-pathogen interaction
Rights and permissions
Creative Commons License This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.
How to Cite
1.
Dsouza N, Chellasamy S. A comparative genomic approach to decipher the mutations associated with Nipah viral human isolates from southeast Asia. Iran J Microbiol. 2024;16(1):104-113.