1887

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Volume 99, Issue 2

Evaluation of the population heterogeneity of TBEV laboratory variants using high-throughput sequencing Free

Abstract

We studied minor variants within two tick-borne encephalitis virus (TBEV) populations with a common ancestor: the mouse brain-adapted variant EK-328c and the tick-adapted variant M. High-throughput sequencing with custom amplicons from RT-PCR viral RNA was performed on Illumina MiSeq 2*250 paired-end v2 chemistry. Using the LowFreq program (default settings) and Sanger-sequenced consensus as a reference, variants with an abundance of 1 % and above within the studied populations were identified. Using the obtained data in the context of our previous studies, we concluded that TBEV variants, which are different from the major population phenotype and can become a major part of the viral population under favourable environmental conditions, can exist at abundances of less than 1 % in the long-term. The comparison of our data with the literature allowed us to conclude that the laboratory variant EK-328c and variant M have similar SNV counts to TBEV variants from natural populations and some fast-evolving RNA viruses.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): HTS , molecular memory , NGS , population , SNV and TBEV
© 2018 The Authors
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2018-02-01
2024-04-18
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References

  1. Domingo E, Sheldon J, Perales C. Viral quasispecies evolution. Microbiol Mol Biol Rev 2012; 76:159–216 [View Article][PubMed]
     [Google Scholar]
  2. Sanjuán R, Nebot MR, Chirico N, Mansky LM, Belshaw R. Viral mutation rates. J Virol 2010; 84:9733–9748 [View Article][PubMed]
     [Google Scholar]
  3. Lauring AS, Andino R. Quasispecies theory and the behavior of RNA viruses. PLoS Pathog 2010; 6:e10010051001008 [View Article][PubMed]
     [Google Scholar]
  4. Arias A, Lázaro E, Escarmís C, Domingo E. Molecular intermediates of fitness gain of an RNA virus: characterization of a mutant spectrum by biological and molecular cloning. J Gen Virol 2001; 82:1049–1060 [View Article][PubMed]
     [Google Scholar]
  5. Briones C, de Vicente A, Molina-París C, Domingo E. Minority memory genomes can influence the evolution of HIV-1 quasispecies in vivo. Gene 2006; 384:129–138 [View Article][PubMed]
     [Google Scholar]
  6. Ruiz-Jarabo CM, Arias A, Baranowski E, Escarmís C, Domingo E. Memory in viral quasispecies. J Virol 2000; 74:3543–3547 [View Article][PubMed]
     [Google Scholar]
  7. Ruíz-Jarabo CM, Arias A, Molina-París C, Briones C, Baranowski E et al. Duration and fitness dependence of quasispecies memory. J Mol Biol 2002; 315:285–296 [View Article][PubMed]
     [Google Scholar]
  8. Briones C, Domingo E, Molina-París C. Memory in retroviral quasispecies: experimental evidence and theoretical model for human immunodeficiency virus. J Mol Biol 2003; 331:213–229 [View Article][PubMed]
     [Google Scholar]
  9. Chumakov KM, Powers LB, Noonan KE, Roninson IB, Levenbook IS. Correlation between amount of virus with altered nucleotide sequence and the monkey test for acceptability of oral poliovirus vaccine. Proc Natl Acad Sci USA 1991; 88:199–203 [View Article][PubMed]
     [Google Scholar]
  10. Jerzak GV, Bernard K, Kramer LD, Shi PY, Ebel GD. The West Nile virus mutant spectrum is host-dependant and a determinant of mortality in mice. Virology 2007; 360:469–476 [View Article][PubMed]
     [Google Scholar]
  11. Sim S, Aw PP, Wilm A, Teoh G, Hue KD et al. Tracking dengue virus intra-host genetic diversity during human-to-mosquito transmission. PLoS Negl Trop Dis 2015; 9:e000405221 [View Article][PubMed]
     [Google Scholar]
  12. Asghar N, Pettersson JH, Dinnetz P, Andreassen Å, Johansson M. Deep sequencing analysis of tick-borne encephalitis virus from questing ticks at natural foci reveals similarities between quasispecies pools of the virus. J Gen Virol 2017; 98:413–421 [View Article][PubMed]
     [Google Scholar]
  13. Ehrbar DJ, Ngo KA, Campbell SR, Kramer LD, Ciota AT. High levels of local inter- and intra-host genetic variation of West Nile virus and evidence of fine-scale evolutionary pressures. Infect Genet Evol 2017; 51:219–226 [View Article][PubMed]
     [Google Scholar]
  14. Süss J. Tick-borne encephalitis 2010: epidemiology, risk areas, and virus strains in Europe and Asia-an overview. Ticks Tick Borne Dis 2011; 2:2–15 [View Article][PubMed]
     [Google Scholar]
  15. Lindenbach BD, Thiel H-J, Rice CM. Flaviviridae: the viruses and their replication. In Knipe DM, Howley PM. (editors) Fields Virology, 5th ed. Philadelphia: Lippincott-Raven Publishers; 2007 pp. 1101–1152
     [Google Scholar]
  16. Gritsun TS, Lashkevich VA, Gould EA. Tick-borne encephalitis. Antiviral Res 2003; 57:129–146 [View Article][PubMed]
     [Google Scholar]
  17. Ciota AT, Kramer LD. Insights into arbovirus evolution and adaptation from experimental studies. Viruses 2010; 2:2594–2617 [View Article][PubMed]
     [Google Scholar]
  18. Grubaugh ND, Rückert C, Armstrong PM, Bransfield A, Anderson JF et al. Transmission bottlenecks and RNAi collectively influence tick-borne flavivirus evolution. Virus Evol 2016; 2:vew033 [View Article][PubMed]
     [Google Scholar]
  19. Belova OA, Litov AG, Kholodilov IS, Kozlovskaya LI, Bell-Sakyi L et al. Properties of the tick-borne encephalitis virus population during persistent infection of ixodid ticks and tick cell lines. Ticks Tick Borne Dis 2017; 8:895–906 [Epub ahead of print] [View Article][PubMed]
     [Google Scholar]
  20. Romanova LIu, Gmyl AP, Dzhivanian TI, Bakhmutov DV, Lukashev AN et al. Microevolution of tick-borne encephalitis virus in course of host alternation. Virology 2007; 362:75–84 [View Article][PubMed]
     [Google Scholar]
  21. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 2014; 30:2114–2120 [View Article][PubMed]
     [Google Scholar]
  22. Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods 2012; 9:357–359 [View Article][PubMed]
     [Google Scholar]
  23. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 2009; 25:2078–2079 [View Article][PubMed]
     [Google Scholar]
  24. Wilm A, Aw PP, Bertrand D, Yeo GH, Ong SH et al. LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets. Nucleic Acids Res 2012; 40:11189–11201 [View Article][PubMed]
     [Google Scholar]
  25. Acevedo A, Andino R. Library preparation for highly accurate population sequencing of RNA viruses. Nat Protoc 2014; 9:1760–1769 [View Article][PubMed]
     [Google Scholar]
  26. Sobel Leonard A, McClain MT, Smith GJ, Wentworth DE, Halpin RA 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:JVI.01657-16 [View Article][PubMed]
     [Google Scholar]
  27. Chen SP. Molecular evolution and epidemiology of four serotypes of dengue virus in Thailand from 1973 to 2007. Epidemiol Infect 2013; 141:419–424 [View Article][PubMed]
     [Google Scholar]
  28. Jorba J, Campagnoli R, De L, Kew O. Calibration of multiple poliovirus molecular clocks covering an extended evolutionary range. J Virol 2008; 82:4429–4440 [View Article][PubMed]
     [Google Scholar]
  29. Cattoli G, Fusaro A, Monne I, Coven F, Joannis T et al. Evidence for differing evolutionary dynamics of A/H5N1 viruses among countries applying or not applying avian influenza vaccination in poultry. Vaccine 2011; 29:9368–9375 [View Article][PubMed]
     [Google Scholar]
  30. Uzcátegui NY, Sironen T, Golovljova I, Jääskeläinen AE, Välimaa H et al. Rate of evolution and molecular epidemiology of tick-borne encephalitis virus in Europe, including two isolations from the same focus 44 years apart. J Gen Virol 2012; 93:786–796 [View Article][PubMed]
     [Google Scholar]
  31. Jerzak G, Bernard KA, Kramer LD, Ebel GD. Genetic variation in West Nile virus from naturally infected mosquitoes and birds suggests quasispecies structure and strong purifying selection. J Gen Virol 2005; 86:2175–2183 [View Article][PubMed]
     [Google Scholar]
  32. Batschelet E, Domingo E, Weissmann C. The proportion of revertant and mutant phage in a growing population, as a function of mutation and growth rate. Gene 1976; 1:27–32 [View Article][PubMed]
     [Google Scholar]
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Evaluation of the population heterogeneity of TBEV laboratory variants using high-throughput sequencing
J. Gen. Virol. 99, 240 (2018); https://doi.org/10.1099/jgv.0.001003
/content/journal/jgv/10.1099/jgv.0.001003
/content/journal/jgv/10.1099/jgv.0.001003
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