1887

Abstract

Naturally occurring isolates of baculoviruses, such as the Bombyx mori nucleopolyhedrovirus (BmNPV), usually consist of numerous genetically different haplotypes. Deciphering the different haplotypes of such isolates is hampered by the large size of the dsDNA genome, as well as the short read length of next generation sequencing (NGS) techniques that are widely applied for baculovirus isolate characterization. In this study, we addressed this challenge by combining the accuracy of NGS to determine single nucleotide variants (SNVs) as genetic markers with the long read length of Nanopore sequencing technique. This hybrid approach allowed the comprehensive analysis of genetically homogeneous and heterogeneous isolates of BmNPV. Specifically, this allowed the identification of two putative major haplotypes in the heterogeneous isolate BmNPV-Ja by SNV position linkage. SNV positions, which were determined based on NGS data, were linked by the long Nanopore reads in a Position Weight Matrix. Using a modified Expectation–Maximization algorithm, the Nanopore reads were assigned according to the occurrence of variable SNV positions by machine learning. The cohorts of reads were assembled, which led to the identification of BmNPV haplotypes. The method demonstrated the strength of the combined approach of short- and long-read sequencing techniques to decipher the genetic diversity of baculovirus isolates.

Loading

Article metrics loading...

/content/journal/jgv/10.1099/jgv.0.001983
2024-05-20
2024-06-19
Loading full text...

Full text loading...

References

  1. Harrison RL, Herniou EA, Jehle JA, Theilmann DA, Burand JP et al. ICTV virus taxonomy profile: Baculoviridae. J Gen Virol 2018; 99:1185–1186 [View Article] [PubMed]
    [Google Scholar]
  2. van Oers MM. Opportunities and challenges for the baculovirus expression system. J Invertebr Pathol 2011; 107:S3–15 [View Article] [PubMed]
    [Google Scholar]
  3. Eberle KE, Jehle JA, Huber J. Microbial control of crop pests using insect viruses. In Abrol DP, Shanker U. eds Integrated Pest Management: Principles and Practice CABI Publishing; 2012 pp 281–298 [View Article]
    [Google Scholar]
  4. Grzywacz D, Moore S. Production, formulation, and bioassay of baculoviruses for pest control. In Microbial Control of Insect and Mite Pests Elsevier; 2017 pp 109–124 [View Article]
    [Google Scholar]
  5. Cox MMJ. Innovations in the insect cell expression system for industrial recombinant vaccine antigen production. Vaccines 2021; 9:1504 [View Article] [PubMed]
    [Google Scholar]
  6. Rodríguez-Hernández AP, Martínez-Flores D, Cruz-Reséndiz A, Padilla-Flores T, González-Flores R et al. Baculovirus display of peptides and proteins for medical applications. Viruses 2023; 15:411 [View Article] [PubMed]
    [Google Scholar]
  7. Rahman MM, Gopinathan KP. Systemic and in vitro infection process of Bombyx mori nucleopolyhedrovirus. Virus Res 2004; 101:109–118 [View Article] [PubMed]
    [Google Scholar]
  8. Braxton SM, Onstad DW, Dockter DE, Giordano R, Larsson R et al. Description and analysis of two internet-based databases of insect pathogens: EDWIP and VIDIL. J Invertebr Pathol 2003; 83:185–195 [View Article] [PubMed]
    [Google Scholar]
  9. Dallas TA, Carlson CJ, Stephens PR, Ryan SJ, Onstad DW. insectDisease: programmatic access to the ecological database of the world’s insect pathogens. Ecography 2022; 2022:e06152 [View Article]
    [Google Scholar]
  10. Wennmann JT, Keilwagen J, Jehle JA. Baculovirus Kimura two-parameter species demarcation criterion is confirmed by the distances of 38 core gene nucleotide sequences. J Gen Virol 2018; 99:1307–1320 [View Article] [PubMed]
    [Google Scholar]
  11. Afonso CL, Tulman ER, Lu Z, Balinsky CA, Moser BA et al. Genome sequence of a baculovirus pathogenic for Culex nigripalpus. J Virol 2001; 75:11157–11165 [View Article] [PubMed]
    [Google Scholar]
  12. Jehle JA, Lange M, Wang H, Hu Z, Wang Y et al. Molecular identification and phylogenetic analysis of baculoviruses from Lepidoptera. Virology 2006; 346:180–193 [View Article] [PubMed]
    [Google Scholar]
  13. Lauzon HAM, Lucarotti CJ, Krell PJ, Feng Q, Retnakaran A et al. Sequence and organization of the Neodiprion lecontei nucleopolyhedrovirus genome. J Virol 2004; 78:7023–7035 [View Article] [PubMed]
    [Google Scholar]
  14. van Oers MM, Vlak JM. Baculovirus genomics. Curr Drug Targets 2007; 8:1051–1068 [View Article] [PubMed]
    [Google Scholar]
  15. Chateigner A, Bézier A, Labrousse C, Jiolle D, Barbe V et al. Ultra deep sequencing of a Baculovirus population reveals widespread genomic variations. Viruses 2015; 7:3625–3646 [View Article] [PubMed]
    [Google Scholar]
  16. Ewing B, Green P. Base-calling of automated sequencer traces using Phred. II. Error probabilities. Genome Res 1998; 8:186–194 [View Article] [PubMed]
    [Google Scholar]
  17. Ewing B, Hillier L, Wendl MC, Green P. Base-calling of automated sequencer traces using Phred. I. Accuracy assessment. Genome Res 1998; 8:175–185 [View Article] [PubMed]
    [Google Scholar]
  18. Harrison RL, Rowley DL. The Parapoynx stagnalis nucleopolyhedrovirus (PastNPV), a divergent member of the Alphabaculovirus group I clade, encodes a homolog of ran GTPase. Viruses 2022; 14:2289 [View Article] [PubMed]
    [Google Scholar]
  19. Liu L, Zhang Z, Liu C, Qu L, Wang D. Genome analysis of an alphabaculovirus isolated from the Larch Looper, Erannis ankeraria. Viruses 2021; 14:34 [View Article] [PubMed]
    [Google Scholar]
  20. Marsberg T, Jukes MD, Krejmer-Rabalska M, Rabalski L, Knox CM et al. Morphological, genetic and biological characterisation of a novel alphabaculovirus isolated from Cryptophlebia peltastica (Lepidoptera: Tortricidae). J Invertebr Pathol 2018; 157:90–99 [View Article] [PubMed]
    [Google Scholar]
  21. Cory JS, Green BM, Paul RK, Hunter-Fujita F. Genotypic and phenotypic diversity of a baculovirus population within an individual insect host. J Invertebr Pathol 2005; 89:101–111 [View Article] [PubMed]
    [Google Scholar]
  22. Gettig RR, McCarthy WJ. Genotypic variation among wild isolates of Heliothis spp nuclear polyhedrosis viruses from different geographical regions. Virology 1982; 117:245–252 [View Article] [PubMed]
    [Google Scholar]
  23. Harrison RL. Concentration- and time-response characteristics of plaque isolates of Agrotis ipsilon multiple nucleopolyhedrovirus derived from a field isolate. J Invertebr Pathol 2013; 112:159–161 [View Article] [PubMed]
    [Google Scholar]
  24. Hodgson DJ, Vanbergen AJ, Hartley SE, Hails RS, Cory JS. Differential selection of baculovirus genotypes mediated by different species of host food plant. Ecol Lett 2002; 5:512–518 [View Article]
    [Google Scholar]
  25. Fan J, Wennmann JT, Wang D, Jehle JA. Single nucleotide polymorphism (SNP) frequencies and distribution reveal complex genetic composition of seven novel natural isolates of Cydia pomonella granulovirus. Virology 2020; 541:32–40 [View Article] [PubMed]
    [Google Scholar]
  26. Masson T, Fabre ML, Pidre ML, Niz JM, Berretta MF et al. Genomic diversity in a population of Spodoptera frugiperda nucleopolyhedrovirus. Infect Genet Evol 2021; 90:104749 [View Article] [PubMed]
    [Google Scholar]
  27. Fan J, Jehle JA, Wennmann JT. Population structure of Cydia pomonella granulovirus isolates revealed by quantitative analysis of genetic variation. Virus Evol 2021; 7:veaa073 [View Article] [PubMed]
    [Google Scholar]
  28. Gani M, Senger S, Lokanath S, Saini P, Bali K et al. Patterns in genotype composition of Indian isolates of the Bombyx mori nucleopolyhedrovirus and Bombyx mori bidensovirus. Viruses 2021; 13:901 [View Article] [PubMed]
    [Google Scholar]
  29. Wennmann JT, Fan J, Jehle JA. Bacsnp: using single nucleotide polymorphism (SNP) specificities and frequencies to identify genotype composition in baculoviruses. Viruses 2020; 12:625 [View Article] [PubMed]
    [Google Scholar]
  30. Eisenstein M. Oxford nanopore announcement sets sequencing sector abuzz. Nat Biotechnol 2012; 30:295–296 [View Article] [PubMed]
    [Google Scholar]
  31. Heather JM, Chain B. The sequence of sequencers: the history of sequencing DNA. Genomics 2016; 107:1–8 [View Article] [PubMed]
    [Google Scholar]
  32. El-Salamouny S, Wennmann JT, Kleespies RG, Richert-Pöggeler KR, Mansour A et al. Identification of a new nucleopolyhedrovirus isolated from the olive leaf moth, Palpita vitrealis, from two locations in Egypt. J Invertebr Pathol 2022; 192:107770 [View Article] [PubMed]
    [Google Scholar]
  33. Moldován N, Tombácz D, Szűcs A, Csabai Z, Balázs Z et al. Third-generation sequencing reveals extensive polycistronism and transcriptional overlapping in a baculovirus. Sci Rep 2018; 8:8604 [View Article] [PubMed]
    [Google Scholar]
  34. Sereika M, Kirkegaard RH, Karst SM, Michaelsen TY, Sørensen EA et al. Oxford nanopore R10.4 long-read sequencing enables the generation of near-finished bacterial genomes from pure cultures and metagenomes without short-read or reference polishing. Nat Methods 2022; 19:823–826 [View Article] [PubMed]
    [Google Scholar]
  35. Kumar P, Baig M, Sengupta K. Handbook on Pest and Disease Control of Mulberry and Silkworm UN; 1990
    [Google Scholar]
  36. van Oers MM, Herniou EA, Jehle JA, Krell PJ, Abd-Alla AMM et al. Developments in the classification and nomenclature of arthropod-infecting large DNA viruses that contain pif genes. Arch Virol 2023; 168:182 [View Article] [PubMed]
    [Google Scholar]
  37. Cheng R-L, Xu Y-P, Zhang C-X. Genome sequence of a Bombyx mori nucleopolyhedrovirus strain with cubic occlusion bodies. J Virol 2012; 86:10245 [View Article] [PubMed]
    [Google Scholar]
  38. Fan H-W, Zhang X-C, Xu Y-P, Cheng X-W, Zhang C-X. Genome of a Bombyx mori nucleopolyhedrovirus strain isolated from India. J Virol 2012; 86:11941 [View Article] [PubMed]
    [Google Scholar]
  39. Gomi S, Majima K, Maeda S. Sequence analysis of the genome of Bombyx mori nucleopolyhedrovirus. J Gen Virol 1999; 80:1323–1337 [View Article] [PubMed]
    [Google Scholar]
  40. Xu Y-P, Gu L-Z, Lou Y-H, Cheng R-L, Xu H-J et al. A baculovirus isolated from wild silkworm encompasses the host ranges of Bombyx mori nucleopolyhedrosis virus and Autographa californica multiple nucleopolyhedrovirus in cultured cells. J Gen Virol 2012; 93:2480–2489 [View Article] [PubMed]
    [Google Scholar]
  41. Wood DE, Lu J, Langmead B. Improved metagenomic analysis with Kraken 2. Genome Biol 2019; 20:257 [View Article] [PubMed]
    [Google Scholar]
  42. Breitwieser FP, Salzberg SL. Pavian: interactive analysis of metagenomics data for microbiome studies and pathogen identification. Bioinformatics 2020; 36:1303–1304 [View Article] [PubMed]
    [Google Scholar]
  43. Gary S, Schneider TD, Gold L, Ehrenfreuch A. “Use of the “Perceptron” algorithm to distinguish transitional initiation sites in E. Coli”. Nucleic Acids Res 1982
    [Google Scholar]
  44. Aitkin M, Wilson GT. Mixture models, outliers, and the EM algorithm. Technometrics 1980; 22:325–331 [View Article]
    [Google Scholar]
  45. Grau J, Keilwagen J, Gohr A, Haldemann B, Posch S et al. Jstacs: a Java framework for statistical analysis and classification of biological sequences. J Mach Learn Res 2012; 13:1967–1971
    [Google Scholar]
  46. Lin Y, Yuan J, Kolmogorov M, Shen MW, Chaisson M et al. Assembly of long error-prone reads using de Bruijn graphs. Proc Natl Acad Sci U S A 2016; 113:E8396–E8405 [View Article] [PubMed]
    [Google Scholar]
  47. Zheng Z, Li S, Su J, Leung A-S, Lam T-W et al. Symphonizing pileup and full-alignment for deep learning-based long-read variant calling. Bioinformatics 2021 [View Article]
    [Google Scholar]
  48. Koren S, Rhie A, Walenz BP, Dilthey AT, Bickhart DM et al. De novo assembly of haplotype-resolved genomes with trio binning. Nat Biotechnol 2018; 36:1174–1182 [View Article] [PubMed]
    [Google Scholar]
  49. Koren S, Walenz BP, Berlin K, Miller JR, Bergman NH et al. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res 2017; 27:722–736 [View Article] [PubMed]
    [Google Scholar]
  50. Nurk S, Walenz BP, Rhie A, Vollger MR, Logsdon GA et al. HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads. Genome Res 2020; 30:1291–1305 [View Article] [PubMed]
    [Google Scholar]
  51. Wick RR, Judd LM, Gorrie CL, Holt KE. Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol 2017; 13:e1005595 [View Article] [PubMed]
    [Google Scholar]
  52. Krueger F. Trim Galore: a wrapper tool around cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files [WWW document]; 2015
  53. Knyazev S, Tsyvina V, Shankar A, Melnyk A, Artyomenko A et al. Accurate assembly of minority viral haplotypes from next-generation sequencing through efficient noise reduction. Nucleic Acids Res 2021; 49:e102 [View Article] [PubMed]
    [Google Scholar]
  54. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2009; 25:1754–1760 [View Article] [PubMed]
    [Google Scholar]
  55. Li H, Durbin R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 2010; 26:589–595 [View Article] [PubMed]
    [Google Scholar]
  56. Luo X, Kang X, Schönhuth A. Strainline: full-length de novo viral haplotype reconstruction from noisy long reads. Genome Biol 2022; 23:29 [View Article] [PubMed]
    [Google Scholar]
  57. Darling ACE, Mau B, Blattner FR, Perna NT. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res 2004; 14:1394–1403 [View Article] [PubMed]
    [Google Scholar]
  58. Kumar S, Stecher G, Tamura K. MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article] [PubMed]
    [Google Scholar]
  59. Rohrmann GF. Baculovirus molecular biology, 4th. edn Bethesda (MD): National Center for Biotechnology Information (US); 2019
    [Google Scholar]
  60. Larem A, Ben-Tiba S, Wennmann JT, Gueli Alletti G, Jehle JA. Elucidating the genetic diversity of Phthorimaea operculella granulovirus (PhopGV). J Gen Virol 2019; 100:679–690 [View Article] [PubMed]
    [Google Scholar]
  61. do Lago BV, Bezerra CS, Moreira DA, Parente TE, Portilho MM et al. Genetic diversity of hepatitis B virus quasispecies in different biological compartments reveals distinct genotypes. Sci Rep 2023; 13:17023 [View Article] [PubMed]
    [Google Scholar]
  62. Lin P, Jin T, Yu X, Liang L, Liu G et al. Composition and dynamics of H1N1 and H7N9 influenza A virus quasispecies in a co-infected patient analyzed by single molecule sequencing technology. Front Genet 2021; 12:754445 [View Article] [PubMed]
    [Google Scholar]
  63. Meleshko D, Hajirasouliha I, Korobeynikov A. coronaSPAdes: from biosynthetic gene clusters to RNA viral assemblies. Bioinformatics 2021; 38:1–8 [View Article] [PubMed]
    [Google Scholar]
  64. Prabhakaran S, Rey M, Zagordi O, Beerenwinkel N, Roth V. HIV haplotype inference using a propagating Dirichlet process mixture model. IEEE/ACM Trans Comput Biol Bioinform 2014; 11:182–191 [View Article] [PubMed]
    [Google Scholar]
  65. Ahn S, Vikalo H. aBayesQR: a Bayesian method for reconstruction of viral populations characterized by low diversity. J Comput Biol 2018; 25:637–648 [View Article] [PubMed]
    [Google Scholar]
  66. Töpfer A, Marschall T, Bull RA, Luciani F, Schönhuth A et al. Viral quasispecies assembly via maximal clique enumeration. PLoS Comput Biol 2014; 10:e1003515 [View Article] [PubMed]
    [Google Scholar]
  67. Zagordi O, Bhattacharya A, Eriksson N, Beerenwinkel N. ShoRAH: estimating the genetic diversity of a mixed sample from next-generation sequencing data. BMC Bioinform 2011; 12:119 [View Article] [PubMed]
    [Google Scholar]
  68. Baaijens JA, Aabidine AZE, Rivals E, Schönhuth A. De novo assembly of viral quasispecies using overlap graphs. Genome Res 2017; 27:835–848 [View Article] [PubMed]
    [Google Scholar]
  69. Chen J, Zhao Y, Sun Y. De novo haplotype reconstruction in viral quasispecies using paired-end read guided path finding. Bioinformatics 2018; 34:2927–2935 [View Article] [PubMed]
    [Google Scholar]
  70. Freire B, Ladra S, Parama JR, Salmela L. ViQUF: De novo viral quasispecies reconstruction using unitig-based flow networks. IEEE/ACM Trans Comput Biol Bioinform 2023; 20:1550–1562 [View Article] [PubMed]
    [Google Scholar]
  71. Freire B, Ladra S, Paramá JR, Salmela L. Inference of viral quasispecies with a paired de Bruijn graph. Bioinformatics 2021; 37:473–481 [View Article] [PubMed]
    [Google Scholar]
  72. Bateman KS, Kerr R, Stentiford GD, Bean TP, Hooper C et al. Identification and full characterisation of two novel Crustacean infecting members of the family Nudiviridae provides support for two subfamilies. Viruses 2021; 13:1694 [View Article] [PubMed]
    [Google Scholar]
  73. Hikida H, Okazaki Y, Zhang R, Nguyen TT, Ogata H. A rapid genome-wide analysis of isolated giant viruses using MinION sequencing. Microbiology 2023; 25:2621–2635 [View Article]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/jgv/10.1099/jgv.0.001983
Loading
/content/journal/jgv/10.1099/jgv.0.001983
Loading

Data & Media loading...

Supplements

Supplementary material 1

EXCEL

Supplementary material 2

EXCEL

Supplementary material 3

EXCEL
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error