Archives of Virology

, Volume 161, Issue 4, pp 1019–1026 | Cite as

Identification and in silico characterisation of defective molecules associated with isolates of banana bunchy top virus

  • Daisy Stainton
  • Darren P. Martin
  • David A. Collings
  • John E. Thomas
  • Arvind VarsaniEmail author
Brief Report


Banana bunchy top virus (BBTV) is a multi-component single-stranded DNA virus. From 267 potentially infected Musa plants, 24 apparently ‘defective’ BBTV components have been identified. Interestingly, 23/24 of these defective molecules were apparently derived from DNA-R. All of the identified defective molecules had retained at least part of the CR-SL and CR-M but had insertions and/or deletions that in most cases resulted in open reading frame disruptions. Our detection of three monophyletic but diverse (and therefore likely circulating) defective DNA-R lineages suggests that, in many cases, defective DNA-R molecules might remain associated with BBTV genomes for prolonged periods.


Banana bunchy top virus Nanovirus Defective molecules 



D.S was supported by a postgraduate scholarship from the Marsden Fund of New Zealand (UOC0903). AV and DPM are supported by the National Research Foundation of South Africa. This work was supported by the Marsden Fund Council from government funding, administered by the Royal Society of New Zealand (grant UOC0903) awarded to AV.

Supplementary material

705_2015_2736_MOESM1_ESM.txt (26 kb)
Supplementary Data 1 Fasta file of defective BBTV sequences (TXT 25 kb)
705_2015_2736_MOESM2_ESM.pdf (361 kb)
Supplementary Figure 1 Insert and deletion breakpoint distribution plot where total numbers of breakpoints falling within a 200-nt moving window have been plotted across DNA-R (black line). Points where the black line emerges above the dark grey (95% confidence interval on the expected number of breakpoints at particular genome sites) and light grey (99% confidence interval) areas indicate statistically significant degrees of breakpoint clustering. Two breakpoint hotspots detected at a p–value significance threshold ≤ 0.01) are highlighted in red. (PDF 361 kb)
705_2015_2736_MOESM3_ESM.pdf (977 kb)
Supplementary Figure 2 Maximum-likelihood phylogenetic tree of the rep coding region of the defective DNA-R molecule sequences (insert regions removed) and 302 DNA-R components (see Supplementary Table 1). The phylogenetic tree was rooted with ABTV DNA-R sequences, and branches with < 60% bootstrap support were collapsed. Isolate information is available in Supplementary Table 1 for the DNA-R sequences and in Table 1 for the defective genomes (PDF 977 kb)
705_2015_2736_MOESM4_ESM.doc (282 kb)
Supplementary Table 1 List of DNA-R sequences used in Figure 2 with two-letter country codes: AU, Australia; BI, Burundi; CD, Democratic Republic of Congo; CG, Congo; CN, China; EG, Egypt; FJ, Fiji; ID, Indonesia; IN, India; JP, Japan; LK, Sri Lanka; MM, Myanmar; MY, Malaysia; MW, Malawi; PH, Philippines; PK, Pakistan; RW, Rwanda; TO, Tonga; TW, Taiwan; US, United States of America; VN, Vietnam; WS, Samoa (DOC 282 kb)


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Copyright information

© Springer-Verlag Wien 2016

Authors and Affiliations

  1. 1.School of Biological Sciences and Biomolecular Interaction CentreUniversity of CanterburyChristchurchNew Zealand
  2. 2.Department of Clinical Laboratory SciencesUniversity of Cape TownCape TownSouth Africa
  3. 3.Ecosciences Precinct, Queensland Alliance for Agriculture and Food Innovation, Centre for Plant ScienceThe University of QueenslandBrisbaneAustralia
  4. 4.Department of Plant Pathology, Emerging Pathogens InstituteUniversity of FloridaGainesvilleUSA

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