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A new African streak virus species from Nigeria

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Abstract

The African streak viruses (AfSVs) are a diverse group of mastrevirus species (family Geminiviridae) that infect a wide variety of annual and perennial grass species across the African continent and its nearby Indian Ocean islands. Six AfSV species (of which maize streak virus is the best known) have been described. Here we report the full genome sequences of eight isolates of a seventh AfSV species: Urochloa streak virus (USV), sampled from various locations in Nigeria. Despite there being good evidence of recombination in many other AfSV species, we found no convincing evidence that any of the USV sequences were either inter- or intra-species recombinants. The USV isolates, all of which appear to be variants of the same strain (their genome sequences are all more than 98% identical), share less than 69% nucleotide sequence identity with other currently described AfSV species.

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Acknowledgments

This research was partially funded by the National Research Foundation (South Africa). A. V. is supported by the Carnegie Corporation of New York. D. N. S. is supported by PANNAR (Pty) Ltd; D. P. M. is supported by the Wellcome trust; B. O. is supported by the Rockefeller foundation through the USHEPiA programme; A. L. M. is supported by the Canon Collins Trust for Southern Africa and a University of Cape Town International Scholarship.

Author information

Authors and Affiliations

  1. Department of Crop, Soil and Environmental Management, Bowen University, P.M.B 284, Iwo, Osun State, Nigeria

    Sunday Oluwafemi

  2. Electron Microscope Unit, University of Cape Town, Private Bag, Rondebosch, Cape Town, 7701, South Africa

    Arvind Varsani

  3. Department of Molecular and Cell Biology, University of Cape Town, Private Bag, Rondebosch, 7701, South Africa

    Arvind Varsani, Adérito L. Monjane, Dionne N. Shepherd, Betty E. Owor & Edward P. Rybicki

  4. Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, Anzio Rd, Cape Town, 7925, South Africa

    Edward P. Rybicki & Darren P. Martin

Authors
  1. Sunday Oluwafemi
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  2. Arvind Varsani
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  3. Adérito L. Monjane
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  4. Dionne N. Shepherd
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  5. Betty E. Owor
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  6. Edward P. Rybicki
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  7. Darren P. Martin
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Corresponding author

Correspondence to Arvind Varsani.

Electronic supplementary material

Below is the link to the electronic supplementary material.

705_2008_123_MOESM1_ESM.doc

Supplementary Figure 1. Annotated genome sequence alignments of four of the new USV sequences together with a selection of major strain variants from other publicly available African streak virus species. Sequences either known or believed to have some role in mastrevirus replication and transcription are marked together with a corresponding label on the nucleotide sequence alignments. To highlight differences between the sequences, wherever nucleotides in a particular alignment column are identical to that of USV-[NIwo] they are replaced with a “-” character. In columns where they differ from USV-[NIwo] they are shown in lower case. “.” Characters denote gaps that have been inserted during alignment. [1] Stenger, et al., 1991. Proc Natl Acad Sci U S A.88:8029-8033; [2] Sunter, et al. 1985. Nucleic Acids Res. 13:4645-4659; [3] Argüello-Astorga et al. 1994. Virology. 203:90-100; [4] Suárez-López et al. 1995. Virology. 208:303-311; [5] Morris-Krsinich et al. 1985.. Nucleic Acids Res.13:7237-7256; [6] Boulton et al. 1989. J Gen Virol. 70:2309-2323; [7] Wright et al.1997 Plant J. 2:1285-1297; [8] Donson et al. 1984. EMBO J. 3:3069-3073; [9] Dekker et al. 1991. Nucleic Acids Res. 19:4075-4081; [10] Fenoll et al. 1990. Plant. Mol. Biol. 15:865-877. (DOC 253 kb)

705_2008_123_MOESM2_ESM.doc

Supplementary Figure 2. Annotated predicted movement protein amino acid sequence alignments of four of the new USV sequences, together with a selection of major strain variants from other publicly available African streak virus species. The hydrophobic, potentially membrane-spanning internal domain of the sequences is highlighted. Wherever amino acids in a particular alignment column are identical to that of USV-[NIwo] they are replaced with a “-” character. In columns where they differ from USV-[NIwo] they are shown in lower case. “.” Characters denote gaps that have been inserted during alignment. [1] Wright et al.1997 Plant J. 2:1285-1297. (DOC 26 kb)

705_2008_123_MOESM3_ESM.doc

Supplementary Figure 3. Annotated predicted coat protein amino acid sequence alignments of four of the new USV sequences, together with a selection of major strain variants from other publicly available African streak virus species. The potential nuclear localization signal and DNA binding domains (inferred by analogy with those determined for MSV) are highlighted on the sequence. Wherever amino acids in a particular alignment column are identical to that of USV-[NIwo] they are replaced with a “-” character. In columns where they differ from USV-[NIwo] they are shown in lower case. “.” Characters denote gaps that have been inserted during alignment. [1] Liu et al. 1999. Mol. Plant Microbe Interact. 12:894-900; [2] Liu et al. 1997. J. Gen. Virol. 78: 1265-1270. (DOC 33 kb)

705_2008_123_MOESM4_ESM.doc

Supplementary Figure 4. Annotated predicted replication-associated protein amino acid sequence alignments of four of the new USV sequences, together with a selection of major strain variants from other publicly available African streak virus species. Potential rolling-circle replication motifs and interaction domains inferred by analogy with MSV and wheat dwarf virus are highlighted. Wherever amino acids in a particular alignment column are identical to that of USV-[NIwo] they are replaced with a “-” character. In columns where they differ from USV-[NIwo] they are shown in lower case. “.” Characters denote gaps that have been inserted during alignment. [1] Koonin & Ilyina. 1992. J Gen Virol. 73:2763-2766; [2] Horvath et al. 1998. Plant Mol. Biol. 38:699-712; [3] Xie et al. 1995. EMBO J. 14:4073-4082; [4] Gorbalenya & Koonin. 1989. Nucl. Acids Res. 17:8413-8440. (DOC 39 kb)

705_2008_123_MOESM5_ESM.doc

Supplementary Figure 5. Annotated predicted RepA amino acid sequence alignments of four of the new USV sequences, together with a selection of major strain variants from other publicly available African streak virus species. Potential rolling-circle replication motifs and interaction domains inferred by analogy with MSV and wheat dwarf virus are highlighted. Wherever amino acids in a particular alignment column are identical to that of USV-[NIwo] they are replaced with a “-” character. In columns where they differ from USV-[NIwo] they are shown in lower case. “.” Characters denote gaps that have been inserted during alignment. [1] Koonin & Ilyina. 1992. J Gen Virol, 73:2763-2766; [2] Horvath et al. 1998. Plant Mol. Biol. 38:699-712; [3] Xie et al. 1995. EMBO J. 14:4073-4082; [4] Xie et al. 1999. Plant Mol. Biol. 39:647-656. (DOC 39 kb)

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Oluwafemi, S., Varsani, A., Monjane, A.L. et al. A new African streak virus species from Nigeria. Arch Virol 153, 1407–1410 (2008). https://doi.org/10.1007/s00705-008-0123-9

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