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Genetic analysis of maize streak virus isolates from Uganda reveals widespread distribution of a recombinant variant

¹ Department of Molecular and Cell Biology, University of Cape Town, Private Bag, Rondebosch 7701, South Africa
² Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Anzio Rd, Observatory 7925, South Africa
³ Department of Crop Science, Faculty of Agriculture, Makerere University, PO Box 7062, Kampala, Uganda
⁴ Electron Microscope Unit, University of Cape Town, Private Bag, Rondebosch 7701, South Africa

Correspondence
Arvind Varsani
arvind.varsani{at}uct.ac.za

Maize streak virus (MSV) contributes significantly to the problem of extremely low African maize yields. Whilst a diverse range of MSV and MSV-like viruses are endemic in sub-Saharan Africa and neighbouring islands, only a single group of maize-adapted variants – MSV subtypes A₁–A₆ – causes severe enough disease in maize to influence yields substantially. In order to assist in designing effective strategies to control MSV in maize, a large survey covering 155 locations was conducted to assess the diversity, distribution and genetic characteristics of the Ugandan MSV-A population. PCR–restriction fragment-length polymorphism analyses of 391 virus isolates identified 49 genetic variants. Sixty-two full-genome sequences were determined, 52 of which were detectably recombinant. All but two recombinants contained predominantly MSV-A₁-like sequences. Of the ten distinct recombination events observed, seven involved inter-MSV-A subtype recombination and three involved intra-MSV-A₁ recombination. One of the intra-MSV-A₁ recombinants, designated MSV-A₁UgIII, accounted for >60 % of all MSV infections sampled throughout Uganda. Although recombination may be an important factor in the emergence of novel geminivirus variants, it is demonstrated that its characteristics in MSV are quite different from those observed in related African cassava-infecting geminivirus species.

The GenBank/EMBL/DDBJ accession numbers for sequences of MSV isolates determined in this study are EF547063–EF547124 (also shown individually in Table 1).

Supplementary figures, Excel tables and alignment files are available with the online version of this paper.

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