Browsing by Author "Owor, Betty E"

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    Genetic analysis of maize streak virus isolates from Uganda reveals widespread distribution of a recombinant variant.
    (Microbiology Society, 2007) Owor, Betty E; Martin, Darren P; Shepherd, Dionne N; Edema, Richard; Monjane, Ade´rito L; Rybicki, Edward P; Thomson, Jennifer A; Vasani, Arvind
    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.
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    A new African streak virus species from Nigeria
    (Springer Verlag, 2008) Oluwafemi, Sunday; Varsani, Arvind; Monjane, Ade´rito L; Shepherd, Dionne N; Owor, Betty E; Rybicki, Edward P; Martin, Darren P
    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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    A novel species of mastrevirus (family Geminiviridae) isolated from Digitaria didactyla grass from Australia
    (Springer Verlag, 2010) Briddon, Rob W; Martin, Darren P; Owor, Betty E; Donaldson, Lara; Markham, Peter G; Varsani, Arvind; Greber, Ray S
    Mastreviruses (family Geminiviridae) that infect monocotyledonous plants occur throughout the temperate and tropical regions of Asia, Africa, Europe and Australia. Despite the identification of a very diverse array of mastrevirus species whose members infect African monocots, few such species have been discovered in other parts of the world. For example, the sequence of only a single monocot-infecting mastrevirus, Chloris striate mosaic virus (CSMV), has been reported so far from Australia, even though earlier biological and serological studies suggested that other distinct mastreviruses were present. Here, we have obtained the complete nucleotide sequence of a virus from the grass Digitaria didactyla originating from Australia. Analysis of the sequence shows the virus to be a typical mastrevirus, with four open reading frames, two in each orientation, separated by two noncoding intergenic regions. Although it showed the highest levels of sequence identity to CSMV (68.7%), their sequences are sufficiently diverse for the virus to be considered a member of a new species in the genus Mastrevirus, based on the present species demarcation criteria. We propose that the name first used during the 1980s be used for this species, Digitaria didactyla striate mosaic virus (DDSMV).
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    Novel sugarcane streak and sugarcane streak Reunion mastreviruses from southern Africa and La Réunion.
    (Springer Verlag, 2008) Shepherd, Dionne N; Varsani, Arvind; Windram, Oliver P; Lefeuvre, Pierre; Monjane, Ade´rito L; Owor, Betty E; Martin, Darren P
    The sugarcane infecting streak viruses (SISVs) are mastreviruses (Family Geminiviridae) belonging to a group of ‘‘African streak viruses’’ (AfSVs) that includes the economically devastating Maize streak virus (MSV). Although there are three currently described SISV species (Sugarcane streak virus [SSV], Sugarcane streak Egypt virus [SSEV] and Sugarcane streak Re´union virus [SSRV]), only one strain variant has been fully sequenced for each of these species and as a result very little is known about the diversity and evolutionary origins of the SCISVs. Here we present annotated full genome sequences of four new SISV isolates, including a new strain of both SSRV and SSV, and one potentially new SISV species, sampled from wild grasses in La Re´union and Zimbabwe. For the first time, we report the finding of SSRV isolates in Zimbabwe and SSV isolates on the island of La Re´union. Phylogenetic and recombination analyses indicate continent-wide SSRV strain diversity and that our isolate potentially representing a new SISV species is a recombinant.
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    A protocol for the rapid isolation of full geminivirus genomes from dried plant tissue
    (Elsevier, 2008) Shepherd, Dionne N; Martin, Darren P; Lefeuvre, Pierre; Monjane, Aderito L; Owor, Betty E; Rybicki, Edward P; Varsani, Arvind
    A high-throughput method of isolating and cloning geminivirus genomes from dried plant material, by combining an Extract-n-AmpTM-based DNA isolation technique with rolling circle amplification (RCA) of viral DNA, is presented. Using this method an attempt was made to isolate and clone full geminivirus genomes/genome components from 102 plant samples, including dried leaves stored at room temperature for between 6 months and 10 years, with an average hands-on-time to RCA-ready DNA of 15 min per 20 samples. While storage of dried leaves for up to 6 months did not appreciably decrease cloning success rates relative to those achieved with fresh samples, efficiency of the method decreased with increasing storage time. However, it was still possible to clone virus genomes from 47% of 10-year-old samples. To illustrate the utility of this simple method for high-throughput geminivirus diversity studies, six Maize streak virus genomes, an Abutilon mosaic virus DNA-B component and the DNA-A component of a previously unidentified New Word begomovirus species were fully sequenced. Genomic clones of the 69 other viruses were verified as such by end sequencing. This method should be extremely useful for the study of any circular DNA plant viruses with genome component lengths smaller than the maximum size amplifiable by RCA.
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    Recombination, decreased host specificity and increased mobility may have driven the emergence of maize streak virus as an agricultural pathogen.
    (Microbiology Society, 2008) Varsani, Arvind; Shepherd, Dionne N; Monjane, Ade´rito L; Owor, Betty E; Erdmann, Julia B; Rybicki, Edward P; Peterschmitt, Michel; Briddon, Rob W; Markham, Peter G; Oluwafemi, Sunday; Windram, Oliver P; Lefeuvre, Pierre; Lett, Jean-Michel; Martin, Darren P
    Maize streak virus (MSV; family Geminiviridae, genus Mastrevirus), the causal agent of maize streak disease, ranks amongst the most serious biological threats to food security in subSaharan Africa. Although five distinct MSV strains have been currently described, only one of these – MSV-A – causes severe disease in maize. Due primarily to their not being an obvious threat to agriculture, very little is known about the ‘grass-adapted’ MSV strains, MSV-B, -C, -D and -E. Since comparing the genetic diversities, geographical distributions and natural host ranges of MSV-A with the other MSV strains could provide valuable information on the epidemiology, evolution and emergence of MSV-A, we carried out a phylogeographical analysis of MSVs found in uncultivated indigenous African grasses. Amongst the 83 new MSV genomes presented here, we report the discovery of six new MSV strains (MSV-F to -K). The non-random recombination breakpoint distributions detectable with these and other available mastrevirus sequences partially mirror those seen in begomoviruses, implying that the forces shaping these breakpoint patterns have been largely conserved since the earliest geminivirus ancestors. We present evidence that the ancestor of all MSV-A variants was the recombinant progeny of ancestral MSV-B and MSV-G/-F variants. While it remains unknown whether recombination influenced the emergence of MSV-A in maize, our discovery that MSV-A variants may both move between and become established in different regions of Africa with greater ease, and infect more grass species than other MSV strains, goes some way towards explaining why MSV-A is such a successful maize pathogen.
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    Successful application of FTA Classic Card technology and use of bacteriophage phi29 DNA polymerase for large-scale field sampling and cloning of complete maize streak virus genomes
    (Elsevier, 2007) Owor, Betty E; Shepherd, Dionne N; Taylor, Nigel J; Edema, Richard; Monjane, Aderito L; Thomson, Jennifer A; Martin, Darren P; Varsani, Arvind
    Leaf samples from 155 maize streak virus (MSV)-infected maize plants were collected from 155 farmers’ fields in 23 districts in Uganda in May/June 2005 by leaf-pressing infected samples onto FTA® Classic Cards. Viral DNA was successfully extracted from cards stored at room temperature for 9 months. The diversity of 127 MSV isolates was analysed by PCR-generated RFLPs. Six representative isolates having different RFLP patterns and causing either severe, moderate or mild disease symptoms, were chosen for amplification from FTA cards by bacteriophage 29 DNA polymerase using the TempliPhiTM system. Full-length genomes were inserted into a cloning vector using a unique restriction enzyme site, and sequenced. The 1.3-kb PCR product amplified directly from FTA-eluted DNA and used for RFLP analysis was also cloned and sequenced. Comparison of cloned whole genome sequences with those of the original PCR products indicated that the correct virus genome had been cloned and that no errors were introduced by the 29 polymerase. This is the first successful large-scale application of FTA card technology to the field, and illustrates the ease with which large numbers of infected samples can be collected and stored for downstream molecular applications such as diversity analysis and cloning of potentially new virus genomes.