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1.
Arch Virol ; 165(5): 1231-1234, 2020 May.
Article in English | MEDLINE | ID: mdl-32152787

ABSTRACT

Severe mottling symptoms were observed on Carica papaya L. in Koyonzo, Kakamega County, Kenya. Total RNA was sequenced via an RNAtag-seq workflow. Assembled contigs indicated the presence of a divergent strain of Moroccan watermelon mosaic virus (genus Potyvirus) with a complete genome length of 9,733 nt (GenBank accession no. MN418119). Additionally, the complete genome sequence of a novel member of the viral genus Allexivirus was determined (GenBank accession no. MN418120). The genome contains six open reading frames (ORFs) that show varying degrees of sequence similarity to members of the genus Allexivirus; however, it appears to lack an ORF encoding a nucleic-acid-binding homolog. The tentative name "papaya virus A" (PaVA) has been proposed for this virus.


Subject(s)
Carica/virology , Flexiviridae/classification , Flexiviridae/isolation & purification , Metagenome , Plant Diseases/virology , Potyvirus/classification , Potyvirus/isolation & purification , Coinfection/virology , Flexiviridae/genetics , Genome, Viral , Kenya , Open Reading Frames , Phylogeny , Potyvirus/genetics , RNA, Viral/genetics , Sequence Analysis, DNA , Sequence Homology
2.
Arch Virol ; 164(6): 1711-1715, 2019 Jun.
Article in English | MEDLINE | ID: mdl-30900068

ABSTRACT

RNAtag-seq of maize samples collected in Tanzania revealed the presence of a previously undescribed nucleorhabdovirus, tentatively named "Morogoro maize-associated virus" (MMaV), in three samples. The MMaV genome is 12,185-12,187 nucleotides long and shares a 69-70% nucleotide sequence identity with taro vein chlorosis virus. Annotation of the genomes showed a typical nucleorhabdovirus gene organization. PCR was unable to detect the same virus in the remaining 35 samples collected in the region.


Subject(s)
Plant Diseases/virology , Rhabdoviridae/genetics , Sequence Analysis, RNA/methods , Zea mays/virology , Genome Size , Genome, Viral , Molecular Sequence Annotation , Open Reading Frames , Phylogeny , Plant Leaves/virology , Rhabdoviridae/classification , Rhabdoviridae/isolation & purification , Tanzania
3.
Virus Genes ; 55(3): 429-432, 2019 Jun.
Article in English | MEDLINE | ID: mdl-30790190

ABSTRACT

Typically associated with fungal species, members of the viral family Totiviridae have recently been shown to be associated with plants, including important crop species, such as Carica papaya (papaya) and Zea mays (maize). Maize-associated totivirus (MATV) was first described in China and more recently in Ecuador, where it has been found to co-occur with other viruses known to elicit maize lethal necrosis disease (MLND). In a survey for maize-associated viruses, 35 samples were selected for Illumina HiSeq sequencing, from the Tanzanian maize producing regions of Mara, Arusha, Manyara, Kilimanjaro, Morogoro and Pwani. Libraries were prepared using an RNA-tag-seq methodology. Taxonomic classification of the resulting datasets showed that 6 of the 35 samples from the regions of Arusha, Kilimanjaro, Morogoro and Mara, contained reads that were assigned to MATV reference sequences. This was confirmed with PCR and Sanger sequencing. Read assembly of the six MATV-associated datasets yielded partial MATV genomes, two of which were selected for further characterization, using RACE. This yielded two full-length MATV genomes, one of which is divergent from other available MATV genomes.


Subject(s)
Genetic Variation , Plant Diseases/virology , Totivirus/genetics , Zea mays/virology , China , Genome, Viral/genetics , Phylogeny , Plant Diseases/genetics , Totivirus/pathogenicity , Zea mays/genetics
4.
J Virol Methods ; 237: 107-113, 2016 11.
Article in English | MEDLINE | ID: mdl-27599411

ABSTRACT

Citrus tristeza virus (CTV) is present in almost all of the major citrus production areas where it continues to reduce the profitability of citriculture. The accurate characterisation of CTV populations, which are usually made up of a number of disparate strains, requires the use of robust PCR protocols. Mismatches between primers and their corresponding binding sites may introduce primer-associated bias during amplification. The primer-associated bias of four sets of CTV specific primers, targeting the A and F regions and the p33 and p23 genes, were evaluated. This was done through the amplification of defined templates followed by their characterisation using the sequencing of multiple clones, as well as Illumina next generation sequencing. High levels of bias were found to be associated with the primer pairs targeting the A and F regions. The p33 gene primers were found to be biased against two genotypes and suggestions for preventing this apparent bias are discussed. The primer pair targeting the conserved p23 gene was found to have very little associated bias. Primers should undergo rigorous screening before being used to characterize virus populations that are known to exhibit high levels of variation, especially within primer binding sites.


Subject(s)
Closterovirus/genetics , Genetic Variation , High-Throughput Nucleotide Sequencing/methods , Polymerase Chain Reaction , Binding Sites , Citrus/virology , DNA Primers , Genotype , High-Throughput Nucleotide Sequencing/standards , Phylogeny , Plant Diseases/virology , Polymerase Chain Reaction/methods , Polymerase Chain Reaction/standards
5.
Genome Announc ; 3(4)2015 Jul 16.
Article in English | MEDLINE | ID: mdl-26184931

ABSTRACT

We report here the complete genome sequence of "Candidatus Liberibacter africanus" strain PTSAPSY. The 1,192,232-bp genome with 34.5% G+C content comprises 1,017 open reading frames, 44 tRNAs, and three complete rRNAs in a circular chromosome.

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