Browsing by Author "Varsani, Arvind"

Now showing 1 - 6 of 6
  • Thumbnail Image
    Item
    Avihepadnavirus diversity in parrots is comparable to that found amongst all other avian species
    (Elsevier, 2013) Piasecki, Tomasz; Harkins, Gordon William; Chrzastek, Klaudia; Julian, Laurel; Martin, Darren Patrick; Varsani, Arvind
    Avihepadna viruses have previously been isolated from various species of duck ,goose, stork, heron and crane. Recently the first parrot avihepadna virus was isolated from a Ring-necked Parakeet in Poland. In this study, 41 psittacineliver samples archived in Poland over the last nine years were tested for presence of Parrot hepatitis B virus(PHBV). We cloned and sequenced PHBVisolates from 18 birds including a Crimson Rosella, an African grey parrot and sixteen Ring-necked Parakeets. PHBVisolates display a degree of diversity (478% genome wide pair wise identity) that is comparable to that found amongst all other avihepadna viruses (479% genome wide pair wise identity). The PHBV viruses can be subdivided into seven genetically distinct groups (tentatively named A-G) of which the two isolated of PHBV-Gare the most divergent sharing 79% genome wide pair wise identity with all their PHBVs. All PHBV isolates display classical avihepadnavirus genome architecture.
  • Thumbnail Image
    Item
    Diverse genomoviruses representing twenty-nine species identified associated with plants
    (Springer Nature, 2020) Fontenele, Rafaela Salgado; Varsani, Arvind; Lefeuvre, Pierre F.
    Genomoviruses (family Genomoviridae) are circular single-stranded DNA viruses that have been mainly identifed through metagenomics studies in a wide variety of samples from various environments. Here, we describe 98 genomes of genomoviruses found associated with members of 19 plant families from Australia, Brazil, France, South Africa and the USA. These 98 genomoviruses represent 29 species, 26 of which are new, in the genera Gemykolovirus (n = 37), Gemyduguivirus (n = 9), Gemygorvirus (n = 8), Gemykroznavirus (n = 6), Gemycircularvirus (n = 21) and Gemykibivirus (n = 17).
  • Thumbnail Image
    Item
    Evidence of pervasive biologically functional secondary structures within the Genomes of Eukaryotic Single-Stranded DNA Viruses
    (American Society for Microbiology, 2013) Muhire, Brejnev Muhizi; Golden, Michael; Tanov, Emil Pavlov; Harkins, Gordon William; Murrell, Ben; Lefeuvre, Pierre; Lett, Jean-Michel; Gray, Alistair; Poon, Art Y. F.; Ngandu, Nobubelo Kwanele; Semegni, Yves; Monjane, Adérito Luis; Varsani, Arvind; Shepherd, Dionne Natalie; Martin, Darren Patrick
    Single-stranded DNA (ssDNA) viruses have genomes that are potentially capable of forming complex secondary structures through Watson-Crick base pairing between their constituent nucleotides. A few of the structural elements formed by such base pairings are, in fact, known to have important functions during the replication of many ssDNA viruses. Unknown, however, are (i) whether numerous additional ssDNA virus genomic structural elements predicted to exist by computational DNA folding methods actually exist and (ii) whether those structures that do exist have any biological relevance. We therefore computationally inferred lists of the most evolutionarily conserved structures within a diverse selection of animal- and plant-infecting ssDNA viruses drawn from the families Circoviridae, Anelloviridae, Parvoviridae, Nanoviridae, and Geminiviridae and analyzed these for evidence of natural selection favoring the maintenance of these structures. While we find evidence that is consistent with purifying selection being stronger at nucleotide sites that are predicted to be base paired than at sites predicted to be unpaired, we also find strong associations between sites that are predicted to pair with one another and site pairs that are apparently coevolving in a complementary fashion. Collectively, these results indicate that natural selection actively preserves much of the pervasive secondary structure that is evident within eukaryote-infecting ssDNA virus genomes and, therefore, that much of this structure is biologically functional. Lastly, we provide examples of various highly conserved but completely uncharacterized structural elements that likely have important functions within some of the ssDNA virus genomes analyzed here.
  • Thumbnail Image
    Item
    Evidence that dicot-infecting mastreviruses are particularly prone to inter-species recombination and have likely been circulating in Australia for longer than in Africa and the Middle East
    (Elsevier, 2013) Kraberger, Simona; Harkins, Gordon William; Kumari, Safaa G.; Thomas, John E.; Schwinghamer, Mark W.; Sharman, Murray; Collings, David A.; Briddon, Rob W.; Martin, Darren Patrick; Varsani, Arvind
    Viruses of the genus Mastrevirus (family Geminiviridae) are transmitted by leafhoppers and infect either mono- or dicotyledonous plants. Here we have determined the full length sequences of 49 dicot-infecting mastrevirus isolates sampled in Australia, Eritrea, India, Iran, Pakistan, Syria, Turkey and Yemen. Comprehensive analysis of all available dicot-infecting mastrevirus sequences showed the diversity of these viruses in Australia to be greater than in the rest of their known range, consistent with earlier studies, and that, in contrast with the situation in monocot-infecting mastreviruses, detected inter-species recombination events outnumbered intra-species recombination events. Consistent with Australia having the greatest diversity of known dicot-infecting mastreviruses phylogeographic analyses indicating the most plausible scheme for the spread of these viruses to their present locations, suggest that most recent common ancestor of these viruses is likely nearer Australia than it is to the other regions investigated.
  • Thumbnail Image
    Item
    Extensive recombination detected among beak and feather disease virus isolates from breeding facilities in Poland
    (Microbiology Society, 2013) Julian, Laurel; Piasecki, Tomasz; Chrzastek, Klaudia; Walters, Matthew; Muhire, Brejnev; Harkins, Gordon William; Martin, Darren Patrick; Varsani, Arvind
    Beak and feather disease virus (BFDV) causes the highly contagious, in some cases fatal, psittacine beak and feather disease in parrots. The European continent has no native parrots, yet in the past has been one of the world’s biggest importers of wild-caught exotic parrot species. Following the banning of this practice in 2007, the demand for exotic pet parrots has largely been met by established European breeding facilities, which can also supply buyers outside Europe. However, the years of unregulated importation have provided numerous opportunities for BFDV to enter Europe, meaning the likelihood of birds within captive breeding facilities being BFDV positive is high. This study examined the BFDV status of such facilities in Poland, a country previously shown to have BFDV among captive birds. A total of 209 birds from over 50 captive breeding facilities across Poland were tested, and 43 birds from 18 different facilities tested positive for BFDV. The full BFDV genomes from these 43 positive birds were determined, and phylogenetic analysis revealed that these samples harboured a relatively high degree of diversity and that they were highly recombinant. It is evident that there have been multiple introductions of BFDV into Poland over a long period of time, and the close association of different species of birds in the captive environment has probably facilitated the evolution of new BFDV strains through recombination.
  • Thumbnail Image
    Item
    Post-translational cleavage of recombinantly expressed nitrilase from Rhodococcus rhodochrous J1 yields a stable, active helical form
    (Wiley, 2007) Thuku, Ndoria R.; Weber, Brandon W.; Varsani, Arvind
    Nitrilases convert nitriles to the corresponding carboxylic acids and ammonia. The nitrilase from Rhodococcus rhodochrous J1 is known to be inactive as a dimer but to become active on oligomerization. The recombinant enzyme undergoes post-translational cleavage at approximately residue 327, resulting in the formation of active, helical homo-oligomers. Determining the 3D structure of these helices using electron microscopy, followed by fitting the stain envelope with a model based on homology with other members of the nitrilase superfamily, enables the interacting surfaces to be identified. This also suggests that the reason for formation of the helices is related to the removal of steric hindrance arising from the 39 C-terminal amino acids from the wild-type protein. The helical form can be generated by expressing only residues 1–327.