Browsing by Author "Harkins, Gordon William"

Now showing 1 - 7 of 7
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    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.
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    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.
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    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.
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    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.
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    Genome sequence of the tsetse fly (glossina morsitans): vector of African trypanosomiasis
    (American Association for the Advancement of Science, 2014) Christoffels, Alan; Obiero, George F.; Harkins, Gordon William
    Tsetse flies are the sole vectors of human African trypanosomiasis throughout sub-Saharan Africa. Both sexes of adult tsetse feed exclusively on blood and contribute to disease transmission. Notable differences between tsetse and other disease vectors include obligate microbial symbioses, viviparous reproduction, and lactation. Here, we describe the sequence and annotation of the 366-megabase Glossina morsitans morsitans genome. Analysis of the genome and the 12,308 predicted protein-encoding genes led to multiple discoveries, including chromosomal integrations of bacterial (Wolbachia) genome sequences, a family of lactation-specific proteins, reduced complement of host pathogen recognition proteins, and reduced olfaction/chemosensory associated genes. These genome data provide a foundation for research into trypanosomiasis prevention and yield important insights with broad implications for multiple aspects of tsetse biology.
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    Geometagenomics illuminates the impact of agriculture on the distribution and prevalence of plant viruses at the ecosystem scale
    (Nature Publishing Group, 2018) Bernardo, Pauline; Charles-Dominique, Tristan; Barakat, Mohamed; Ortet, Philippe; Harkins, Gordon William
    Disease emergence events regularly result from human activities such as agriculture, which frequently brings large populations of genetically uniform hosts into contact with potential pathogens. Although viruses cause nearly 50% of emerging plant diseases, there is little systematic information about virus distribution across agro-ecological interfaces and large gaps in understanding of virus diversity in nature. Here we applied a novel landscape-scale geometagenomics approach to examine relationships between agricultural land use and distributions of plantassociated viruses in two Mediterranean-climate biodiversity hotspots (Western Cape region of South Africa and Rhône river delta region of France). In total, we analysed 1725 geo-referenced plant samples collected over two years from 4.5 × 4.5 km2 grids spanning farmlands and adjacent uncultivated vegetation. We found substantial virus prevalence (25.8–35.7%) in all ecosystems, but prevalence and identified family-level virus diversity were greatest in cultivated areas, with some virus families displaying strong agricultural associations. Our survey revealed 94 previously unknown virus species, primarily from uncultivated plants. This is the first effort to systematically evaluate plant-associated viromes across broad agro-ecological interfaces. Our findings indicate that agriculture substantially influences plant virus distributions and highlight the extent of current ignorance about the diversity and roles of viruses in nature.
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    Self-maintaining or continuously refreshed? The genetic structure of Euphausia lucens populations in the Benguela upwelling ecosystem
    (Oxford University Press, 2013) Harkins, Gordon William; D'Amato, Maria Eugenia; Gibbons, Mark J.
    Populations of Euphausia lucens over the shelf of the southern Benguela upwelling region could be self-maintaining. Alternatively, they could be continually refreshed by expatriates from the SW Atlantic that enter the system via South Atlantic Central Water in the south, before developing and then being lost through advection off Namibia. These two hypotheses are investigated here by examining geographic heterogeneity and molecular variation (cox1 and ND1) of the species across its distributional range in the Southern Hemisphere. Comparisons are made with E. vallentini, which is assumed to show panmixia associated with its circumglobal distribution between 50 and 60°S. Phylogenetic analysis with mitochondrial 16S ribosomal RNA and cytochrome oxidase 1 (cox1) confirmed that E. lucens and E. vallentinirepresent sister taxa. Strong geographic structuring of cox1 and ND1 mtDNA genetic variation by ocean basin was recorded in E. lucens, indicating that neritic populations off South Africa are likely self-maintaining. This contrasts with the results for E. vallentini, which appears to occur as a single panmictic population across its distributional range. These differences are likely related to the habitats (neritic, E. lucens; oceanic, E. vallentini) occupied by each species. The results of the neutrality tests are consistent with demographic processes and suggest growth in E. lucens and equilibrium or shrinkage in E. vallentini. Although purifying selection cannot be ruled out in the former, the very few haplotypes recovered from E. vallentini could indicate that any population expansion following a crash is not yet reflected in the relatively slowly evolving mtDNA markers used here. Further work using other methods is recommended.