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Browsing by Author "Martin, Darren P"

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Appearances can be deceptive: revealing a hidden viral infection with deep sequencing in a plant quarantine context

Author: Candresse, Thierry ; Filloux, Denis ; Muhire, Brejnev ; Julian, Charlotte ; Galzi, Serge ; Fort, Guillaume ; Bernardo, Pauline ; Daugrois, Jean-Heindrich ; Fernandez, Emmanuel ; Martin, Darren P Date: 2014 Comprehensive inventories of plant viral diversity are essential for effective quarantine and sanitation efforts. The safety of regulated plant material exchanges presently relies heavily on techniques such as PCR or nucleic acid hybridisation, ... Read more c b
Avoidance of Protein Fold Disruption in Natural Virus Recombinants

Author: Lefeuvre, Pierre ; Lett, Jean-Michel ; Reynaud, Bernard ; Martin, Darren P Date: 2007 Author Summary The exchange of genetic material between different virus species, called inter-species recombination, has the potential to generate, within a single genome replication cycle, an almost unimaginable number of genetically distinct ... Read more c b
Comparative genomic and phylogenetic approaches to characterize the role of genetic recombination in mycobacterial evolution

Author: Smith, Silvia E ; Showers-Corneli, Patrice ; Dardenne, Caitlin N ; Harpending, Henry H ; Martin, Darren P ; Beiko, Robert G Date: 2012 The genus Mycobacterium encompasses over one hundred named species of environmental and pathogenic organisms, including the causative agents of devastating human diseases such as tuberculosis and leprosy. The success of these human pathogens ... Read more c b
Complex recombination patterns arising during geminivirus coinfections preserve and demarcate biologically important intra-genome interaction networks

Author: Martin, Darren P ; Lefeuvre, Pierre ; Varsani, Arvind ; Hoareau, Murielle ; Semegni, Jean-Yves ; Dijoux, Betty ; Vincent, Claire ; Reynaud, Bernard ; Lett, Jean-Michel Date: 2011 Author Summary Genetic recombination between viruses is a form of parasexual reproduction during which two parental viruses each contribute genetic information to an offspring, or recombinant, virus. Unlike with sexual reproduction, however, ... Read more c b
Conserved positive selection signals in gp41 across multiple subtypes and difference in selection signals detectable in gp41 sequences sampled during acute and chronic HIV-1 subtype C infection

Author: Bandawe, Gama P ; Martin, Darren P ; Treurnicht, Florette ; Mlisana, Koleka ; Karim, Salim S A ; Williamson, Carolyn Date: 24 Nov 2008 Background: The high diversity of HIV variants driving the global AIDS epidemic has caused many to doubt whether an effective vaccine against the virus is possible. However, by identifying the selective forces that are driving the ongoing ... Read more
Differences in genotype and virulence among four multidrug-resistant Streptococcus pneumoniae isolates belonging to the PMEN1 clone

Author: Hiller, N Luisa ; Eutsey, Rory A ; Powell, Evan ; Earl, Joshua P ; Janto, Benjamin ; Martin, Darren P ; Dawid, Suzanne ; Ahmed, Azad ; Longwell, Mark J ; Dahlgren, Margaret E Date: 2011 We report on the comparative genomics and characterization of the virulence phenotypes of four S. pneumoniae strains that belong to the multidrug resistant clone PMEN1 (Spain 23F ST81). Strains SV35-T23 and SV36-T3 were recovered in 1996 from ... Read more c b
Evaluating the predictive performance of cytotoxic T lymphocyte epitope prediction tools using Elispot assay data

Author: Meraba, Rebone Leboreng Date: 2018 Computational T-cell epitope prediction tools have been previously devised to predict potential human leukocyte antigen (HLA) binding peptides from protein sequences. These tools are complements of Enzyme-linked immunosorbent spot (ELISpot) ... Read more
Evidence of ancient papillomavirus recombination

Author: Varsani, Arvind ; van der Walt, Eric ; Heath, Livio ; Rybicki, Edward P ; Williamson, Anna Lise ; Martin, Darren P Date: 2006 An open question amongst papillomavirus taxonomists is whether recombination has featured in the evolutionary history of these viruses. Since the onset of the global AIDS epidemic, the question is somewhat less academic, because immune-compromised ... Read more
Evolutionary dynamics of ten novel Gamma-PVs: insights from phylogenetic incongruence, recombination and phylodynamic analyses

Author: Murahwa, Alltalents T ; Nindo, Fredrick ; Onywera, Harris ; Meiring, Tracy L ; Martin, Darren P ; Williamson, Anna-Lise Date: 14 May 2019 Abstract Background Human papillomaviruses (HPVs) are genetically diverse, belonging to five distinct genera: Alpha, Beta, Gamma, Mu and Nu. All papillomaviruses have double stranded DNA genomes ... Read more
The evolutionary impacts of secondary structures within genomes of eukaryote-infecting single-stranded DNA viruses

Author: Muhire, Brejnev Muhizi Date: 2015 Secondary structures forming through base-pairing in virus genomes have been proven to regulate several processes during viral replication cycles, including genome replication, transcription, post-transcriptional activities, protein synthesis, ... Read more
Evolutionary time-scale of the begomoviruses: evidence from integrated sequences in the Nicotiana genome

Author: Lefeuvre, Pierre ; Harkins, Gordon W ; Lett, Jean-Michel ; Briddon, Rob W ; Chase, Mark W ; Moury, Benoit ; Martin, Darren P Date: 2011 Despite having single stranded DNA genomes that are replicated by host DNA polymerases, viruses in the family Geminiviridae are apparently evolving as rapidly as some RNA viruses. The observed substitution rates of geminiviruses in the genera ... Read more c b
The Evolutionary Value of Recombination Is Constrained by Genome Modularity

Author: Martin, Darren P ; Walt, Eric van der ; Posada, David ; Rybicki, Edward P Date: 2005 Genetic recombination is a fundamental evolutionary mechanism promoting biological adaptation. Using engineered recombinants of the small single-stranded DNA plant virus, Maize streak virus (MSV), we experimentally demonstrate that fragments ... Read more c b
Generation of genic diversity among Streptococcus pneumoniae strains via horizontal gene transfer during a chronic polyclonal pediatric infection

Author: Hiller, N Luisa ; Ahmed, Azad ; Powell, Evan ; Martin, Darren P ; Eutsey, Rory ; Earl, Josh ; Janto, Benjamin ; Boissy, Robert J ; Hogg, Justin ; Barbadora, Karen Date: 2010 Although there is tremendous interest in understanding the evolutionary roles of horizontal gene transfer (HGT) processes that occur during chronic polyclonal infections, to date there have been few studies that directly address this topic. ... Read more c b
Genetic analysis of maize streak virus isolates from Uganda reveals widespread distribution of a recombinant variant.

Author: Owor, Betty E ; Martin, Darren P ; Shepherd, Dionne N ; Edema, Richard ; Monjane, Ade´rito L ; Rybicki, Edward P ; Thomson, Jennifer A ; Vasani, Arvind Date: 2007 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 ... Read more
Genetic variability among complete human respiratory syncytial virus subgroup A genomes: bridging molecular evolutionary dynamics and epidemiology

Author: Tan, Lydia ; Lemey, Philippe ; Houspie, Lieselot ; Viveen, Marco C ; Jansen, Nicolaas J G ; Loon, Anton M van ; Wiertz, Emmanuel ; Bleek, Grada M van ; Martin, Darren P ; Coenjaerts, Frank E Date: 2012 Human respiratory syncytial virus (RSV) is an important cause of severe lower respiratory tract infections in infants and the elderly. In the vast majority of cases, however, RSV infections run mild and symptoms resemble those of a common ... Read more c b
A highly divergent South African geminivirus species illuminates the ancient evolutionary history of this family

Author: Varsani, Arvind ; Shepherd, Dionne N ; Dent, Kyle ; Monjane, Aderito L ; Rybicki, Edward P ; Martin, Darren P Date: 2009 Background: We have characterised a new highly divergent geminivirus species, Eragrostis curvula streak virus (ECSV), found infecting a hardy perennial South African wild grass. ECSV represents a new genus-level geminivirus lineage, and has ... Read more c b
HIV type 1 subtype C gag and nef diversity in Southern Africa.

Author: Bredell, Helba ; Martin, Darren P ; Van Harmelen Joanne ; Varsani, Arvind ; Sheppard, Haynes W ; Donovan, R ; Gray, C ; HIVNET028 Study Team ; Williamson, C Date: 2007 Several HIV-1 subtype C-specific gag- and/or nef-based vaccines are currently intended for clinical trial in southern Africa. Here we provide sequences of 64 gag and 45 nef genes sampled in Malawi, Zambia, Zimbabwe, and South Africa and assess ... Read more
Maize streak virus: an old and complex 'emerging' pathogen

Author: Shepherd, Dionne N ; Martin, Darren P ; Van der Walt, Eric ; Dent, Kyle ; Varsani, Arvind ; Rybicki, Edward P Date: 2010 Maize streak virus (MSV; Genus Mastrevirus, Family Geminiviridae) occurs throughout Africa, where it causes what is probably the most serious viral crop disease on the continent. It is obligately transmitted by as many as six leafhopper species ... Read more
Metagenomic-based screening and molecular characterization of cowpea-infecting viruses in Burkina Faso

Author: Palanga, Essowè ; Filloux, Denis ; Martin, Darren P ; Fernandez, Emmanuel ; Gargani, Daniel ; Ferdinand, Romain ; Zabré, Jean ; Bouda, Zakaria ; Neya, James Bouma ; Sawadogo, Mahamadou ; Traore, Oumar ; Peterschmitt, Michel ; Roumagnac, Philippe Date: 2016 Cowpea, ( Vigna unguiculata L. (Walp)) is an annual tropical grain legume. Often referred to as "poor man's meat", cowpea is one of the most important subsistence legumes cultivated in West Africa due to the high protein content of its seeds. ... Read more c b
Molecular characterization and prevalence of two capulaviruses: Alfalfa leaf curl virus from France and Euphorbia caput-medusae latent virus from South Africa

Author: Bernardo, Pauline ; Muhire, Brejnev ; François, Sarah ; Deshoux, Maëlle ; Hartnady, Penelope ; Farkas, Kata ; Kraberger, Simona ; Filloux, Denis ; Fernandez, Emmanuel ; Galzi, Serge ; Ferdinand, Romain ; Granier, Martine ; Marais, Armelle ; Blasco, Pablo Monge ; Candresse, Thierry ; Escriu, Fernando ; Varsani, Arvind ; Harkins, Gordon W ; Martin, Darren P ; Roumagnac, Philippe Date: 2016 Little is known about the prevalence, diversity, evolutionary processes, genomic structures and population dynamics of viruses in the divergent geminivirus lineage known as the capulaviruses. We determined and analyzed full genome sequences ... Read more c b n d

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