Viral metagenomics of aphids present in bean and maize plots on mixed-use farms in Kenya reveals the presence of three dicistroviruses including a novel Big Sioux River virus-like dicistrovirus

[1]  J. Carr,et al.  Engineering resistance to virus transmission. , 2017, Current opinion in virology.

[2]  K. Dorman,et al.  Discovery of Known and Novel Viral Genomes in Soybean Aphid by Deep Sequencing , 2017 .

[3]  A. Firth,et al.  ICTV Virus Taxonomy Profile: Dicistroviridae , 2017, The Journal of general virology.

[4]  Andrew J. Davison,et al.  Consensus statement: Virus taxonomy in the age of metagenomics , 2017, Nature Reviews Microbiology.

[5]  O. Edwards,et al.  Metagenomic Analysis of Cucumber RNA from East Timor Reveals an Aphid lethal paralysis virus Genome , 2017, Genome Announcements.

[6]  Xiaomin Hu,et al.  A Metagenomic Survey of Viral Abundance and Diversity in Mosquitoes from Hubei Province , 2015, PloS one.

[7]  E. Genersch,et al.  Honey bee colony losses and associated viruses. , 2015, Current opinion in insect science.

[8]  W. Miller,et al.  Analysis of new aphid lethal paralysis virus (ALPV) isolates suggests evolution of two ALPV species. , 2014, The Journal of general virology.

[9]  I. Tzanetakis,et al.  Development of a virus detection and discovery pipeline using next generation sequencing. , 2014, Virology.

[10]  Arvind Varsani,et al.  SDT: A Virus Classification Tool Based on Pairwise Sequence Alignment and Identity Calculation , 2014, PloS one.

[11]  Caspar Zialor.  DNA sequencing with chain terminating inhibitors , 2014 .

[12]  Koichiro Tamura,et al.  MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. , 2013, Molecular biology and evolution.

[13]  A. Dombrovsky,et al.  The Nerium oleander aphid Aphis nerii is tolerant to a local isolate of Aphid lethal paralysis virus (ALPV) , 2013, Virus Genes.

[14]  J. Sánchez-Vizcaíno,et al.  Metagenomic Detection of Viral Pathogens in Spanish Honeybees: Co-Infection by Aphid Lethal Paralysis, Israel Acute Paralysis and Lake Sinai Viruses , 2013, PloS one.

[15]  P. Zhou,et al.  Metagenomic Analysis of Viruses from Bat Fecal Samples Reveals Many Novel Viruses in Insectivorous Bats in China , 2012, Journal of Virology.

[16]  J. Derisi,et al.  Temporal Analysis of the Honey Bee Microbiome Reveals Four Novel Viruses and Seasonal Prevalence of Known Viruses, Nosema, and Crithidia , 2011, PloS one.

[17]  E. Holmes,et al.  RNA Viruses in Hymenopteran Pollinators: Evidence of Inter-Taxa Virus Transmission via Pollen and Potential Impact on Non-Apis Hymenopteran Species , 2010, PloS one.

[18]  Patrick J. Biggs,et al.  SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data , 2010, BMC Bioinformatics.

[19]  V. Brault,et al.  Aphids as transport devices for plant viruses. , 2010, Comptes rendus biologies.

[20]  D. Winstanley,et al.  Densovirus induces winged morphs in asexual clones of the rosy apple aphid, Dysaphis plantaginea , 2009, Proceedings of the National Academy of Sciences.

[21]  N. Nakashima,et al.  Functional analysis of structural motifs in dicistroviruses. , 2009, Virus research.

[22]  N. Nakashima,et al.  Cleavage sites of the “P3 region” in the nonstructural polyprotein precursor of a dicistrovirus , 2008, Archives of Virology.

[23]  P. Scotti,et al.  Dicistroviruses , 2008, Encyclopedia of Virology.

[24]  L. Ban,et al.  Infection with an insect virus affects olfactory behaviour and interactions with host plant and natural enemies in an aphid , 2008 .

[25]  F. Schurr,et al.  Spread of Infectious Chronic Bee Paralysis Virus by Honeybee (Apis mellifera L.) Feces , 2007, Applied and Environmental Microbiology.

[26]  R. Glinwood,et al.  An improved detection method for the Rhopalosiphum padi virus (RhPV) allows monitoring of its presence in aphids and movement within plants. , 2007, Journal of virological methods.

[27]  David Posada,et al.  An Exact Nonparametric Method for Inferring Mosaic Structure in Sequence Triplets , 2007, Genetics.

[28]  E. Holmes,et al.  A phylogenetic survey of recombination frequency in plant RNA viruses , 2006, Archives of Virology.

[29]  Y. P. Chen,et al.  Prevalence and Transmission of Honeybee Viruses , 2006, Applied and Environmental Microbiology.

[30]  Colin Favret,et al.  Speciation by host-switching in pinyon Cinara (Insecta: Hemiptera: Aphididae). , 2004, Molecular phylogenetics and evolution.

[31]  Robert C. Edgar,et al.  MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.

[32]  M. van Munster,et al.  Sequence analysis and genomic organization of Aphid lethal paralysis virus: a new member of the family Dicistroviridae. , 2002, The Journal of general virology.

[33]  M. Mayo.  Virus taxonomy - Houston 2002. , 2002, Archives of virology.

[34]  K. Crandall,et al.  Evaluation of methods for detecting recombination from DNA sequences: Computer simulations , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[35]  P. Sarnow,et al.  Naturally Occurring Dicistronic Cricket Paralysis Virus RNA Is Regulated by Two Internal Ribosome Entry Sites , 2000, Molecular and Cellular Biology.

[36]  Mark J. Gibbs,et al.  Sister-Scanning: a Monte Carlo procedure for assessing signals in recombinant sequences , 2000, Bioinform..

[37]  Darren Martin,et al.  RDP: detection of recombination amongst aligned sequences , 2000, Bioinform..

[38]  J. Bujarski,et al.  Frequent Homologous Recombination Events between Molecules of One RNA Component in a Multipartite RNA Virus , 2000, Journal of Virology.

[39]  S. Sawyer,et al.  Possible emergence of new geminiviruses by frequent recombination. , 1999, Virology.

[40]  H. Jin,et al.  Nucleotide sequence analysis shows that Rhopalosiphum padi virus is a member of a novel group of insect-infecting RNA viruses. , 1998, Virology.

[41]  M. Aranda,et al.  Genetic exchange by recombination or reassortment is infrequent in natural populations of a tripartite RNA plant virus , 1997, Journal of virology.

[42]  T. Candresse,et al.  Frequent occurrence of recombinant potyvirus isolates. , 1996, The Journal of general virology.

[43]  John Maynard Smith,et al.  Analyzing the mosaic structure of genes , 1992, Journal of Molecular Evolution.

[44]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[45]  C. D'arcy,et al.  Cytopathology and experimental host range of Rhopalosiphum padi virus, a small isometric RNA virus infecting cereal grain aphids , 1990 .

[46]  C. D'arcy,et al.  Barley and oats as reservoirs for an aphid virus and the influence on barley yellow dwarf virus transmission , 1988 .

[47]  C. Williamson,et al.  Characterization of a New Picorna-like Virus Isolated from Aphids , 1988 .

[48]  Lloyd M. Smith,et al.  Fluorescence detection in automated DNA sequence analysis , 1986, Nature.

[49]  C. D'arcy,et al.  Detection, biological effects, and transmission of a virus of the aphid Rhopalosiphum padi. , 1981, Virology.

[50]  R. M. Goodman,et al.  Purification and characterization of a virus from the aphid Rhopalosiphum padi. , 1981, Virology.

[51]  V. Eastop.  The Periodicity of Aphid Flight in East Africa , 1957 .

[52]  E. Koonin,et al.  Virus taxonomy in the age of metagenomics , 2017 .

[53]  N. Mitter,et al.  Bean Common Mosaic Virus and Bean Common Mosaic Necrosis Virus: Relationships, Biology, and Prospects for Control. , 2015, Advances in virus research.

[54]  Elliot J. Lefkowitz,et al.  Virus taxonomy: classification and nomenclature of viruses , 2012 .

[55]  C. Williamson,et al.  A comparative study on the cell-free translation of the genomic RNAs of two aphid picorna-like viruses , 2005, Archives of Virology.

[56]  M. V. Regenmortel,et al.  Virus taxonomy: classification and nomenclature of viruses. Seventh report of the International Committee on Taxonomy of Viruses. , 2000 .

[57]  M. Nei,et al.  The neighbor-joining method , 1987 .

[58]  H. Y. Kulkarni.  Survey of viruses affecting East African major food crops , 1972 .