Virus discovery reveals frequent infection by diverse novel members of the Flaviviridae in wild lemurs

[1]  R. Junge,et al.  The microbiome of Haemaphysalis lemuris (Acari: Ixodidae), a possible vector of pathogens of endangered lemur species in Madagascar. , 2018, Ticks and tick-borne diseases.

[2]  P. Becher,et al.  Mutational Analysis of the Bovine Hepacivirus Internal Ribosome Entry Site , 2018, Journal of Virology.

[3]  Travis S. Steffens,et al.  Lemur species-specific metapopulation responses to habitat loss and fragmentation , 2018, PloS one.

[4]  Joost T P Verhoeven,et al.  ViDiT-CACTUS: an inexpensive and versatile library preparation and sequence analysis method for virus discovery and other microbiology applications. , 2018, Canadian journal of microbiology.

[5]  E. Holmes,et al.  The evolutionary history of vertebrate RNA viruses , 2018, Nature.

[6]  C. Rice,et al.  miRNA independent hepacivirus variants suggest a strong evolutionary pressure to maintain miR-122 dependence , 2017, PLoS pathogens.

[7]  E. Gould,et al.  ICTV Virus Taxonomy Profile: Flaviviridae , 2017, The Journal of general virology.

[8]  E. Gould,et al.  Proposed update to the taxonomy of the genera Hepacivirus and Pegivirus within the Flaviviridae family , 2016, The Journal of general virology.

[9]  J. Cullen,et al.  The Strange, Expanding World of Animal Hepaciviruses. , 2016, Annual review of virology.

[10]  D. Todt,et al.  Acute and chronic infections with nonprimate hepacivirus in young horses , 2016, Veterinary Research.

[11]  Daniel H. Huson,et al.  MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data , 2016, PLoS Comput. Biol..

[12]  Chase W. Nelson,et al.  Arteriviruses, Pegiviruses, and Lentiviruses Are Common among Wild African Monkeys , 2016, Journal of Virology.

[13]  Sudhir Kumar,et al.  MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. , 2016, Molecular biology and evolution.

[14]  O. Pybus,et al.  Hepacivirus cross-species transmission and the origins of the hepatitis C virus. , 2016, Current opinion in virology.

[15]  P. Simmonds,et al.  Proposed reference sequences for hepatitis E virus subtypes. , 2016, The Journal of general virology.

[16]  M. Canuti,et al.  Driving forces behind the evolution of the Aleutian mink disease parvovirus in the context of intensive farming , 2016, Virus evolution.

[17]  G. Dawson,et al.  Discovery of a Novel Human Pegivirus in Blood Associated with Hepatitis C Virus Co-Infection , 2015, PLoS pathogens.

[18]  Nikos Vasilakis,et al.  Divergent Viruses Discovered in Arthropods and Vertebrates Revise the Evolutionary History of the Flaviviridae and Related Viruses , 2015, Journal of Virology.

[19]  O. Pybus,et al.  Evolutionary and Phylogenetic Analysis of the Hepaciviruses and Pegiviruses , 2015, Genome biology and evolution.

[20]  P. Simmonds,et al.  Virome Analysis of Transfusion Recipients Reveals a Novel Human Virus That Shares Genomic Features with Hepaciviruses and Pegiviruses , 2015, mBio.

[21]  R. Junge,et al.  Ectoparasites of Propithecus diadema (Primates: Indriidae) with Notes on Unusual Attachment Site Selection by Haemaphysalis lemuris (Parasitiformes: Ixodidae) , 2015, Journal of medical entomology.

[22]  V. Corman,et al.  Highly Divergent Hepaciviruses from African Cattle , 2015, Journal of Virology.

[23]  B. Murrell,et al.  RDP4: Detection and analysis of recombination patterns in virus genomes , 2015, Virus evolution.

[24]  C. Rice,et al.  Characterization of nonprimate hepacivirus and construction of a functional molecular clone , 2015, Proceedings of the National Academy of Sciences.

[25]  D. Huson,et al.  Fast and sensitive protein alignment using DIAMOND , 2014, Nature Methods.

[26]  J. Cullen,et al.  Persistent viremia by a novel parvovirus in a slow loris (Nycticebus coucang) with diffuse histiocytic sarcoma , 2014, Front. Microbiol..

[27]  D. O’Connor,et al.  Discovery and Characterization of Distinct Simian Pegiviruses in Three Wild African Old World Monkey Species , 2014, PloS one.

[28]  K. Lambert,et al.  A novel flavivirus in the soybean cyst nematode. , 2014, The Journal of general virology.

[29]  P. Kellam,et al.  Full Genome Virus Detection in Fecal Samples Using Sensitive Nucleic Acid Preparation, Deep Sequencing, and a Novel Iterative Sequence Classification Algorithm , 2014, PloS one.

[30]  R. Mittermeier,et al.  Averting Lemur Extinctions amid Madagascar's Political Crisis , 2014, Science.

[31]  T. Pietschmann,et al.  Natural reservoirs for homologs of hepatitis C virus , 2014, Emerging Microbes & Infections.

[32]  Henry T. Wright,et al.  Stone tools and foraging in northern Madagascar challenge Holocene extinction models , 2013, Proceedings of the National Academy of Sciences.

[33]  Colin A. Chapman,et al.  A Novel Hepacivirus with an Unusually Long and Intrinsically Disordered NS5A Protein in a Wild Old World Primate , 2013, Journal of Virology.

[34]  J. Epstein,et al.  Bats are a major natural reservoir for hepaciviruses and pegiviruses , 2013, Proceedings of the National Academy of Sciences.

[35]  K. Vandegrift,et al.  Identification of Rodent Homologs of Hepatitis C Virus and Pegiviruses , 2013, mBio.

[36]  K. Katoh,et al.  MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability , 2013, Molecular biology and evolution.

[37]  M. Batzer,et al.  An Alu-Based Phylogeny of Lemurs (Infraorder: Lemuriformes) , 2012, PloS one.

[38]  Sergey I. Nikolenko,et al.  SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing , 2012, J. Comput. Biol..

[39]  J. Stapleton,et al.  GB virus C: the good boy virus? , 2012, Trends in microbiology.

[40]  C. Jopling,et al.  Liver-specific microRNA-122 , 2012, RNA biology.

[41]  P. Simmonds,et al.  Evaluating the evidence for virus/host co-evolution. , 2011, Current opinion in virology.

[42]  S. Brunak,et al.  SignalP 4.0: discriminating signal peptides from transmembrane regions , 2011, Nature Methods.

[43]  C. Guérin,et al.  Les plus anciennes traces d’activités anthropiques de Madagascar sur des ossements d’hippopotames subfossiles d’Anjohibe (Province de Mahajanga) , 2011 .

[44]  Jack T. Stapleton,et al.  The GB viruses: a review and proposed classification of GBV-A, GBV-C (HGV), and GBV-D in genus Pegivirus within the family Flaviviridae , 2011, The Journal of general virology.

[45]  B. Crowley.  A refined chronology of prehistoric Madagascar and the demise of the megafauna , 2010 .

[46]  C. Guérin,et al.  Le plus ancien hippopotame fossile (Hippopotamus laloumena) de Madagascar (Belobaka, Province de Mahajanga) , 2010 .

[47]  Thomas L. Madden,et al.  BLAST+: architecture and applications , 2009, BMC Bioinformatics.

[48]  V. Sousa,et al.  Influence of forest fragmentation on an endangered large-bodied lemur in northwestern Madagascar , 2009 .

[49]  M. Hasegawa,et al.  Molecular phylogeny and evolution of prosimians based on complete sequences of mitochondrial DNAs. , 2009, Gene.

[50]  Cathy V. Williams,et al.  Neoplasia in Prosimians: Case Series from a Captive Prosimian Population and Literature Review , 2009, Veterinary pathology.

[51]  Toni Gabaldón,et al.  trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses , 2009, Bioinform..

[52]  Peter J. Lukavsky,et al.  Structure and function of HCV IRES domains , 2009, Virus research.

[53]  O. Gascuel,et al.  An improved general amino acid replacement matrix. , 2008, Molecular biology and evolution.

[54]  M. Irwin.  Diademed Sifaka (Propithecus diadema) Ranging and Habitat Use in Continuous and Fragmented Forest: Higher Density but Lower Viability in Fragments? , 2008 .

[55]  Rodrigo Lopez,et al.  Clustal W and Clustal X version 2.0 , 2007, Bioinform..

[56]  P. Sarnow,et al.  Modulation of Hepatitis C Virus RNA Abundance by a Liver-Specific MicroRNA , 2005, Science.

[57]  M. Hayashi,et al.  Species-independent detection of RNA virus by representational difference analysis using non-ribosomal hexanucleotides for reverse transcription , 2005, Nucleic acids research.

[58]  Rodrigo Lopez,et al.  Multiple sequence alignment with the Clustal series of programs , 2003, Nucleic Acids Res..

[59]  Jean Dubuisson,et al.  Glycosylation of hepatitis C virus envelope proteins. , 2003, Biochimie.

[60]  J. Hoofnagle.  Course and outcome of hepatitis C , 2002, Hepatology.

[61]  J. Hoofnagle.  Course and outcome of hepatitis C , 2002 .

[62]  M. Honda,et al.  Stability of a stem-loop involving the initiator AUG controls the efficiency of internal initiation of translation on hepatitis C virus RNA. , 1996, RNA.

[63]  T. Pilot‐Matias,et al.  Molecular and serologic analysis in the transmission of the GB hepatitis agents , 1995, Journal of medical virology.

[64]  M. Nei,et al.  Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. , 1993, Molecular biology and evolution.

[65]  K. Tamura,et al.  Estimation of the number of nucleotide substitutions when there are strong transition-transversion and G+C-content biases. , 1992, Molecular biology and evolution.

[66]  M. Nei,et al.  Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. , 1986, Molecular biology and evolution.

[67]  J. Felsenstein.  CONFIDENCE LIMITS ON PHYLOGENIES: AN APPROACH USING THE BOOTSTRAP , 1985, Evolution; international journal of organic evolution.

[68]  V. ter meulen,et al.  Studies on Persistent Infections of Tissue Culture VI. Reversible Changes in Newcastle Disease Virus Populations as a Result of Passage in L Cells or Chick Embryos , 1967, Journal of virology.

[69]  Hideyuki Takahashi,et al.  Gentian Kobu-sho-associated virus: a tentative, novel double-stranded RNA virus that is relevant to gentian Kobu-sho syndrome , 2012, Journal of General Plant Pathology.

[70]  Angela C. M. Luyf,et al.  UvA-DARE ( Digital Academic Repository ) A Sensitive Assay for Virus Discovery in Respiratory Clinical Samples , 2011 .

[71]  Michael Zuker,et al.  UNAFold: software for nucleic acid folding and hybridization. , 2008, Methods in molecular biology.

[72]  J. Felsenstein.  Evolutionary trees from DNA sequences: A maximum likelihood approach , 2005, Journal of Molecular Evolution.