Edward C Holmes

Edward C Holmes

UNVERIFIED PROFILE

Are you Edward C Holmes?   Register this Author

Register author
Edward C Holmes

Edward C Holmes

Publications by authors named "Edward C Holmes"

Are you Edward C Holmes?   Register this Author

100Publications

1703Reads

-Profile Views

Fecal Viral Diversity of Captive and Wild Tasmanian Devils Characterized Using Virion-Enriched Metagenomics and Metatranscriptomics.

J Virol 2019 Jun 15;93(11). Epub 2019 May 15.

Marie Bashir Institute for Infectious Diseases and Biosecurity, Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia

View Article

Download full-text PDF

Source
http://jvi.asm.org/lookup/doi/10.1128/JVI.00205-19
Publisher Site
http://dx.doi.org/10.1128/JVI.00205-19DOI Listing
June 2019

Evolutionary stasis of viruses?

Nat Rev Microbiol 2019 May;17(5):329

Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Australia.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41579-019-0168-7DOI Listing
May 2019

Discovery of a highly divergent hepadnavirus in shrews from China.

Virology 2019 May 11;531:162-170. Epub 2019 Mar 11.

State Key Laboratory for Infectious Disease Prevention and Control; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases; Department of Zoonoses, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China; Shanghai Public Health Clinical Center & Institute of Biomedical Sciences, Fudan University, Shanghai, China. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.virol.2019.03.007DOI Listing
May 2019

Entrezpy: A Python library to dynamically interact with the NCBI Entrez databases.

Bioinformatics 2019 May 11. Epub 2019 May 11.

Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW, Australia.

View Article

Download full-text PDF

Source
https://academic.oup.com/bioinformatics/advance-article/doi/
Publisher Site
http://dx.doi.org/10.1093/bioinformatics/btz385DOI Listing
May 2019

Expanding the RNA Virosphere by Unbiased Metagenomics.

Annu Rev Virol 2019 May 17. Epub 2019 May 17.

Shanghai Public Health Clinical Center and Institute of Biomedical Sciences, Fudan University, Shanghai 200433, China; email:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1146/annurev-virology-092818-015851DOI Listing
May 2019

Punctuated Evolution of Myxoma Virus: Rapid and Disjunct Evolution of a Recent Viral Lineage in Australia.

J Virol 2019 Apr 3;93(8). Epub 2019 Apr 3.

Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1128/JVI.01994-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6450118PMC
April 2019

Can Sequence Phylogenies Safely Infer the Origin of the Global Virome?

MBio 2019 04 16;10(2). Epub 2019 Apr 16.

Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia.

View Article

Download full-text PDF

Source
http://mbio.asm.org/lookup/doi/10.1128/mBio.00289-19
Publisher Site
http://dx.doi.org/10.1128/mBio.00289-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6469966PMC
April 2019

Fogarty International Center collaborative networks in infectious disease modeling: Lessons learnt in research and capacity building.

Epidemics 2019 03 23;26:116-127. Epub 2018 Oct 23.

Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda MD, USA. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.epidem.2018.10.004DOI Listing
March 2019

Identification of A Novel Picorna-Like Virus, Burpengary Virus, that is Negatively Associated with Chlamydial Disease in the Koala.

Viruses 2019 Mar 2;11(3). Epub 2019 Mar 2.

Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia.

View Article

Download full-text PDF

Source
https://www.mdpi.com/1999-4915/11/3/211
Publisher Site
http://dx.doi.org/10.3390/v11030211DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6466430PMC
March 2019

Extensive Diversity of RNA Viruses in Australian Ticks.

J Virol 2019 Feb 17;93(3). Epub 2019 Jan 17.

Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, Australia

View Article

Download full-text PDF

Source
http://jvi.asm.org/lookup/doi/10.1128/JVI.01358-18
Publisher Site
http://dx.doi.org/10.1128/JVI.01358-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6340049PMC
February 2019

Tracking virus outbreaks in the twenty-first century.

Nat Microbiol 2019 01 13;4(1):10-19. Epub 2018 Dec 13.

Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.

View Article

Download full-text PDF

Source
http://www.nature.com/articles/s41564-018-0296-2
Publisher Site
http://dx.doi.org/10.1038/s41564-018-0296-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6345516PMC
January 2019

Human Tick-Borne Diseases in Australia.

Front Cell Infect Microbiol 2019 28;9. Epub 2019 Jan 28.

Neuroinflammation Group, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.3389/fcimb.2019.00003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6360175PMC
January 2019

A reptilian endogenous foamy virus sheds light on the early evolution of retroviruses.

Virus Evol 2019 Jan 27;5(1):vez001. Epub 2019 Feb 27.

Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/ve/vez001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6393741PMC
January 2019

The discovery of three new hare lagoviruses reveals unexplored viral diversity in this genus.

Virus Evol 2019 Jan 9;5(1):vez005. Epub 2019 Apr 9.

Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia.

View Article

Download full-text PDF

Source
https://academic.oup.com/ve/article/doi/10.1093/ve/vez005/54
Publisher Site
http://dx.doi.org/10.1093/ve/vez005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6456799PMC
January 2019

The phylogenomics of evolving virus virulence.

Nat Rev Genet 2018 Dec;19(12):756-769

Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41576-018-0055-5DOI Listing
December 2018

Virus-virus interactions and host ecology are associated with RNA virome structure in wild birds.

Mol Ecol 2018 12 22;27(24):5263-5278. Epub 2018 Nov 22.

Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia.

View Article

Download full-text PDF

Source
http://doi.wiley.com/10.1111/mec.14918
Publisher Site
http://dx.doi.org/10.1111/mec.14918DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6312746PMC
December 2018

Evolutionary Virology at 40.

Genetics 2018 12;210(4):1151-1162

Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, New South Wales 2006, Australia

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1534/genetics.118.301556DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6283181PMC
December 2018

A Divergent Hepatitis D-Like Agent in Birds.

Viruses 2018 12 17;10(12). Epub 2018 Dec 17.

WHO Collaborating Centre for Reference and Research on Influenza, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.3390/v10120720DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6315422PMC
December 2018

A Simple Method to Detect Candidate Overlapping Genes in Viruses Using Single Genome Sequences.

Mol Biol Evol 2018 10;35(10):2572-2581

Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW , Australia.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/molbev/msy155DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6188560PMC
October 2018

An Atypical Parvovirus Drives Chronic Tubulointerstitial Nephropathy and Kidney Fibrosis.

Cell 2018 Oct 13;175(2):530-543.e24. Epub 2018 Sep 13.

Centenary Institute, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2050, Australia; Discipline of Dermatology, Faculty of Medicine and Health, University of Sydney, NSW 2006, Australia; Department of Dermatology, Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia; Department of Dermatology, Medical University of Vienna, Vienna 1090, Austria. Electronic address:

View Article

Download full-text PDF

Source
https://linkinghub.elsevier.com/retrieve/pii/S00928674183102
Publisher Site
http://dx.doi.org/10.1016/j.cell.2018.08.013DOI Listing
October 2018

Author Correction: The evolutionary history of vertebrate RNA viruses.

Nature 2018 09;561(7722):E6

State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41586-018-0310-0DOI Listing
September 2018

Evolution of Human Respiratory Syncytial Virus (RSV) over Multiple Seasons in New South Wales, Australia.

Viruses 2018 09 6;10(9). Epub 2018 Sep 6.

Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia.

View Article

Download full-text PDF

Source
http://www.mdpi.com/1999-4915/10/9/476
Publisher Site
http://dx.doi.org/10.3390/v10090476DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6164696PMC
September 2018

Multiple Incursions and Recurrent Epidemic Fade-Out of H3N2 Canine Influenza A Virus in the United States.

J Virol 2018 08 31;92(16). Epub 2018 Jul 31.

Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1128/JVI.00323-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6069211PMC
August 2018

The diversity, evolution and origins of vertebrate RNA viruses.

Curr Opin Virol 2018 08 13;31:9-16. Epub 2018 Aug 13.

Shanghai Public Health Clinical Center & Institute of Biomedical Sciences, Fudan University, Shanghai, China; Department of Zoonosis, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China; Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, Australia.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.coviro.2018.07.017DOI Listing
August 2018

Transcriptome Analysis and In Situ Hybridization for FcaGHV1 in Feline Lymphoma.

Viruses 2018 08 30;10(9). Epub 2018 Aug 30.

Sydney School of Veterinary Science, Faculty of Science, University of Sydney, Sydney, NSW 2006, Australia.

View Article

Download full-text PDF

Source
http://www.mdpi.com/1999-4915/10/9/464
Publisher Site
http://dx.doi.org/10.3390/v10090464DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6165513PMC
August 2018

Low evolutionary rate of infectious pancreatic necrosis virus (IPNV) in Italy is associated with reduced virulence in trout.

Virus Evol 2018 Jul 18;4(2):vey019. Epub 2018 Jul 18.

Department of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie, viale dell'Università 10, Legnaro, Padova, Italy.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/ve/vey019DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6054257PMC
July 2018

No detectable effect of Mel on the prevalence and abundance of the RNA virome of .

Proc Biol Sci 2018 07 25;285(1883). Epub 2018 Jul 25.

Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, University of Sydney, Sydney, New South Wales 2006, Australia

View Article

Download full-text PDF

Source
http://rspb.royalsocietypublishing.org/lookup/doi/10.1098/rs
Publisher Site
http://dx.doi.org/10.1098/rspb.2018.1165DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6083246PMC
July 2018

Hidden diversity and evolution of viruses in market fish.

Virus Evol 2018 Jul 31;4(2):vey031. Epub 2018 Oct 31.

Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, Australia.

View Article

Download full-text PDF

Source
http://fdslive.oup.com/www.oup.com/pdf/production_in_progres
Publisher Site
http://dx.doi.org/10.1093/ve/vey031DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6208713PMC
July 2018

Complete genome of Aedes aegypti anphevirus in the Aag2 mosquito cell line.

J Gen Virol 2018 06 9;99(6):832-836. Epub 2018 May 9.

3​Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1099/jgv.0.001079DOI Listing
June 2018

Virological Sampling of Inaccessible Wildlife with Drones.

Viruses 2018 06 2;10(6). Epub 2018 Jun 2.

Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.3390/v10060300DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6024715PMC
June 2018

The Biological Object Notation (BON): a structured file format for biological data.

Sci Rep 2018 Jun 25;8(1):9644. Epub 2018 Jun 25.

Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, the University of Sydney, Sydney, New South Wales, 2006, Australia.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41598-018-28016-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6018389PMC
June 2018

Publisher Correction: Sudden emergence of human infections with H7N9 avian influenza A virus in Hubei province, central China.

Sci Rep 2018 May 10;8(1):7588. Epub 2018 May 10.

CAS Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41598-018-25257-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5945859PMC
May 2018

A Novel Hepadnavirus Identified in an Immunocompromised Domestic Cat in Australia.

Viruses 2018 05 17;10(5). Epub 2018 May 17.

Sydney School of Veterinary Science, Faculty of Science, University of Sydney, Sydney, NSW 2006, Australia.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.3390/v10050269DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5977262PMC
May 2018

The evolutionary history of vertebrate RNA viruses.

Nature 2018 04 4;556(7700):197-202. Epub 2018 Apr 4.

State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41586-018-0012-7DOI Listing
April 2018

Interplay between co-divergence and cross-species transmission in the evolutionary history of bat coronaviruses.

Infect Genet Evol 2018 03 30;58:279-289. Epub 2018 Jan 30.

National Reference Centre, OIE Collaborating Centre for Diseases at the Animal-Human Interface, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Universita' 10, Legnaro, Padova 35020, Italy.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.meegid.2018.01.012DOI Listing
March 2018

Using Metagenomics to Characterize an Expanding Virosphere.

Cell 2018 03;172(6):1168-1172

Shanghai Public Health Clinical Center & Institutes of Biomedical Sciences, Fudan University, Shanghai, China; State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China; Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, Australia.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.cell.2018.02.043DOI Listing
March 2018

The impact of host genetic diversity on virus evolution and emergence.

Ecol Lett 2018 02 5;21(2):253-263. Epub 2017 Dec 5.

Centro de Biotecnología y Genómica de Plantas (Universidad Politécnica de Madrid - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria), Madrid, 28223, Spain.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1111/ele.12890DOI Listing
February 2018

Sudden emergence of human infections with H7N9 avian influenza A virus in Hubei province, central China.

Sci Rep 2018 02 6;8(1):2486. Epub 2018 Feb 6.

CAS Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China.

View Article

Download full-text PDF

Source
http://www.nature.com/articles/s41598-018-20988-9
Publisher Site
http://dx.doi.org/10.1038/s41598-018-20988-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5802767PMC
February 2018

Meta-transcriptomics and the evolutionary biology of RNA viruses.

Virus Res 2018 01 27;243:83-90. Epub 2017 Oct 27.

Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, Australia; State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Department of Zoonoses, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.virusres.2017.10.016DOI Listing
January 2018

Extensive diversity and evolution of hepadnaviruses in bats in China.

Virology 2018 01 16;514:88-97. Epub 2017 Nov 16.

State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Department of Zoonoses, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China. Electronic address:

View Article

Download full-text PDF

Source
https://linkinghub.elsevier.com/retrieve/pii/S00426822173037
Publisher Site
http://dx.doi.org/10.1016/j.virol.2017.11.005DOI Listing
January 2018

The paradox of HBV evolution as revealed from a 16th century mummy.

PLoS Pathog 2018 01 4;14(1):e1006750. Epub 2018 Jan 4.

McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, ON, Canada.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.ppat.1006750DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5754119PMC
January 2018

Continental synchronicity of human influenza virus epidemics despite climatic variation.

PLoS Pathog 2018 01 11;14(1):e1006780. Epub 2018 Jan 11.

Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.ppat.1006780DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5764404PMC
January 2018

Estimating evolutionary rates in giant viruses using ancient genomes.

Virus Evol 2018 Jan 27;4(1):vey006. Epub 2018 Feb 27.

Marie Bashir Institute of Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, University of Sydney, Sydney, NSW 2006, Australia.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/ve/vey006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5829572PMC
January 2018

Predicting virus emergence amid evolutionary noise.

Open Biol 2017 10;7(10)

Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, New South Wales 2006, Australia

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1098/rsob.170189DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5666085PMC
October 2017

High-Resolution Metatranscriptomics Reveals the Ecological Dynamics of Mosquito-Associated RNA Viruses in Western Australia.

J Virol 2017 09 10;91(17). Epub 2017 Aug 10.

Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Biological Sciences and Sydney Medical School, The University of Sydney, Sydney, Australia

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1128/JVI.00680-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5553174PMC
September 2017

Discovery of a Highly Divergent Coronavirus in the Asian House Shrew from China Illuminates the Origin of the Alphacoronaviruses.

J Virol 2017 Sep 10;91(17). Epub 2017 Aug 10.

State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Department of Zoonoses, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1128/JVI.00764-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5553162PMC
September 2017

Characterizing the virome of Ixodes ricinus ticks from northern Europe.

Sci Rep 2017 09 7;7(1):10870. Epub 2017 Sep 7.

Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, the University of Sydney, Sydney, New South Wales, 2006, Australia.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41598-017-11439-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5589870PMC
September 2017

Comment: Characterization of Two Historic Smallpox Specimens from a Czech Museum.

Viruses 2017 09 28;9(10). Epub 2017 Sep 28.

Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.3390/v9100276DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5691628PMC
September 2017

A Diverse Range of Novel RNA Viruses in Geographically Distinct Honey Bee Populations.

J Virol 2017 08 27;91(16). Epub 2017 Jul 27.

School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1128/JVI.00158-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5533899PMC
August 2017

Next step in the ongoing arms race between myxoma virus and wild rabbits in Australia is a novel disease phenotype.

Proc Natl Acad Sci U S A 2017 08 14;114(35):9397-9402. Epub 2017 Aug 14.

Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, PA 16802;

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.1710336114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5584459PMC
August 2017

Extensive diversity of coronaviruses in bats from China.

Virology 2017 07 3;507:1-10. Epub 2017 Apr 3.

State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Department of Zoonoses, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.virol.2017.03.019DOI Listing
July 2017

Persistent infections in immunocompromised hosts are rarely sources of new pathogen variants.

Virus Evol 2017 Jul 28;3(2):vex018. Epub 2017 Jul 28.

School of Biotechnology and Biomolecular Sciences, and Evolution & Ecology Research Centre, University of New South Wales, Sydney, NSW 2052, Australia.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/ve/vex018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5534129PMC
July 2017

Multiple Sources of Genetic Diversity of Influenza A Viruses during the Hajj.

J Virol 2017 06 12;91(11). Epub 2017 May 12.

Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1128/JVI.00096-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5432881PMC
June 2017

Benign Rabbit Calicivirus in New Zealand.

Appl Environ Microbiol 2017 06 17;83(11). Epub 2017 May 17.

Wildlife Ecology and Management Group, Landcare Research, Lincoln, New Zealand

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1128/AEM.00090-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5440710PMC
June 2017

Molecular Evolution and Emergence of H5N6 Avian Influenza Virus in Central China.

J Virol 2017 06 26;91(12). Epub 2017 May 26.

CAS Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1128/JVI.00143-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5446651PMC
June 2017

Extensive diversity of rickettsiales bacteria in ticks from Wuhan, China.

Ticks Tick Borne Dis 2017 06 24;8(4):574-580. Epub 2017 Mar 24.

State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Department of Zoonoses, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.ttbdis.2017.03.006DOI Listing
June 2017

Diversity, evolution and population dynamics of avian influenza viruses circulating in the live poultry markets in China.

Virology 2017 05 20;505:33-41. Epub 2017 Feb 20.

State Key Laboratory of Virology/Institute of Medical Virology, School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China; State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, 102206 Beijing, China. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.virol.2017.02.009DOI Listing
May 2017

The impact of migratory flyways on the spread of avian influenza virus in North America.

BMC Evol Biol 2017 05 25;17(1):118. Epub 2017 May 25.

Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, Australia.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12862-017-0965-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5445350PMC
May 2017

Dinucleotide Composition in Animal RNA Viruses Is Shaped More by Virus Family than by Host Species.

J Virol 2017 Apr 29;91(8). Epub 2017 Mar 29.

Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences, and Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1128/JVI.02381-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5375695PMC
April 2017

Virus genomes reveal factors that spread and sustained the Ebola epidemic.

Nature 2017 04 12;544(7650):309-315. Epub 2017 Apr 12.

Institute of Evolutionary Biology, University of Edinburgh, King's Buildings, Edinburgh EH9 3FL, UK.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nature22040DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5712493PMC
April 2017

Genomic and phenotypic characterization of myxoma virus from Great Britain reveals multiple evolutionary pathways distinct from those in Australia.

PLoS Pathog 2017 03 2;13(3):e1006252. Epub 2017 Mar 2.

Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and Sydney Medical School, University of Sydney, Sydney, New South Wales 2006, Australia.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.ppat.1006252DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5349684PMC
March 2017

Comparative analysis estimates the relative frequencies of co-divergence and cross-species transmission within viral families.

PLoS Pathog 2017 02 8;13(2):e1006215. Epub 2017 Feb 8.

Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.ppat.1006215DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5319820PMC
February 2017

Redefining the invertebrate RNA virosphere.

Nature 2016 Dec 23;540(7634):539-543. Epub 2016 Nov 23.

State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, 100206 Beijing, China.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nature20167DOI Listing
December 2016

Plasmodium falciparum malaria in 1-2 century CE southern Italy.

Curr Biol 2016 12;26(23):R1220-R1222

McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, Ontario L8S 4L9, Canada; Department of Anthropology, McMaster University, Hamilton, Ontario L8S 4L9, Canada; Department of Biology, McMaster University, Hamilton, Ontario L8S 4L9, Canada; DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario L8S 4L9, Canada; Humans & the Microbiome Program, Canadian Institute for Advanced Research, Toronto, Ontario M5G 1Z8, Canada. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.cub.2016.10.016DOI Listing
December 2016

Cyprinid herpesvirus 3 and its evolutionary future as a biological control agent for carp in Australia.

Virol J 2016 12 8;13(1):206. Epub 2016 Dec 8.

Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, the University of Sydney, Sydney, NSW, 2006, Australia.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12985-016-0666-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5146810PMC
December 2016

Extensive genetic diversity of Rickettsiales bacteria in multiple mosquito species.

Sci Rep 2016 12 9;6:38770. Epub 2016 Dec 9.

State Key Laboratory of Infectious Disease Prevention and Control, Department of Zoonoses, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/srep38770DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5146937PMC
December 2016

17 Century Variola Virus Reveals the Recent History of Smallpox.

Curr Biol 2016 12 8;26(24):3407-3412. Epub 2016 Dec 8.

McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, ON L8S 4L8, Canada; Department of Biology, McMaster University, Hamilton, ON L8S 4L8, Canada; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4L8, Canada; Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ON M5G 1Z8, Canada. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.cub.2016.10.061DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5196022PMC
December 2016

Large-Scale Phylogenomic Analysis Reveals the Complex Evolutionary History of Rabies Virus in Multiple Carnivore Hosts.

PLoS Pathog 2016 Dec 15;12(12):e1006041. Epub 2016 Dec 15.

Institut Pasteur, Unit Lyssavirus Dynamics and Host Adaptation, WHO Collaborating Centre for Reference and Research on Rabies, Paris, France.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.ppat.1006041DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5158080PMC
December 2016

Estimating evolutionary rates using time-structured data: a general comparison of phylogenetic methods.

Bioinformatics 2016 11 13;32(22):3375-3379. Epub 2016 Jul 13.

School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btw421DOI Listing
November 2016

Human Adaptation of Ebola Virus during the West African Outbreak.

Cell 2016 11;167(4):1079-1087.e5

School of Life Sciences, The University of Nottingham, Nottingham NG7 2RD, UK; NIHR Nottingham Digestive Diseases Biomedical Research Unit, The University of Nottingham, Nottingham University Hospitals NHS Trust, Nottingham NG7 2UH, UK. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.cell.2016.10.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5101188PMC
November 2016

Genome-scale rates of evolutionary change in bacteria.

Microb Genom 2016 11 30;2(11):e000094. Epub 2016 Nov 30.

Marie Bashir Institute of Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney , Sydney, NSW 2006 , Australia.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1099/mgen.0.000094DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5320706PMC
November 2016

Benign Rabbit Caliciviruses Exhibit Evolutionary Dynamics Similar to Those of Their Virulent Relatives.

J Virol 2016 10 29;90(20):9317-29. Epub 2016 Sep 29.

Commonwealth Scientific and Industrial Research Organization, Health and Biosecurity, Black Mountain, ACT, Australia Invasive Animals Cooperative Research Centre, University of Canberra, Bruce, ACT, Australia

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1128/JVI.01212-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5044836PMC
October 2016

The evolution of Ebola virus: Insights from the 2013-2016 epidemic.

Nature 2016 10;538(7624):193-200

The Scripps Research Institute, Department of Immunology and Microbial Science, La Jolla, San Diego, California 92037, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nature19790DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5580494PMC
October 2016

Molecular Evolution and Phylogeography of Co-circulating IHNV and VHSV in Italy.

Front Microbiol 2016 23;7:1306. Epub 2016 Aug 23.

Department of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie Padova, Italy.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.3389/fmicb.2016.01306DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4994472PMC
September 2016

The Expanding Virosphere.

Authors:
Edward C Holmes

Cell Host Microbe 2016 09;20(3):279-280

Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, the University of Sydney, Sydney NSW 2006, Australia. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.chom.2016.08.007DOI Listing
September 2016

A Bat-Derived Putative Cross-Family Recombinant Coronavirus with a Reovirus Gene.

PLoS Pathog 2016 Sep 27;12(9):e1005883. Epub 2016 Sep 27.

National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.ppat.1005883DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5038965PMC
September 2016

Comment on "Mutation rate and genotype variation of Ebola virus from Mali case sequences".

Science 2016 Aug 11;353(6300):658. Epub 2016 Aug 11.

The Scripps Research Institute, Department of Immunology and Microbial Science, La Jolla, CA 92037, USA. Scripps Translational Science Institute, La Jolla, CA 92037, USA. Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1126/science.aaf3823DOI Listing
August 2016

Pathogen population bottlenecks and adaptive landscapes: overcoming the barriers to disease emergence.

Proc Biol Sci 2016 08;283(1837)

Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, New South Wales 2006, Australia

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1098/rspb.2016.0727DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5013787PMC
August 2016