Edward C Holmes

Edward C Holmes

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Comparative Analysis of RNA Virome Composition in Rabbits and Associated Ectoparasites.

J Virol 2020 May 18;94(11). Epub 2020 May 18.

Marie Bashir Institute for Infectious Disease and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW, Australia

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http://dx.doi.org/10.1128/JVI.02119-19DOI Listing
May 2020

A Novel Bat Coronavirus Closely Related to SARS-CoV-2 Contains Natural Insertions at the S1/S2 Cleavage Site of the Spike Protein.

Curr Biol 2020 May 11. Epub 2020 May 11.

Key Laboratory of Etiology and Epidemiology of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University, and Shandong Academy of Medical Sciences, Taian 271000, China; The First Affiliated Hospital of Shandong First Medical University (Shandong Provincial Qianfoshan Hospital), Ji'nan 250014, China. Electronic address:

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http://dx.doi.org/10.1016/j.cub.2020.05.023DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7211627PMC
May 2020

We shouldn't worry when a virus mutates during disease outbreaks.

Nat Microbiol 2020 04;5(4):529-530

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

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http://dx.doi.org/10.1038/s41564-020-0690-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7095397PMC
April 2020

A Genomic Perspective on the Origin and Emergence of SARS-CoV-2.

Cell 2020 Apr 26;181(2):223-227. Epub 2020 Mar 26.

Shanghai Public Health Clinical Center and School of Life Science, Fudan University, Shanghai, China; Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, Australia. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2020.03.035DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7194821PMC
April 2020

The proximal origin of SARS-CoV-2.

Nat Med 2020 04;26(4):450-452

Tulane University, School of Medicine, Department of Microbiology and Immunology, New Orleans, LA, USA.

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http://dx.doi.org/10.1038/s41591-020-0820-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7095063PMC
April 2020

Sustained RNA virome diversity in Antarctic penguins and their ticks.

ISME J 2020 Apr 14. Epub 2020 Apr 14.

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

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http://dx.doi.org/10.1038/s41396-020-0643-1DOI Listing
April 2020

CCMetagen: comprehensive and accurate identification of eukaryotes and prokaryotes in metagenomic data.

Genome Biol 2020 Apr 28;21(1):103. Epub 2020 Apr 28.

Marie Bashir Institute for Infectious Diseases and Biosecurity and Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, The University of Sydney, Sydney, NSW, 2006, Australia.

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http://dx.doi.org/10.1186/s13059-020-02014-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7189439PMC
April 2020

An Ecosystems Perspective on Virus Evolution and Emergence.

Trends Microbiol 2020 Mar 16;28(3):165-175. Epub 2019 Nov 16.

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:

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http://dx.doi.org/10.1016/j.tim.2019.10.010DOI Listing
March 2020

High resolution metagenomic characterization of complex infectomes in paediatric acute respiratory infection.

Sci Rep 2020 Mar 3;10(1):3963. Epub 2020 Mar 3.

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

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http://dx.doi.org/10.1038/s41598-020-60992-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7054269PMC
March 2020

Correction for Batovska et al., "Coding-Complete Genome Sequence of Yada Yada Virus, a Novel Alphavirus Detected in Australian Mosquitoes".

Microbiol Resour Announc 2020 Mar 5;9(10). Epub 2020 Mar 5.

Agriculture Victoria Research, AgriBio Centre for AgriBioscience, Bundoora, Victoria, Australia.

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http://dx.doi.org/10.1128/MRA.00103-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7171210PMC
March 2020

Identifying SARS-CoV-2 related coronaviruses in Malayan pangolins.

Nature 2020 Mar 26. Epub 2020 Mar 26.

Joint Institute of Virology (Shantou University / The University of Hong Kong) & Guangdong-Hongkong Joint Laboratory of Emerging Infectious Diseases, Shantou University, Shantou, Guangdong, 515063, P. R. China.

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http://dx.doi.org/10.1038/s41586-020-2169-0DOI Listing
March 2020

Human pegivirus in brain tissue of a patient with encephalitis.

Diagn Microbiol Infect Dis 2020 Feb 5;96(2):114898. Epub 2019 Oct 5.

Nepean Hospital, PO Box 63, Penrith, NSW 2751, Australia. Electronic address:

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http://dx.doi.org/10.1016/j.diagmicrobio.2019.114898DOI Listing
February 2020

Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding.

Lancet 2020 02 30;395(10224):565-574. Epub 2020 Jan 30.

NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China; Central Theater, People's Liberation Army General Hospital, Wuhan, China; Center for Biosafety Mega-Science, Chinese Academy of Sciences, Beijing, China. Electronic address:

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http://dx.doi.org/10.1016/S0140-6736(20)30251-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7159086PMC
February 2020

The use of taxon-specific reference databases compromises metagenomic classification.

BMC Genomics 2020 Feb 27;21(1):184. Epub 2020 Feb 27.

Marie Bashir Institute for Infectious Diseases and Biosecurity and Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, The University of Sydney, Sydney, NSW, 2006, Australia.

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http://dx.doi.org/10.1186/s12864-020-6592-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7045516PMC
February 2020

Coding-Complete Genome Sequence of Yada Yada Virus, a Novel Alphavirus Detected in Australian Mosquitoes.

Microbiol Resour Announc 2020 Jan 9;9(2). Epub 2020 Jan 9.

Agriculture Victoria Research, AgriBio Centre for AgriBioscience, Bundoora, Victoria, Australia.

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http://dx.doi.org/10.1128/MRA.01476-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6952676PMC
January 2020

Properties and abundance of overlapping genes in viruses.

Virus Evol 2020 Jan 13;6(1):veaa009. Epub 2020 Feb 13.

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

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http://dx.doi.org/10.1093/ve/veaa009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7017920PMC
January 2020

Newly identified viral genomes in pangolins with fatal disease.

Virus Evol 2020 Jan 12;6(1):veaa020. Epub 2020 Apr 12.

Department of Zoonosis, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.

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http://dx.doi.org/10.1093/ve/veaa020DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7151644PMC
January 2020

An emergent clade of SARS-CoV-2 linked to returned travellers from Iran.

Virus Evol 2020 Jan 10;6(1):veaa027. Epub 2020 Apr 10.

Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead, NSW 2145, Australia.

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http://dx.doi.org/10.1093/ve/veaa027DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7147362PMC
January 2020

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.

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

Co-circulation and persistence of multiple A/H3N2 influenza variants in China.

Emerg Microbes Infect 2019 ;8(1):1157-1167

a Chinese National Influenza Center, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention , Beijing , People's Republic of China.

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http://dx.doi.org/10.1080/22221751.2019.1648183DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6713139PMC
December 2019

Meta-transcriptomic identification of hepatitis B virus in cerebrospinal fluid in patients with central nervous system disease.

Diagn Microbiol Infect Dis 2019 Dec 1;95(4):114878. Epub 2019 Aug 1.

Unité des Virus Émergents (UVE: Aix-Marseille Univ - IRD 190 - Inserm 1207 - IHU Méditerranée Infection), Marseille, France; Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Churchill Hospital, University of Oxford, Oxford, United Kingdom.

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http://dx.doi.org/10.1016/j.diagmicrobio.2019.114878DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6892275PMC
December 2019

Influenza Viruses in Mice: Deep Sequencing Analysis of Serial Passage and Effects of Sialic Acid Structural Variation.

J Virol 2019 12 13;93(23). Epub 2019 Nov 13.

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

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http://dx.doi.org/10.1128/JVI.01039-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6854484PMC
December 2019

Limited Intrahost Diversity and Background Evolution Accompany 40 Years of Canine Parvovirus Host Adaptation and Spread.

J Virol 2019 12 12;94(1). Epub 2019 Dec 12.

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

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http://dx.doi.org/10.1128/JVI.01162-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6912114PMC
December 2019

Intra-host growth kinetics of dengue virus in the mosquito Aedes aegypti.

PLoS Pathog 2019 12 2;15(12):e1008218. Epub 2019 Dec 2.

School of Biological Sciences, Monash University, Melbourne, Victoria, Australia.

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http://dx.doi.org/10.1371/journal.ppat.1008218DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6907869PMC
December 2019

The Ecology and Evolution of Influenza Viruses.

Cold Spring Harb Perspect Med 2019 Dec 30. Epub 2019 Dec 30.

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 2006, Australia.

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http://dx.doi.org/10.1101/cshperspect.a038489DOI Listing
December 2019

Novel RNA viruses associated with Plasmodium vivax in human malaria and Leucocytozoon parasites in avian disease.

PLoS Pathog 2019 12 30;15(12):e1008216. Epub 2019 Dec 30.

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.

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http://dx.doi.org/10.1371/journal.ppat.1008216DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6953888PMC
December 2019

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

Bioinformatics 2019 Nov;35(21):4511-4514

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.

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https://academic.oup.com/bioinformatics/advance-article/doi/
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http://dx.doi.org/10.1093/bioinformatics/btz385DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6821292PMC
November 2019

Evolution of Termite Symbiosis Informed by Transcriptome-Based Phylogenies.

Curr Biol 2019 11 17;29(21):3728-3734.e4. Epub 2019 Oct 17.

Okinawa Institute of Science & Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan; Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Kamycka 129, 16521 Prague, Czech Republic. Electronic address:

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http://dx.doi.org/10.1016/j.cub.2019.08.076DOI Listing
November 2019

Meta-Transcriptomic Comparison of the RNA Viromes of the Mosquito Vectors and in Northern Europe.

Viruses 2019 11 6;11(11). Epub 2019 Nov 6.

Department of Medical Biochemistry and Microbiology/Zoonosis Science Center, Uppsala University, 75237 Uppsala, Sweden.

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http://dx.doi.org/10.3390/v11111033DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6893722PMC
November 2019

Diversity and Evolution of Novel Invertebrate DNA Viruses Revealed by Meta-Transcriptomics.

Viruses 2019 11 25;11(12). Epub 2019 Nov 25.

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

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http://dx.doi.org/10.3390/v11121092DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6950620PMC
November 2019

Virome heterogeneity and connectivity in waterfowl and shorebird communities.

ISME J 2019 10 25;13(10):2603-2616. Epub 2019 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, Australia.

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http://dx.doi.org/10.1038/s41396-019-0458-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6775988PMC
October 2019

Expanding the RNA Virosphere by Unbiased Metagenomics.

Annu Rev Virol 2019 09 17;6(1):119-139. Epub 2019 May 17.

Shanghai Public Health Clinical Center and School of Public Health, Fudan University, Shanghai 200433, China; email:

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

Evolutionary history of Simbu serogroup orthobunyaviruses in the Australian episystem.

Virology 2019 09 26;535:32-44. Epub 2019 Jun 26.

School of Biological Sciences, The University of Queensland, St Lucia, 4072, Queensland, Australia. Electronic address:

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http://dx.doi.org/10.1016/j.virol.2019.06.013DOI Listing
September 2019

Identification of diverse arthropod associated viruses in native Australian fleas.

Virology 2019 09 9;535:189-199. Epub 2019 Jul 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, NSW, 2006, Australia. Electronic address:

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http://dx.doi.org/10.1016/j.virol.2019.07.010DOI Listing
September 2019

Reply to 'Reconciling disparate estimates of viral genetic diversity during human influenza infections'.

Nat Genet 2019 09;51(9):1301-1303

Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA.

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http://dx.doi.org/10.1038/s41588-019-0486-8DOI Listing
September 2019

Epidemiology and Diversity of Rickettsiales Bacteria in Humans and Animals in Jiangsu and Jiangxi provinces, China.

Sci Rep 2019 Sep 11;9(1):13176. Epub 2019 Sep 11.

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.

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http://dx.doi.org/10.1038/s41598-019-49059-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6739303PMC
September 2019

Identification of a Novel Equine Papillomavirus in Semen from a Thoroughbred Stallion with a Penile Lesion.

Viruses 2019 08 4;11(8). Epub 2019 Aug 4.

Royal North Shore Hospital, Clinical Microbiology & Infectious Diseases, Reserve Road, St Leonards, NSW 2065, Australia.

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http://dx.doi.org/10.3390/v11080713DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6723834PMC
August 2019

Metatranscriptomics as a tool to identify fungal species and subspecies in mixed communities - a proof of concept under laboratory conditions.

IMA Fungus 2019 8;10:12. Epub 2019 Aug 8.

1Marie Bashir Institute for Infectious Diseases and Biosecurity and Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, The University of Sydney, Sydney, NSW 2006 Australia.

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http://dx.doi.org/10.1186/s43008-019-0012-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7184889PMC
August 2019

Novel hepatitis D-like agents in vertebrates and invertebrates.

Virus Evol 2019 Jul 15;5(2):vez021. Epub 2019 Jul 15.

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

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http://dx.doi.org/10.1093/ve/vez021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6628682PMC
July 2019

Identification and evolution of avian endogenous foamy viruses.

Virus Evol 2019 Jul 25;5(2):vez049. Epub 2019 Nov 25.

Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.

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http://dx.doi.org/10.1093/ve/vez049DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6875641PMC
July 2019

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

J Virol 2019 06 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

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http://jvi.asm.org/lookup/doi/10.1128/JVI.00205-19
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http://dx.doi.org/10.1128/JVI.00205-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6532096PMC
June 2019

Comparison of intra- and inter-host genetic diversity in rabies virus during experimental cross-species transmission.

PLoS Pathog 2019 06 20;15(6):e1007799. Epub 2019 Jun 20.

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

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http://dx.doi.org/10.1371/journal.ppat.1007799DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6615636PMC
June 2019

Evolutionary stasis of viruses?

Nat Rev Microbiol 2019 05;17(5):329

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

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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 05 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:

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http://dx.doi.org/10.1016/j.virol.2019.03.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7172195PMC
May 2019

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

J Virol 2019 04 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

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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.

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http://mbio.asm.org/lookup/doi/10.1128/mBio.00289-19
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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:

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https://linkinghub.elsevier.com/retrieve/pii/S17554365183002
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http://dx.doi.org/10.1016/j.epidem.2018.10.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7105018PMC
March 2019

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

Viruses 2019 03 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.

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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 02 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

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http://jvi.asm.org/lookup/doi/10.1128/JVI.01358-18
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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.

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

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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.

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https://academic.oup.com/ve/article/doi/10.1093/ve/vez005/54
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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 12;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.

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http://dx.doi.org/10.1038/s41576-018-0055-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7096893PMC
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.

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http://doi.wiley.com/10.1111/mec.14918
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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

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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.

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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.

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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 10 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:

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https://linkinghub.elsevier.com/retrieve/pii/S00928674183102
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http://dx.doi.org/10.1016/j.cell.2018.08.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6800251PMC
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.

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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.

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http://www.mdpi.com/1999-4915/10/9/476
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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

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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.

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http://dx.doi.org/10.1016/j.coviro.2018.07.017DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7102767PMC
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.

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http://www.mdpi.com/1999-4915/10/9/464
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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.

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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

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http://rspb.royalsocietypublishing.org/lookup/doi/10.1098/rs
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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.

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http://fdslive.oup.com/www.oup.com/pdf/production_in_progres
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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.

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.

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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.

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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 06 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.

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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.

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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.

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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.

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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.

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http://dx.doi.org/10.1016/j.meegid.2018.01.012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7106311PMC
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.

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

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

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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.

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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.

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