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

Zhang YZ, Holmes EC.

Cell. 2020 Mar 26. pii: S0092-8674(20)30328-7. doi: 10.1016/j.cell.2020.03.035. [Epub ahead of print]


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

Lam TT, Shum MH, Zhu HC, Tong YG, Ni XB, Liao YS, Wei W, Cheung WY, Li WJ, Li LF, Leung GM, Holmes EC, Hu YL, Guan Y.

Nature. 2020 Mar 26. doi: 10.1038/s41586-020-2169-0. [Epub ahead of print]


Comparative analysis of RNA virome composition in rabbits and associated ectoparasites.

Mahar JE, Shi M, Hall RN, Strive T, Holmes EC.

J Virol. 2020 Mar 18. pii: JVI.02119-19. doi: 10.1128/JVI.02119-19. [Epub ahead of print]


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

Batovska J, Buchmann JP, Holmes EC, Lynch SE.

Microbiol Resour Announc. 2020 Mar 5;9(10). pii: e00103-20. doi: 10.1128/MRA.00103-20. No abstract available.


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

Li CX, Li W, Zhou J, Zhang B, Feng Y, Xu CP, Lu YY, Holmes EC, Shi M.

Sci Rep. 2020 Mar 3;10(1):3963. doi: 10.1038/s41598-020-60992-6.


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

R Marcelino V, Holmes EC, Sorrell TC.

BMC Genomics. 2020 Feb 27;21(1):184. doi: 10.1186/s12864-020-6592-2.


Properties and abundance of overlapping genes in viruses.

Schlub TE, Holmes EC.

Virus Evol. 2020 Feb 13;6(1):veaa009. doi: 10.1093/ve/veaa009. eCollection 2020 Jan.


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

Grubaugh ND, Petrone ME, Holmes EC.

Nat Microbiol. 2020 Apr;5(4):529-530. doi: 10.1038/s41564-020-0690-4. No abstract available.


A new coronavirus associated with human respiratory disease in China.

Wu F, Zhao S, Yu B, Chen YM, Wang W, Song ZG, Hu Y, Tao ZW, Tian JH, Pei YY, Yuan ML, Zhang YL, Dai FH, Liu Y, Wang QM, Zheng JJ, Xu L, Holmes EC, Zhang YZ.

Nature. 2020 Mar;579(7798):265-269. doi: 10.1038/s41586-020-2008-3. Epub 2020 Feb 3.


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

Lu R, Zhao X, Li J, Niu P, Yang B, Wu H, Wang W, Song H, Huang B, Zhu N, Bi Y, Ma X, Zhan F, Wang L, Hu T, Zhou H, Hu Z, Zhou W, Zhao L, Chen J, Meng Y, Wang J, Lin Y, Yuan J, Xie Z, Ma J, Liu WJ, Wang D, Xu W, Holmes EC, Gao GF, Wu G, Chen W, Shi W, Tan W.

Lancet. 2020 Feb 22;395(10224):565-574. doi: 10.1016/S0140-6736(20)30251-8. Epub 2020 Jan 30.


Identification of A Novel Papillomavirus Associated with Squamous Cell Carcinoma in A Domestic Cat.

Carrai M, Van Brussel K, Shi M, Li CX, Chang WS, Munday JS, Voss K, McLuckie A, Taylor D, Laws A, Holmes EC, Barrs VR, Beatty JA.

Viruses. 2020 Jan 20;12(1). pii: E124. doi: 10.3390/v12010124.


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

Batovska J, Buchmann JP, Holmes EC, Lynch SE.

Microbiol Resour Announc. 2020 Jan 9;9(2). pii: e01476-19. doi: 10.1128/MRA.01476-19. Erratum in: Microbiol Resour Announc. 2020 Mar 5;9(10):.


Discovery and Prevalence of Divergent RNA Viruses in European Field Voles and Rabbits.

Tsoleridis T, Chappell JG, Monchatre-Leroy E, Umhang G, Shi M, Bennett M, Tarlinton RE, McClure CP, Holmes EC, Ball JK.

Viruses. 2019 Dec 31;12(1). pii: E47. doi: 10.3390/v12010047.


Origin of the São Paulo Yellow Fever epidemic of 2017-2018 revealed through molecular epidemiological analysis of fatal cases.

Cunha MDP, Duarte-Neto AN, Pour SZ, Ortiz-Baez AS, Černý J, Pereira BBS, Braconi CT, Ho YL, Perondi B, Sztajnbok J, Alves VAF, Dolhnikoff M, Holmes EC, Saldiva PHN, Zanotto PMA.

Sci Rep. 2019 Dec 31;9(1):20418. doi: 10.1038/s41598-019-56650-1.


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

Charon J, Grigg MJ, Eden JS, Piera KA, Rana H, William T, Rose K, Davenport MP, Anstey NM, Holmes EC.

PLoS Pathog. 2019 Dec 30;15(12):e1008216. doi: 10.1371/journal.ppat.1008216. eCollection 2019 Dec.


The Ecology and Evolution of Influenza Viruses.

Wille M, Holmes EC.

Cold Spring Harb Perspect Med. 2019 Dec 30. pii: a038489. doi: 10.1101/cshperspect.a038489. [Epub ahead of print]


Distinct Lineages of Feline Parvovirus Associated with Epizootic Outbreaks in Australia, New Zealand and the United Arab Emirates.

Van Brussel K, Carrai M, Lin C, Kelman M, Setyo L, Aberdein D, Brailey J, Lawler M, Maher S, Plaganyi I, Lewis E, Hawkswell A, Allison AB, Meers J, Martella V, Beatty JA, Holmes EC, Decaro N, Barrs VR.

Viruses. 2019 Dec 13;11(12). pii: E1155. doi: 10.3390/v11121155.


Bat IFITM3 restriction depends on S-palmitoylation and a polymorphic site within the CD225 domain.

Benfield CT, MacKenzie F, Ritzefeld M, Mazzon M, Weston S, Tate E, Teo BH, Smith SE, Kellam P, Holmes EC, Marsh M.

Life Sci Alliance. 2019 Dec 11;3(1). pii: e201900542. doi: 10.26508/lsa.201900542. Print 2020 Jan.


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

Novelo M, Hall MD, Pak D, Young PR, Holmes EC, McGraw EA.

PLoS Pathog. 2019 Dec 2;15(12):e1008218. doi: 10.1371/journal.ppat.1008218. eCollection 2019 Dec.


Identification and evolution of avian endogenous foamy viruses.

Chen Y, Wei X, Zhang G, Holmes EC, Cui J.

Virus Evol. 2019 Nov 25;5(2):vez049. doi: 10.1093/ve/vez049. eCollection 2019 Jul.


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

Porter AF, Shi M, Eden JS, Zhang YZ, Holmes EC.

Viruses. 2019 Nov 25;11(12). pii: E1092. doi: 10.3390/v11121092.


Human pegivirus in brain tissue of a patient with encephalitis.

Tuddenham R, Eden JS, Gilbey T, Dwyer DE, Jennings Z, Holmes EC, Branley JM.

Diagn Microbiol Infect Dis. 2020 Feb;96(2):114898. doi: 10.1016/j.diagmicrobio.2019.114898. Epub 2019 Oct 5.


An Ecosystems Perspective on Virus Evolution and Emergence.

French RK, Holmes EC.

Trends Microbiol. 2020 Mar;28(3):165-175. doi: 10.1016/j.tim.2019.10.010. Epub 2019 Nov 16. Review.


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

Pettersson JH, Shi M, Eden JS, Holmes EC, Hesson JC.

Viruses. 2019 Nov 6;11(11). pii: E1033. doi: 10.3390/v11111033.


An engineered pathway for N-hydroxy-pipecolic acid synthesis enhances systemic acquired resistance in tomato.

Holmes EC, Chen YC, Sattely ES, Mudgett MB.

Sci Signal. 2019 Oct 22;12(604). pii: eaay3066. doi: 10.1126/scisignal.aay3066.


Evolution of Termite Symbiosis Informed by Transcriptome-Based Phylogenies.

Bucek A, Šobotník J, He S, Shi M, McMahon DP, Holmes EC, Roisin Y, Lo N, Bourguignon T.

Curr Biol. 2019 Nov 4;29(21):3728-3734.e4. doi: 10.1016/j.cub.2019.08.076. Epub 2019 Oct 17.


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

Voorhees IEH, Lee H, Allison AB, Lopez-Astacio R, Goodman LB, Oyesola OO, Omobowale O, Fagbohun O, Dubovi EJ, Hafenstein SL, Holmes EC, Parrish CR.

J Virol. 2019 Dec 12;94(1). pii: e01162-19. doi: 10.1128/JVI.01162-19. Print 2019 Dec 12.


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

Lu M, Li F, Liao Y, Shen JJ, Xu JM, Chen YZ, Li JH, Holmes EC, Zhang YZ.

Sci Rep. 2019 Sep 11;9(1):13176. doi: 10.1038/s41598-019-49059-3.


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

Wasik BR, Voorhees IEH, Barnard KN, Alford-Lawrence BK, Weichert WS, Hood G, Nogales A, Martínez-Sobrido L, Holmes EC, Parrish CR.

J Virol. 2019 Nov 13;93(23). pii: e01039-19. doi: 10.1128/JVI.01039-19. Print 2019 Dec 1.


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

Pettersson JH, Piorkowski G, Mayxay M, Rattanavong S, Vongsouvath M, Davong V, Alfsnes K, Eldholm V, de Lamballerie X, Holmes EC, Newton PN, Dubot-Pérès A.

Diagn Microbiol Infect Dis. 2019 Dec;95(4):114878. doi: 10.1016/j.diagmicrobio.2019.114878. Epub 2019 Aug 1.


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

Poon LLM, Song T, Wentworth DE, Holmes EC, Greenbaum BD, Peiris JSM, Cowling BJ, Ghedin E.

Nat Genet. 2019 Sep;51(9):1301-1303. doi: 10.1038/s41588-019-0486-8. No abstract available.


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

Li CX, Chang WS, Mitsakos K, Rodger J, Holmes EC, Hudson BJ.

Viruses. 2019 Aug 4;11(8). pii: E713. doi: 10.3390/v11080713.


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

Shi W, Ke C, Fang S, Li J, Song H, Li X, Hu T, Wu J, Chen T, Yi L, Song Y, Wang X, Xing W, Huang W, Xiao H, Liang L, Peng B, Wu W, Liu H, Liu WJ, Holmes EC, Gao GF, Wang D.

Emerg Microbes Infect. 2019;8(1):1157-1167. doi: 10.1080/22221751.2019.1648183.


Novel hepatitis D-like agents in vertebrates and invertebrates.

Chang WS, Pettersson JH, Le Lay C, Shi M, Lo N, Wille M, Eden JS, Holmes EC.

Virus Evol. 2019 Jul 15;5(2):vez021. doi: 10.1093/ve/vez021. eCollection 2019 Jul.


Identification of diverse arthropod associated viruses in native Australian fleas.

Harvey E, Rose K, Eden JS, Lawrence A, Doggett SL, Holmes EC.

Virology. 2019 Sep;535:189-199. doi: 10.1016/j.virol.2019.07.010. Epub 2019 Jul 9.


Evolutionary history of Simbu serogroup orthobunyaviruses in the Australian episystem.

Wang J, Firth C, Amos-Ritchie R, Davis SS, Yin H, Holmes EC, Blasdell KR, Walker PJ.

Virology. 2019 Sep;535:32-44. doi: 10.1016/j.virol.2019.06.013. Epub 2019 Jun 26.


Virome heterogeneity and connectivity in waterfowl and shorebird communities.

Wille M, Shi M, Klaassen M, Hurt AC, Holmes EC.

ISME J. 2019 Oct;13(10):2603-2616. doi: 10.1038/s41396-019-0458-0. Epub 2019 Jun 25.


Reagent contamination in viromics: all that glitters is not gold.

Holmes EC.

Clin Microbiol Infect. 2019 Oct;25(10):1167-1168. doi: 10.1016/j.cmi.2019.06.019. Epub 2019 Jun 22. No abstract available.


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

Bonnaud EM, Troupin C, Dacheux L, Holmes EC, Monchatre-Leroy E, Tanguy M, Bouchier C, Cliquet F, Barrat J, Bourhy H.

PLoS Pathog. 2019 Jun 20;15(6):e1007799. doi: 10.1371/journal.ppat.1007799. eCollection 2019 Jun.


Sustained Wolbachia-mediated blocking of dengue virus isolates following serial passage in Aedes aegypti cell culture.

Koh C, Audsley MD, Di Giallonardo F, Kerton EJ, Young PR, Holmes EC, McGraw EA.

Virus Evol. 2019 Jun 8;5(1):vez012. doi: 10.1093/ve/vez012. eCollection 2019 Jan.


Limited Sustained Local Transmission of HIV-1 CRF01_AE in New South Wales, Australia.

Di Giallonardo F, Pinto AN, Keen P, Shaik A, Carrera A, Salem H, Telfer B, Cooper C, Price K, Selvey C, Holden J, Bachmann N, Lee FJ, Dwyer DE, Duchêne S, Holmes EC, Grulich AE, Kelleher AD.

Viruses. 2019 May 27;11(5). pii: E482. doi: 10.3390/v11050482.


Expanding the RNA Virosphere by Unbiased Metagenomics.

Zhang YZ, Chen YM, Wang W, Qin XC, Holmes EC.

Annu Rev Virol. 2019 Sep 29;6(1):119-139. doi: 10.1146/annurev-virology-092818-015851. Epub 2019 May 17.


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

Buchmann JP, Holmes EC.

Bioinformatics. 2019 Nov 1;35(21):4511-4514. doi: 10.1093/bioinformatics/btz385.


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

Mahar JE, Hall RN, Shi M, Mourant R, Huang N, Strive T, Holmes EC.

Virus Evol. 2019 Apr 9;5(1):vez005. doi: 10.1093/ve/vez005. eCollection 2019 Jan.


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

Holmes EC, Duchêne S.

mBio. 2019 Apr 16;10(2). pii: e00289-19. doi: 10.1128/mBio.00289-19. No abstract available.


Meta-transcriptomics reveals a diverse antibiotic resistance gene pool in avian microbiomes.

Marcelino VR, Wille M, Hurt AC, González-Acuña D, Klaassen M, Schlub TE, Eden JS, Shi M, Iredell JR, Sorrell TC, Holmes EC.

BMC Biol. 2019 Apr 8;17(1):31. doi: 10.1186/s12915-019-0649-1.


Discovery of a highly divergent hepadnavirus in shrews from China.

Nie FY, Tian JH, Lin XD, Yu B, Xing JG, Cao JH, Holmes EC, Ma RZ, Zhang YZ.

Virology. 2019 May;531:162-170. doi: 10.1016/j.virol.2019.03.007. Epub 2019 Mar 11.


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

Chong R, Shi M, Grueber CE, Holmes EC, Hogg CJ, Belov K, Barrs VR.

J Virol. 2019 May 15;93(11). pii: e00205-19. doi: 10.1128/JVI.00205-19. Print 2019 Jun 1.


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

Wei X, Chen Y, Duan G, Holmes EC, Cui J.

Virus Evol. 2019 Feb 27;5(1):vez001. doi: 10.1093/ve/vez001. eCollection 2019 Jan.


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

Harvey E, Madden D, Polkinghorne A, Holmes EC.

Viruses. 2019 Mar 2;11(3). pii: E211. doi: 10.3390/v11030211.

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