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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. 2019 Oct 5:114898. doi: 10.1016/j.diagmicrobio.2019.114898. [Epub ahead of print]


An Ecosystems Perspective on Virus Evolution and Emergence.

French RK, Holmes EC.

Trends Microbiol. 2019 Nov 16. pii: S0966-842X(19)30265-3. doi: 10.1016/j.tim.2019.10.010. [Epub ahead of print] 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 Jul 9;535:189-199. doi: 10.1016/j.virol.2019.07.010. [Epub ahead of print]


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 Jun 26;535:32-44. doi: 10.1016/j.virol.2019.06.013. [Epub ahead of print]


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.


Evolutionary stasis of viruses?

Holmes EC, Duchêne S.

Nat Rev Microbiol. 2019 May;17(5):329. doi: 10.1038/s41579-019-0168-7. No abstract available.


Human Tick-Borne Diseases in Australia.

Dehhaghi M, Kazemi Shariat Panahi H, Holmes EC, Hudson BJ, Schloeffel R, Guillemin GJ.

Front Cell Infect Microbiol. 2019 Jan 28;9:3. doi: 10.3389/fcimb.2019.00003. eCollection 2019. Review.


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

Kerr PJ, Eden JS, Di Giallonardo F, Peacock D, Liu J, Strive T, Read AF, Holmes EC.

J Virol. 2019 Apr 3;93(8). pii: e01994-18. doi: 10.1128/JVI.01994-18. Print 2019 Apr 15.


Shared Common Ancestry of Rodent Alphacoronaviruses Sampled Globally.

Tsoleridis T, Chappell JG, Onianwa O, Marston DA, Fooks AR, Monchatre-Leroy E, Umhang G, Müller MA, Drexler JF, Drosten C, Tarlinton RE, McClure CP, Holmes EC, Ball JK.

Viruses. 2019 Jan 30;11(2). pii: E125. doi: 10.3390/v11020125.


A Divergent Hepatitis D-Like Agent in Birds.

Wille M, Netter HJ, Littlejohn M, Yuen L, Shi M, Eden JS, Klaassen M, Holmes EC, Hurt AC.

Viruses. 2018 Dec 17;10(12). pii: E720. doi: 10.3390/v10120720.


Tracking virus outbreaks in the twenty-first century.

Grubaugh ND, Ladner JT, Lemey P, Pybus OG, Rambaut A, Holmes EC, Andersen KG.

Nat Microbiol. 2019 Jan;4(1):10-19. doi: 10.1038/s41564-018-0296-2. Epub 2018 Dec 13. Review.


Evolutionary Virology at 40.

Geoghegan JL, Holmes EC.

Genetics. 2018 Dec;210(4):1151-1162. doi: 10.1534/genetics.118.301556. Review.


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

Nelson MI, Lloyd-Smith JO, Simonsen L, Rambaut A, Holmes EC, Chowell G, Miller MA, Spiro DJ, Grenfell B, Viboud C.

Epidemics. 2019 Mar;26:116-127. doi: 10.1016/j.epidem.2018.10.004. Epub 2018 Oct 23. Review.


Extensive Diversity of RNA Viruses in Australian Ticks.

Harvey E, Rose K, Eden JS, Lo N, Abeyasuriya T, Shi M, Doggett SL, Holmes EC.

J Virol. 2019 Jan 17;93(3). pii: e01358-18. doi: 10.1128/JVI.01358-18. Print 2019 Feb 1.


Hidden diversity and evolution of viruses in market fish.

Geoghegan JL, Di Giallonardo F, Cousins K, Shi M, Williamson JE, Holmes EC.

Virus Evol. 2018 Oct 31;4(2):vey031. doi: 10.1093/ve/vey031. eCollection 2018 Jul.


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

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

Mol Ecol. 2018 Dec;27(24):5263-5278. doi: 10.1111/mec.14918. Epub 2018 Nov 22.


The phylogenomics of evolving virus virulence.

Geoghegan JL, Holmes EC.

Nat Rev Genet. 2018 Dec;19(12):756-769. doi: 10.1038/s41576-018-0055-5. Review.


An Atypical Parvovirus Drives Chronic Tubulointerstitial Nephropathy and Kidney Fibrosis.

Roediger B, Lee Q, Tikoo S, Cobbin JCA, Henderson JM, Jormakka M, O'Rourke MB, Padula MP, Pinello N, Henry M, Wynne M, Santagostino SF, Brayton CF, Rasmussen L, Lisowski L, Tay SS, Harris DC, Bertram JF, Dowling JP, Bertolino P, Lai JH, Wu W, Bachovchin WW, Wong JJ, Gorrell MD, Shaban B, Holmes EC, Jolly CJ, Monette S, Weninger W.

Cell. 2018 Oct 4;175(2):530-543.e24. doi: 10.1016/j.cell.2018.08.013. Epub 2018 Sep 13.


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

Di Giallonardo F, Kok J, Fernandez M, Carter I, Geoghegan JL, Dwyer DE, Holmes EC, Eden JS.

Viruses. 2018 Sep 6;10(9). pii: E476. doi: 10.3390/v10090476.


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

Aghazadeh M, Shi M, Pesavento PA, Durham AC, Polley T, Donahoe SL, Troyer RM, Barrs VR, Holmes EC, Beatty JA.

Viruses. 2018 Aug 30;10(9). pii: E464. doi: 10.3390/v10090464.


The diversity, evolution and origins of vertebrate RNA viruses.

Zhang YZ, Wu WC, Shi M, Holmes EC.

Curr Opin Virol. 2018 Aug;31:9-16. doi: 10.1016/j.coviro.2018.07.017. Epub 2018 Aug 13. Review.


Draft genome assembly of the invasive cane toad, Rhinella marina.

Edwards RJ, Tuipulotu DE, Amos TG, O'Meally D, Richardson MF, Russell TL, Vallinoto M, Carneiro M, Ferrand N, Wilkins MR, Sequeira F, Rollins LA, Holmes EC, Shine R, White PA.

Gigascience. 2018 Sep 1;7(9). doi: 10.1093/gigascience/giy095.

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