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Items: 28

1.

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.

2.

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.

3.

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.

4.

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.

5.

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.

6.

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

Di Giallonardo F, Audsley MD, Shi M, Young PR, McGraw EA, Holmes EC.

J Gen Virol. 2018 Jun;99(6):832-836. doi: 10.1099/jgv.0.001079. Epub 2018 May 9.

PMID:
29741476
7.

RNA-Seq analysis of chikungunya virus infection and identification of granzyme A as a major promoter of arthritic inflammation.

Wilson JA, Prow NA, Schroder WA, Ellis JJ, Cumming HE, Gearing LJ, Poo YS, Taylor A, Hertzog PJ, Di Giallonardo F, Hueston L, Le Grand R, Tang B, Le TT, Gardner J, Mahalingam S, Roques P, Bird PI, Suhrbier A.

PLoS Pathog. 2017 Feb 16;13(2):e1006155. doi: 10.1371/journal.ppat.1006155. eCollection 2017 Feb.

8.

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

Di Giallonardo F, Schlub TE, Shi M, Holmes EC.

J Virol. 2017 Mar 29;91(8). pii: e02381-16. doi: 10.1128/JVI.02381-16. Print 2017 Apr 15.

9.

Distinct Viral Lineages from Fish and Amphibians Reveal the Complex Evolutionary History of Hepadnaviruses.

Dill JA, Camus AC, Leary JH, Di Giallonardo F, Holmes EC, Ng TF.

J Virol. 2016 Aug 12;90(17):7920-33. doi: 10.1128/JVI.00832-16. Print 2016 Sep 1.

10.

Cross-validation to select Bayesian hierarchical models in phylogenetics.

Duchêne S, Duchêne DA, Di Giallonardo F, Eden JS, Geoghegan JL, Holt KE, Ho SY, Holmes EC.

BMC Evol Biol. 2016 May 26;16(1):115. doi: 10.1186/s12862-016-0688-y.

11.

Monocyte-derived macrophages exhibit distinct and more restricted HIV-1 integration site repertoire than CD4(+) T cells.

Kok YL, Vongrad V, Shilaih M, Di Giallonardo F, Kuster H, Kouyos R, Günthard HF, Metzner KJ.

Sci Rep. 2016 Apr 12;6:24157. doi: 10.1038/srep24157.

12.

Virological factors that increase the transmissibility of emerging human viruses.

Geoghegan JL, Senior AM, Di Giallonardo F, Holmes EC.

Proc Natl Acad Sci U S A. 2016 Apr 12;113(15):4170-5. doi: 10.1073/pnas.1521582113. Epub 2016 Mar 21.

13.

A Follow-Up of the Multicenter Collaborative Study on HIV-1 Drug Resistance and Tropism Testing Using 454 Ultra Deep Pyrosequencing.

St John EP, Simen BB, Turenchalk GS, Braverman MS, Abbate I, Aerssens J, Bouchez O, Gabriel C, Izopet J, Meixenberger K, Di Giallonardo F, Schlapbach R, Paredes R, Sakwa J, Schmitz-Agheguian GG, Thielen A, Victor M, Metzner KJ, Däumer MP; 454 HIV-1 Alpha Study Group.

PLoS One. 2016 Jan 12;11(1):e0146687. doi: 10.1371/journal.pone.0146687. eCollection 2016.

14.

A Comprehensive Analysis of Primer IDs to Study Heterogeneous HIV-1 Populations.

Seifert D, Di Giallonardo F, Töpfer A, Singer J, Schmutz S, Günthard HF, Beerenwinkel N, Metzner KJ.

J Mol Biol. 2016 Jan 16;428(1):238-250. doi: 10.1016/j.jmb.2015.12.012. Epub 2015 Dec 19.

15.

Fluid Spatial Dynamics of West Nile Virus in the United States: Rapid Spread in a Permissive Host Environment.

Di Giallonardo F, Geoghegan JL, Docherty DE, McLean RG, Zody MC, Qu J, Yang X, Birren BW, Malboeuf CM, Newman RM, Ip HS, Holmes EC.

J Virol. 2015 Oct 28;90(2):862-72. doi: 10.1128/JVI.02305-15. Print 2016 Jan 15.

16.

Contribution of APOBEC3G/F activity to the development of low-abundance drug-resistant human immunodeficiency virus type 1 variants.

Noguera-Julian M, Cozzi-Lepri A, Di Giallonardo F, Schuurman R, Däumer M, Aitken S, Ceccherini-Silberstein F, D'Arminio Monforte A, Geretti AM, Booth CL, Kaiser R, Michalik C, Jansen K, Masquelier B, Bellecave P, Kouyos RD, Castro E, Furrer H, Schultze A, Günthard HF, Brun-Vezinet F, Metzner KJ, Paredes R; CHAIN Minority HIV-1 Variants Working group.

Clin Microbiol Infect. 2016 Feb;22(2):191-200. doi: 10.1016/j.cmi.2015.10.004. Epub 2015 Oct 23.

17.

Substitution Model Adequacy and Assessing the Reliability of Estimates of Virus Evolutionary Rates and Time Scales.

Duchêne S, Di Giallonardo F, Holmes EC.

Mol Biol Evol. 2016 Jan;33(1):255-67. doi: 10.1093/molbev/msv207. Epub 2015 Sep 28.

PMID:
26416981
18.

Exploring Host-Pathogen Interactions through Biological Control.

Di Giallonardo F, Holmes EC.

PLoS Pathog. 2015 Jun 25;11(6):e1004865. doi: 10.1371/journal.ppat.1004865. eCollection 2015 Jun. Review. No abstract available.

19.

Viral biocontrol: grand experiments in disease emergence and evolution.

Di Giallonardo F, Holmes EC.

Trends Microbiol. 2015 Feb;23(2):83-90. doi: 10.1016/j.tim.2014.10.004. Epub 2014 Oct 31. Review.

20.

A framework for inferring fitness landscapes of patient-derived viruses using quasispecies theory.

Seifert D, Di Giallonardo F, Metzner KJ, Günthard HF, Beerenwinkel N.

Genetics. 2015 Jan;199(1):191-203. doi: 10.1534/genetics.114.172312. Epub 2014 Nov 17. Erratum in: Genetics. 2015 Apr;199(4):1271.

21.

Low-frequency drug-resistant HIV-1 and risk of virological failure to first-line NNRTI-based ART: a multicohort European case-control study using centralized ultrasensitive 454 pyrosequencing.

Cozzi-Lepri A, Noguera-Julian M, Di Giallonardo F, Schuurman R, Däumer M, Aitken S, Ceccherini-Silberstein F, D'Arminio Monforte A, Geretti AM, Booth CL, Kaiser R, Michalik C, Jansen K, Masquelier B, Bellecave P, Kouyos RD, Castro E, Furrer H, Schultze A, Günthard HF, Brun-Vezinet F, Paredes R, Metzner KJ; CHAIN Minority HIV-1 Variants Working Group.

J Antimicrob Chemother. 2015 Mar;70(3):930-40. doi: 10.1093/jac/dku426. Epub 2014 Oct 21.

22.

An international multicenter study on HIV-1 drug resistance testing by 454 ultra-deep pyrosequencing.

Simen BB, Braverman MS, Abbate I, Aerssens J, Bidet Y, Bouchez O, Gabriel C, Izopet J, Kessler HH, Stelzl E, Di Giallonardo F, Schlapbach R, Radonic A, Paredes R, Recordon-Pinson P, Sakwa J, St John EP, Schmitz-Agheguian GG, Metzner KJ, Däumer MP; 454 HIV Alphastudy Group.

J Virol Methods. 2014 Aug;204:31-7. doi: 10.1016/j.jviromet.2014.04.007. Epub 2014 Apr 13.

PMID:
24731928
23.

Next-generation sequencing of HIV-1 RNA genomes: determination of error rates and minimizing artificial recombination.

Di Giallonardo F, Zagordi O, Duport Y, Leemann C, Joos B, Künzli-Gontarczyk M, Bruggmann R, Beerenwinkel N, Günthard HF, Metzner KJ.

PLoS One. 2013 Sep 18;8(9):e74249. doi: 10.1371/journal.pone.0074249. eCollection 2013.

24.

EH3 (ABHD9): the first member of a new epoxide hydrolase family with high activity for fatty acid epoxides.

Decker M, Adamska M, Cronin A, Di Giallonardo F, Burgener J, Marowsky A, Falck JR, Morisseau C, Hammock BD, Gruzdev A, Zeldin DC, Arand M.

J Lipid Res. 2012 Oct;53(10):2038-45. doi: 10.1194/jlr.M024448. Epub 2012 Jul 12.

25.

Tailored enrichment strategy detects low abundant small noncoding RNAs in HIV-1 infected cells.

Althaus CF, Vongrad V, Niederöst B, Joos B, Di Giallonardo F, Rieder P, Pavlovic J, Trkola A, Günthard HF, Metzner KJ, Fischer M.

Retrovirology. 2012 Mar 29;9:27. doi: 10.1186/1742-4690-9-27.

26.

Reappearance of minority K103N HIV-1 variants after interruption of ART initiated during primary HIV-1 infection.

Metzner KJ, Leemann C, Di Giallonardo F, Grube C, Scherrer AU, Braun D, Kuster H, Weber R, Guenthard HF.

PLoS One. 2011;6(7):e21734. doi: 10.1371/journal.pone.0021734. Epub 2011 Jul 6.

27.

A suicide gene approach using the human pro-apoptotic protein tBid inhibits HIV-1 replication.

Huelsmann PM, Hofmann AD, Knoepfel SA, Popp J, Rauch P, Di Giallonardo F, Danke C, Gueckel E, Schambach A, Wolff H, Metzner KJ, Berens C.

BMC Biotechnol. 2011 Jan 11;11:4. doi: 10.1186/1472-6750-11-4.

28.

In-depth analysis of G-to-A hypermutation rate in HIV-1 env DNA induced by endogenous APOBEC3 proteins using massively parallel sequencing.

Knoepfel SA, Di Giallonardo F, Däumer M, Thielen A, Metzner KJ.

J Virol Methods. 2011 Feb;171(2):329-38. doi: 10.1016/j.jviromet.2010.11.016. Epub 2010 Nov 24.

PMID:
21111003

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