Select Publications

Journal articles

Spedicato M; Compagni ED; Caporale M; Teodori L; Leone A; Ancora M; Mangone I; Perletta F; Portanti O; Di Giallonardo F; Bonfini B; Savini G; Lorusso A, 2022, 'Reemergence of an atypical bluetongue virus strain in goats, Sardinia, Italy', Research in Veterinary Science, vol. 151, pp. 36 - 41, http://dx.doi.org/10.1016/j.rvsc.2022.07.003

Molini U; Curini V; Jacobs E; Tongo E; Berjaoui S; Hemberger MY; Puglia I; Jago M; Khaiseb S; Cattoli G; Dundon WG; Lorusso A; Di Giallonardo F, 2022, 'First influenza D virus full-genome sequence retrieved from livestock in Namibia, Africa', Acta Tropica, vol. 232, http://dx.doi.org/10.1016/j.actatropica.2022.106482

Curini V; Marcacci M; Abid S; Ouederni M; Elmoussi A; Charaa L; Achour W; Ouhichi R; Maazaoui L; Di Pasquale A; Elghord H; Gzara A; Ripani A; Di Giallonardo F; Cammà C; Lorusso A; Boubaker IBB, 2022, 'Full Genome Characterization of Respiratory Syncytial Virus Causing a Fatal Infection in an Immunocompromised Patient in Tunisia', Pathogens, vol. 11, pp. 758 - 758, http://dx.doi.org/10.3390/pathogens11070758

Amato L; Candeloro L; Di Girolamo A; Savini L; Puglia I; Marcacci M; Caporale M; Mangone I; Cammà C; Conte A; Torzi G; Mancinelli A; Di Giallonardo F; Lorusso A; Migliorati G; Schael T; D'Alterio N; Calistri P, 2022, 'Epidemiological and genomic findings of the first documented Italian outbreak of SARS-CoV-2 Alpha variant of concern', Epidemics, vol. 39, pp. 100578, http://dx.doi.org/10.1016/j.epidem.2022.100578

Featherstone LA; Di Giallonardo F; Holmes EC; Vaughan TG; Duchêne S, 2021, 'Infectious disease phylodynamics with occurrence data', Methods in Ecology and Evolution, vol. 12, pp. 1498 - 1507, http://dx.doi.org/10.1111/2041-210X.13620

Geoghegan JL; Di Giallonardo F; Wille M; Ortiz-Baez AS; Costa VA; Ghaly T; Mifsud JCO; Turnbull OMH; Bellwood DR; Williamson JE; Holmes EC, 2021, 'Virome composition in marine fish revealed by meta-transcriptomics (vol 7, veab005, 2021)', VIRUS EVOLUTION, vol. 7, http://dx.doi.org/10.1093/ve/veab035

Kok YL; Vongrad V; Chaudron SE; Shilaih M; Leemann C; Neumann K; Kusejko K; Di Giallonardo F; Kuster H; Braun DL; Kouyos RD; Günthard HF; Metzner KJ, 2021, 'HIV-1 integration sites in CD4+ T cells during primary, chronic, and late presentation of HIV-1 infection', JCI Insight, vol. 6, http://dx.doi.org/10.1172/jci.insight.143940

Di Giallonardo F; Puglia I; Curini V; Cammà C; Mangone I; Calistri P; Cobbin JCA; Holmes EC; Lorusso A, 2021, 'Emergence and spread of sars-cov-2 lineages b.1.1.7 and p.1 in Italy', Viruses, vol. 13, pp. 794 - 794, http://dx.doi.org/10.3390/v13050794

Amato L; Jurisic L; Puglia I; Di Lollo V; Curini V; Torzi G; Di Girolamo A; Mangone I; Mancinelli A; Decaro N; Calistri P; Di Giallonardo F; Lorusso A; D’Alterio N, 2021, 'Multiple detection and spread of novel strains of the SARS-CoV-2 B.1.177 (B.1.177.75) lineage that test negative by a commercially available nucleocapsid gene real-time RT-PCR', Emerging Microbes and Infections, vol. 10, pp. 1148 - 1155, http://dx.doi.org/10.1080/22221751.2021.1933609

Di Giallonardo F; Pinto AN; Keen P; Shaik A; Carrera A; Salem H; Selvey C; Nigro SJ; Fraser N; Price K; Holden J; Lee FJ; Dwyer DE; Bavinton BR; Geoghegan JL; Grulich AE; Kelleher AD; Guy R; Prestage G; Zablotska I; Duck T; Cooper C; Holt M; de Wit J; Kaldor J; Wilson D; Brotherton A; Cooper DA; Crooks L; Whittaker B; Callander D; Madeddu D; Schmidt HM; Telfer B; Boyd M; McGill S; Patel P; Power C; Gordon T; Feeney L; Bath K; Mackie B, 2021, 'Subtype-specific differences in transmission cluster dynamics of HIV-1 B and CRF01_AE in New South Wales, Australia', Journal of the International AIDS Society, vol. 24, pp. e25655, http://dx.doi.org/10.1002/jia2.25655

Geoghegan JL; Di Giallonardo F; Wille M; Ortiz-Baez AS; Costa VA; Ghaly T; Mifsud JCO; Turnbull OMH; Bellwood DR; Williamson JE; Holmes EC, 2021, 'Virome composition in marine fish revealed by meta-transcriptomics', Virus Evolution, vol. 7, http://dx.doi.org/10.1093/ve/veab005

Adikari TN; Di Giallonardo F; Leung P; Grifoni A; Sette A; Weiskopf D; Bull RA; Luciani F, 2020, 'Conserved epitopes with high HLA-I population coverage are targets of CD8+ T cells associated with high IFN-γ responses against all dengue virus serotypes', Scientific Reports, vol. 10, http://dx.doi.org/10.1038/s41598-020-77565-2

Di Giallonardo F; Duchene S; Puglia I; Curini V; Profeta F; Cammà C; Marcacci M; Calistri P; Holmes EC; Lorusso A, 2020, 'Genomic epidemiology of the first wave of sars-cov-2 in Italy', Viruses, vol. 12, http://dx.doi.org/10.3390/v12121438

Di Giallonardo F; Pinto AN; Keen P; Shaik A; Carrera A; Salem H; Selvey C; Nigro SJ; Fraser N; Price K; Holden J; Lee FJ; Dwyer DE; Bavinton BR; Grulich AE; Kelleher AD, 2020, 'Increased hiv subtype diversity reflecting demographic changes in the hiv epidemic in new south wales, australia', Viruses, vol. 12, http://dx.doi.org/10.3390/v12121402

Campbell SJ; Ashley W; Gil-Fernandez M; Newsome TM; Di Giallonardo F; Ortiz-Baez AS; Mahar JE; Towerton AL; Gillings M; Holmes EC; Carthey AJR; Geoghegan JL, 2020, 'Red fox viromes in urban and rural landscapes', Virus Evolution, vol. 6, http://dx.doi.org/10.1093/ve/veaa065

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, 2019, 'Limited sustained local transmission of HIV-1 CRF01_AE in New South Wales, Australia', Viruses, vol. 11, http://dx.doi.org/10.3390/v11050482

Kerr PJ; Eden JS; Di Giallonardo F; Peacock D; Liu J; Strive T; Read AF; Holmes EC, 2019, 'Punctuated evolution of myxoma virus: Rapid and disjunct evolution of a recent viral lineage in Australia', Journal of Virology, vol. 93, http://dx.doi.org/10.1128/JVI.01994-18

Koh C; Audsley MD; Di Giallonardo F; Kerton EJ; Young PR; Holmes EC; McGraw EA, 2019, 'Sustained Wolbachia-mediated blocking of dengue virus isolates following serial passage in Aedes aegypti cell culture', Virus Evolution, vol. 5, http://dx.doi.org/10.1093/ve/vez012

Di Giallonardo F; Geoghegan JL; Cousins K; Shi M; Williamson JE; Holmes EC, 2018, 'Hidden diversity and evolution of viruses in market fish', Virus Evolution, vol. 4, pp. vey031 - vey031, http://dx.doi.org/10.1093/ve/vey031

Di Giallonardo F; Kok J; Fernandez M; Carter I; Geoghegan JL; Dwyer DE; Holmes EC; Eden JS, 2018, 'Evolution of human respiratory syncytial virus (RSV) over multiple seasons in New South Wales, Australia', Viruses, vol. 10, http://dx.doi.org/10.3390/v10090476

Pinto AN; Hawke K; Castley A; Chibo D; Giallonardo FD; Cooper C; Sawleshwarkar S; Kelleher A; Dwyer DE, 2018, 'HIV-1 subtype diversity, transmitted drug resistance and phylogenetics in Australia', Future Virology, vol. 13, pp. 575 - 584, http://dx.doi.org/10.2217/fvl-2018-0031

Di Giallonardo F; Audsley MD; Shi M; Young PR; McGraw EA; Holmes EC, 2018, 'Complete genome of Aedes aegypti anphevirus in the Aag2 mosquito cell line', Journal of General Virology, vol. 99, pp. 832 - 836, http://dx.doi.org/10.1099/jgv.0.001079

Pinto A; Di Giallonardo F; Keen P; Cooper C; Telfer B; Cooper D; Grulich A; Kelleher A, 2018, 'A10 Using the molecular epidemiology of HIV transmission in New South Wales to inform public health response: Assessing the representativeness of linked phylogenetic data', Virus Evolution, vol. 4, http://dx.doi.org/10.1093/ve/vey010.009

Giallonardo FD; Schlub TE; Shi M; Holmes EC, 2017, 'Dinucleotide composition in animal RNA viruses is shaped more by virus family than by host species', Journal of Virology, vol. 91, http://dx.doi.org/10.1128/JVI.02381-16

Wilson JAC; 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, 2017, 'RNA-Seq analysis of chikungunya virus infection and identification of granzyme A as a major promoter of arthritic inflammation', PLoS Pathogens, vol. 13, http://dx.doi.org/10.1371/journal.ppat.1006155

Duchêne S; Duchêne DA; Di Giallonardo F; Eden JS; Geoghegan JL; Holt KE; Ho SYW; Holmes EC, 2016, 'Cross-validation to select Bayesian hierarchical models in phylogenetics', BMC Evolutionary Biology, vol. 16, http://dx.doi.org/10.1186/s12862-016-0688-y

Kok YL; Vongrad V; Shilaih M; Di Giallonardo F; Kuster H; Kouyos R; Günthard HF; Metzner KJ, 2016, 'Monocyte-derived macrophages exhibit distinct and more restricted HIV-1 integration site repertoire than CD4 + T cells', Scientific Reports, vol. 6, http://dx.doi.org/10.1038/srep24157

Geoghegan JL; Senior AM; Giallonardo FD; Holmes EC, 2016, 'Virological factors that increase the transmissibility of emerging human viruses', Proceedings of the National Academy of Sciences of the United States of America, vol. 113, pp. 4170 - 4175, http://dx.doi.org/10.1073/pnas.1521582113

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; Paredes R; Schuurman R; Günthard H; Reqaeui F; Kaiser R; Geretti AM; Brockmeyer N, 2016, 'Contribution of APOBEC3G/F activity to the development of low-abundance drug-resistant human immunodeficiency virus type 1 variants', Clinical Microbiology and Infection, vol. 22, pp. 191 - 200, http://dx.doi.org/10.1016/j.cmi.2015.10.004

Seifert D; Di Giallonardo F; Töpfer A; Singer J; Schmutz S; Günthard HF; Beerenwinkel N; Metzner KJ, 2016, 'A Comprehensive Analysis of Primer IDs to Study Heterogeneous HIV-1 Populations', Journal of Molecular Biology, vol. 428, pp. 238 - 250, http://dx.doi.org/10.1016/j.jmb.2015.12.012

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; Danzer M; Stabentheiner S; Pröll J; Hofer K; Mostmans W; Thys K; Van Marck H; Dubois M; Nicot F; Milan D; Thiele B; Kuecherer C; Nitsche A; Radonic A; Dabrowski PW; Lengauer T; Capobianchi MR; Bruselles A; Giombini E; Rozera G; Bartolini B; Codoñer FM; Pou C; Günthard HF; Yang WL; Aquino C; Bruggmann R; Künzli-Gontarczyk M; Stephens D; Makgamathe M; Khan G; Gordon M; Moreno E, 2016, 'A follow-up of the multicenter collaborative study on HIV-1 drug resistance and tropism testing using 454 ultra deep pyrosequencing', PLoS ONE, vol. 11, http://dx.doi.org/10.1371/journal.pone.0146687

Dill JA; Camus AC; Leary JH; Di Giallonardo F; Holmes EC; Nga TFF, 2016, 'Distinct viral lineages from fish and amphibians reveal the complex evolutionary history of hepadnaviruses', Journal of Virology, vol. 90, pp. 7920 - 7933, http://dx.doi.org/10.1128/JVI.00832-16

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, 2016, 'Fluid spatial dynamics of West Nile virus in the United States: Rapid spread in a permissive host environment', Journal of Virology, vol. 90, pp. 862 - 872, http://dx.doi.org/10.1128/JVI.02305-15

Duchene S; Di Giallonardo F; Holmes EC, 2016, 'Substitution model adequacy and assessing the reliability of estimates of virus evolutionary rates and time scales', Molecular Biology and Evolution, vol. 33, pp. 255 - 267, http://dx.doi.org/10.1093/molbev/msv207

Di Giallonardo F; Holmes EC, 2015, 'Exploring Host–Pathogen Interactions through Biological Control', PLoS Pathogens, vol. 11, http://dx.doi.org/10.1371/journal.ppat.1004865

Seifert D; Di Giallonardo F; Metzner KJ; Guenthard HF; Beerenwinkel N, 2015, 'A Framework for Inferring Fitness Landscapes of Patient-Derived Viruses Using Quasispecies Theory (vol 199, pg 191, 2014)', GENETICS, vol. 199, pp. 1271 - 1271, http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000352734400028&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1

Cozzi-Lepri A; Noguera-Julian M; Di Giallonardo F; Schuurman R; Däumer M; Aitken S; Ceccherini-Silberstein F; Monforte ADA; 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; Brockmeyer N, 2015, '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', Journal of Antimicrobial Chemotherapy, vol. 70, pp. 930 - 940, http://dx.doi.org/10.1093/jac/dku426

Di Giallonardo F; Holmes EC, 2015, 'Viral biocontrol: Grand experiments in disease emergence and evolution', Trends in Microbiology, vol. 23, pp. 83 - 90, http://dx.doi.org/10.1016/j.tim.2014.10.004

Seifert D; Giallonardo FD; Metzner KJ; Günthard HF; Beerenwinke N, 2015, 'A framework for inferring fitness landscapes of patient-derived viruses using quasispecies theory', Genetics, vol. 199, pp. 191 - 203, http://dx.doi.org/10.1534/genetics.114.172312

Di Giallonardo F; Töpfer A; Rey M; Prabhakaran S; Duport Y; Leemann C; Schmutz S; Campbell NK; Joos B; Lecca MR; Patrignani A; Däumer M; Beisel C; Rusert P; Trkola A; Günthard HF; Roth V; Beerenwinkel N; Metzner KJ, 2014, 'Full-length haplotype reconstruction to infer the structure of heterogeneous virus populations', Nucleic Acids Research, vol. 42, http://dx.doi.org/10.1093/nar/gku537

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; Danzer M; Hackl C; Pröll J; Niklas N; Bizon B; Van Eygen V; Vandenbroucke I; Van Marck H; Dubois M; Nicot F; Milan D; Masquelier B; Fleury H; Viala S; Marell R; Thiele B; Kuecherer C; Meixenberger K; Nitsche A; Dabrowski PW; Ihlenfeldt HG; Capobianchi MR; Bruselles A; Rozera G; Bartolini B; Stephens D; Makgamathe M; Pillay D; Gordon M; Green T; Codoñer FM; Pou C; Günthard HF; Künzli-Gontarczyk M; Bruggmann R; Qi W; Turenchalk G; Hanczaruk B, 2014, 'An international multicenter study on HIV-1 drug resistance testing by 454 ultra-deep pyrosequencing', Journal of Virological Methods, vol. 204, pp. 31 - 37, http://dx.doi.org/10.1016/j.jviromet.2014.04.007

Di Giallonardo F; Zagordi O; Duport Y; Leemann C; Joos B; Künzli-Gontarczyk M; Bruggmann R; Beerenwinkel N; Günthard HF; Metzner KJ, 2013, 'Next-Generation Sequencing of HIV-1 RNA Genomes: Determination of Error Rates and Minimizing Artificial Recombination', PLoS ONE, vol. 8, http://dx.doi.org/10.1371/journal.pone.0074249

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, 2012, 'EH3 (ABHD9): The first member of a new epoxide hydrolase family with high activity for fatty acid epoxides', Journal of Lipid Research, vol. 53, pp. 2038 - 2045, http://dx.doi.org/10.1194/jlr.M024448

Althaus CF; Vongrad V; Niederöst B; Joos B; Di Giallonardo F; Rieder P; Pavlovic J; Trkola A; Günthard HF; Metzner KJ; Fischer M, 2012, 'Tailored enrichment strategy detects low abundant small noncoding RNAs in HIV-1 infected cells', Retrovirology, vol. 9, http://dx.doi.org/10.1186/1742-4690-9-27

Metzner KJ; Leemann C; Di Giallonardo F; Grube C; Scherrer AU; Braun D; Kuster H; Weber R; Guenthard HF, 2011, 'Reappearance of minority K103N HIV-1 variants after interruption of ART initiated during primary HIV-1 infection', PLoS ONE, vol. 6, http://dx.doi.org/10.1371/journal.pone.0021734

Knoepfel SA; Di Giallonardo F; Däumer M; Thielen A; Metzner KJ, 2011, 'In-depth analysis of G-to-A hypermutation rate in HIV-1 env DNA induced by endogenous APOBEC3 proteins using massively parallel sequencing', Journal of Virological Methods, vol. 171, pp. 329 - 338, http://dx.doi.org/10.1016/j.jviromet.2010.11.016

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, 2011, 'A suicide gene approach using the human pro-apoptotic protein tBid inhibits HIV-1 replication', BMC Biotechnology, vol. 11, http://dx.doi.org/10.1186/1472-6750-11-4

Conference Papers

Topfer A; Di Giallonardo F; Metzner KJ; Gunthard HF; Beerenwinkel N, 2013, 'Probing of viral diversity by global haplotype prediction', in 2013 IEEE 3rd International Conference on Computational Advances in Bio and medical Sciences (ICCABS), IEEE, presented at 2013 IEEE 3rd International Conference on Computational Advances in Bio and Medical Sciences (ICCABS), 12 June 2013 - 14 June 2013, http://dx.doi.org/10.1109/iccabs.2013.6629231

Cozzi-Lepri A; Noguera-Julian M; Di Giallonardo F; Schuurman R; Daeumer M; Aitken S; Guenthard HF; Brun-Vezinet F; Metzner KJ; Paredes R, 2013, 'Low-frequency drug-resistant HIV-1 and risk of virological failure to first-line NNRTI-based ART: a multi-cohort European case-control study using centralized ultrasensitive 454 sequencing', in ANTIVIRAL THERAPY, INT MEDICAL PRESS LTD, Toronto, CANADA, pp. A41 - A41, presented at International Workshop on HIV and Hepatitis Virus Drug Resistance and Curative Strategies, Toronto, CANADA, 04 June 2013 - 08 June 2013, http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000335229500037&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1

Adamska M; Bekteshi M; Cronin A; Decker M; di Giallonardo F; Arand M, 2008, 'Characterisation of a new human epoxide hydrolase capable of metabolizing epoxyeicosatrienoic acids', in FASEB JOURNAL, FEDERATION AMER SOC EXP BIOL, http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000208467808115&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1


Back to profile page