Nuno Faria

Sir Henry Dale Research Fellow

Department of Zoology

University of Oxford

Peter Medawar Building

South Parks Road

Oxford, OX1 3SY, UK

My research focuses on investigating the patterns of gene flow in pathogen populations. I am particularly interested in phylogenetic methods of sequence analysis that combine genetic, spatial and ecological information. Specific questions involve (i) uncovering the spatiotemporal dynamics of human and animal pathogens, (ii) identifying factors underlying pathogen spread and dynamics at different scales (e.g. geographic regions, body compartments) and (iii) investigating the drivers of cross-species transmission and host shifts.

Research Interests

Kraemer MUG, Faria NR, Reiner Jr RC, Golding N, Nikolay, B, Johansson MA, Salje H, Faye O, Wint GRW, Niedrig M, Shearer FM, Hill SC, Bisanzi D, Nax HH, Pradelski BS, Murphy NR, Bogoch II, Khan K, Brownstein JS, Tatem AJ, de Oliveira T, Smith DL, Sall A, Pybus OG, Hay SI, Cauchemez S (2017) Spread of yellow fever virus outbreak in Angola and the Democratic Republic Congo 2015-2016. Lancet Infectious Diseases 17:330-38

Faria NR*, Azevedo RD*, Kraemer MU, Souza R, Cunha MS, Hill SC, Thézé J, Bonsall MB, Bowden TA, Rissanen I, Rocco IM, Nogueira JS, Maeda AY, Vasami FG, Macedo FL, Suzuki A, Rodrigues SG, Cruz AC, Nunes BT, Medeiros DB, Rodrigues DS, Nunes Queiroz AL, Silva EV, Henriques DF, Travassos da Rosa ES, de Oliveira CS, Martins LC, Vasconcelos HB, Casseb LM, Simith DB, Messina JP, Abade L, Lourenço J, Alcantara LC, Lima MM, Giovanetti M, Hay SI, de Oliveira RS, Lemos PD, Oliveira LF, de Lima CP, da Silva SP, Vasconcelos JM, Franco L, Cardoso JF, Vianez-Junior JL, Mir D, Bello G, Delatorre E, Khan K, Creatore M, Coelho GE, de Oliveira WK, Tesh R, Pybus OG, Nunes MR, Vasconcelos PF (2016) Zika virus in the Americas: early epidemiological and genetic findings. Science 352:345-9

Faria NR, Sabino EC, Nunes MRT, Alcantara LCJ, Loman N, Pybus OG (2016) Mobile real-time surveillance of Zika virus in Brazil. Genome Medicine 8:97

Wu J, Lu J, Faria NR, Zeng X, Song Y, Zou L, Yi L, Liang L, Ni H, Kang M, Zhang X, Huang G, Zhong H, Bowden TA, Raghwani J, He J, He X, Lin J, Koopmans M, Pybus OG, Ke C (2016) Live poultry market interventions for influenza A(H7N9) virus, Guangdong, China. Emerging Infectious Diseases 22:2104–12

Faria NR, Lourenço J, de Cerqueira EM, de Lima MM, Pybus O, Alcantara LC (2016) Epidemiology of chikungunya virus in Bahia, Brazil, 2014-2015. PLOS Currents Outbreaks DOI: 10.1371/currents.outbreaks.c97507e3e48efb946401755d468c28b2

Lu J, Fang L, Zheng H, Lao J, Yang F, Sun L, Xiao J, Lin J, Song T, Ni T, Raghwani J, Ke C, Faria NR, Bowden TA, Pybus OG*, Li H* (2016). The evolution and transmission of epidemic GII.17 noroviruses. Journal of Infectious Disease 214:556–64

Dellicour S, Rose R, Faria NR, Lemey P, Pybus OG (2016) SERAPHIM: studying environmental rasters and phylogenetically-informed movements. Bioinformatics 32:3204–6

PS Born, MM Siqueira, NR Faria, PC Resende, FC Motta, G Bello (2016) Phylodynamics of influenza A (H3N2) in South America, 1999–2012. Infection, Genetics and Evolution 43:312-320

Arias A, Watson SJ, Asogun D, Ekaete Alice Tobin, Thorne L, Caddy S, Lu J, Phan MVT, Meredith L, Langat P, Dudas G, Faria NR, Dellicour S, Kamara A, Kargbo B, Kamara BO, Gevao S, Jah U, Cooper D, Newport M, Horby P, Dunning J, Sahr F, Brooks T, Simpson AJH, Groppelli E, Liu G, Mulakken N, Rhodes K, Akpablie J, Yoti Z, Lamunu M, Vitto E, Otim P, Owilli C, Boateng I, Okoror L, Omomoh E, Oyakhilome J, Omiunu R, Yemisis I, Donatus A, Ehikhiametalor S, Akhilomen P, Aire C, Kurth A, Cook N, Baumann J, Gabriel M, Wölfel R, Di Caro A, Carroll MW, Günther S, Redd J, Naidoo D, Pybus OG, Rambaut A, Kellam P, Goodfellow I, Cotton M (2016) Rapid outbreak sequencing of Ebola virus in Sierra Leone identifies transmission chains linked to sporadic cases. Virus Evolution 2:vew016

Giovanetti M, Faria NR, Nunes MRT, Lourenço J, de Vasconcelos JM, Rodrigues SG, do Rosário MS, Siqueira I, Ciccozzi M, Vasconcelos PF, Pybus OG, de Oliveira T, Alcantara LCJ (2016) Zika virus genome from Salvador - Bahia, Brazil 2015. Infection, Genetics & Evolution 41:142-5

Nunes MR*, Faria NR*, de Vasconcelos JM, Golding N, Kraemer M, de Oliveira LF, Socorro R, Vieira EP, Coelho GE, Goncalves Vianez JL, Cardoso JF, Tesh RB, Hay SI, Pybus OG, Vasconcelos PF (2015) Emergence and potential for spread of chikungunya virus in Brazil. BMC Medicine 13:102

Bezemer D, Cori A, Ratmann O, van Sighem A, Hermanides HS, Dutilh BE, Gras L, Faria NR, van den Hengel R, Duits AJ, Reiss P, de Wolf F, Fraser C, ATHENA Observational Cohort (2015) Dispersion of the HIV-1 epidemic in men having sex with men in the Netherlands: a combined mathematical model and phylogenetic analysis. PLOS Medicine 12:e1001898

Pineda-Pena AC*, Faria NR*, Mina T, Amini-Bavil-Olyaee S, Alavian SM, Lemey P, Maes P, Van Ranst M, Pourkarim MR (2015) Epidemiological history and genomic characterization of non-D1 HBV strains identified in Iran. Journal of Clinical Virology 63:38-41

von Stockenstrom S, Odevall L, Lee E, Sinclair E, Bacchetti P, Killian M, Epling L, Shao W, Hoh R, Ho T, Faria NR, Lemey P, Albert J, Hunt P, Loeb L, Pilcher C, Poole C, Hatano H, Somsouk M, Douek D, Boritz E, Deeks SG, Hecht MF, Palmer, S (2015) Longitudinal genetic characterization reveals that cell proliferation maintains a persistent HIV type 1 DNA pool during effective HIV therapy. Journal of Infectious Diseases 212:596-607

Li G, Piampongsant S, Faria NR, Voet A, Pineda-Peña AC, Khouri R, Lemey P, Vandamme AM, Theys K (2015) An integrated map of HIV genome-wide variation from a population perspective. Retrovirology 12:18

Faria NR, Esbjornsson J, Lemey P (2015) Phylogeographic insights into the origins and epidemic history of the Human Immunodeficiency Virus Type 2. In Encyclopedia of AIDS p1-9 (eds. TJ Hope, M Stevenson, D Richman). Springer New York.

Faria NR, Rambaut A, Suchard MA, Baele G, Bedford T, Ward MJ, Tatem AJ, Sousa JD, Arinaminpathy N, Pepin J, Posada D, Peeters M, Pybus OG, Lemey P (2014) The early spread and epidemic ignition of HIV-1 in human populations. Science 346:56-61

Lemey P, Rambaut A, Bedford T, Faria N, Bielejec F, Baele G, Russell CA, Smith DJ, Pybus OG, Brockmann D, Suchard MA (2014) Unifying viral genetics and human transportation data to predict the global transmission dynamics of human influenza H3N2. PLOS Pathogens 10:e1003932

Nunes MR*, Palacios G*, Faria NR*, Sousa EC, Pantoja JA, Rodrigues SG, Carvalho VL, Medeiros DBA, Savji N, Baele G, Suchard MA, Lemey P, Vasconcelos PF, Lipkin WI (2014) Air travel is associated with intracontinental spread of dengue virus serotypes 1-3 in Brazil. PLOS Neglected Tropical Diseases 8:e2769

Bezemer D, Faria NR, Hassan A, Hamers RL, Mutua G, Anzala O, Mandaliya K, Cane P, Berkley JA, Rinke de Wit TF, Wallis C, Graham SM, Price MA, Coutinho RA, Sanders EJ (2014) HIV Type 1 transmission networks among men having sex with men and heterosexuals in Kenya. AIDS Research & Human Retroviruses 30:118-26

Faria NR, Suchard MA, Rambaut A, Streicker DG, Lemey P (2013) Simultaneously reconstructing viral cross-species transmission history and identifying the underlying constraints. Philosophical Transactions of the Royal Society Series B 368:20120196

Josefsson L, Stockenstrom SV, Faria NR, Sinclair E, Bacchetti P, Killian M, Epling L, Tan A, Ho T, Lemey P, Shao W, Hunt P, Somsouk M, Wylie W, Douek D, Loeb L, Custer J, Ho R, Poole L, Deeks S, Hecht FM, Palmer D (2013) The HIV-1 reservoir in eight patients on long-term suppressive antiretroviral therapy is stable with few genetic changes over time. Proceedings of the National Academy of Sciences USA E4987-96

Josefsson L, Palmer S, Faria NR, Lemey P, Casazza J, Ambrozak D, Kearney M, Shao W, Kottilil S, Sneller M, Mellors J, Coffin JM, Maldarelli F (2013) Single cell analysis of lymph node tissue from HIV-1 infected patients reveals that the majority of CD4+ T-cells contain one HIV-1 DNA molecule. PLOS Pathogens 9:e1003432

Pineda-Pena AC, Faria NR, Imbrechts S, Libin P, Abecasis AB, Deforche K, Gomez-Lopez A, Camacho RJ, de Oliveira T, Vandamme AM (2013) Automated subtyping of HIV-1 genetic sequences for clinical and surveillance purposes: Performance evaluation of the new REGA version 3 and seven other tools. Infection, Genetics & Evolution 19:337-48

Gill MS, Lemey P, Faria NR, Rambaut A, Shapiro B, Suchard MA (2013) Improving Bayesian population dynamics inference: a coalescent-based model for multiple loci. Molecular Biology & Evolution 30:713-24

de Carvalho LM, Santos LB, Faria NR, de Castro Silveira W (2013) Phylogeography of foot-and-mouth disease virus serotype O in Ecuador. Infection, Genetics & Evolution 13:76-88

Faria NR, Hodges-Mameletzis I, Silva JC, Rodés B, Erasmus S, Paolucci S, Ruelle J, Pieniazek D, Taveira N, Treviño A, Gonçalves MF, Jallow S, Xu L, Camacho RJ, Soriano V, Goubau P, de Sousa JD, Vandamme AM, Suchard MA, Lemey P (2012) Phylogeographical footprint of colonial history in the global dispersal of human immunodeficiency virus type 2 group A. Journal of General Virology 93:889-99

Faria NR, Suchard MA, Abecasis A, Sousa JD, Ndembi N, Bonfim I, Camacho RJ, Vandamme AM, Lemey P (2012) Phylodynamics of the HIV-1 CRF02_AG clade in Cameroon. Infection, Genetics & Evolution 12:453-60

Nunes MR, Faria NR, Vasconcelos HB, Medeiros DB, Silva de Lima CP, Carvalho VL, Pinto da Silva EV, Cardoso JF, Sousa EC Jr, Nunes KN, Rodrigues SG, Abecasis AB, Suchard MA, Lemey P, Vasconcelos PF (2012) Phylogeography of dengue virus serotype 4, Brazil, 2010-2011. Emerging Infectious Diseases 18:1858-64

Faria NR, Suchard MA, Rambaut A, Lemey P (2011) Toward a quantitative understanding of viral phylogeography. Current Opinion in Virology 1:423-9 

de Vries M, Deijs M, Canuti M, van Schaik BD, Faria NR, van de Garde MD, Jachimowski LC, Jebbink MF, Jakobs M, Luyf AC, Coenjaerts FE, Claas EC, Molenkamp R, Koekkoek SM, Lammens C, Leus F, Goossens H, Ieven M, Baas F, van der Hoek L (2011) A sensitive assay for virus discovery in respiratory clinical samples. PLOS One 6:e161182

Faria NR, de Vries M, van Hemert FJ, Benschop K, van der Hoek L (2009) Rooting human parechovirus evolution in time. BMC Evolutionary Biology 9:164


* denotes equal contributions