Dr Nuno R. Faria

Faculty of Medicine, School of Public Health

Reader in Viral Evolution

Contact

Location

Sir Alexander Fleming BuildingSouth Kensington Campus

Summary

My research programme is focused on studying the evolution and epidemiology of rapidly evolving viruses that circulate in human and animal populations, such as SARS-CoV-2, yellow fever, chikungunya, Zika and dengue. Current research topics include: epidemiology, evolution and phylodynamics of viral epidemics; local and regional genomic capacity and outbreak preparedness; and implementation of One Health approaches in hotspots of emerging infectious diseases.

Current Initiatives

I coordinate the Brazil-UK CADDE Centre (Centre for Arbovirus Discovery, Diagnostics, Genomics and Epidemiology) with Prof. Ester Sabino from the University of São Paulo. In February 2020, CADDE led the initiative that resulted in the generation, analysis and report of the first SARS-CoV-2 genomes from Latin America in <48 hours. Our team then provided early insights into the epidemiology and genetic diversity of SARS-CoV-2 in Brazil and uncovered a three-quarters attack rate of SARS-CoV-2 in the Amazon region by October 2020. In January 2021, our team discovered the first cases of the SARS-CoV-2 Gamma variant of concern in Manaus. I also lead the ArboSPREAD project, a network for surveillance of arbovirus spread and persistence across corridors of ecological suitability between Angola and Brazil that characterised a Zika outbreak caused by Asian genotype lineage in Angola. I have previously co-led the ZiBRA project in northeast Brazil for real-time genome sequencing of Zika virus in Brazil.

Affiliations

I am currently a Reader in Virus Evolution at the Faculty of Medicine, School of Public Health, Imperial College, and I hold a Wellcome Trust and Royal Society Sir Henry Dale Fellowship. I am also an Associate Professor at the Department of Zoology, University of Oxford since 2019, an Associate of the Oxford Martin School Programme on Pandemic Genomics and an invited Professor in Infectious Diseases at the Institute Tropical Medicine, University of São Paulo, Brazil. In December 2021 I became part of the World Health Organization Technical Advisory Group (TAG) on Arboviruses. Between 2013 and 2017 I was a Research Lecturer in Infectious Disease Control in University of Oxford. My research is currently funded by the Wellcome Trust and Royal Society, Medical Research Council, Bill & Melinda Gates Foundation and the John Fell Fund from Oxford University.

Our Team

I am currently supervising PhD students Darlan Candido (University of Oxford), Jocelyne Vasconcelos (DIDE-ICL), Jean Paul Carrera (University of Oxford), Nilani Chandradeva (DIDE-ICL) and co-supervising PhD student Victoria Cox (DIDE-ICL) and Mayara Bertanhe and Ian Nunes (University of São Paulo, Brazil). Dr. Lewis Buss has recently joined our team as a Research Assistant, and Dr. Jaqueline Goes de Jesus (University of São Paulo, Brazil) is currently visiting our team as part of a FAPESP exchange programme. Lucy Matkin, is the Scientific program manager of the CADDE and ArboSPREAD projects.

Dr. Sarah Hill worked with me in the ArboSPREAD grant and his now a Research Fellow (Henry Wellcome) at The Royal Veterinary College, UK. Dr. Tetyana Vasylyeva did her PhD with me and is now an Assistant Professor at the University of San Diego, USA. I also co-supervised the PhD of Dr. Felipe Iani who is now Head of Virology Centre at Fundação Ezequiel Dias, Brazil.

Selected Publications

Journal Articles

Faria NR, Mellan TA, Whittaker C, et al.Faria NR, Mellan TA, Whittaker C, Claro IM, Candido DDS, Mishra S, Crispim MAE, Sales FC, Hawryluk I, McCrone JT, Hulswit RJG, Franco LAM, Ramundo MS, de Jesus JG, Andrade PS, Coletti TM, Ferreira GM, Silva CAM, Manuli ER, Pereira RHM, Peixoto PS, Kraemer MU, Gaburo N, Camilo CDC, Hoeltgebaum H, Souza WM, Rocha EC, de Souza LM, de Pinho MC, Araujo LJT, Malta FS, de Lima AB, Silva JDP, Zauli DAG, Ferreira ACDS, Schnekenberg RP, Laydon DJ, Walker PGT, Schlueter HM, dos Santos ALP, Vidal MS, Del Caro VS, Filho RMF, dos Santos HM, Aguiar RS, Proenca-Modena JLP, Nelson B, Hay JA, Monod M, Miscouridou X, Coupland H, Sonabend R, Vollmer M, Gandy A, Prete CA, Nascimento VH, Suchard MA, Bowden TA, Pond SLK, Wu C-H, Ratmann O, Ferguson NM, Dye C, Loman NJ, Lemey P, Rambaut A, Fraiji NA, Carvalho MDPSS, Pybus OG, Flaxman S, Bhatt S, Sabino EC close, 2021, Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil, Science, Vol:372, ISSN:0036-8075, Pages:815-821

du Plessis L, McCrone JT, Zarebski AE, et al.du Plessis L, McCrone JT, Zarebski AE, Hill V, Ruis C, Gutierrez B, Raghwani J, Ashworth J, Colquhoun R, Connor TR, Faria NR, Jackson B, Loman NJ, O'Toole A, Nicholls SM, Parag K, Scher E, Vasylyeva T, Volz EM, Watts A, Bogoch II, Khan K, Aanensen DM, Kraemer MUG, Rambaut A, Pybus OG close, 2021, Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK, Science, Vol:371, ISSN:0036-8075, Pages:708-+

Sabino EC, Buss LF, Carvalho MPS, et al.Sabino EC, Buss LF, Carvalho MPS, Prete CA, Crispim MAE, Fraiji NA, Pereira RHM, Parag KV, Peixoto PDS, Kraemer MUG, Oikawa MK, Salomon T, Cucunuba ZM, Castro MC, Santos AADS, Nascimento VH, Pereira HS, Ferguson NM, Pybus OG, Kucharski A, Busch MP, Dye C, Faria NR close, 2021, Resurgence of COVID-19 in Manaus, Brazil, despite high seroprevalence, The Lancet, Vol:397, ISSN:0140-6736, Pages:452-455

Buss LF, Prete CA, Abrahim CMM, et al.Buss LF, Prete CA, Abrahim CMM, Mendrone A, Salomon T, de Almeida-Neto C, França RFO, Belotti MC, Carvalho MPSS, Costa AG, Crispim MAE, Ferreira SC, Fraiji NA, Gurzenda S, Whittaker C, Kamaura LT, Takecian PL, da Silva Peixoto P, Oikawa MK, Nishiya AS, Rocha V, Salles NA, de Souza Santos AA, da Silva MA, Custer B, Parag KV, Barral-Netto M, Kraemer MUG, Pereira RHM, Pybus OG, Busch MP, Castro MC, Dye C, Nascimento VH, Faria NR, Sabino EC close, 2021, Three-quarters attack rate of SARS-CoV-2 in the Brazilian Amazon during a largely unmitigated epidemic., Science, Vol:371, ISSN:1095-9203, Pages:288-292

de Souza WM, Buss LF, Candido DDS, et al.de Souza WM, Buss LF, Candido DDS, Carrera J-P, Li S, Zarebski AE, Pereira RHM, Prete CA, de Souza-Santos AA, Parag KV, Belotti MCTD, Vincenti-Gonzalez MF, Messina J, da Silva Sales FC, Andrade PDS, Nascimento VH, Ghilardi F, Abade L, Gutierrez B, Kraemer MUG, Braga CKV, Aguiar RS, Alexander N, Mayaud P, Brady OJ, Marcilio I, Gouveia N, Li G, Tami A, de Oliveira SB, Porto VBG, Ganem F, de Almeida WAF, Fantinato FFST, Macario EM, de Oliveira WK, Nogueira ML, Pybus OG, Wu C-H, Croda J, Sabino EC, Faria NR close, 2020, Epidemiological and clinical characteristics of the COVID-19 epidemic in Brazil, Nature Human Behaviour, Vol:4, ISSN:2397-3374, Pages:856-+

Candido DDS, Claro IM, de Jesus JG, et al.Candido DDS, Claro IM, de Jesus JG, Souza WMD, Moreira FRR, Dellicour S, Mellan T, du Plessis L, Pereira RHM, Sales FCDS, Manuli ER, Theze J, Almeida L, de Menezes MT, Voloch CM, Fumagalli MJ, Coletti TDM, Silva CAM, Ramundo MS, Amorim MR, Hoeltgebaum H, Mishra S, Gill M, Carvalho LM, Buss LF, Prete CA, Ashworth J, Nakaya H, Peixoto PDS, Brady O, Nicholls S, Tanuri A, Rossi AD, Braga CKV, Gerber AL, Guimaraes AP, Gaburo N, Alencar CS, Ferreira ACDS, Lima CX, Levi JE, Granato C, Ferreira GM, Francisco RDS, Granja F, Garcia MT, Moretti ML, Perroud MW, Castineiras TMPP, Lazari CDS, Hill S, Santos AADS, Simeoni CL, Forato J, Sposito AC, Schreiber AZ, Santos MNN, Sa CZ, Souza RP, Resende Moreira LC, Teixeira MM, Hubner J, Leme PAF, Moreira RG, Nogueira ML, Ferguson N, Costa SF, Proenca-Modena JL, Vasconcelos AT, Bhatt S, Lemey P, Wu C-H, Rambaut A, Loman N, Aguiar RS, Pybus O, Sabino EC, Faria NR, CADDE-Genomic-Network close, 2020, Evolution and epidemic spread of SARS-CoV-2 in Brazil, Science, Vol:369, ISSN:0036-8075, Pages:1255-1260

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