Jayna Raghwani

Ho CKY, Raghwani J, Koekkoek S, Liang R, Van der Meer JTM, Van Der Valk M, De Jong M, Pybus OG, Schinkel J, Molenkamp R, MOSAIC study group (2017) Characterization of HCV envelope diversification from acute to chronic infection using SMRT sequencing within a sexually-transmitted hepatitis C virus cluster. Journal of Virology 91:e02262-16

Faria NR, Quick J, Claro IM, Thézé J, de Jesus JG, Giovanetti M, Kraemer MUG, Hill SC, Black A, da Costa AC, Franco LC, Silva SP, Wu CH, Raghwani J, Cauchemez S, du Plessis L, Verotti MP, de Oliveira WK, Carmo EH, Coelho GE, Santelli ACFS, Vinhal LC, Henriques CM, Simpson JT, Loose M, Andersen KG, Grubaugh ND, Somasekar S, Chiu CY, Muñoz-Medina JE, Gonzalez-Bonilla CR, Arias CF, Lewis-Ximenez LL, Baylis SA, Chieppe AO, Aguiar SF, Fernandes CA, Lemos PS, Nascimento BLS, Monteiro HAO, Siqueira IC, de Queiroz MG, de Souza TR, Bezerra JF, Lemos MR, Pereira GF, Loudal D, Moura LC, Dhalia R, França RF, Magalhães T, Marques ET Jr, Jaenisch T, Wallau GL, de Lima MC, Nascimento V, de Cerqueira EM, de Lima MM, Mascarenhas DL, Neto JPM, Levin AS, Tozetto-Mendoza TR, Fonseca SN, Mendes-Correa MC, Milagres FP, Segurado A, Holmes EC, Rambaut A, Bedford T, Nunes MR, Sabino EC*, Alcantara LCJ, Loman NJ, Pybus OG (2017) Establishment and cryptic transmission of Zika virus in Brazil and the Americas. Nature 546:406-10

Jacka B, Bray B, Applegate TL, Marshall BD, Dias Lima V, Hayashi K, DeBeck K, Raghwani J, Harrigan PR, Krajden M, Montaner J, Grebely J (2017) Drug use and phylogenetic clustering of hepatitis C virus infection among people who use drugs in Vancouver, Canada: A latent class analysis approach. Journal of Viral Hepatitis In press

Raghwani J, Rose R, Sheridan I, Lemey P, Suchard M, Farci P, Klenerman P, Pybus OG (2016) Exceptional heterogeneity in viral evolutionary dynamics characterises chronic hepatitis C virus infection. PLOS Pathogens 12:e1005894

Raghwani J, Bhatt S, Pybus OG (2016) Faster adaptation in smaller populations: counter-intuitive evolution of HIV during infection. PLOS Computational Biology 12:e1004694

Dialdestoro K, Sibbesen J, Maretty L, Raghwani J, Gall A, Kellam P, Pybus OG, Hein J, Jenkins PA (2016) Coalescent inference using serially sampled, high-throughput sequencing data from intra-host HIV infection. Genetics 202:1449-72

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

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) Effect of live poultry market interventions on influenza A (H7N9) virus, Guangdong, China. Emerging Infectious Diseases 22:2104–12

Li S, Rissanen I, Zeltina A, Hepojoki J, Raghwani J, Harlos K, Pybus OG, Huiskonen JT, Bowden TA (2016) A molecular-level account of the antigenic hantaviral surface. Cell Reports 15:959–67

Bradshaw D, Raghwani J, Jacka B, Sacks-Davis R, Lamoury F, Down I, Prestage G, Applegate TL, Hellard M, Sasadeusz J, Dore GJ, Pybus OG, Matthews GV, Danta M (2016) Venue-based networks may underpin HCV transmissions amongst HIV-infected gay and bisexual men. PLOS One 11:e0162002

Jacka B, Applegate TL, Poon AF, Raghwani J, Harrigan PR, DeBeck K, Milloy M-J, Krajden M, Olmstead A, Joy JB, Marshall BD, Hayashi K, Pybus OG, Lima V, Magiorkinis G, Montaner J, Lamoury F, Dore GJ, Wood E, Grebely J (2016) Transmission of hepatitis C virus infection among younger and older people who inject drugs in Vancouver, Canada. Journal of Hepatology 64:1247–55

Raghwani J, Pybus OG, Illingworth CJR (2016) Population genetic modelling of viruses. In Virus Evolution: Current Research & Future Directions (S. Weaver, M. Denison, M. Roossinck, M. Vignuzzi, eds.) pp. 293-327. Caister Academic Press

Liu W*, Fan H*, Raghwani J*, Lam TT, Li J, Pybus OG, Yao HW, Wo Y, Liu K, An XP, Pei GQ, Li H, Wang HY, Zhao JJ, Jiang T, Ma MJ, Xia X, Dong YD, Zhao TY, Jiang JF, Yang YH, Guan Y, Tong YG, Cao W (2014) Occurrence and reassortment of avian influenza A (H7N9) viruses derived from coinfected birds in China. Journal of Virology 88:13344-51

Takebe Y, Naito Y, Raghwani J, Fearnhill E, Sano T, Kusagawa S, Mbisa JL, Zhang H, Matano T, Leigh Brown AJ, Pybus OG, Dunn D, Kondo M, the UK Collaborative Group on HIV Drug Resistance (2014) Inter-continental dispersal of HIV-1 subtype B associated with transmission among men-having-sex-with-men in Japan. Journal of Virology 88:9864-76

Iles JC, Raghwani J, Harrison GLA, Pepin J, Djoko CF, Tamoufe U, Lebreton M, Schneider BS, Fair JN, Tshala FM, Kayembe PK, Muyembe JJ, Edidi-Basepeo S, Wolfe ND, Simmonds P, Klenerman P, Pybus OG (2014) Phylogeography and molecular epidemiology of hepatitis C virus genotype 4 in Africa. Virology 464-465:233-43

Raghwani J, Thomas XV, Koekkoek SM, Schinkel J, Molenkamp R, van de Laar TJ, Takebe Y, Tanaka Y, Mizokami M, Rambaut A, Pybus OG (2012) The origin and evolution of the unique hepatitis C virus circulating recombinant form 2k/1b. Journal of Virology 86:2212-20

Raghwani J, Rambaut A, Holmes EC, Hang VT, Hien TT, Farrar J, Wills B, Lennon NJ, Birren BW, Henn MR, Simmons CP (2011) Endemic dengue associated with the co-circulation of multiple viral lineages and localized density-dependent transmission. PLOS Pathogens 7:e1002064

Smith GJD, Vijaykrishna D, Bahl J, Lycett SJ, Worobey M, Pybus OG, Ma SK, Cheung CM, Raghwani J, Bhatt S, Peiris JS, Guan Y, Rambaut A (2009) Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic. Nature 459:1122-5

Post-doctoral Researcher

Department of Zoology

University of Oxford

Peter Medawar Building

South Parks Road

Oxford, OX1 3SY, UK

Publications

I am an evolutionary geneticist with broad interests in virus evolution and ecology. My current projects involve (i) developing analytical methods for investigating the within-host dynamics of chronic viral infections, such as HIV and HCV, using deep-sequence viral genetic data, and (ii) understanding the mechanisms underlying adaptive evolution in fast-evolving viruses.

Research Interests

* denotes equal contributions