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Dr. Jayna Raghwani

Research Interests

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.


Oxford Martin School Research Fellow, Room D59, Department of Zoology

University of Oxford, South Parks Road, Oxford, OX1 3PS, UK


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 In press 

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 

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