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Items: 29

1.

Link between the numbers of particles and variants founding new HIV-1 infections depends on the timing of transmission.

Thompson RN, Wymant C, Spriggs RA, Raghwani J, Fraser C, Lythgoe KA.

Virus Evol. 2019 Jan 30;5(1):vey038. doi: 10.1093/ve/vey038. eCollection 2019 Jan.

2.

High-Resolution Evolutionary Analysis of Within-Host Hepatitis C Virus Infection.

Raghwani J, Wu CH, Ho CKY, De Jong M, Molenkamp R, Schinkel J, Pybus OG, Lythgoe KA.

J Infect Dis. 2019 May 5;219(11):1722-1729. doi: 10.1093/infdis/jiy747.

3.

A Protective Monoclonal Antibody Targets a Site of Vulnerability on the Surface of Rift Valley Fever Virus.

Allen ER, Krumm SA, Raghwani J, Halldorsson S, Elliott A, Graham VA, Koudriakova E, Harlos K, Wright D, Warimwe GM, Brennan B, Huiskonen JT, Dowall SD, Elliott RM, Pybus OG, Burton DR, Hewson R, Doores KJ, Bowden TA.

Cell Rep. 2018 Dec 26;25(13):3750-3758.e4. doi: 10.1016/j.celrep.2018.12.001.

4.

Molecular Evolution, Diversity, and Adaptation of Influenza A(H7N9) Viruses in China.

Lu J, Raghwani J, Pryce R, Bowden TA, Thézé J, Huang S, Song Y, Zou L, Liang L, Bai R, Jing Y, Zhou P, Kang M, Yi L, Wu J, Pybus OG, Ke C.

Emerg Infect Dis. 2018 Oct;24(10):1795-1805. doi: 10.3201/eid2410.171063.

5.

Where do all the subtypes go? Temporal dynamics of H8-H12 influenza A viruses in waterfowl.

Wille M, Latorre-Margalef N, Tolf C, Halpin R, Wentworth D, Fouchier RAM, Raghwani J, Pybus OG, Olsen B, Waldenström J.

Virus Evol. 2018 Aug 14;4(2):vey025. doi: 10.1093/ve/vey025. eCollection 2018 Jul.

6.

Evolution of HIV-1 within untreated individuals and at the population scale in Uganda.

Raghwani J, Redd AD, Longosz AF, Wu CH, Serwadda D, Martens C, Kagaayi J, Sewankambo N, Porcella SF, Grabowski MK, Quinn TC, Eller MA, Eller LA, Wabwire-Mangen F, Robb ML, Fraser C, Lythgoe KA.

PLoS Pathog. 2018 Jul 27;14(7):e1007167. doi: 10.1371/journal.ppat.1007167. eCollection 2018 Jul.

7.

Structure of the Lassa virus glycan shield provides a model for immunological resistance.

Watanabe Y, Raghwani J, Allen JD, Seabright GE, Li S, Moser F, Huiskonen JT, Strecker T, Bowden TA, Crispin M.

Proc Natl Acad Sci U S A. 2018 Jul 10;115(28):7320-7325. doi: 10.1073/pnas.1803990115. Epub 2018 Jun 25.

8.

Genome-wide evolutionary dynamics of influenza B viruses on a global scale.

Langat P, Raghwani J, Dudas G, Bowden TA, Edwards S, Gall A, Bedford T, Rambaut A, Daniels RS, Russell CA, Pybus OG, McCauley J, Kellam P, Watson SJ.

PLoS Pathog. 2017 Dec 28;13(12):e1006749. doi: 10.1371/journal.ppat.1006749. eCollection 2017 Dec.

9.

Selection on non-antigenic gene segments of seasonal influenza A virus and its impact on adaptive evolution.

Raghwani J, Thompson RN, Koelle K.

Virus Evol. 2017 Nov 9;3(2):vex034. doi: 10.1093/ve/vex034. eCollection 2017 Jul.

10.

Role of HIV-specific CD8+ T cells in pediatric HIV cure strategies after widespread early viral escape.

Leitman EM, Thobakgale CF, Adland E, Ansari MA, Raghwani J, Prendergast AJ, Tudor-Williams G, Kiepiela P, Hemelaar J, Brener J, Tsai MH, Mori M, Riddell L, Luzzi G, Jooste P, Ndung'u T, Walker BD, Pybus OG, Kellam P, Naranbhai V, Matthews PC, Gall A, Goulder PJR.

J Exp Med. 2017 Nov 6;214(11):3239-3261. doi: 10.1084/jem.20162123. Epub 2017 Oct 5.

11.

A10 The evolution and molecular epidemiology of epidemic GII.17 noroviruses.

Lu J, Fang L, Zheng H, Lao J, Yang F, Sun L, Xiao J, Lin J, Song T, Raghwani J, Ke C, Faria NR, Bowden TA, Pybus OG, Li H.

Virus Evol. 2017 Mar 5;3(Suppl 1). pii: vew036.009. doi: 10.1093/ve/vew036.009. eCollection 2017 Mar. No abstract available.

12.

Drug use and phylogenetic clustering of hepatitis C virus infection among people who use drugs in Vancouver, Canada: A latent class analysis approach.

Jacka B, Bray BC, Applegate TL, Marshall BDL, Lima VD, Hayashi K, DeBeck K, Raghwani J, Harrigan PR, Krajden M, Montaner JSG, Grebely J Senior.

J Viral Hepat. 2018 Jan;25(1):28-36. doi: 10.1111/jvh.12758. Epub 2017 Sep 4.

13.

Establishment and cryptic transmission of Zika virus in Brazil and the Americas.

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 MRT, Sabino EC, Alcantara LCJ, Loman NJ, Pybus OG.

Nature. 2017 Jun 15;546(7658):406-410. doi: 10.1038/nature22401. Epub 2017 May 24.

14.

Characterization of Hepatitis C Virus (HCV) Envelope Diversification from Acute to Chronic Infection within a Sexually Transmitted HCV Cluster by Using Single-Molecule, Real-Time Sequencing.

Ho CKY, Raghwani J, Koekkoek S, Liang RH, Van der Meer JTM, Van Der Valk M, De Jong M, Pybus OG, Schinkel J, Molenkamp R.

J Virol. 2017 Feb 28;91(6). pii: e02262-16. doi: 10.1128/JVI.02262-16. Print 2017 Mar 15.

15.

Effect of Live Poultry Market Interventions on Influenza A(H7N9) Virus, Guangdong, China.

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.

Emerg Infect Dis. 2016 Dec;22(12):2104-2112. doi: 10.3201/eid2212.160450.

16.

Exceptional Heterogeneity in Viral Evolutionary Dynamics Characterises Chronic Hepatitis C Virus Infection.

Raghwani J, Rose R, Sheridan I, Lemey P, Suchard MA, Santantonio T, Farci P, Klenerman P, Pybus OG.

PLoS Pathog. 2016 Sep 15;12(9):e1005894. doi: 10.1371/journal.ppat.1005894. eCollection 2016 Sep.

17.

Venue-Based Networks May Underpin HCV Transmissions amongst HIV-Infected Gay and Bisexual Men.

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.

PLoS One. 2016 Sep 1;11(9):e0162002. doi: 10.1371/journal.pone.0162002. eCollection 2016.

18.

A Molecular-Level Account of the Antigenic Hantaviral Surface.

Li S, Rissanen I, Zeltina A, Hepojoki J, Raghwani J, Harlos K, Pybus OG, Huiskonen JT, Bowden TA.

Cell Rep. 2016 Jun 28;16(1):278. doi: 10.1016/j.celrep.2016.06.039. Epub 2016 Jun 28. No abstract available.

19.

The Evolution and Transmission of Epidemic GII.17 Noroviruses.

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.

J Infect Dis. 2016 Aug 15;214(4):556-64. doi: 10.1093/infdis/jiw208. Epub 2016 May 24.

20.

A Molecular-Level Account of the Antigenic Hantaviral Surface.

Li S, Rissanen I, Zeltina A, Hepojoki J, Raghwani J, Harlos K, Pybus OG, Huiskonen JT, Bowden TA.

Cell Rep. 2016 May 3;15(5):959-967. doi: 10.1016/j.celrep.2016.03.082. Epub 2016 Apr 21. Erratum in: Cell Rep. 2016 Jun 28;16(1):278.

21.

Transmission of hepatitis C virus infection among younger and older people who inject drugs in Vancouver, Canada.

Jacka B, Applegate T, Poon AF, Raghwani J, Harrigan PR, DeBeck K, Milloy MJ, Krajden M, Olmstead A, Joy JB, Marshall BD, Hayashi K, Pybus OG, Lima VD, Magiorkinis G, Montaner J, Lamoury F, Dore GJ, Wood E, Grebely J.

J Hepatol. 2016 Jun;64(6):1247-55. doi: 10.1016/j.jhep.2016.02.031. Epub 2016 Feb 26.

22.

Coalescent Inference Using Serially Sampled, High-Throughput Sequencing Data from Intrahost HIV Infection.

Dialdestoro K, Sibbesen JA, Maretty L, Raghwani J, Gall A, Kellam P, Pybus OG, Hein J, Jenkins PA.

Genetics. 2016 Apr;202(4):1449-72. doi: 10.1534/genetics.115.177931. Epub 2016 Feb 8.

23.

Faster Adaptation in Smaller Populations: Counterintuitive Evolution of HIV during Childhood Infection.

Raghwani J, Bhatt S, Pybus OG.

PLoS Comput Biol. 2016 Jan 7;12(1):e1004694. doi: 10.1371/journal.pcbi.1004694. eCollection 2016 Jan.

24.

Occurrence and reassortment of avian influenza A (H7N9) viruses derived from coinfected birds in China.

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 Y, Cao WC.

J Virol. 2014 Nov;88(22):13344-51. doi: 10.1128/JVI.01777-14. Epub 2014 Sep 10.

25.

Phylogeography and epidemic history of hepatitis C virus genotype 4 in Africa.

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.

Virology. 2014 Sep;464-465:233-243. doi: 10.1016/j.virol.2014.07.006. Epub 2014 Aug 6.

26.

Intercontinental dispersal of HIV-1 subtype B associated with transmission among men who have sex with men in Japan.

Takebe Y, Naito Y, Raghwani J, Fearnhill E, Sano T, Kusagawa S, Mbisa JL, Zhang H, Matano T, Brown AJ, Pybus OG, Dunn D, Kondo M; UK Collaborative Group on HIV Drug Resistance.

J Virol. 2014 Sep 1;88(17):9864-76. doi: 10.1128/JVI.01354-14. Epub 2014 Jun 18.

27.

Origin and evolution of the unique hepatitis C virus circulating recombinant form 2k/1b.

Raghwani J, Thomas XV, Koekkoek SM, Schinkel J, Molenkamp R, van de Laar TJ, Takebe Y, Tanaka Y, Mizokami M, Rambaut A, Pybus OG.

J Virol. 2012 Feb;86(4):2212-20. doi: 10.1128/JVI.06184-11. Epub 2011 Nov 23.

28.

Endemic dengue associated with the co-circulation of multiple viral lineages and localized density-dependent transmission.

Raghwani J, Rambaut A, Holmes EC, Hang VT, Hien TT, Farrar J, Wills B, Lennon NJ, Birren BW, Henn MR, Simmons CP.

PLoS Pathog. 2011 Jun;7(6):e1002064. doi: 10.1371/journal.ppat.1002064. Epub 2011 Jun 2.

29.

Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic.

Smith GJ, Vijaykrishna D, Bahl J, Lycett SJ, Worobey M, Pybus OG, Ma SK, Cheung CL, Raghwani J, Bhatt S, Peiris JS, Guan Y, Rambaut A.

Nature. 2009 Jun 25;459(7250):1122-5. doi: 10.1038/nature08182.

PMID:
19516283

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