Publications                                                    Publications before 2000

Journal Publications

Ssemwanga D, Bbosa N, Nsubuga RN, Ssekagiri A, Kapaata A, Nannyonjo M, Nassolo F, Seeley J, Yebra G, Leigh Brown A, Kaleebu P. The Molecular Epidemiology and Transmission Dynamics of HIV type 1 in a General Population Cohort in Uganda. Viruses 12: 1283, 2020. link to journal article

Grant HE, Hodcroft EB, Ssemwanga D, Kitayimbwa J, Yebra G, Esquivel Gomez LR, Gall A, Kellam P, de Oliveira T, Roy S, Breuer J, Bbosa N, Nsubuga R, Kibengo F, Kwan TH, Lycett S, Kao R, Robertson DL, Ratmann O, Fraser C, Pillay D, Kaleebu P, Leigh Brown AJ, on behalf of the PANGEA consortium. Pervasive and non-random recombination in near full-length HIV genomes from Uganda. Virus Evolution 6(1): veaa004 2020. link to journal article

Ratmann O, Grabowski MK, Hall M, Golubchik T, Wymant C, Abeler-Dörner L, Bonsall D, Hoppe A, Leigh Brown A, de Oliveira T, Gall A, Kellam P, Pillay D, Kagaayi J, Kigozi K, Quinn T, Wawer M, Laeyendecker O, Serwadda D, Gray R, Fraser C on behalf of the PANGEA consortium and Rakai Health Sciences Program. Inferring HIV-1 transmission networks and sources of ongoing viral spread in Africa with deep sequencing. Nature Communications 10:1411, 2019. link to journal article

Hey-Nguyen WJ, Bailey M, Xu Y, Suzuki K, Van Bockel D, Finlayson, R, Leigh Brown A, Carr A, Cooper D, Kelleher AD, Koelsch KK and Zaunders JJ. HIV-1 DNA is maintained in antigen-specific CD4+ T cell subsets in patients on long-term antiretroviral therapy regardless of recurrent antigen exposure. AIDS Res Hum Retroviruses 35:112-120, 2019. link to journal article

Bbosa N, Ssemwanga D, Nsubuga RN, Salazar-Gonzalez JF, Salazar M, Nanyonjo M, Kuteesa M, Seeley J, Kiwanuka N, Bagaya BS, Yebra G, Leigh Brown AJ, Kaleebu P. Complex phylogeography of HIV-1 suggests that Ugandan fishing communities are a sink for, not a source of, virus from general populations. Scientific Reports, 9: 1051, 2019. link to journal article

Ragonnet-Cronin M, Hué S, Hodcroft EB, Tostevin A, Dunn D, Fawcett T, Pozniak A, Brown AE, Delpech V and Leigh Brown AJ on behalf of the UK HIV Drug Resistance Database. Nondisclosed MSM link together in HIV transmission networks. Lancet HIV 5: e 309-316, 2018. link to journal article

Kosakovsky Pond SL, Weaver S, Leigh Brown AJ, and Wertheim JO. HIV-TRACE (Transmission Cluster Engine): a tool for large scale molecular epidemiology of HIV-1 and other rapidly evolving pathogens. Mol Biol Evol 35: 1812-1819, 2018. link to journal article

Ragonnet-Cronin M, Jackson C, Bradley-Stewart A, Aitken C, McAuley A, Palmateer N, Goldberg D, Milosevic C, Leigh Brown AJ. Recent and rapid transmission of HIV among people who inject drugs in Scotland revealed through phylogenetic analysis. J Infect Dis 217: 1885-1882, 2018.link to journal article

Yebra G, Frampton D, Gallo Cassarino T, Raffle J, Hubb J, Ferns RB, Waters L, Tong CY, Kozlakidis Z, Hayward A, Kellam P, Pillay D, Clark D, Nastouli E, Leigh Brown AJ. A high HIV-1 strain variability in London, UK, revealed by full-genome analysis: Results from the ICONIC project. PLoS One 2018 Feb 1; 13:e0192081.link to journal article

Yebra G, Hodcroft EB, Ragonnet-Cronin R, Pillay D & Leigh Brown AJ on behalf of the PANGEA_HIV Consortium and the ICONIC Project.Using full-genome HIV sequence data improves phylogeny reconstruction in a simulated epidemic. Sci Rep 2016; 6:39489. link to journal article

Ratmann O, Hodcroft EB, Pickles M, Cori A, Hall M, Lycett S, Colijn C, Kendall M, Didelot X, Plazotta G, Poon A, Joy J, Leventhal G, Rasmussen D, Kuehnert D, Stadler T, Volz E, Dearlove B, Hossain M, Frost SDW, Leigh Brown AJ and Fraser C.Using phylogenetic tools to estimate aspects of HIV transmission dynamics in generalized HIV epidemics: findings from the PANGEA-HIV methods comparison exercise. Mol. Biol. Evol.; 34: 185-203 2017. link to journal article

Ragonnet-Cronin, M, Shilaih, M, Gunthard H, Hodcroft E, Boni J, Fearnhill E, Dunn D, Yerly S, Klimkait T, Aubert V, Yang W-L, Delpech V, Lycett S, Kouyos R and Leigh Brown AJ. A Direct Comparison of Two Densely Sampled Western European HIV Epidemics: The UK and Switzerland. Sci Rep 2016; 6:32251. link to journal article

Yebra G, Kalish ML, Leigh Brown AJ.Reconstructing the HIV-1 CRF02_AG and CRF06_cpx epidemics in Burkina Faso and West Africa using early samples.Infect. Genet. Evol. 2016. link to journal article

Ragonnet-Cronin M, Lycett S, Hodcroft E, Hue S, Fearnhill E, Brown AE, Delpech V, Dunn DT and Leigh Brown AJ on behalf of the UK HIV Drug Resistance Database. Transmission of non-B HIV in the UK is increasingly driven by large non-heterosexual clusters. J Infect Dis 213: 1410-1418 2016; doi: 10.1093/infdis/jiv758. link to journal article

Yebra G, Ragonnet-Cronin M, Ssemwanga D, Parry C, Logue C, Cane PA, Kaleebu P and Leigh Brown AJ.Analysis of the history and spread of HIV-1 in Uganda using phylodynamics.J. Gen Virol. 96: 1890-1898. 2015 link to journal article

Lu L, Lycett SJ, Leigh Brown AJ.Determining the phylogenetic and phylogeographic origin of Highly Pathogenic Avian Influenza (H7N3) in Mexico.Plos One 2014 Sep 16;9:e107330. link to journal article

Dennis AM, Herbeck JT, Garnett GP, Fraser C, Leigh Brown A, Kellam P, Pillay D, Cohen MS. Phylogenetic studies of transmission dynamics in generalized HIV epidemics: An essential tool where the burden is greatest? J. AIDS. in press 2014. link to journal article

Hue S, Brown AE, Ragonnet-Cronin M, Lycett SJ, Dunn DT, Fearnhill E, Dolling DI, Delpech VC, Pozniak A, Pillay D, and Leigh Brown AJ on behalf of the UK HIV Drug Resistance Database and the Collaborative HIV and Anti-HIV Drug Resistance Network (CHAIN). Misclassification of HIV-1 heterosexual transmissions quantified by phylogenetic means. AIDS 2014 Jul 2;28:1967-75. Link to pdf

Schuh, AJ, Ward, MJ, Leigh Brown, AJ, Barrett, ADT. Dynamics of the emergence and establishment of a newly dominant genotype of Japanese encephalitis virus throughout Asia. J. Virol. 2014; 88: (8) 4522-4532. link to journal article

Lu L, Lycett, SJ, Leigh Brown AJ. Diverse reassortment patterns of avian influenza viruses among different subtypes. BMC Evol Biol 2014 Jan 24;14(1):16. link to journal article

Hodcroft E., Hadfield J, Fearnhill E, Phillips A, Dunn DT, O'Shea S, Tong W, Pillay D and Leigh Brown AJ on behalf of the UK HIV Drug Resistance Database and UK CHIC Study. Estimating the contribution of viral genotype to plasma viral set-point in HIV infection. PLoS Path.; 10(5):e1004112 2014 link to journal article

Schuh, AJ, Ward, MJ, Leigh Brown, AJ, Barrett, ADT. Phylogeography of Japanese Encephalitis Virus: genotype is associated with climate. PLoS Negl Trop Dis;7:e2411 2013 link to journal article

Ragonnet-Cronin M, Lycett SJ, Hodcroft E, Hue S, Fearnhill E, Dunn D, Delpech V, Leigh Brown AJ. Automated analysis of phylogenetic clusters. BMC Bioinformatics 14:317; 2013 link to journal article

Ward,MJ, Lycett,SJ, Avila, D, Bollback, JP, Leigh Brown AJ Evolutionary interactions between haemagglutinin and neuraminidase in avian influenza. BMC Evolutionary Biology 13:222; 2013 link to journal article

Wertheim JO, Leigh Brown AJ, Hepler NH, Mehta S, Richman DD, Smith DM, Kosakovsky Pond SL. The global transmission network of HIV-1. J. Infect. Dis. 209; 304-313, 2013. link to journal article

Ward, MJ, Lycett, SJ, Kalish, ML, Rambaut, A, Leigh Brown AJ. Estimating the rate of inter-subtype recombination in early HIV-1 group M strains. J Virol 2013; 87:1967-73. link to journal article

Bhatt S, Lam TT, Lycett SJ, Leigh Brown AJ, Bowden TA, Holmes EC, Wood JLN, Brown IH, Kellam P, Combatting Swine Influenza Consortium, Pybus OG. The evolutionary dynamics of influenza A virus adaptation to mammalian hosts. Phil. Trans R Soc Lond B Biol Sci 2013;368(1614):20120382 link to journal article

Lycett, S, Baillie,G, Coulter,E, Bhatt,S, Pybus,O, Kellam,P, Wood,J, Brown,I, COSI, Leigh Brown,A.J. Estimating Reassortment Rates in Co-Circulating Eurasian Swine Influenza Strains. J Gen Virol 2012 Nov;93(Pt 11):2326-36. link to journal article

Lycett, SJ, McLeish, NJ, Robertson,C, Carman,W, Baillie,G, McMenamin,J, Rambaut, A, Simmonds, P, Woolhouse,ME, Leigh Brown,AJ. Origin and fate of A/H1N1 influenza in Scotland during 2009. J. Gen Virol. 2012 Feb 15 93:1253-60 link to journal article

Volz EM, Koopman JS, Ward MJ, Leigh Brown AJ, Frost SD. Simple epidemiological dynamics explain phylogenetic clustering of HIV from patients with recent infection. PLoS Comput Biol 2012;8(6):e1002552 link to journal article

Vermund, SH, Leigh Brown, A.J., The HIV Epidemic: High-Income Countries. Chapter 21 in HIV: From Biology to Prevention and Treatment, Bushman, F.D., Nabel, G., Swanstrom, R., eds. Cold Spring Harbor Laboratory Press. 2012.

Leigh Brown AJ, Lycett SJ, Weinert L, Hughes GJ, Fearnhill E, Dunn DT, UK HIV Drug Resistance Collaboration. Transmission network parameters estimated from HIV sequences for a nationwide epidemic. J. Infect. Dis. 2011. 204: 1463-1469 link to journal article

McLeish NJ, Simmonds P, Robertson C, Handel I, McGilchrist M, Singh BK, Kerr S, Chase-Topping ME, Sinka K, Bronsvoort M, Porteous DJ, Carman W, McMenamin J, Leigh-Brown A, Woolhouse ME. Sero-Prevalence and Incidence of A/H1N1 2009 Influenza Infection in Scotland in Winter 2009-2010. PLoS One 6:e20358; 2011. link to journal article

Kosakovsky Pond, S. L., Posada, D., Stawiski, E., Chappey, C., Poon, A. F., Hughes, G., Fearnhill, E., Gravenor, M. B., Leigh Brown, A. J., and Frost, S. D. An evolutionary model-based algorithm for accurate phylogenetic breakpoint mapping and subtype prediction in HIV-1. PLoS Comput.Biol. 5(11), e1000581. 2009. link to journal article

Volz, E., Kosakovsky Pond, S.L., Ward, M.J., Leigh Brown A.J. and Frost, S.D. Phylodynamics of infectious disease epidemics. Genetics. 2009 183: 1421-1430. link to journal article

Lycett,S.J. Ward, M., Lewis, F.I., Poon, A.F.Y., Kosakovsky Pond, S.L. and Leigh Brown, A.J. A Bayesian graphical model for the genetic determination of virulence of H5N1 influenza in mammals. J.Virol. 2009 83:9901-10. link to journal article

Hughes, G.J. Fearnhill, E., Dunn, D., Lycett, S.J., Rambaut,A. and Leigh Brown A.J. (on behalf of the UK HIV Drug Resistance Collaboration) Molecular phylodynamics of the heterosexual HIV epidemic in the United Kingdom. PLoS Pathogens 2009 5:e1000590. link to journal article

Kosakovsky Pond SL, Poon AF, Leigh Brown AJ, Frost SD. A maximum likelihood method for detecting directional evolution in protein sequences and its application to influenza A virus. Mol Biol Evol 2008;25:1809-24. pdf

Murray RJ, Lewis F, Miller, MD, Leigh Brown AJ Genetic basis of variation in tenofovir drug susceptibility. AIDS 2008, 22: 1113-1123. pdf

Lewis FI, Hughes GJ, Rambaut A, Pozniak A, Leigh Brown AJ. Episodic sexual transmission of HIV revealed by molecular phylodynamics. PLoS Med 5(3): e50 2008. link to journal article

Pillay D, Rambaut A, Geretti AM, Leigh Brown AJ. HIV phylogenetics. BMJ 2007 Sep 8;335(7618):460-1. pdf

Poon A.F.Y., Kosakovsky Pond S.L., Bennett P., Richman D.D., Leigh Brown A.J., Frost, S.D.W. Adaptation to human populations is revealed by within-host polymorphisms in HIV-1 and hepatitis C virus. PLoS Pathog 3(3), 2007: e45. pdf

Kosakovsky Pond S.L, Frost S.D.W, Grossman Z., Gravenor M.B., Richman D.D., Leigh Brown A.J. Adaptation to different human populations by HIV-1 revealed by codon-based analyses. PLoS Comput Biol. 2; e62, 2006. pdf

Yang, O.O., Daar, E.S., Jamieson, B.D., Balamururugam, A., Smith, D.M., Pitt, J.A., Petropoulos, C.J., Richman, D.D., Little, S.J. and Leigh Brown A.J. HIV-1 Clade B superinfection: evidence for differential immune containment of distinct clade B strains. J. Virol. 79, 860-868, 2005. pdf

Froebel, K. Howard, W., Schafer, J., Howie, F., Whitworth, J., Kaleebu, P., Leigh Brown, A. and Riley, E. Activation by malaria antigenes renders mononuclear cells susceptible to HIV infection and reactivates replication of endogenous HIV in cells from HIV infected donors. Parasite Immunol. 26, 213-217, 2004 pdf

Leigh Brown, A.J., Frost, S.D.W., Good, B., Daar, E.S., Simon, V., Markowitz, M., Collier, A.C., Connick, E., Conway, B., Margolick, J.B., Routy, J-P., Corbeil, J., Hellmann, N.S., Richman, D.D., Little, S.J. Genetic basis of hypersusceptibility to protease inhibitors and low replicative capacity of Human Immunodeficiency Virus Type strains in primary infection. J.Virol. 78, 2242-2246, 2004. pdf

De Pasquale, M.P., Leigh Brown, A.J., Allega, J., Caliendo, A.M., Sutton, L., Donahue, S., CuUvin, S., D'Aquila, R.T. Differences in HIV-1 pol sequences from female genital tract and blood during antiretroviral therapy. Journal of Acquired Immune Deficiency Syndromes, 34, 37-44, 2003.

Koelsch, K.K., Smith, D.M., Little, S.J., Ignacio, C.C., Leigh Brown, A.J., Petropoulos, C.C., Richman D.D. and Wong, J.K. Clade B HIV-1 Superinfection with Wild Type Virus Following Infection with Drug Resistant Clade B Virus. AIDS 17: F11-F16, 2003.

Strain, M.C., Gunthard, H.F., Havlir, D.V., Ignacio, C.C., Smith, D.M., Leigh Brown, A.J., Macaranas, T.R., Lam, R.Y., Daly, O.A., Fischer, M., Opravil, M., Levine, H., Bacheler, L., Spina, C., Richman, D.D. and Wong, J.K. Heterogeneous clearance rates of long-lived lymphocytes infected with HIV: intrinsic stability predicts lifelong persistence. Proc. Natl. Acad. Sci USA, 100, 4819-48 2003

Leigh Brown, A.J., Frost, S.D.W., Mathews, W. C., Whitcomb, J.M., Hellmann, N.S., Daar, E.S., Richman, D.D. and Little, S.J. Transmission fitness of drug resistant virus and the prevalence of resistance in the treated population, JID, 187, 683-686, 2003. pdf

Raposo, G., Moore, M., Innes, D., Leijendekker, R., Leigh-Brown, A., Benaroch, P., and Geuze, H. Human macrophages accumulate HIV-1 particles in MHC II compartments. Traffic, 3, 718-729, 2002

Quigg, M. Frost, S.D.W., McDonagh, S., Burns, S.M., Clutterbuck, D., MacMillan, A., Leen, C.S. and Leigh Brown, A.J. Association of antiretroviral resistance genotypes with response to therapy - comparison of three models. Antiviral Therapy, 7, 151-157, 2002. pdf

Bird, S.M. and Leigh Brown, A.J., Criminalisation of HIV transmission: implications for public health in Scotland. BMJ, 323, 1174-1177 2001. pdf

Frost, S.D.W., Martinez-Picado, J., Ruiz, L., Clotet, B. and Leigh Brown A.J. Viral dynamics during structured treatment interruptions of chronic human immunodeficiency virus type 1 infection. J. Virol., 76, 968-979, 2002. pdf

Jassal, S.R., Lairmore, M.D., Leigh Brown, A.J. and Brighty, D.W. Soluble recombinant HTLV-1 surface glycoprotein competitively inhibits syncytia formation and viral infection of cells. Virus Res. 78, 17-34, 2001.

Frost, S.D.W., Gunthard, H.F., Wong, J.K., Havlir,D., Richman, D.D and Leigh Brown,A.J. Evidence for positive selection driving the evolution of HIV env under potent antiretroviral therapy. Virology 284, 250-258, 2001. pdf

Lockett, S.F., Robertson, J.R., Brettle, R.P., Middleton, D., Yap, P.L. and Leigh Brown, A.J. Mismatched HLA alleles protect against HIV transmission in heterosexual infection. J. Acquir. Immun. Defic. Syndr. 27, 277-280, 2001. pdf

Frost, S.D.W. Dumaurier, M-J., Wain-Hobson, S. and Leigh Brown, A.J. Genetic drift and within-host metapopulation dynamics of HIV-1 infection. Proc. Natl. Acad. Sci. USA 98, 6975-6980, 2001. pdf

Leigh Brown, A.J., Precious, H.M., Whitcomb, J., Wong, J.K., Quigg, M., Daar, E., D'Aquila, R.T., Keiser, P., Connick, E., Hellmann, N., Petropoulos, C., Richman, D.D. and Little, S.J. Novel amino acid change affecting susceptibility to non-nucleoside reverse transcriptase inhibitors detected in primary HIV infection. J.Virol., 74, 10269-10273, 2000 pdf

Frost, S.D.W., Nijhuis, M., Schuurman, R., Boucher, C.A.B. and Leigh Brown, A.J. Variation in the rate of evolution of lamivudine (3TC) resistance in HIV-1 infected individuals and its relationship to effective population size. J. Virol., 74, 6262-6268, 2000. pdf

Hanna, G.J. Johnson, V.A. , Kuritzkes, D.R., Richman, D.D., Leigh Brown, A.J., Savara, A.V. Hazelwood, J.D. and D'Aquila, R.T. Patterns of resistance mutations selected by treatment of human immunodeficiency virus type 1 infection with zidovudine, didanosine and nevirapine. J.Infect.Dis., 181, 904-911, 2000.

Precious, H., Gunthard, H., Wong, J., D'Aquila, R.T., Johnson, V.A., Kuritzkes, D.R., Richman, D.D. and Leigh Brown, A.J., Multiple sites in HIV-1 reverse transcriptase associated with virological response to combination therapy. AIDS, 14, 31-36, 2000. pdf