Edinburgh Research Explorer

Prof Andrew Leigh-Brown

Professor of Evolutionary Genetics

  1. 2020
  2. Pervasive and non-random recombination in near full-length HIV genomes from Uganda

    Grant, H., Hodcroft, E., Ssemwanga, D., Kitayimbwa, J., Yebra, G., Esquivel Gomez, L. R., Frampton, D., Gall, A., Kellam, P., de Oliveira, T., Bbosa, N., Nsubuga, R. N., Kibengo, F., Kwan, T. H., Lycett, S., Kao, R., Robertson, D., Ratmann, O., Fraser, C., Pillay, D. & 2 others, Kaleebu, P. & Leigh-Brown, A., 2 Jan 2020, (Accepted/In press) In : Virus Evolution.

    Research output: Contribution to journalArticle

  3. 2019
  4. Inferring HIV-1 transmission networks and sources of epidemic spread in Africa with deep-sequence phylogenetic analysis

    Ratmann, O., Grabowski, M. K., Hall, M., Golubchik, T., Wymant, C., Abeler-Dörner, L., Bonsall, D., Hoppe, A., Brown, A. L., de Oliveira, T., Gall, A., Kellam, P., Pillay, D., Kagaayi, J., Kigozi, G., Quinn, T. C., Wawer, M. J., Laeyendecker, O., Serwadda, D., Gray, R. H. & 1 others, Fraser, C., 29 Mar 2019, In : Nature Communications. 10, 1411.

    Research output: Contribution to journalArticle

  5. Phylogeography of HIV-1 suggests that Ugandan fishing communities are a sink for, not a source of, virus from general populations

    Bbosa, N., Ssemwanga, D., Nsubuga, R. N., Salazar-Gonzalez, J. F., Salazar, M. G., Nanyonjo, M., Kuteesa, M., Seeley, J., Kiwanuka, N., Bagaya, B. S., Yebra, G., Leigh-Brown, A. & Kaleebu, P., 31 Jan 2019, In : Scientific Reports. 9, 1, 8 p., 1051.

    Research output: Contribution to journalArticle

  6. HIV-1 DNA is Maintained in Antigen-Specific CD4+ T Cell Subsets in Patients on Long-Term Antiretroviral Therapy Regardless of Recurrent Antigen Exposure

    Hey-Nguyen, W., Bailey, M., Xu, Y., Suzuki, K., van Bockel, D., Finlayson, R., Leigh Brown, A., Carr, A., Cooper, D. A., Kelleher, A. D., Koelsch, K. K. & Zaunders, J., 11 Jan 2019, In : Aids research and human retroviruses. 35, 1, p. 112-120 9 p.

    Research output: Contribution to journalArticle

  7. 2018
  8. Non-disclosed men who have sex with men in UK HIV transmission networks: phylogenetic analysis of surveillance data

    Ragonnet-Cronin, M., Hué, S., Hodcroft, E. B., Tostevin, A., Dunn, D., Fawcett, T., Pozniak, A., Brown, A. E., Delpech, V. & Leigh-Brown, A., 1 Jun 2018, In : Lancet HIV. 5, 6, p. e309–e316

    Research output: Contribution to journalArticle

  9. Recent and rapid transmission of HIV among people who inject drugs in Scotland revealed through phylogenetic analysis

    Ragonnet-Cronin, M., Jackson, C., Bradley-Stewart, A., Aitken, C., McAuley, A., Palmateer, N., Gunson, R., Goldberg, D. J., Milosevic, C. & Leigh Brown, A. J., 10 Apr 2018, In : The Journal of Infectious Diseases. 217, 12, p. 1875-1882 8 p.

    Research output: Contribution to journalArticle

  10. A high HIV-1 strain variability in London, UK, revealed by full-genome analysis: Results from the ICONIC project

    Yebra, G., Frampton, D., Gallo Cassarino, T., Raffle, J., Hubb, J., Ferns, R. B., Waters, L., Tong, C. Y. W., Kozlakidis, Z., Hayward, A., Kellam, P., Pillay, D., Clark, D. A., Nastouli, E., Leigh Brown, A. J. & ICONIC Consortium, 1 Feb 2018, In : PLoS ONE. 13, 2, p. e0192081

    Research output: Contribution to journalArticle

  11. HIV-TRACE (Transmission Cluster Engine): a tool for large scale molecular epidemiology of HIV-1 and other rapidly evolving pathogens

    Kosakovsky Pond, S. L., Weaver, S., Leigh Brown, A. J. & Wertheim, J. O., 31 Jan 2018, In : Molecular Biology and Evolution. 16 p., msy016.

    Research output: Contribution to journalArticle

  12. 2017
  13. Recent trends and patterns in HIV-1 transmitted drug resistance in the United Kingdom

    Tostevin, A., White, E., Dunn, D., Croxford, S., Delpech, V., Williams, I., Asboe, D., Pozniak, A., Churchill, D., Geretti, A., Pillay, D., Sabin, C., Leigh-Brown, A. & Smit, E., Mar 2017, In : HIV Medicine.

    Research output: Contribution to journalArticle

  14. Quantifying predictors for the spatial diffusion of avian influenza virus in China

    Lu, L., Leigh-Brown, A. & Lycett, S., 13 Jan 2017, In : BMC Evolutionary Biology. 17, 1, 16.

    Research output: Contribution to journalArticle

  15. Phylogenetic Tools for Generalized HIV-1 Epidemics: Findings from the PANGEA-HIV Methods Comparison

    Ratmann, O., Hodcroft, E., Pickles, M., Cori, A., Hall, M., Lycett, S., Colijn, C., Leigh Brown, A. & Fraser, C., Jan 2017, In : Molecular Biology and Evolution. 34, 10, p. 185-203 31 p.

    Research output: Contribution to journalArticle

  16. 2016
  17. Reconstructing the HIV-1 CRF02_AG and CRF06_cpx Epidemics in Burkina Faso and West Africa using early samples

    Yebra, G., Kalish, M. L. & Leigh Brown, A. J., Dec 2016, In : Infection, Genetics and Evolution. 46, p. 209-218 10 p.

    Research output: Contribution to journalArticle

  18. A Direct Comparison of Two Densely Sampled HIV Epidemics: The UK and Switzerland

    Ragonnet-Cronin, M. L., Shilaih, M., Günthard, H. F., Hodcroft, E. B., Böni, J., Fearnhill, E., Dunn, D., Yerly, S., Klimkait, T., Aubert, V., Yang, W-L., Brown, A. E., Lycett, S. J., Kouyos, R. & Leigh Brown, A., 19 Sep 2016, In : Scientific Reports. 6, 32251.

    Research output: Contribution to journalArticle

  19. 2015
  20. Transmission of non-B HIV subtypes in the UK is increasingly driven by large non-heterosexual clusters

    Ragonnet-Cronin, M., Lycett, S., Hodcroft, E., Hué, S., Fearnhill, E., Brown, A. E., Delpech, V., Dunn, D., Leigh Brown, A. J. & UK HIV Drug Resistance Database, 23 Dec 2015, In : The Journal of Infectious Diseases. 213, 9, p. 1410-1418

    Research output: Contribution to journalArticle

  21. Analysis of the History and Spread of HIV-1 in Uganda using phylodynamics

    Yebra, G., Ragonnet-Cronin, M., Ssemwanga, D., Parry, C. M., Logue, C. H., Cane, P. A., Kaleebu, P. & Leigh-Brown, A. J., 1 Jul 2015, In : Journal of General Virology. 96, p. 1890–1898

    Research output: Contribution to journalArticle

  22. PANGEA-HIV: phylogenetics for generalised epidemics in Africa

    Pillay, D., Herbeck, J., Cohen, M. S., de Oliveira, T., Fraser, C., Ratmann, O., Brown, A. L., Kellam, P. & PANGEA-HIV Consortium, Mar 2015, In : The Lancet Infectious Diseases. 15, 3, p. 259-61 3 p.

    Research output: Contribution to journalComment/debate

  23. 2014
  24. Phylogenetic studies of transmission dynamics in generalized HIV epidemics: An essential tool where the burden is greatest?

    Dennis, A. M., Herbeck, J. T., Leigh Brown, A., Kellam, P., de Oliveira, T., Pillay, D., Fraser, C. & Cohen, M. S., 1 Oct 2014, In : Journal of Acquired Immune Deficiency Syndromes. 67, 2, p. 181-95 15 p.

    Research output: Contribution to journalArticle

  25. Determining the Phylogenetic and Phylogeographic Origin of Highly Pathogenic Avian Influenza (H7N3) in Mexico

    Lu, L., Lycett, S. J. & Leigh Brown, A. J., 16 Sep 2014, In : PLoS ONE. 9, 9, 13 p., e107330.

    Research output: Contribution to journalArticle

  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, J. L., Zhang, H., Matano, T., Leigh-Brown, A., Pybus, O. G., Dunn, D., Kondo, M. & UK Collaborative Group on HIV Drug Resistance, 1 Sep 2014, In : Journal of Virology. 88, 17, p. 9864-76 13 p.

    Research output: Contribution to journalArticle

  27. Phylogenetic analyses reveal HIV-1 infections between men misclassified as heterosexual transmissions

    Hué, S., Brown, A. E., Ragonnet-Cronin, M., Lycett, S. J., Dunn, D. T., Fearnhill, E., Dolling, D. I., Pozniak, A., Pillay, D., Delpech, V. C. & Leigh Brown, A. J., 24 Aug 2014, In : AIDS. 28, 13, p. 1967-75 9 p.

    Research output: Contribution to journalArticle

  28. The Contribution of Viral Genotype to Plasma Viral Set-Point in HIV Infection

    Hodcroft, E., Hadfield, J. D., Fearnhill, E., Phillips, A., Dunn, D., O'Shea, S., Pillay, D., Leigh Brown, A. J. & on behalf of the UK HIV Drug Resistance Database and the UK CHIC Study, May 2014, In : Plos pathogens. 10, 5, e1004112.

    Research output: Contribution to journalArticle

  29. Dynamics of the emergence and establishment of a newly dominant genotype of Japanese encephalitis virus throughout Asia

    Schuh, A. J., Ward, M. J., Leigh Brown, A. J. & Barrett, A. D. T., 5 Feb 2014, In : Journal of Virology.

    Research output: Contribution to journalArticle

  30. Reassortment patterns of avian influenza virus internal segments among different subtypes

    Lu, L., Lycett, S. J. & Leigh Brown, A. J., 24 Jan 2014, In : BMC Evolutionary Biology. 14, 1, 15 p., 16.

    Research output: Contribution to journalArticle

  31. Novel HIV-1 Recombinants Spreading across Multiple Risk Groups in the United Kingdom: The Identification and Phylogeography of Circulating Recombinant Form (CRF) 50_A1D

    Foster, G. M., Ambrose, J. C., Hué, S., Delpech, V. C., Fearnhill, E., Abecasis, A. B., Leigh Brown, A. J., Geretti, A. M. & UK HIV Drug Resistance Database, 15 Jan 2014, In : PLoS ONE. 9, 1, e83337.

    Research output: Contribution to journalArticle

  32. The global transmission network of HIV-1

    Wertheim, J. O., Leigh Brown, A. J., Hepler, N. L., Mehta, S. R., Richman, D. D., Smith, D. M. & Kosakovsky Pond, S. L., 15 Jan 2014, In : The Journal of Infectious Diseases. 209, 2, p. 304-13 10 p.

    Research output: Contribution to journalArticle

  33. 2013
  34. The evolutionary dynamics of influenza A virus adaptation to mammalian hosts

    Bhatt, S., Lam, T. T., Lycett, S. J., Leigh Brown, A. J., Bowden, T. A., Holmes, E. C., Guan, Y., Wood, J. L. N., Brown, I. H., Kellam, P., Pybus, O. G. & Combating Swine Influenza Consortium, Mar 2013, In : Philosophical Transactions of the Royal Society B: Biological Sciences. 368, 1614, 20120382.

    Research output: Contribution to journalArticle

  35. Estimating the rate of intersubtype recombination in early HIV-1 group M strains

    Ward, M. J., Lycett, S. J., Kalish, M. L., Rambaut, A. & Leigh Brown, A., Feb 2013, In : Journal of Virology. 87, 4, p. 1967-1973 7 p.

    Research output: Contribution to journalArticle

  36. Automated analysis of phylogenetic clusters

    Ragonnet-Cronin, M., Hodcroft, E., Hué, S., Fearnhill, E., Delpech, V., Leigh Brown, A., Lycett, S. & UK HIV Drug Resistance Database, 2013, In : BMC Bioinformatics. 14, 317.

    Research output: Contribution to journalArticle

  37. Evolutionary interactions between haemagglutinin and neuraminidase in avian influenza

    Ward, M. J., Lycett, S. J., Avila, D., Bollback, J. P. & Leigh Brown, A. J., 2013, In : BMC Evolutionary Biology. 13, 222.

    Research output: Contribution to journalArticle

  38. Phylogeography of Japanese encephalitis virus: genotype is associated with climate

    Schuh, A. J., Ward, M. J., Leigh Brown, A. & Barrett, A. D. T., 2013, In : PLoS Neglected Tropical Diseases. 7, 8, e2411.

    Research output: Contribution to journalArticle

  39. 2012
  40. Simple Epidemiological Dynamics Explain Phylogenetic Clustering of HIV from Patients with Recent Infection

    Volz, E. M., Koopman, J. S., Ward, M. J., Brown, A. L. & Frost, S. D. W., 28 Jun 2012, In : PLoS Computational Biology. 8, 6, e1002552.

    Research output: Contribution to journalArticle

  41. Origin and Fate of A/H1N1 Influenza in Scotland during 2009

    Lycett, S., McLeish, N. J., Robertson, C., Carman, W., Baillie, G., McMenamin, J., Rambaut, A., Simmonds, P., Woolhouse, M. & Leigh Brown, A. J., Jun 2012, In : Journal of General Virology. 93, 6, p. 1253-1260 8 p.

    Research output: Contribution to journalArticle

  42. Immune responses in pigs vaccinated with adjuvanted and non-adjuvanted A(H1N1)pdm/09 influenza vaccines used in human immunization programmes

    Lefevre, E. A., Carr, B. V., Inman, C. F., Prentice, H., Brown, I. H., Brookes, S. M., Garcon, F., Hill, M. L., Iqbal, M., Elderfield, R. A., Barclay, W. S., Gubbins, S., Bailey, M., Charleston, B., COSI, Leigh Brown, A., Woolhouse, M. & Archibald, A., 9 Mar 2012, In : PLoS ONE. 7, 3, p. e32400

    Research output: Contribution to journalArticle

  43. Estimating reassortment rates in co-circulating Eurasian swine influenza viruses

    Combating Swine Influenza Initiative (COSI) Consortium, 2012, In : Journal of General Virology. 93, 11, p. 2326-2336

    Research output: Contribution to journalArticle

  44. The HIV Epidemic: High-Income Countries

    Vermund, SH. & Leigh Brown, AJ., 2012, In : Cold spring harbor perspectives in medicine. 2, 5

    Research output: Contribution to journalArticle

  45. Time trends in drug resistant HIV-1 infections in the United Kingdom up to 2009: multicentre observational study

    Dolling, D., Sabin, C., Delpech, V., Smit, E., Pozniak, A., Asboe, D., Brown, A. L., Churchill, D., Williams, I., Geretti, A. M., Phillips, A., Mackie, N., Murphy, G., Castro, H., Pillay, D., Cane, P., Dunn, D. & UK Collaborative Group on HIV Drug Resistance, 2012, In : BMJ. 345, p. e5253

    Research output: Contribution to journalArticle

  46. 2011
  47. Transmission Network Parameters Estimated From HIV Sequences for a Nationwide Epidemic

    Leigh Brown, A. J., Lycett, S. J., Weinert, L., Hughes, G. J., Fearnhill, E. & Dunn, D. T., Nov 2011, In : The Journal of Infectious Diseases. 204, 9, p. 1463-1469 7 p.

    Research output: Contribution to journalArticle

  48. Sero-Prevalence and Incidence of A/H1N1 2009 Influenza Infection in Scotland in Winter 2009-2010

    McLeish, N. J., Simmonds, P., Robertson, C., Handel, I., McGilchrist, M., Singh, B. K., Kerr, S., Chase-Topping, M. E., Sinka, K., Bronsvoort, M., Porteous, D. J., Carman, W., McMenamin, J., Leigh-Brown, A. & Woolhouse, M. E. J., 8 Jun 2011, In : PLoS ONE. 6, 6, p. - 8 p., e20358.

    Research output: Contribution to journalArticle

  49. 2009
  50. Phylodynamics of Infectious Disease Epidemics

    Volz, E. M., Pond, S. L. K., Ward, M. J., Leigh Brown, A. J. & Frost, S. D. W., Dec 2009, In : Genetics. 183, 4, p. 1421-1430 10 p.

    Research output: Contribution to journalArticle

  51. Detection of Mammalian Virulence Determinants in Highly Pathogenic Avian Influenza H5N1 Viruses: Multivariate Analysis of Published Data

    Lycett, S. J., Ward, M. J., Lewis, F. I., Poon, A. F. Y., Pond, S. L. K. & Leigh Brown, A., Oct 2009, In : Journal of Virology. 83, 19, p. 9901-9910 10 p.

    Research output: Contribution to journalArticle

  52. Molecular Phylodynamics of the Heterosexual HIV Epidemic in the United Kingdom

    Hughes, G. J., Fearnhill, E., Dunn, D., Lycett, S. J., Rambaut, A. & Leigh Brown, A. J., Sep 2009, In : Plos pathogens. 5, 9, 8 p., e1000590.

    Research output: Contribution to journalArticle

  53. An Evolutionary Model-Based Algorithm for Accurate Phylogenetic Breakpoint Mapping and Subtype Prediction in HIV-1

    Pond, S. L. K., Posada, D., Stawiski, E., Chappey, C., Poon, A. F. Y., Hughes, G., Fearnhill, E., Gravenor, M. B., Leigh Brown, A. J. & Frost, S. D. W., 2009, In : PLoS Computational Biology. 5, 11, p. 1-21 21 p., e1000581.

    Research output: Contribution to journalArticle

  54. 2008
  55. A maximum likelihood method for detecting directional evolution in protein sequences and its application to influenza a virus

    Pond, S. L. K., Poon, A. F. Y., Leigh Brown, A. J. & Frost, S. D. W., Oct 2008, In : Molecular Biology and Evolution. 25, 9, p. 1809-1824 16 p.

    Research output: Contribution to journalArticle

  56. Genetic basis of variation in tenofovir drug susceptibility in HIV-1

    Murray, R. J., Lewis, F. I., Miller, M. D. & Leigh Brown, A. J., Jun 2008, In : AIDS. 22, 10, p. 1113-1123 11 p.

    Research output: Contribution to journalArticle

  57. Episodic sexual transmission of HIV revealed by molecular phylodynamics

    Lewis, F., Hughes, G. J., Rambaut, A., Pozniak, A. & Leigh Brown, A. J., Mar 2008, In : PLOS Medicine. 5, 3, p. 0392-0402 11 p., e50.

    Research output: Contribution to journalArticle

  58. Estimating selection pressures on HIV-1 using phylogenetic likelihood models

    Pond, S. L. K., Poon, A. F. Y., Zarate, S., Smith, D. M., Little, S. J., Pillai, S. K., Ellis, R. J., Wong, J. K., Leigh Brown, A., Richman, D. D. & Frost, S. D. W., 2008, In : STATISTICS IN MEDICINE. 27, 23, SI, p. 4779-4789 11 p.

    Research output: Contribution to journalArticle

  59. 2007
  60. Adaptation to human populations is revealed by within-host polymorphisms in HIV-1 and hepatitis C virus

    Poon, A. F. Y., Pond, S. L. K., Bennett, P., Richman, D. D., Leigh Brown, A. J. & Frost, S. D. W., Apr 2007, In : Plos pathogens. 3, 3

    Research output: Contribution to journalArticle

  61. Evidence of a decline in transmitted HIV-1 drug resistance in the United Kingdom

    Burns, S., Cameron, S., Cane, P., Down, P., Chrystie, I., Churchill, D., Delpech, V., Pillay, D., Dunn, D., Fearnhill, E., Green, H., Porter, K., Easterbrook, P., Zuckerman, M., Geretti, A. M., Gifford, R., Kellam, P., Phillips, A., Sabin, C., Goldberg, D. & 32 others, Gompels, M., Hale, A., Kaye, S., Leigh Brown, A., Orkin, C., Pozniak, A., Robb, G., Smit, E., Tilston, P., Williams, I., Ainsworth, J., Anderson, J., Babiker, A., Fisher, M., Gazzard, B., Gilson, R., Hill, T., Johnson, M., Leen, C., Sadiq, T., Schwenk, A., Walsh, J., Brettle, R., Darbyshire, J., Fidler, S., Hawkins, D., Jaffe, H., Johnson, A., McLean, K., Resistance, UK. C. G. HIV. D., Comm, UK. CHIC. S. & Ste, UK. R. HIV. S., 2007, In : AIDS. 21, 8, p. 1035-1039 5 p.

    Research output: Contribution to journalArticle

  62. HIV phylogenetics: Criminal convictions relying solely on this to establish transmission are unsafe

    Pillay, D., Rambaut, A., Geretti, A. M. & Leigh Brown, A. J., 2007, In : BMJ. 335, 7618, p. 460-461 2 p.

    Research output: Contribution to journalArticle

  63. 2006
  64. Adaptation to Different Human Populations by HIV-1 Revealed by Codon-Based Analyses

    Kosakovsky Pond, S. L., Frost, S. D. W., Grossman, Z., Gravenor, M. B., Richman, D. D. & Leigh Brown, A. J., Jun 2006, In : PLoS Computational Biology. 2, 6, p. 530-538 9 p., e62.

    Research output: Contribution to journalArticle

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