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Department of Pathology

I am interested in viruses of global health significance. I have studied within-host evolution of both HIV-1 and SARS-CoV-2. In HIV-1, I have been particularly interested in independent replication of the virus in the central nervous system (CNS) and characterising the genotypic and phenotypic properties of these CNS viruses. To do this I set up a clinical cohort study of HIV-1 positive patients with mild-moderate neurocognitive disorder at the Africa Health Research Institute in Durban, South Africa. In addition, I have worked collaboratively with the Malawi-Liverpool Wellcome Trust and have access to over 100 paired plasma and cerebrospinal fluid (CSF) samples. I discovered that although CSF escape is uncommon, genetically distinct, independently replicating viral populations can be found in the CSF. These viruses have adapted to the constraints of the niche in which they find themselves, for example, I found that there is heterogeneity of broadly neutralising antibody activity and affinity for CCR5 coreceptors in these viruses compared with plasma-derived virus.
In SARS-CoV-2, I have studied virus diversity within a chronically infected patient by NGS and discovered that the intrahost viral evolution was driven by immune escape from neutralising antibodies in the absence of adequate B and T cell responses. This not only provided insights into the dynamic evolution of a virus thought to be slowly evolving on a population level, but turned out to be the blueprint for emergence of virus variants that threaten the success of vaccines and longer term control of the pandemic.
Central nervous system escape


Key publications: 

• Collier, D. A.*, I. A. T. M. Ferreira, P. Kotagiri, R. Datir, E. Lim, E. Touizer, B. Meng, A. Abdullahi, S.Baker, G. Dougan, C. Hess, N. Kingston, P. J. Lehner, P. A. Lyons, N. J. Matheson, W. H. Owehand, C.Saunders, C. Summers, J. E. D. Thaventhiran, M. Toshner, M. P. Weekes, P. Maxwell, A. Shaw, A. Bucke, J. Calder, L. Canna, J. Domingo, A. Elmer, S. Fuller, J. Harris, S. Hewitt, J. Kennet, S. Jose, J. Kourampa, A. Meadows, C. O’Brien, J. Price, C. Publico, R. Rastall, C. Ribeiro, J. Rowlands, V. Ruffolo, H. Tordesillas, B. Bullman, B. J. Dunmore, S. Fawke, S. Gräf, J. Hodgson, C. Huang, K. Hunter, E. Jones, E. Legchenko, C. Matara, J. Martin, F. Mescia, C. O’Donnell, L. Pointon, N. Pond, J. Shih, R. Sutcliffe, T. Tilly, C. Treacy, Z. Tong, J. Wood, M. Wylot, L. Bergamaschi, A. Betancourt, G. Bower, C. Cossetti, A. De Sa, M. Epping, S. Fawke, N. Gleadall, R. Grenfell, A. Hinch, O. Huhn, S. Jackson, I. Jarvis, B. Krishna, D. Lewis, J. Marsden, F. Nice, G. Okecha, O. Omarjee, M. Perera, M. Potts, N. Richoz, V. Romashova, N. S. Yarkoni, R. Sharma, L. Stefanucci, J. Stephens, M. Strezlecki, L. Turner, E. M. D. D. De Bie, K. Bunclark, M. Josipovic, M. Mackay, S. Rossi, M. Selvan, S. Spencer, C. Yong, A. Ansaripour, A. Michael, L. Mwaura, C. Patterson, G. Polwarth, P. Polgarova, G. di Stefano, C. Fahey, R. Michel, S.-H. Bong, J. D. Coudert, E. Holmes, J. Allison, H. Butcher, D. Caputo, D. Clapham-Riley, E. Dewhurst, A. Furlong, B. Graves, J. Gray, T. Ivers, M. Kasanicki, E. Le Gresley, R. Linger, S. Meloy, F. Muldoon, N. Ovington, S. Papadia, I. Phelan, H. Stark, K.E. Stirrups, P. Townsend, N. Walker, J. Webster, A. Elmer, N. Kingston, B. Graves, E. Le Gresley, D. Caputo, L. Bergamaschi, K. G. C. Smith, J. R. Bradley, L. Ceron-Gutierrez, P. Cortes-Acevedo, G. Barcenas-Morales, M. A. Linterman, L. McCoy, C. Davis, E. Thomson, P. A. Lyons, E. McKinney, R. Doffinger, M. Wills, R. K. Gupta, Citiid-Nihr Covid BioResource Collaboration. Age-related immune response heterogeneity to SARS-CoV-2 vaccine BNT162b2. Nature 596, 417–422 (2021).

• Collier DA*, De Marco A, Ferreira IATM, Meng B, Datir RP, Walls AC, Kemp SA, Bassi J, Pinto D, Silacci-Fregni C, Bianchi S, Tortorici MA, Bowen J, Culap K, Jaconi S, Cameroni E, Snell G, Pizzuto MS, Pellanda, AF, Garzoni C, Riva A; CITIID-NIHR BioResource COVID-19 Collaboration, Elmer A, Kingston N, Graves B, McCoy LE, Smith KGC, Bradley JR, Temperton N, Ceron-Gutierrez L, Barcenas-Morales G; COVID-19 Genomics UK (COG-UK) Consortium, Harvey W, Virgin HW, Lanzavecchia A, Piccoli L, Doffinger R, Wills, M, Veesler D, Corti D, Gupta RK. Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies. Nature 593, 136–141 (2021).

• Kemp, S. A., Collier, D. A.*, Datir, R. P., Ferreira, I.A.T.M., Gayed, S., Jahun, A., Hosmillo, M., Rees-Spear, C., Mlcochova, P., Lumb, I. U., Roberts, D. J., Chandra, A., Temperton, N., Sharrocks, K., Blane, E., Modis, Y., Leigh, K. E., Briggs, J. A. G., van Gils, M. J., Smith, K. G. C., Bradley, J. R., Smith, C., Doffinger, R., Ceron-Gutierrez, L., Barcenas-Morales, G., Pollock, D. D., Goldstein, R. A., Smielewska, A., Skittrall, J. P., Gouliouris, T., Goodfellow, I. G., Gkrania-Klotsas, E., Illingworth, C. J. R., McCoy, L. E., Gupta, R. K. SARS-CoV-2 evolution during treatment of chronic infection. Nature. 2021;592(7853):277-82. • Collier, D. A*, Assennato, S. M, Warne, B, Sithole, N, Sharrocks, K, Ritchie, A, Ravji, P, Routledge, M, Sparkes, D, Skittrall, J, Smielewska, A, Ramsey, I, Goel, N, Curran, M, Enoch, D, Tassell, R, Lineham, M, Vaghela, D, Leong, C, Mok, H. P, Bradley, J, Smith, K. G. C, Mendoza, V, Demiris, N, Besser, M, Dougan, G, Lehner, P. J, Siedner, M. J, Zhang, H, Waddington, C. S, Lee, H, Gupta, R. K, Citiid-Nihr Covid BioResource Collaboration. Point of Care Nucleic Acid Testing for SARS-CoV-2 in Hospitalized Patients: A Clinical Validation Trial and Implementation Study. Cell Rep Med. 2020;1(5):100062.

• Collier DA*, Haddow L, Brijkumar J, Moosa MS, Benjamin L, Gupta RK. HIV Cerebrospinal Fluid Escape and Neurocognitive Pathology in the Era of Combined Antiretroviral Therapy: What Lies Beneath the Tip of the Iceberg in Sub-Saharan Africa? Brain Sci. 2018;8(10).

• Kugathasan R, Collier DA*, Haddow LJ, El Bouzidi K, Edwards SG, Cartledge JD, Miller RF, Gupta RK. Diffuse White Matter Signal Abnormalities on Magnetic Resonance Imaging Are Associated With Human Immunodeficiency Virus Type 1 Viral Escape in the Central Nervous System Among Patients With Neurological Symptoms. Clin Infect Dis. 2017;64(8):1059-65.

Other publications: 

• Collier, D., et al., HIV escape and resistance in the central nervous system in treatment experienced South Africans. medRxiv, 2023: p. 2023.03.03.23286708.

• Collier, D. A.*, R. Bousfiled, E. Gkrania-Klotsas, R. Gupta. Point of care SARS-CoV-2 nucleic acid testing in schools improves school attendance. Wellcome Open Res. 2022; 7: 8.

• Mlcochova, P., S. A. Kemp, M. S. Dhar, G. Papa, B. Meng, I. A. T. M. Ferreira, R. Datir, D. A. Collier*, A. Albecka, S. Singh, R. Pandey, J. Brown, J. Zhou, N. Goonawardane, S. Mishra, C. Whittaker, T. Mellan, R. Marwal, M. Datta, S. Sengupta, K. Ponnusamy, V. S. Radhakrishnan, A. Abdullahi, O. Charles, P. Chattopadhyay, P. Devi, D. Caputo, T. Peacock, C. Wattal, N. Goel, A. Satwik, R. Vaishya, M. Agarwal, The Indian SARS-CoV-2 Genomics Consortium (INSACOG), The Genotype to Phenotype Japan (G2P-Japan) Consortium, The CITIID-NIHR BioResource COVID-19 Collaboration, A. Mavousian, J. H Lee, J. Bassi, C. Silacci-Fegni, C. Saliba, D. Pinto, T. Irie, I. Yoshida, W. L. Hamilton, K. Sato, S. Bhatt, S. Flaxman, L. C. James, D. Corti, L. Piccoli, W. S. Barclay, P. Rakshit, A. Agrawal, R. K. Gupta. SARS-CoV-2 B.1.617.2 Delta variant replication and immune evasion. Nature 599, 114–119 (2021).

• Meng, B., S. A. Kemp, G. Papa, R. Datir, I. A. T. M. Ferreira, S. Marelli, W. T. Harvey, S. Lytras, A. Mohamed, G. Gallo, N. Thakur, D. A. Collier*, P. Mlcochova, The COVID-19 Genomics UK (COG-UK) Consortium and Gupta, R.K. Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7. Cell Rep. 2021:109292.

• Mlcochova, P., D. Collier*, A. Ritchie, S. M. Assennato, M. Hosmillo, N. Goel, B. Meng, K. Chatterjee, V. Mendoza, N. Temperton, L. Kiss, L. C. James, K. A. Ciazynska, X. Xiong, J. A. G. Briggs, J. A. Nathan, F. Mescia, L. Bergamaschi, H. Zhang, P. Barmpounakis, N. Demeris, R. Skells, P. A. Lyons, J. Bradley, S. Baker, J. P. Allain, K. G. C. Smith, R. Bousfield, M. Wilson, D. Sparkes, G. Amoroso, E. Gkrania-Klotsas, S. Hardwick, A. Boyle, I. Goodfellow, R. K. Gupta and Citiid-Nihr Covid BioResource Collaboration. Combined Point-of-Care Nucleic Acid and Antibody Testing for SARS-CoV-2 following Emergence of D614G Spike Variant. Cell Rep Med. 2020;1(6):100099.

• Saunders, M. J., M. A. Tovar, D. Collier*, M. R. Baldwin, R. Montoya, T. R. Valencia, R. H. Gilman and C. A. Evans. Active and passive case-finding in tuberculosis-affected households in Peru: a 10-year prospective cohort study. The Lancet Infectious Diseases, Volume 19, Issue 5, 519–528, MAY 01, 2019

• Collier DA*, Monit C, Gupta RK. The Impact of HIV-1 Drug Escape on the Global Treatment Landscape. Cell Host Microbe. 2019;26(1):48-60.

Clinical Lecturer in Medical Virology
Not available for consultancy