• Mark Tsz Kin Cheng, Mazharul Altaf, Jesu Castin, Ann-Kathrin Reuschl, Benjamin L Sievers, Kimia Kamelian, Dejan Mesner, Rebecca B Morse, Adam Abdullahi, Bo Meng, Kata Csiba; Cambridge NIHR Bioresource - The members of CITIID-NIHR BioResource COVID-19 Collaboration , Steven A Kemp, Darren P Martin, Clare Jolly, Christopher Ruis, Lipi Thukral, Ravindra K Gupta. Signatures of omicron-like adaptation in early SARS-CoV-2 variants and chronic infection. Cell Rep. 2025 Aug 26;44(8):116135. doi: 10.1016/j.celrep.2025.116135. Epub 2025 Aug 13.

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• Omolara O Baiyegunhi, Kensane Mthembu, Ann-Kathrin Reuschl, Doty Ojwach, Omotayo Farinre, Murunwa Maimela, Sheila Balinda, Matt Price, Madeleine J Bunders, Marcus Altfeld, Clare Jolly, Jaclyn Mann, Thumbi Ndung'u. HIV-1 Gag-protease-driven replicative capacity influences T-cell metabolism, cytokine induction, and viral cell-to-cell spread. 2025 Apr 9;16(4):e0356524. doi: 10.1128/mbio.03565-24. Epub 2025 Feb 25.

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• Lydia S Newton, Clara Gathmann, Sophie Ridewood, Robert J Smith, Andre J Wijaya, Thomas W Hornsby, Kate L Morling, Dara Annett, Riccardo Zenezini Chiozzi, Ann-Kathrin Reuschl, Morten L Govasli, Ying Ying Tan, Lucy G Thorne, Clare Jolly, Konstantinos Thalassinos, Alessio Ciulli, Greg J Towers, David L Selwood. Macrocycle-based PROTACs selectively degrade cyclophilin A and inhibit HIV-1 and HCV. Nat Commun. 2025 Feb 10;16(1):1484. doi: 10.1038/s41467-025-56317-8.

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• Ann-Kathrin Reuschl, Lucy G Thorne, Matthew V X Whelan, Roberta Ragazzini, Wilhelm Furnon, Vanessa M Cowton, Giuditta De Lorenzo, Dejan Mesner, Jane L E Turner, Giulia Dowgier, Nathasha Bogoda, Paola Bonfanti, Massimo Palmarini, Arvind H Patel, Clare Jolly, Greg J Towers. Evolution of enhanced innate immune suppression by SARS-CoV-2 Omicron subvariants. Nat Microbiol. 2024 Feb;9(2):451-463. doi: 10.1038/s41564-023-01588-4. Epub 2024 Jan 16.

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• Mehdi Bouhaddou, Ann-Kathrin Reuschl, Benjamin J Polacco, Lucy G Thorne, Manisha R Ummadi, Chengjin Ye, Romel Rosales, Adrian Pelin, Jyoti Batra, Gwendolyn M Jang, Jiewei Xu, Jack M Moen, Alicia L Richards, Yuan Zhou, Bhavya Harjai, Erica Stevenson, Ajda Rojc, Roberta Ragazzini, Matthew V X Whelan, Wilhelm Furnon, Giuditta De Lorenzo, Vanessa Cowton, Abdullah M Syed, Alison Ciling, Noa Deutsch, Daniel Pirak, Giulia Dowgier, Dejan Mesner, Jane L Turner, Briana L McGovern, M Luis Rodriguez, Rocio Leiva-Rebollo, Alistair S Dunham, Xiaofang Zhong, Manon Eckhardt, Andrea Fossati, Nicholas F Liotta, Thomas Kehrer, Anastasija Cupic, Magdalena Rutkowska, Ignacio Mena, Sadaf Aslam, Alyssa Hoffert, Helene Foussard, Charles Ochieng' Olwal, Weiqing Huang, Thomas Zwaka, John Pham, Molly Lyons, Laura Donohue, Aliesha Griffin, Rebecca Nugent, Kevin Holden, Robert Deans, Pablo Aviles, Jose A Lopez-Martin, Jose M Jimeno, Kirsten Obernier, Jacqueline M Fabius, Margaret Soucheray, Ruth Hüttenhain, Irwin Jungreis, Manolis Kellis, Ignacia Echeverria, Kliment Verba, Paola Bonfanti, Pedro Beltrao, Roded Sharan, Jennifer A Doudna, Luis Martinez-Sobrido, Arvind H Patel, Massimo Palmarini, Lisa Miorin, Kris White, Danielle L Swaney, Adolfo Garcia-Sastre, Clare Jolly, Lorena Zuliani-Alvarez, Greg J Towers, Nevan J Krogan. SARS-CoV-2 variants evolve convergent strategies to remodel the host response. Cell. 2023 Oct 12;186(21):4597-4614.e26. doi: 10.1016/j.cell.2023.08.026. Epub 2023 Sep 21.

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• Dejan Mesner, Ann-Kathrin Reuschl, Matthew V X Whelan, Taylor Bronzovich, Tafhima Haider, Lucy G Thorne, Roberta Ragazzini, Paola Bonfanti, Greg J Towers, Clare Jolly. SARS-CoV-2 evolution influences GBP and IFITM sensitivity. Proc Natl Acad Sci U S A. 2023 Jan 31;120(5):e2212577120. doi: 10.1073/pnas.2212577120. Epub 2023 Jan 24.

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• Ann-Kathrin Reuschl, Dejan Mesner, Maitreyi Shivkumar, Matthew V X Whelan, Laura J Pallett, José Afonso Guerra-Assunção, Rajhmun Madansein, Kaylesh J Dullabh, Alex Sigal, John P Thornhill, Carolina Herrera, Sarah Fidler, Mahdad Noursadeghi, Mala K Maini, Clare Jolly. HIV-1 Vpr drives a tissue residency-like phenotype during selective infection of resting memory T cells. Cell Rep 2022 Apr 12;39(2):110650. doi: 10.1016/j.celrep.2022.110650.

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• Lucy G Thorne, Mehdi Bouhaddou, Ann-Kathrin Reuschl, Lorena Zuliani-Alvarez, Ben Polacco, Adrian Pelin, Jyoti Batra, Matthew V X Whelan, Myra Hosmillo, Andrea Fossati, Roberta Ragazzini, Irwin Jungreis, Manisha Ummadi, Ajda Rojc, Jane Turner, Marie L Bischof, Kirsten Obernier, Hannes Braberg, Margaret Soucheray, Alicia Richards, Kuei-Ho Chen, Bhavya Harjai, Danish Memon, Joseph Hiatt, Romel Rosales, Briana L McGovern, Aminu Jahun, Jacqueline M Fabius, Kris White, Ian G Goodfellow, Yasu Takeuchi, Paola Bonfanti, Kevan Shokat, Natalia Jura, Klim Verba, Mahdad Noursadeghi, Pedro Beltrao, Manolis Kellis, Danielle L Swaney, Adolfo García-Sastre, Clare Jolly, Greg J Towers, Nevan J Krogan. Evolution of enhanced innate immune evasion by SARS-CoV-2. Nature 2021 Dec 23. doi: 10.1038/s41586-021-04352-y.

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• Tafhima Haider, Xenia Snetkov, Clare Jolly. HIV envelope tail truncation confers resistance to SERINC5 restriction. Proc Natl Acad Sci U S A. 2021 May 25;118(21):e2101450118. doi: 10.1073/pnas.2101450118.

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• Nathalie M Schmidt, Peter A C Wing, Mariana O Diniz, Laura J Pallet, Leo Swadling, James M Harris, Alice R Burton, Anna Jeffery-Smith, Nekisa Zakeri, Oliver E Amin, Stephanie Kucykowicz, Mirjam H Heemskerk, Brian Davidson, Tim Meyer, Joe Grove, Hans J Stauss, Ines Pineda-Torra, Clare Jolly, Elizabeth C Jury, Jane A McKeating, Mala K Maini. Targeting human Acyl-CoA:cholesterol acyltransferase as a dual viral and T cell metabolic checkpoint. Nat Commun. 2021 May 14;12(1):2814.doi: 10.1038/s41467-021-22967-7.

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• Jenny O'Nions, Luke Muir, Jiexin Zheng, Chloe Rees-Spear, Annachiara Rosa, Christopher Earl, Peter Cherepanov, Rajeev Gupta, Asim Khwaja, Clare Jolly, Laura E McCoy 'SARS-CoV-2 antibody responses in patients with aggressive haematological malignancies' Leukemia. 2021 Jan;35(1):289-292. doi: 10.1038/s41375-020-01103-2. Epub 2020 Dec 9

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• Mesner D, Hotter D, Kirchhoff F, Jolly C. Loss of Nef-mediated CD3 down-regulation in the HIV-1 lineage increases viral infectivity and spread. Proc Natl Acad Sci U S A. 2020 Mar 31;117(13):7382-7391. doi: 10.1073/pnas.1921135117. Epub 2020 Mar 16.

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• Titanji BK., Pillay D., and Jolly C. (2017). Combination antiretroviral therapy and cell-cell spread of wild-type and drug-resistant human immunodeficiency virusu-1. Journal of General Virology 98: 821-834.

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• Len AC., Starling S., Shivkumar M. and Jolly C. (2017) HIV-1 activates signaling independently of antigen to drive viral spread. Cell Reports 18: 1062-1074.

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• Starling S, Jolly C. LFA-1 Engagement Triggers T Cell Polarization at the HIV-1 Virological Synapse. J Virol. 2016 Nov 1;90(21):9841-9854. PubMed PMID: 27558417.

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• Zhang C., Zhou S., Groppelli E., Pellegrino P., Williams I., Borrow P., Chain B. and Jolly C. (2015) Hybrid spreading mechanisms and T cell activation shape the dynamics of HIV-1 infection. PloS Computational Biology. 11:e1004179

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• Groppelli E., Starling S. and Jolly C. (2015) Contact-induced mitochondria polarization supports HIV-1 virological synapse formation. Journal of Virology. 89: 14-24.

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• Groppelli E., Len A., Granger L., and Jolly C. (2014) Retromer regulates HIV-1 envelope glycoprotein trafficking and incorporation into virions. PLoS Pathogens 10:e1004518

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• McCoy L., Groppelli E., Blanchetot C., de Haard H., Verrips T., Rutten L., Weiss R. and Jolly C. (2014) Neutralisation of HIV-1 cell-cell spread by human and llama antibodies Retrovirology 11:83.

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• Titanji B., Aasa-Chapman M., Pillay D. and Jolly C. (2013) Protease inhibitors effectively block cell-to-cell spread of HIV-1 between T cells. Retrovirology 10: 161.

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• Wei B., Han L., Abbink T., Groppelli E., Lim D., Thaker Y., Gao W., Zhai R., Wang J., Lever A., Jolly C., Wang H. and Rudd C. (2013) Immune adaptor ADAP in T cells regulates HIV-1 transcription and cell-cell viral spread via different co-receptors. Retrovirology 10:101

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• Jolly C., Welsch S., Michor S. and Sattentau Q. (2011) The regulated secretory pathway in CD4+ T cells contributes to Human Immunodeficiency Virus type-1 cell-to-cell spread at the virological synapse. PLoS Pathogens 7, e10022226.

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• Zhou L., Sokolskaja E., Jolly C., James W., Cowley S. and Fassati A. (2011) Transportin 3 promotes a nuclear maturation step required for efficient HIV-1 integration. PLoS Pathogens 7, e1002194

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• Jolly C. (2011) Cell-to-Cell transmission of retroviruses: Innate immunity and interferon induced restriction factors. Virology 411: 251-259

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• Jolly C. (2011) T cell polarization at the Virological Synapse. Viruses 2: 1261-1278

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• Jolly C., Booth N. and Neil S. (2010) Cell-cell spread of human immunodeficiency virus type-1 overcomes tetherin/BST-2 mediated restriction in T cells. Journal of Virology 84: 12185-99

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• Gonzalez N., Bermejo M., Calinge E., Jolly C., Arenzana-Seisdedos F., Pablos J., Sattentau Q.J., Alcami J. (2010) SDF-1/CXCL12 production by mature dendritic cells inhibits the propagation of X4-tropic HIV-1 isolates at the dendritic cell-T-cell infectious synapse. Journal of Virology 84: 4341-51

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• Martin N., Welsch S., Jolly C., Briggs J., Vaux D., and Sattentau Q. (2010) Virological synapse-mediated spread of Human Immunodeficiency Virus Type-1 between T cells is sensitive to entry inhibition. Journal of Virology 84: 3516-27

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• Sowinski S., Jolly C., Berninghausen O., Purboo M., Chauveau A., Kohler K., Oddos S., Eissmann P., Brodsky F., Hopkins C., Onfelt B., Sattentau Q. and Davis D. (2008) Membrane nanotubes physically connect T cells over long distances presenting a novel route for HIV-1 transmission. Nature Cell Biology 10: 211-9

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• Jolly C., and Sattentau Q.J. (2007) Regulated secretion from CD4+ T cells. Trends in Immunology 28: 474-81

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• Jolly C., Mitar I., and Sattentau Q. (2007) Adhesion molecule interactions facilitate human immunodeficiency type-1 induced virological synapse formation between T cells. Journal of Virology 81: 13916-21

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• Jolly C., and Sattentau Q. (2007) Human immunodeficiency type-1 assembly, budding and cell-cell spread in T cells takes place in tetraspanin-enriched plasma membrane domains. Journal of Virology 81: 7873-84

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• Jolly C., Mitar I., and Sattentau Q. (2007) Requirement for an intact T-cell actin and tubulin cytoskeleton for efficient assembly and cell-cell spread of Human Immunodeficiency Virus Type-1. Journal of Virology 81:5547-60

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• Jolly C., and Sattentau Q. (2005) Human Immunodeficiency Virus type-1 virological synapse formation in T cells requires lipid raft integrity. Journal of Virology 79: 12088-94

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• Jolly C., Kashefi K., Hollinshead M., and Sattentau Q. (2004) HIV-1 cell to cell transfer across an Env-induced, actin-dependent synapse. Journal of Experimental Medicine 199: 283-93.