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42 results on '"Ansari, M. Azim"'

1. Sustained aviremia despite anti-retroviral therapy non-adherence in male children after in utero HIV transmission

Author: Bengu, Nomonde, Cromhout, Gabriela, Adland, Emily, Govender, Katya, Herbert, Nicholas, Lim, Nicholas, Fillis, Rowena, Sprenger, Kenneth, Vieira, Vinicius, Kannie, Samantha, van Lobenstein, Jeroen, Chinniah, Kogielambal, Kapongo, Constant, Bhoola, Roopesh, Krishna, Malini, Mchunu, Noxolo, Pascucci, Giuseppe Rubens, Cotugno, Nicola, Palma, Paolo, Tagarro, Alfredo, Rojo, Pablo, Roider, Julia, Garcia-Guerrero, Maria C., Ochsenbauer, Christina, Groll, Andreas, Reddy, Kavidha, Giaquinto, Carlo, Rossi, Paolo, Hong, Seohyun, Dong, Krista, Ansari, M. Azim, Puertas, Maria C., Ndung’u, Thumbi, Capparelli, Edmund, Lichterfeld, Mathias, Martinez-Picado, Javier, Kappes, John C., Archary, Moherndran, and Goulder, Philip
Published: 2024
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2. HepFREEPak: protocol for a multi-centre, prospective observational study examining efficacy and impact of current therapies for the treatment of hepatitis C in Pakistan and reporting resistance to antiviral drugs: study protocol

Author: Arif, Ambreen, Hasnain, Aliya, Chaudhry, Auj, Asim, Muhammad, Shafqat, Muhammad Nabeel, Altaf, Abeer, Saba, Noor, Kemos, Polychronis, Ansari, M. Azim, Barnes, Eleanor, Metcalfe, Chris, Vickerman, Peter, Qureshi, Huma, Hamid, Saeed, Choudhry, Asad Ali, Niaz, Saad Khalid, Foster, Graham R., and Choudhry, Naheed
Published: 2023
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3. Genotyping and population characteristics of the China Kadoorie Biobank

Author: Walters, Robin G., Millwood, Iona Y., Lin, Kuang, Schmidt Valle, Dan, McDonnell, Pandora, Hacker, Alex, Avery, Daniel, Edris, Ahmed, Fry, Hannah, Cai, Na, Kretzschmar, Warren W., Ansari, M. Azim, Lyons, Paul A., Collins, Rory, Donnelly, Peter, Hill, Michael, Peto, Richard, Shen, Hongbing, Jin, Xin, Nie, Chao, Xu, Xun, Guo, Yu, Yu, Canqing, Lv, Jun, Clarke, Robert J., Li, Liming, and Chen, Zhengming
Published: 2023
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4. Sustained aviraemia despite anti-retroviral therapy non-adherence in male children following in utero hiv transmission

Author: Bengu, Nomonde, primary, Cromhout, Gabriela, additional, Adland, Emily, additional, Govender, Katya, additional, Herbert, Nicholas, additional, Lim, Nicholas, additional, Fillis, Rowena, additional, Sprenger, Kenneth, additional, Vieira, Vinicius, additional, Kannie, Samantha, additional, van Lobenstein, Jeroen, additional, Chinniah, Kogielambal, additional, Kapongo, Constant, additional, Bhoola, Roopesh, additional, Krishna, Malini, additional, Mchunu, Noxolo, additional, Pascucci, Giuseppe Rubens, additional, Cotugno, Nicola, additional, Palma, Paolo, additional, Tagarro, Alfredo, additional, Rojo, Pablo, additional, Roider, Julia, additional, Garcia-Guerrero, Maria C., additional, Ochsenbauer, Christina, additional, Groll, Andreas, additional, Reddy, Kavidha, additional, Giaquinto, Carlo, additional, Rossi, Paolo, additional, Hong, Seohyun, additional, Dong, Krista, additional, Ansari, M. Azim, additional, Puertas, Maria C., additional, Ndung’u, Thumbi, additional, Capparelli, Edmund, additional, Lichterfeld, Mathias, additional, Martinez-Picado, Javier, additional, Kappes, John C., additional, Archary, Moherndran, additional, and Goulder, Philip, additional
Published: 2024
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5. Constructing custom-made radiotranscriptomic signatures of vascular inflammation from routine CT angiograms: a prospective outcomes validation study in COVID-19

Author: Ahern, David J, Ai, Zhichao, Ainsworth, Mark, Allan, Chris, Allcock, Alice, Angus, Brian, Ansari, M Azim, Arancibia-Cárcamo, Carolina, Aschenbrenner, Dominik, Attar, Moustafa, Baillie, J Kenneth, Barnes, Eleanor, Bashford-Rogers, Rachael, Bashyal, Archana, Beer, Sally, Berridge, Georgina, Beveridge, Amy, Bibi, Sagida, Bicanic, Tihana, Blackwell, Luke, Bowness, Paul, Brent, Andrew, Brown, Andrew, Broxholme, John, Buck, David, Burnham, Katie, Byrne, Helen, Camara, Susana, Ferreira, Ivan Candido, Charles, Philip, Chen, Wentao, Chen, Yi-Ling, Chong, Amanda, Clutterbuck, Elizabeth, Coles, Mark, Conlon, Christopher, Cornall, Richard, Cribbs, Adam, Curion, Fabiola, Davenport, Emma, Davidson, Neil, Davis, Simon, Dendrou, Calliope, Dequaire, Julie, Dib, Lea, Docker, James, Dold, Christina, Dong, Tao, Downes, Damien, Drakesmith, Hal, Dunachie, Susanna, Duncan, David, Eijsbouts, Chris, Esnouf, Robert, Espinosa, Alexis, Etherington, Rachel, Fairfax, Benjamin, Fairhead, Rory, Fang, Hai, Fassih, Shayan, Felle, Sally, Fernandez Mendoza, Maria, Ferreira, Ricardo, Fischer, Roman, Foord, Thomas, Forrow, Aden, Frater, John, Fries, Anastasia, Gallardo Sanchez, Veronica, Garner, Lucy, Geeves, Clementine, Georgiou, Dominique, Godfrey, Leila, Golubchik, Tanya, Gomez Vazquez, Maria, Green, Angie, Harper, Hong, Harrington, Heather, Heilig, Raphael, Hester, Svenja, Hill, Jennifer, Hinds, Charles, Hird, Clare, Ho, Ling-Pei, Hoekzema, Renee, Hollis, Benjamin, Hughes, Jim, Hutton, Paula, Jackson-Wood, Matthew, Jainarayanan, Ashwin, James-Bott, Anna, Jansen, Kathrin, Jeffery, Katie, Jones, Elizabeth, Jostins, Luke, Kerr, Georgina, Kim, David, Klenerman, Paul, Knight, Julian, Kumar, Vinod, Kumar Sharma, Piyush, Kurupati, Prathiba, Kwok, Andrew, Lee, Angela, Linder, Aline, Lockett, Teresa, Lonie, Lorne, Lopopolo, Maria, Lukoseviciute, Martyna, Luo, Jian, Marinou, Spyridoula, Marsden, Brian, Martinez, Jose, Matthews, Philippa, Mazurczyk, Michalina, McGowan, Simon, McKechnie, Stuart, Mead, Adam, Mentzer, Alexander, Mi, Yuxin, Monaco, Claudia, Montadon, Ruddy, Napolitani, Giorgio, Nassiri, Isar, Novak, Alex, O'Brien, Darragh, O'Connor, Daniel, O'Donnell, Denise, Ogg, Graham, Overend, Lauren, Park, Inhye, Pavord, Ian, Peng, Yanchun, Penkava, Frank, Pereira Pinho, Mariana, Perez, Elena, Pollard, Andrew, Powrie, Fiona, Psaila, Bethan, Quan, T Phuong, Repapi, Emmanouela, Revale, Santiago, Silva-Reyes, Laura, Richard, Jean-Baptiste, Rich-Griffin, Charlotte, Ritter, Thomas, Rollier, Christine, Rowland, Matthew, Ruehle, Fabian, Salio, Mariolina, Sansom, Stephen Nicholas, Sanches Peres, Raphael, Santos Delgado, Alberto, Sauka-Spengler, Tatjana, Schwessinger, Ron, Scozzafava, Giuseppe, Screaton, Gavin, Seigal, Anna, Semple, Malcolm, Sergeant, Martin, Simoglou Karali, Christina, Sims, David, Skelly, Donal, Slawinski, Hubert, Sobrinodiaz, Alberto, Sousos, Nikolaos, Stafford, Lizzie, Stockdale, Lisa, Strickland, Marie, Sumray, Otto, Sun, Bo, Taylor, Chelsea, Taylor, Stephen, Taylor, Adan, Thongjuea, Supat, Thraves, Hannah, Todd, John, Tomic, Adriana, Tong, Orion, Trebes, Amy, Trzupek, Dominik, Tucci, Felicia Anna, Turtle, Lance, Udalova, Irina, Uhlig, Holm, van Grinsven, Erinke, Vendrell, Iolanda, Verheul, Marije, Voda, Alexandru, Wang, Guanlin, Wang, Lihui, Wang, Dapeng, Watkinson, Peter, Watson, Robert, Weinberger, Michael, Whalley, Justin, Witty, Lorna, Wray, Katherine, Xue, Luzheng, Yuen Yeung, Hing, Yin, Zixi, Young, Rebecca, Youngs, Jonathan, Zhang, Ping, Zurke, Yasemin-Xiomara, Banning, Adrian, Antonopoulos, Alexios, Bajaj, Amrita, Kelion, Andrew, Deshpande, Aparna, Kardos, Attila, Hudson, Benjamin, Koo, Bon-Kwon, Shirodaria, Cheerag, Xie, Cheng, Kotanidis, Christos, Mahon, Ciara, Berry, Colin, Adlam, David, Newby, David, Connolly, Derek, Scaletta, Diane, Alexander, Donna, Nicol, Ed, McAlindon, Elisa, Oikonomou, Evangelos, Pugliese, Francesca, Pontone, Gianluca, Benedetti, Giulia, He, Guo-Wei, West, Henry, Kondo, Hidekazu, Benedek, Imre, Das, Intrajeet, Deanfield, John, Graby, John, Greenwood, John, Rodrigues, Jonathan, Ge, Junbo, Channon, Keith, Fabritz, Larissa, Fan, Li-Juan, Kingham, Lucy, Guglielmo, Marco, Lyasheva, Maria, Schmitt, Matthias, Beer, Meinrad, Anderson, Michelle, Desai, Milind, Marwan, Mohamed, Takahashi, Naohiko, Mehta, Nehal, Dai, Neng, Screaton, Nicholas, Sabharwal, Nikant, Maurovich-Horvat, Pál, Rao, Praveen, Kotronias, Rafail, Kharbanda, Rajesh, Preston, Rebecca, Wood, Richard, Blankstein, Ron, Rajani, Ronak, Mirsadraee, Saeed, Munir, Shahzad, Thomas, Sheena, Neubauer, Stefan, Klömpken, Steffen, Petersen, Steffen, Achenbach, Stephan, Anthony, Susan, Mak, Sze, Mittal, Tarun, Benedek, Theodora, Sharma, Vinoda, Lin, Wen-Hua, Kotanidis, Christos P, Rodrigues, Jonathan C L, O’Connor, Daniel, Siddique, Muhammad, Lockstone, Helen, Oikonomou, Evangelos K, Badi, Ileana, Lumley, Sheila F, Constantinides, Bede, Sanderson, Nicholas, Rodger, Gillian, Chau, Kevin K, Lodge, Archie, Tsakok, Maria, Gleeson, Fergus, Indrajeet, Das, Hudson, Benjamin J, Srivastava, Vivek, Farid, Shakil, Krasopoulos, George, Sayeed, Rana, Newby, David E, Channon, Keith M, and Antoniades, Charalambos
Published: 2022
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6. Changes in the prevalence of hepatitis B and C viral infections in Sindh province, Pakistan: Findings from two sero‐surveys in 2007 and 2019.

Author: Alamneh, Tesfa Sewunet, Walker, Josephine G., Lim, Aaron G., Alam, Ejaz, Hamid, Saeed, Foster, Graham R., Choudhry, Naheed, Ansari, M. Azim, Qureshi, Huma, and Vickerman, Peter
Subjects: HEPATITIS C virus, HEPATITIS B virus, DISEASE prevalence, VIRUS diseases, HEPATITIS B
Abstract: Pakistan harbours a large burden of hepatitis B virus (HBV) and hepatitis C virus (HCV) infection. We utilised repeat sero‐surveys to assess progress achieved towards hepatitis elimination in Pakistan. Multilevel logistic regression evaluated the change in HBV infection (HBV surface antigen (HBsAg)‐positive) prevalence and HCV exposure (HCV antibody (HCV‐Ab)‐positive) prevalence between two sero‐surveys from 2007 and 2019 for Sindh province and associated risk factors. Adjusted odds ratios (aORs) were estimated and population‐attributable fractions (PAF) for modifiable risk factors for HCV exposure. The 2007 and 2019 surveys included 8855 and 6672 individuals. HBsAg prevalence decreased from 2.6% (95% confidence intervals (95% CI): 2.2–2.9) in 2007 to 1.1% (95% CI: 0.8–1.3) in 2019, while HCV‐Ab prevalence increased from 5.1% (95% CI: 4.6%–5.5%) to 6.2% (95% CI: 5.6%–6.8%). The age and gender‐adjusted HBsAg prevalence decreased by 80% (aOR = 0.2, 95% CI: 0.1–0.4) among children and 60% (aOR = 0.4, 95% CI: 0.3–0.6) among adults over 2007–2019, while HCV‐Ab prevalence decreased by 60% (aOR = 0.4, 95%CI:0.2–0.7) in children and increased by 40% (aOR = 1.4, 95% CI: 1.2–1.7) in adults. HCV‐Ab prevalence was lower in adults with secondary (aOR = 0.6, 95% CI: 0.5–0.8) and higher (aOR = 0.5, 95%CI:0.3–0.8) education compared to illiterates and higher among adults reporting blood transfusion (aOR = 1.7, 95% CI: 1.2–2.4), family history of hepatitis (aOR = 2.5, 95% CI: 1.9–3.3), past year medical injection (aOR = 2.1, 95% CI: 1.6–2.7), being tattooed (aOR = 1.4, 95% CI: 1.0–1.9) and shaved by traditional barber (aOR = 1.2, 95% CI: 1.0–1.5). Modifiable risk factors accounted for 45% of HCV exposure, with medical injection(s) accounting for 38% (95%CI,25.7–48.4%). Overall HCV has increased over 2007–2019 in Sindh province, while HBV prevalence has decreased. Medical injections should be an important focus of prevention activities. [ABSTRACT FROM AUTHOR]
Published: 2024
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7. Castanet: a pipeline for rapid analysis of targeted multi-pathogen genomic data.

Author: Mayne, Richard, Secret, Shannah, Geoghegan, Cyndi, Trebes, Amy, Kean, Kai, Reid, Kaitlin, Lin, Gu-Lung, Ansari, M Azim, Cesare, Mariateresa de, Bonsall, David, Elliott, Ivo, Piazza, Paolo, Brown, Anthony, Bray, James, Knight, Julian C, Harvala, Heli, Breuer, Judith, Simmonds, Peter, Bowden, Rory J, and Golubchik, Tanya
Subjects: UBUNTU (Operating system), BATCH processing, SOURCE code, PATHOLOGICAL laboratories, METAGENOMICS
Abstract: Motivation Target enrichment strategies generate genomic data from multiple pathogens in a single process, greatly improving sensitivity over metagenomic sequencing and enabling cost-effective, high-throughput surveillance and clinical applications. However, uptake by research and clinical laboratories is constrained by an absence of computational tools that are specifically designed for the analysis of multi-pathogen enrichment sequence data. Here we present an analysis pipeline, Castanet, for use with multi-pathogen enrichment sequencing data. Castanet is designed to work with short-read data produced by existing targeted enrichment strategies, but can be readily deployed on any BAM file generated by another methodology. Also included are an optional graphical interface and installer script. Results In addition to genome reconstruction, Castanet reports method-specific metrics that enable quantification of capture efficiency, estimation of pathogen load, differentiation of low-level positives from contamination, and assessment of sequencing quality. Castanet can be used as a traditional end-to-end pipeline for consensus generation, but its strength lies in the ability to process a flexible, pre-defined set of pathogens of interest directly from multi-pathogen enrichment experiments. In our tests, Castanet consensus sequences were accurate reconstructions of reference sequences, including in instances where multiple strains of the same pathogen were present. Castanet performs effectively on standard computers and can process the entire output of a 96-sample enrichment sequencing run (50M reads) using a single batch process command, in $<$2 h. Availability and implementation Source code freely available under GPL-3 license at https://github.com/MultipathogenGenomics/castanet , implemented in Python 3.10 and supported in Ubuntu Linux 22.04. The data underlying this article are available in Europe Nucleotide Archives, at https://www.ebi.ac.uk/ena/browser/view/PRJEB77004. [ABSTRACT FROM AUTHOR]
Published: 2024
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8. Inference of Host–Pathogen Interaction Matrices from Genome-Wide Polymorphism Data.

Author: Märkle, Hanna, John, Sona, Metzger, Lukas, Consortium, STOP-HCV, Ansari, M Azim, Pedergnana, Vincent, and Tellier, Aurélien
Subjects: SINGLE nucleotide polymorphisms, HEPATITIS C virus, LINKAGE disequilibrium, VIRAL mutation, HUMAN genes
Abstract: Host–pathogen coevolution is defined as the reciprocal evolutionary changes in both species due to genotype × genotype (G×G) interactions at the genetic level determining the outcome and severity of infection. While co-analyses of hosts and pathogen genomes (co-genome-wide association studies) allow us to pinpoint the interacting genes, these do not reveal which host genotype(s) is/are resistant to which pathogen genotype(s). The knowledge of this so-called infection matrix is important for agriculture and medicine. Building on established theories of host–pathogen interactions, we here derive four novel indices capturing the characteristics of the infection matrix. These indices can be computed from full genome polymorphism data of randomly sampled uninfected hosts, as well as infected hosts and their pathogen strains. We use these indices in an approximate Bayesian computation method to pinpoint loci with relevant G×G interactions and to infer their underlying interaction matrix. In a combined single nucleotide polymorphism dataset of 451 European humans and their infecting hepatitis C virus (HCV) strains and 503 uninfected individuals, we reveal a new human candidate gene for resistance to HCV and new virus mutations matching human genes. For two groups of significant human–HCV (G×G) associations, we infer a gene-for-gene infection matrix, which is commonly assumed to be typical of plant–pathogen interactions. Our model-based inference framework bridges theoretical models of G×G interactions with host and pathogen genomic data. It, therefore, paves the way for understanding the evolution of key G×G interactions underpinning HCV adaptation to the European human population after a recent expansion. [ABSTRACT FROM AUTHOR]
Published: 2024
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9. Performance of models to predict hepatocellular carcinoma risk among UK patients with cirrhosis and cured HCV infection

Author: Innes, Hamish, Jepsen, Peter, McDonald, Scott, Dillon, John, Hamill, Victoria, Yeung, Alan, Benselin, Jennifer, Went, April, Fraser, Andrew, Bathgate, Andrew, Ansari, M. Azim, Barclay, Stephen T., Goldberg, David, Hayes, Peter C., Johnson, Philip, Barnes, Eleanor, Irving, William, Hutchinson, Sharon, and Guha, Indra Neil
Published: 2021
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10. Prevalence of resistance-associated viral variants to the HIV-specific broadly neutralising antibody 10-1074 in a UK bNAb-naïve population

Author: Zacharopoulou, Panagiota, primary, Lee, Ming, additional, Oliveira, Thiago, additional, Thornhill, John, additional, Robinson, Nicola, additional, Brown, Helen, additional, Kinloch, Sabine, additional, Goulder, Philip, additional, Fox, Julie, additional, Fidler, Sarah, additional, Ansari, M. Azim, additional, and Frater, John, additional
Published: 2024
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11. Targeted metagenomics reveals association between severity and pathogen co-detection in infants with respiratory syncytial virus

Author: CTI Bont, Infectieziekten onderzoek1 (Bont), Zorg en O&O, Child Health, Infection & Immunity, Lin, Gu-Lung, Drysdale, Simon B, Snape, Matthew D, O'Connor, Daniel, Brown, Anthony, MacIntyre-Cockett, George, Mellado-Gomez, Esther, de Cesare, Mariateresa, Ansari, M Azim, Bonsall, David, Bray, James E, Jolley, Keith A, Bowden, Rory, Aerssens, Jeroen, Bont, Louis, Openshaw, Peter J M, Martinon-Torres, Federico, Nair, Harish, Golubchik, Tanya, Pollard, Andrew J, RESCEU Consortium, CTI Bont, Infectieziekten onderzoek1 (Bont), Zorg en O&O, Child Health, Infection & Immunity, Lin, Gu-Lung, Drysdale, Simon B, Snape, Matthew D, O'Connor, Daniel, Brown, Anthony, MacIntyre-Cockett, George, Mellado-Gomez, Esther, de Cesare, Mariateresa, Ansari, M Azim, Bonsall, David, Bray, James E, Jolley, Keith A, Bowden, Rory, Aerssens, Jeroen, Bont, Louis, Openshaw, Peter J M, Martinon-Torres, Federico, Nair, Harish, Golubchik, Tanya, Pollard, Andrew J, and RESCEU Consortium
Published: 2024

12. A calculated risk: Evaluating HIV resistance to the broadly neutralising antibodies10-1074 and 3BNC117

Author: Zacharopoulou, Panagiota, Ansari, M. Azim, and Frater, John
Published: 2022
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13. Phylogenetic Analysis of Hepatitis C Virus Infections in a Large Belgian Cohort Using Next-Generation Sequencing of Full-Length Genomes

Author: Christensen, Kasper T., primary, Pierard, Florian, additional, Bonsall, David, additional, Bowden, Rory, additional, Barnes, Eleanor, additional, Florence, Eric, additional, Ansari, M. Azim, additional, Nguyen, Dung, additional, de Cesare, Mariateresa, additional, Nevens, Frederik, additional, Robaeys, Geert, additional, Schrooten, Yoeri, additional, Busschots, Dana, additional, Simmonds, Peter, additional, Vandamme, Anne-Mieke, additional, Van Wijngaerden, Eric, additional, Dierckx, Tim, additional, Cuypers, Lize, additional, and Van Laethem, Kristel, additional
Published: 2023
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14. Distinct patterns of within-host virus populations between two subgroups of human respiratory syncytial virus

Author: Lin, Gu-Lung, Drysdale, Simon B., Snape, Matthew D., O’Connor, Daniel, Brown, Anthony, MacIntyre-Cockett, George, Mellado-Gomez, Esther, de Cesare, Mariateresa, Bonsall, David, Ansari, M. Azim, Öner, Deniz, Aerssens, Jeroen, Butler, Christopher, Bont, Louis, Openshaw, Peter, Martinón-Torres, Federico, Nair, Harish, Bowden, Rory, Golubchik, Tanya, and Pollard, Andrew J.
Published: 2021
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15. Prevalence of resistanceassociated viral variants to the HIV-specific broadly neutralising antibody 10-1074 in a UK bNAb-naïve population.

Author: Zacharopoulou, Panagiota, Lee, Ming, Oliveira, Thiago, Thornhill, John, Robinson, Nicola, Brown, Helen, Kinloch, Sabine, Goulder, Philip, Fox, Julie, Fidler, Sarah, Ansari, M. Azim, and Frater, John
Subjects: HIV seroconversion, HIV infections, HIV infection transmission, INFECTION prevention, ANTIRETROVIRAL agents, INFECTION
Abstract: Broadly neutralising antibodies (bNAbs) targeting HIV show promise for both prevention of infection and treatment. Among these, 10-1074 has shown potential in neutralising a wide range of HIV strains. However, resistant viruses may limit the clinical efficacy of 10-1074. The prevalence of both de novo and emergent 10-1074 resistance will determine its use at a population level both to protect against HIV transmission and as an option for treatment. To help understand this further, we report the prevalence of pre-existing mutations associated with 10-1074 resistance in a bNAb-naive population of 157 individuals presenting to UK HIV centres with primary HIV infection, predominantly B clade, receiving antiretroviral treatment. Single genome analysis of HIV proviral envelope sequences showed that 29% of participants' viruses tested had at least one sequence with 10-1074 resistance-associated mutations. Mutations interfering with the glycan binding site at HIV Env position 332 accounted for 95% of all observed mutations. Subsequent analysis of a larger historic dataset of 2425 Bclade envelope sequences sampled from 1983 to 2019 revealed an increase of these mutations within the population over time. Clinical studies have shown that the presence of pre-existing bNAb mutations may predict diminished therapeutic effectiveness of 10-1074. Therefore, we emphasise the importance of screening for these mutations before initiating 10-1074 therapy, and to consider the implications of pre-existing resistance when designing prevention strategies. [ABSTRACT FROM AUTHOR]
Published: 2024
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16. Targeted metagenomics reveals association between severity and pathogen co-detection in infants with respiratory syncytial virus.

Author: Lin, Gu-Lung, Drysdale, Simon B., Snape, Matthew D., O'Connor, Daniel, Brown, Anthony, MacIntyre-Cockett, George, Mellado-Gomez, Esther, de Cesare, Mariateresa, Ansari, M. Azim, Bonsall, David, Bray, James E., Jolley, Keith A., Bowden, Rory, Aerssens, Jeroen, Bont, Louis, Openshaw, Peter J. M., Martinon-Torres, Federico, Nair, Harish, Golubchik, Tanya, and Pollard, Andrew J.
Subjects: RESPIRATORY syncytial virus, RESPIRATORY syncytial virus infections, INFANTS, RESPIRATORY infections in children, METAGENOMICS, PATHOGENIC microorganisms
Abstract: Respiratory syncytial virus (RSV) is the leading cause of hospitalisation for respiratory infection in young children. RSV disease severity is known to be age-dependent and highest in young infants, but other correlates of severity, particularly the presence of additional respiratory pathogens, are less well understood. In this study, nasopharyngeal swabs were collected from two cohorts of RSV-positive infants <12 months in Spain, the UK, and the Netherlands during 2017–20. We show, using targeted metagenomic sequencing of >100 pathogens, including all common respiratory viruses and bacteria, from samples collected from 433 infants, that burden of additional viruses is common (111/433, 26%) but only modestly correlates with RSV disease severity. In contrast, there is strong evidence in both cohorts and across age groups that presence of Haemophilus bacteria (194/433, 45%) is associated with higher severity, including much higher rates of hospitalisation (odds ratio 4.25, 95% CI 2.03–9.31). There is no evidence for association between higher severity and other detected bacteria, and no difference in severity between RSV genotypes. Our findings reveal the genomic diversity of additional pathogens during RSV infection in infants, and provide an evidence base for future causal investigations of the impact of co-infection on RSV disease severity. The impact of other pathogens on disease outcome was studied in European infants with RSV infection. Additional viruses were commonly co-detected during infection but were weakly linked to severity. However, presence of Haemophilus bacteria strongly associated with severe cases. [ABSTRACT FROM AUTHOR]
Published: 2024
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17. A large-scale, multi-centre, prospective observational study to treat hepatitis C in Pakistan and assess resistance to antiviral drugs (HepFREEPak): study protocol

Author: Arif, Ambreen, primary, Hasnain, Aliya, additional, Chaudhry, Auj, additional, Asim, Muhammad, additional, Shafqat, Muhammad Nabeel, additional, Altaf, Abeer, additional, Saba, Noor, additional, Kemos, Polychronis, additional, Ansari, M. Azim, additional, Barnes, Eleanor, additional, Metcalfe, Chris, additional, Vickerman, Peter, additional, Qureshi, Huma, additional, Hamid, Saeed, additional, Choudhry, Asad Ali, additional, Niaz, Saad Khalid, additional, Foster, Graham R, additional, and Choudhry, Naheed, additional
Published: 2023
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18. An enrichment protocol and analysis pipeline for long read sequencing of the hepatitis B virus transcriptome

Author: Ng, Esther, primary, Dobrica, Mihaela-Olivia, additional, Harris, James M., additional, Wu, Yanxia, additional, Tsukuda, Senko, additional, Wing, Peter A. C., additional, Piazza, Paolo, additional, Balfe, Peter, additional, Matthews, Philippa C., additional, Ansari, M. Azim, additional, and McKeating, Jane A., additional
Published: 2023
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19. Pan-genotypic probe-based enrichment to improve efficiency of Hepatitis B virus sequencing

Author: Lumley, Sheila F, primary, Jennings, Daisy, additional, Waddilove, Elizabeth, additional, Trebes, Amy, additional, Delphin, Marion, additional, Downs, Louise O, additional, MacIntyre-Cockett, George, additional, Wu, Yanxia, additional, Chaudron, Sandra, additional, de Lara, Catherine, additional, Chai, Haiting, additional, Maponga, Tongai G, additional, Martin, Jacqueline, additional, Collier, Jane, additional, Ip, Camilla LC, additional, Barnes, Eleanor, additional, Bonsall, David, additional, Piazza, Paolo, additional, Ansari, M. Azim, additional, and Matthews, Philippa C, additional
Published: 2023
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20. Association between disease severity and co-detection of respiratory pathogens in infants with RSV infection

Author: Lin, Gu-Lung, primary, Drysdale, Simon B, additional, Snape, Matthew D, additional, O’Connor, Daniel, additional, Brown, Anthony, additional, MacIntyre-Cockett, George, additional, Mellado-Gomez, Esther, additional, de Cesare, Mariateresa, additional, Ansari, M Azim, additional, Bonsall, David, additional, Bray, James E, additional, Jolley, Keith A, additional, Bowden, Rory, additional, Aerssens, Jeroen, additional, Bont, Louis, additional, Openshaw, Peter J M, additional, Martinon-Torres, Federico, additional, Nair, Harish, additional, Golubchik, Tanya, additional, and Pollard, Andrew J, additional
Published: 2023
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21. A systematic review of Hepatitis B virus (HBV) prevalence and genotypes in Kenya: Data to inform clinical care and health policy

Author: Downs, Louise O., primary, Campbell, Cori, additional, Yonga, Paul, additional, Githinji, George, additional, Ansari, M. Azim, additional, Matthews, Philippa C., additional, and Etyang, Anthony O., additional
Published: 2023
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22. Efficacy of ultra-short, response-guided sofosbuvir and daclatasvir therapy for hepatitis C in a single-arm mechanistic pilot study

Author: Flower, Barnaby, primary, Hung, Le Manh, additional, Mccabe, Leanne, additional, Ansari, M Azim, additional, Le Ngoc, Chau, additional, Vo Thi, Thu, additional, Vu Thi Kim, Hang, additional, Nguyen Thi Ngoc, Phuong, additional, Phuong, Le Thanh, additional, Quang, Vo Minh, additional, Dang Trong, Thuan, additional, Le Thi, Thao, additional, Nguyen Bao, Tran, additional, Kingsley, Cherry, additional, Smith, David, additional, Hoglund, Richard M, additional, Tarning, Joel, additional, Kestelyn, Evelyne, additional, Pett, Sarah L, additional, van Doorn, Rogier, additional, Van Nuil, Jennifer Ilo, additional, Turner, Hugo, additional, Thwaites, Guy E, additional, Barnes, Eleanor, additional, Rahman, Motiur, additional, Walker, Ann Sarah, additional, Day, Jeremy N, additional, Chau, Nguyen VV, additional, and Cooke, Graham S, additional
Published: 2023
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23. Author response: Efficacy of ultra-short, response-guided sofosbuvir and daclatasvir therapy for hepatitis C in a single-arm mechanistic pilot study

Author: Flower, Barnaby, primary, Hung, Le Manh, additional, Mccabe, Leanne, additional, Ansari, M Azim, additional, Le Ngoc, Chau, additional, Vo Thi, Thu, additional, Vu Thi Kim, Hang, additional, Nguyen Thi Ngoc, Phuong, additional, Phuong, Le Thanh, additional, Quang, Vo Minh, additional, Dang Trong, Thuan, additional, Le Thi, Thao, additional, Nguyen Bao, Tran, additional, Kingsley, Cherry, additional, Smith, David, additional, Hoglund, Richard M, additional, Tarning, Joel, additional, Kestelyn, Evelyne, additional, Pett, Sarah L, additional, van Doorn, Rogier, additional, Van Nuil, Jennifer Ilo, additional, Turner, Hugo, additional, Thwaites, Guy E, additional, Barnes, Eleanor, additional, Rahman, Motiur, additional, Walker, Ann Sarah, additional, Day, Jeremy N, additional, Chau, Nguyen VV, additional, and Cooke, Graham S, additional
Published: 2022
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24. Constructing custom-made radiotranscriptomic signatures of vascular inflammation from routine CT angiograms: a prospective outcomes validation study in COVID-19

Author: Kotanidis, Christos P, primary, Xie, Cheng, additional, Alexander, Donna, additional, Rodrigues, Jonathan C L, additional, Burnham, Katie, additional, Mentzer, Alexander, additional, O’Connor, Daniel, additional, Knight, Julian, additional, Siddique, Muhammad, additional, Lockstone, Helen, additional, Thomas, Sheena, additional, Kotronias, Rafail, additional, Oikonomou, Evangelos K, additional, Badi, Ileana, additional, Lyasheva, Maria, additional, Shirodaria, Cheerag, additional, Lumley, Sheila F, additional, Constantinides, Bede, additional, Sanderson, Nicholas, additional, Rodger, Gillian, additional, Chau, Kevin K, additional, Lodge, Archie, additional, Tsakok, Maria, additional, Gleeson, Fergus, additional, Adlam, David, additional, Rao, Praveen, additional, Indrajeet, Das, additional, Deshpande, Aparna, additional, Bajaj, Amrita, additional, Hudson, Benjamin J, additional, Srivastava, Vivek, additional, Farid, Shakil, additional, Krasopoulos, George, additional, Sayeed, Rana, additional, Ho, Ling-Pei, additional, Neubauer, Stefan, additional, Newby, David E, additional, Channon, Keith M, additional, Deanfield, John, additional, Antoniades, Charalambos, additional, Ahern, David J, additional, Ai, Zhichao, additional, Ainsworth, Mark, additional, Allan, Chris, additional, Allcock, Alice, additional, Angus, Brian, additional, Ansari, M Azim, additional, Arancibia-Cárcamo, Carolina, additional, Aschenbrenner, Dominik, additional, Attar, Moustafa, additional, Baillie, J Kenneth, additional, Barnes, Eleanor, additional, Bashford-Rogers, Rachael, additional, Bashyal, Archana, additional, Beer, Sally, additional, Berridge, Georgina, additional, Beveridge, Amy, additional, Bibi, Sagida, additional, Bicanic, Tihana, additional, Blackwell, Luke, additional, Bowness, Paul, additional, Brent, Andrew, additional, Brown, Andrew, additional, Broxholme, John, additional, Buck, David, additional, Byrne, Helen, additional, Camara, Susana, additional, Ferreira, Ivan Candido, additional, Charles, Philip, additional, Chen, Wentao, additional, Chen, Yi-Ling, additional, Chong, Amanda, additional, Clutterbuck, Elizabeth, additional, Coles, Mark, additional, Conlon, Christopher, additional, Cornall, Richard, additional, Cribbs, Adam, additional, Curion, Fabiola, additional, Davenport, Emma, additional, Davidson, Neil, additional, Davis, Simon, additional, Dendrou, Calliope, additional, Dequaire, Julie, additional, Dib, Lea, additional, Docker, James, additional, Dold, Christina, additional, Dong, Tao, additional, Downes, Damien, additional, Drakesmith, Hal, additional, Dunachie, Susanna, additional, Duncan, David, additional, Eijsbouts, Chris, additional, Esnouf, Robert, additional, Espinosa, Alexis, additional, Etherington, Rachel, additional, Fairfax, Benjamin, additional, Fairhead, Rory, additional, Fang, Hai, additional, Fassih, Shayan, additional, Felle, Sally, additional, Fernandez Mendoza, Maria, additional, Ferreira, Ricardo, additional, Fischer, Roman, additional, Foord, Thomas, additional, Forrow, Aden, additional, Frater, John, additional, Fries, Anastasia, additional, Gallardo Sanchez, Veronica, additional, Garner, Lucy, additional, Geeves, Clementine, additional, Georgiou, Dominique, additional, Godfrey, Leila, additional, Golubchik, Tanya, additional, Gomez Vazquez, Maria, additional, Green, Angie, additional, Harper, Hong, additional, Harrington, Heather, additional, Heilig, Raphael, additional, Hester, Svenja, additional, Hill, Jennifer, additional, Hinds, Charles, additional, Hird, Clare, additional, Hoekzema, Renee, additional, Hollis, Benjamin, additional, Hughes, Jim, additional, Hutton, Paula, additional, Jackson-Wood, Matthew, additional, Jainarayanan, Ashwin, additional, James-Bott, Anna, additional, Jansen, Kathrin, additional, Jeffery, Katie, additional, Jones, Elizabeth, additional, Jostins, Luke, additional, Kerr, Georgina, additional, Kim, David, additional, Klenerman, Paul, additional, Kumar, Vinod, additional, Kumar Sharma, Piyush, additional, Kurupati, Prathiba, additional, Kwok, Andrew, additional, Lee, Angela, additional, Linder, Aline, additional, Lockett, Teresa, additional, Lonie, Lorne, additional, Lopopolo, Maria, additional, Lukoseviciute, Martyna, additional, Luo, Jian, additional, Marinou, Spyridoula, additional, Marsden, Brian, additional, Martinez, Jose, additional, Matthews, Philippa, additional, Mazurczyk, Michalina, additional, McGowan, Simon, additional, McKechnie, Stuart, additional, Mead, Adam, additional, Mi, Yuxin, additional, Monaco, Claudia, additional, Montadon, Ruddy, additional, Napolitani, Giorgio, additional, Nassiri, Isar, additional, Novak, Alex, additional, O'Brien, Darragh, additional, O'Connor, Daniel, additional, O'Donnell, Denise, additional, Ogg, Graham, additional, Overend, Lauren, additional, Park, Inhye, additional, Pavord, Ian, additional, Peng, Yanchun, additional, Penkava, Frank, additional, Pereira Pinho, Mariana, additional, Perez, Elena, additional, Pollard, Andrew, additional, Powrie, Fiona, additional, Psaila, Bethan, additional, Quan, T Phuong, additional, Repapi, Emmanouela, additional, Revale, Santiago, additional, Silva-Reyes, Laura, additional, Richard, Jean-Baptiste, additional, Rich-Griffin, Charlotte, additional, Ritter, Thomas, additional, Rollier, Christine, additional, Rowland, Matthew, additional, Ruehle, Fabian, additional, Salio, Mariolina, additional, Sansom, Stephen Nicholas, additional, Sanches Peres, Raphael, additional, Santos Delgado, Alberto, additional, Sauka-Spengler, Tatjana, additional, Schwessinger, Ron, additional, Scozzafava, Giuseppe, additional, Screaton, Gavin, additional, Seigal, Anna, additional, Semple, Malcolm, additional, Sergeant, Martin, additional, Simoglou Karali, Christina, additional, Sims, David, additional, Skelly, Donal, additional, Slawinski, Hubert, additional, Sobrinodiaz, Alberto, additional, Sousos, Nikolaos, additional, Stafford, Lizzie, additional, Stockdale, Lisa, additional, Strickland, Marie, additional, Sumray, Otto, additional, Sun, Bo, additional, Taylor, Chelsea, additional, Taylor, Stephen, additional, Taylor, Adan, additional, Thongjuea, Supat, additional, Thraves, Hannah, additional, Todd, John, additional, Tomic, Adriana, additional, Tong, Orion, additional, Trebes, Amy, additional, Trzupek, Dominik, additional, Tucci, Felicia Anna, additional, Turtle, Lance, additional, Udalova, Irina, additional, Uhlig, Holm, additional, van Grinsven, Erinke, additional, Vendrell, Iolanda, additional, Verheul, Marije, additional, Voda, Alexandru, additional, Wang, Guanlin, additional, Wang, Lihui, additional, Wang, Dapeng, additional, Watkinson, Peter, additional, Watson, Robert, additional, Weinberger, Michael, additional, Whalley, Justin, additional, Witty, Lorna, additional, Wray, Katherine, additional, Xue, Luzheng, additional, Yuen Yeung, Hing, additional, Yin, Zixi, additional, Young, Rebecca, additional, Youngs, Jonathan, additional, Zhang, Ping, additional, Zurke, Yasemin-Xiomara, additional, Banning, Adrian, additional, Antonopoulos, Alexios, additional, Kelion, Andrew, additional, Kardos, Attila, additional, Hudson, Benjamin, additional, Koo, Bon-Kwon, additional, Kotanidis, Christos, additional, Mahon, Ciara, additional, Berry, Colin, additional, Newby, David, additional, Connolly, Derek, additional, Scaletta, Diane, additional, Nicol, Ed, additional, McAlindon, Elisa, additional, Oikonomou, Evangelos, additional, Pugliese, Francesca, additional, Pontone, Gianluca, additional, Benedetti, Giulia, additional, He, Guo-Wei, additional, West, Henry, additional, Kondo, Hidekazu, additional, Benedek, Imre, additional, Das, Intrajeet, additional, Graby, John, additional, Greenwood, John, additional, Rodrigues, Jonathan, additional, Ge, Junbo, additional, Channon, Keith, additional, Fabritz, Larissa, additional, Fan, Li-Juan, additional, Kingham, Lucy, additional, Guglielmo, Marco, additional, Schmitt, Matthias, additional, Beer, Meinrad, additional, Anderson, Michelle, additional, Desai, Milind, additional, Marwan, Mohamed, additional, Takahashi, Naohiko, additional, Mehta, Nehal, additional, Dai, Neng, additional, Screaton, Nicholas, additional, Sabharwal, Nikant, additional, Maurovich-Horvat, Pál, additional, Kharbanda, Rajesh, additional, Preston, Rebecca, additional, Wood, Richard, additional, Blankstein, Ron, additional, Rajani, Ronak, additional, Mirsadraee, Saeed, additional, Munir, Shahzad, additional, Klömpken, Steffen, additional, Petersen, Steffen, additional, Achenbach, Stephan, additional, Anthony, Susan, additional, Mak, Sze, additional, Mittal, Tarun, additional, Benedek, Theodora, additional, Sharma, Vinoda, additional, and Lin, Wen-Hua, additional
Published: 2022
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25. T-cell and antibody responses to first BNT162b2 vaccine dose in previously infected and SARS-CoV-2-naive UK health-care workers: a multicentre prospective cohort study

Author: Angyal, Adrienn, primary, Longet, Stephanie, additional, Moore, Shona C, additional, Payne, Rebecca P, additional, Harding, Adam, additional, Tipton, Tom, additional, Rongkard, Patpong, additional, Ali, Mohammad, additional, Hering, Luisa M, additional, Meardon, Naomi, additional, Austin, James, additional, Brown, Rebecca, additional, Skelly, Donal, additional, Gillson, Natalie, additional, Dobson, Sue L, additional, Cross, Andrew, additional, Sandhar, Gurjinder, additional, Kilby, Jonathan A, additional, Tyerman, Jessica K, additional, Nicols, Alexander R, additional, Spegarova, Jarmila S, additional, Mehta, Hema, additional, Hornsby, Hailey, additional, Whitham, Rachel, additional, Conlon, Christopher P, additional, Jeffery, Katie, additional, Goulder, Philip, additional, Frater, John, additional, Dold, Christina, additional, Pace, Matthew, additional, Ogbe, Ane, additional, Brown, Helen, additional, Ansari, M Azim, additional, Adland, Emily, additional, Brown, Anthony, additional, Chand, Meera, additional, Shields, Adrian, additional, Matthews, Philippa C, additional, Hopkins, Susan, additional, Hall, Victoria, additional, James, William, additional, Rowland-Jones, Sarah L, additional, Klenerman, Paul, additional, Dunachie, Susanna, additional, Richter, Alex, additional, Duncan, Christopher J A, additional, Barnes, Eleanor, additional, Carroll, Miles, additional, Turtle, Lance, additional, de Silva, Thushan I, additional, Watson, Adam, additional, Angyal, Adrienn, additional, Alhussni, Ahmed, additional, Nicols, Alexander, additional, Deeks, Alexandra, additional, Webb-Bridges, Alice, additional, Jämsén, Anni, additional, Chawla, Anu, additional, Duncan, Christopher, additional, Conlon, Christopher, additional, O'Donnell, Denise, additional, Weeks, Esme, additional, Abuelgasim, Hibatullah, additional, Xiao, Huiyuan, additional, Spegarova, Jarmila, additional, Holmes, Jennifer, additional, Haworth, Jenny, additional, Tyerman, Jessica, additional, Kilby, Jonathan, additional, Cutteridge, Joseph, additional, Lillie, Katy, additional, Romaniuk, Leigh, additional, Denly, Lucy, additional, Hering, Luisa, additional, Ansari, M. Azim, additional, Kasanyinga, Mwila, additional, Matthews, Philippa, additional, Payne, Rebecca, additional, Wilson, Robert, additional, Rowland-Jones, Sarah, additional, Thomas, Sarah, additional, Moore, Shona, additional, Gardiner, Siobhan, additional, Tucker, Stephanie, additional, Dobson, Sue, additional, Adlou, Syed, additional, de Silva, Thushan, additional, Lawrie, Allan, additional, Smith, Nikki, additional, Turton, Helena, additional, Zawia, Amira, additional, Bayley, Martin, additional, Fairman, Alex, additional, Harrington, Kate, additional, Kirk, Rosemary, additional, Marsh, Louise, additional, Watson, Lisa, additional, Wood, Steven, additional, Diffey, Benjamin, additional, Jones, Chris, additional, Lett, Lauren, additional, Platt, Gareth, additional, Subramaniam, Krishanthi, additional, Wootton, Daniel, additional, Payne, Brendan, additional, Hambleton, Sophie, additional, Kelly, Sinead, additional, Marston, Judith, additional, Poolan, Sonia, additional, Turner, Dianne, additional, Haniffa, Muzlifah, additional, Stephenson, Emily, additional, Adele, Sandra, additional, Akhter, Hossain Delowar, additional, Chinnakannan, Senthil, additional, de Lara, Catherine, additional, Donnison, Timothy, additional, Hackstein, Carl-Philipp, additional, Lee, Lian, additional, Lim, Nicholas, additional, Malone, Tom, additional, Phillips, Eloise, additional, Ramamurthy, Narayan, additional, Robinson, Nichola, additional, Sampson, Oliver, additional, Eyre, David, additional, Simmons, Beatrice, additional, Stafford, Lizzie, additional, Mentzer, Alexander, additional, Amini, Ali, additional, Arancibia-Cárcamo, Carolina, additional, Provine, Nicholas, additional, Travis, Simon, additional, Dimitriadis, Stavros, additional, Johnson, Sile, additional, Foulkes, Sarah, additional, Khawam, Jameel, additional, Wellington, Edgar, additional, Gilbert-Jaramillo, Javier, additional, Knight, Michael, additional, Dupont, Maeva, additional, Horner, Emily, additional, Thaventhiran, James, additional, and Chalk, Jeremy, additional
Published: 2022
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26. Genetic variation in TERT modifies the risk of hepatocellular carcinoma in alcohol-related cirrhosis: Results from a genome-wide case-control study

Author: Buch, Stephan, Innes, Hamish, Lutz, Philipp Ludwig, Nischalke, Hans Dieter, Marquardt, Jens U, Fischer, Janett, Weiss, Karl Heinz, Rosendahl, Jonas, Marot, Astrid, Krawczyk, Marcin, Casper, Markus, Lammert, Frank, Eyer, Florian, Vogel, Arndt, Marhenke, Silke, Von Felden, Johann, Sharma, Rohini, Atkinson, Stephen Rahul, McQuillin, Andrew, Nattermann, Jacob, Schafmayer, Clemens, Franke, Andre, Strassburg, Christian, Rietschel, Marcella, Altmann, Heidi, Sulk, Stefan, Thangapandi, Veera Raghavan, Brosch, Mario, Lackner, Carolin, Stauber, Rudolf E, Canbay, Ali, Link, Alexander, Reiberger, Thomas, Mandorfer, Mattias, Semmler, Georg, Scheiner, Bernhard, Datz, Christian, Romeo, Stefano, Ginanni Corradini, Stefano, Irving, William Lucien, Morling, Joanne R., Guha, Indra Neil, Barnes, Eleanor, Ansari, M. Azim, Quistrebert, Jocelyn, Valenti, Luca, Morgan, Marsha Yvonne, Trebicka, Jonel, Berg, Thomas, Deltenre, Pierre, Mueller, Sebastian, Hampe, Jochen, and Stickel, Felix
Subjects: Gastroenterology
Abstract: Objective: Hepatocellular carcinoma (HCC) often develops in patients with alcohol-related cirrhosis at an annual risk of up to 2.5%. Some host genetic risk factors have been identified but do not account for the majority of the variance in occurrence. This study aimed to identify novel susceptibility loci for the development of HCC in people with alcohol related cirrhosis. Design: Patients with alcohol-related cirrhosis and HCC (cases: n=1214) and controls without HCC (n=1866), recruited from Germany, Austria, Switzerland, Italy and the UK, were included in a two-stage genome-wide association study using a case-control design. A validation cohort of 1520 people misusing alcohol but with no evidence of liver disease was included to control for possible association effects with alcohol misuse. Genotyping was performed using the InfiniumGlobal Screening Array (V.24v2, Illumina) and the OmniExpress Array (V.24v1-0a, Illumina). Results: Associations with variants rs738409 in PNPLA3 and rs58542926 in TM6SF2 previously associated with an increased risk of HCC in patients with alcohol-related cirrhosis were confirmed at genome-wide significance. A novel locus rs2242652(A) in TERT (telomerase reverse transcriptase) was also associated with a decreased risk of HCC, in the combined meta-Analysis, at genome-wide significance (p=6.41×10-9, OR=0.61 (95% CI 0.52 to 0.70). This protective association remained significant after correction for sex, age, body mass index and type 2 diabetes (p=7.94×10-5, OR=0.63 (95% CI 0.50 to 0.79). Carriage of rs2242652(A) in TERT was associated with an increased leucocyte telomere length (p=2.12×10-44). Conclusion: This study identifies rs2242652 in TERT as a novel protective factor for HCC in patients with alcohol-related cirrhosis.
Published: 2022

27. Efficacy of ultra-short, response-guided sofosbuvir and daclatasvir therapy for Hepatitis C: a single arm mechanistic pilot study

Author: Flower, Barnaby, primary, Hung, Le Manh, additional, McCabe, Leanne, additional, Ansari, M. Azim, additional, Le Ngoc, Chau, additional, Vo Thi, Thu, additional, Vu Thi Kim, Hang, additional, Nguyen Thi Ngoc, Phuong, additional, Phuong, Le Thanh, additional, Quang, Vo Minh, additional, Trong, Thuan Dang, additional, Le Thi, Thao, additional, Bao, Tran Nguyen, additional, Kingsley, Cherry, additional, Smith, David, additional, Hoglund, Richard M., additional, Tarning, Joel, additional, Kestelyn, Evelyne, additional, Pett, Sarah L, additional, van Doorn, Rogier, additional, van Nuil, Jennifer Ilo, additional, Turner, Hugo, additional, Thwaites, Guy, additional, Barnes, Eleanor, additional, Rahman, Motiur, additional, Walker, Ann Sarah, additional, Day, Jeremy, additional, Van Vinh Chau, Nguyen, additional, and Cooke, Graham S, additional
Published: 2022
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28. Genetic variation inTERTmodifies the risk of hepatocellular carcinoma in alcohol-related cirrhosis: results from a genome-wide case-control study

Author: Buch, Stephan, primary, Innes, Hamish, additional, Lutz, Philipp Ludwig, additional, Nischalke, Hans Dieter, additional, Marquardt, Jens U, additional, Fischer, Janett, additional, Weiss, Karl Heinz, additional, Rosendahl, Jonas, additional, Marot, Astrid, additional, Krawczyk, Marcin, additional, Casper, Markus, additional, Lammert, Frank, additional, Eyer, Florian, additional, Vogel, Arndt, additional, Marhenke, Silke, additional, von Felden, Johann, additional, Sharma, Rohini, additional, Atkinson, Stephen Rahul, additional, McQuillin, Andrew, additional, Nattermann, Jacob, additional, Schafmayer, Clemens, additional, Franke, Andre, additional, Strassburg, Christian, additional, Rietschel, Marcella, additional, Altmann, Heidi, additional, Sulk, Stefan, additional, Thangapandi, Veera Raghavan, additional, Brosch, Mario, additional, Lackner, Carolin, additional, Stauber, Rudolf E, additional, Canbay, Ali, additional, Link, Alexander, additional, Reiberger, Thomas, additional, Mandorfer, Mattias, additional, Semmler, Georg, additional, Scheiner, Bernhard, additional, Datz, Christian, additional, Romeo, Stefano, additional, Ginanni Corradini, Stefano, additional, Irving, William Lucien, additional, Morling, Joanne R, additional, Guha, Indra Neil, additional, Barnes, Eleanor, additional, Ansari, M Azim, additional, Quistrebert, Jocelyn, additional, Valenti, Luca, additional, Müller, Sascha A, additional, Morgan, Marsha Yvonne, additional, Dufour, Jean-François, additional, Trebicka, Jonel, additional, Berg, Thomas, additional, Deltenre, Pierre, additional, Mueller, Sebastian, additional, Hampe, Jochen, additional, and Stickel, Felix, additional
Published: 2022
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29. Genetic variation in modifies the risk of hepatocellular carcinoma in alcohol-related cirrhosis: results from a genome-wide case-control study.

Author: UCL - SSS/IREC/MONT - Pôle Mont Godinne, UCL - (MGD) Service de gastro-entérologie, Buch, Stephan, Innes, Hamish, Lutz, Philipp Ludwig, Nischalke, Hans Dieter, Marquardt, Jens U, Fischer, Janett, Weiss, Karl Heinz, Rosendahl, Jonas, Marot, Astrid, Krawczyk, Marcin, Casper, Markus, Lammert, Frank, Eyer, Florian, Vogel, Arndt, Marhenke, Silke, von Felden, Johann, Sharma, Rohini, Atkinson, Stephen Rahul, McQuillin, Andrew, Nattermann, Jacob, Schafmayer, Clemens, Franke, Andre, Strassburg, Christian, Rietschel, Marcella, Altmann, Heidi, Sulk, Stefan, Thangapandi, Veera Raghavan, Brosch, Mario, Lackner, Carolin, Stauber, Rudolf E, Canbay, Ali, Link, Alexander, Reiberger, Thomas, Mandorfer, Mattias, Semmler, Georg, Scheiner, Bernhard, Datz, Christian, Romeo, Stefano, Ginanni Corradini, Stefano, Irving, William Lucien, Morling, Joanne R, Guha, Indra Neil, Barnes, Eleanor, Ansari, M Azim, Quistrebert, Jocelyn, Valenti, Luca, Müller, Sascha A, Morgan, Marsha Yvonne, Dufour, Jean-François, Trebicka, Jonel, Berg, Thomas, Deltenre, Pierre, Mueller, Sebastian, Hampe, Jochen, Stickel, Felix, UCL - SSS/IREC/MONT - Pôle Mont Godinne, UCL - (MGD) Service de gastro-entérologie, Buch, Stephan, Innes, Hamish, Lutz, Philipp Ludwig, Nischalke, Hans Dieter, Marquardt, Jens U, Fischer, Janett, Weiss, Karl Heinz, Rosendahl, Jonas, Marot, Astrid, Krawczyk, Marcin, Casper, Markus, Lammert, Frank, Eyer, Florian, Vogel, Arndt, Marhenke, Silke, von Felden, Johann, Sharma, Rohini, Atkinson, Stephen Rahul, McQuillin, Andrew, Nattermann, Jacob, Schafmayer, Clemens, Franke, Andre, Strassburg, Christian, Rietschel, Marcella, Altmann, Heidi, Sulk, Stefan, Thangapandi, Veera Raghavan, Brosch, Mario, Lackner, Carolin, Stauber, Rudolf E, Canbay, Ali, Link, Alexander, Reiberger, Thomas, Mandorfer, Mattias, Semmler, Georg, Scheiner, Bernhard, Datz, Christian, Romeo, Stefano, Ginanni Corradini, Stefano, Irving, William Lucien, Morling, Joanne R, Guha, Indra Neil, Barnes, Eleanor, Ansari, M Azim, Quistrebert, Jocelyn, Valenti, Luca, Müller, Sascha A, Morgan, Marsha Yvonne, Dufour, Jean-François, Trebicka, Jonel, Berg, Thomas, Deltenre, Pierre, Mueller, Sebastian, Hampe, Jochen, and Stickel, Felix
Abstract: Hepatocellular carcinoma (HCC) often develops in patients with alcohol-related cirrhosis at an annual risk of up to 2.5%. Some host genetic risk factors have been identified but do not account for the majority of the variance in occurrence. This study aimed to identify novel susceptibility loci for the development of HCC in people with alcohol related cirrhosis. Patients with alcohol-related cirrhosis and HCC (cases: n=1214) and controls without HCC (n=1866), recruited from Germany, Austria, Switzerland, Italy and the UK, were included in a two-stage genome-wide association study using a case-control design. A validation cohort of 1520 people misusing alcohol but with no evidence of liver disease was included to control for possible association effects with alcohol misuse. Genotyping was performed using the InfiniumGlobal Screening Array (V.24v2, Illumina) and the OmniExpress Array (V.24v1-0a, Illumina). Associations with variants rs738409 in and rs58542926 in previously associated with an increased risk of HCC in patients with alcohol-related cirrhosis were confirmed at genome-wide significance. A novel locus rs2242652(A) in (telomerase reverse transcriptase) was also associated with a decreased risk of HCC, in the combined meta-analysis, at genome-wide significance (p=6.41×10, OR=0.61 (95% CI 0.52 to 0.70). This protective association remained significant after correction for sex, age, body mass index and type 2 diabetes (p=7.94×10, OR=0.63 (95% CI 0.50 to 0.79). Carriage of rs2242652(A) in was associated with an increased leucocyte telomere length (p=2.12×10). This study identifies rs2242652 in as a novel protective factor for HCC in patients with alcohol-related cirrhosis.
Published: 2022

30. Defining the key intrahepatic gene networks in HCV infection driven by sex.

Author: Marchi, Emanuele, Ramamurthy, Narayan, Ansari, M. Azim, Harrer, Caroline E., Barnes, Eleanor, and Klenerman, Paul
Subjects: GENE regulatory networks, LOCUS (Genetics), TYPE I interferons, IMMUNOGLOBULIN genes, GENE expression, POSTMORTEM changes
Published: 2023
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31. A systematic review of Hepatitis B virus (HBV) prevalence and genotypes in Kenya: Data to inform clinical care and health policy

Author: Downs, Louise, primary, Campbell, Cori, additional, Yonga, Paul, additional, Ansari, M Azim, additional, Matthews, Philippa, additional, and Etyang, Anthony O, additional
Published: 2022
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32. Durability of ChAdOx1 nCoV-19 vaccination in people living with HIV

Author: Ogbe, Ane, primary, Pace, Matthew, additional, Bittaye, Mustapha, additional, Tipoe, Timothy, additional, Adele, Sandra, additional, Alagaratnam, Jasmini, additional, Aley, Parvinder K., additional, Ansari, M. Azim, additional, Bara, Anna, additional, Broadhead, Samantha, additional, Brown, Anthony, additional, Brown, Helen, additional, Cappuccini, Federica, additional, Cinardo, Paola, additional, Dejnirattisai, Wanwisa, additional, Ewer, Katie J., additional, Fok, Henry, additional, Folegatti, Pedro M., additional, Fowler, Jamie, additional, Godfrey, Leila, additional, Goodman, Anna L., additional, Jackson, Bethany, additional, Jenkin, Daniel, additional, Jones, Mathew, additional, Longet, Stephanie, additional, Makinson, Rebecca A., additional, Marchevsky, Natalie G., additional, Mathew, Moncy, additional, Mazzella, Andrea, additional, Mujadidi, Yama F., additional, Parolini, Lucia, additional, Petersen, Claire, additional, Plested, Emma, additional, Pollock, Katrina M., additional, Rajeswaran, Thurkka, additional, Ramasamy, Maheshi N., additional, Rhead, Sarah, additional, Robinson, Hannah, additional, Robinson, Nicola, additional, Sanders, Helen, additional, Serrano, Sonia, additional, Tipton, Tom, additional, Waters, Anele, additional, Zacharopoulou, Panagiota, additional, Barnes, Eleanor, additional, Dunachie, Susanna, additional, Goulder, Philip, additional, Klenerman, Paul, additional, Screaton, Gavin R., additional, Winston, Alan, additional, Hill, Adrian V.S., additional, Gilbert, Sarah C., additional, Carroll, Miles, additional, Pollard, Andrew J., additional, Fidler, Sarah, additional, Fox, Julie, additional, Lambe, Teresa, additional, and Frater, John, additional
Published: 2022
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33. A blood atlas of COVID-19 defines hallmarks of disease severity and specificity

Author: Ahern, David J., primary, Ai, Zhichao, additional, Ainsworth, Mark, additional, Allan, Chris, additional, Allcock, Alice, additional, Angus, Brian, additional, Ansari, M. Azim, additional, Arancibia-Cárcamo, Carolina V., additional, Aschenbrenner, Dominik, additional, Attar, Moustafa, additional, Baillie, J. Kenneth, additional, Barnes, Eleanor, additional, Bashford-Rogers, Rachael, additional, Bashyal, Archana, additional, Beer, Sally, additional, Berridge, Georgina, additional, Beveridge, Amy, additional, Bibi, Sagida, additional, Bicanic, Tihana, additional, Blackwell, Luke, additional, Bowness, Paul, additional, Brent, Andrew, additional, Brown, Andrew, additional, Broxholme, John, additional, Buck, David, additional, Burnham, Katie L., additional, Byrne, Helen, additional, Camara, Susana, additional, Candido Ferreira, Ivan, additional, Charles, Philip, additional, Chen, Wentao, additional, Chen, Yi-Ling, additional, Chong, Amanda, additional, Clutterbuck, Elizabeth A., additional, Coles, Mark, additional, Conlon, Christopher P., additional, Cornall, Richard, additional, Cribbs, Adam P., additional, Curion, Fabiola, additional, Davenport, Emma E., additional, Davidson, Neil, additional, Davis, Simon, additional, Dendrou, Calliope A., additional, Dequaire, Julie, additional, Dib, Lea, additional, Docker, James, additional, Dold, Christina, additional, Dong, Tao, additional, Downes, Damien, additional, Drakesmith, Hal, additional, Dunachie, Susanna J., additional, Duncan, David A., additional, Eijsbouts, Chris, additional, Esnouf, Robert, additional, Espinosa, Alexis, additional, Etherington, Rachel, additional, Fairfax, Benjamin, additional, Fairhead, Rory, additional, Fang, Hai, additional, Fassih, Shayan, additional, Felle, Sally, additional, Fernandez Mendoza, Maria, additional, Ferreira, Ricardo, additional, Fischer, Roman, additional, Foord, Thomas, additional, Forrow, Aden, additional, Frater, John, additional, Fries, Anastasia, additional, Gallardo Sanchez, Veronica, additional, Garner, Lucy C., additional, Geeves, Clementine, additional, Georgiou, Dominique, additional, Godfrey, Leila, additional, Golubchik, Tanya, additional, Gomez Vazquez, Maria, additional, Green, Angie, additional, Harper, Hong, additional, Harrington, Heather A., additional, Heilig, Raphael, additional, Hester, Svenja, additional, Hill, Jennifer, additional, Hinds, Charles, additional, Hird, Clare, additional, Ho, Ling-Pei, additional, Hoekzema, Renee, additional, Hollis, Benjamin, additional, Hughes, Jim, additional, Hutton, Paula, additional, Jackson-Wood, Matthew A., additional, Jainarayanan, Ashwin, additional, James-Bott, Anna, additional, Jansen, Kathrin, additional, Jeffery, Katie, additional, Jones, Elizabeth, additional, Jostins, Luke, additional, Kerr, Georgina, additional, Kim, David, additional, Klenerman, Paul, additional, Knight, Julian C., additional, Kumar, Vinod, additional, Kumar Sharma, Piyush, additional, Kurupati, Prathiba, additional, Kwok, Andrew, additional, Lee, Angela, additional, Linder, Aline, additional, Lockett, Teresa, additional, Lonie, Lorne, additional, Lopopolo, Maria, additional, Lukoseviciute, Martyna, additional, Luo, Jian, additional, Marinou, Spyridoula, additional, Marsden, Brian, additional, Martinez, Jose, additional, Matthews, Philippa C., additional, Mazurczyk, Michalina, additional, McGowan, Simon, additional, McKechnie, Stuart, additional, Mead, Adam, additional, Mentzer, Alexander J., additional, Mi, Yuxin, additional, Monaco, Claudia, additional, Montadon, Ruddy, additional, Napolitani, Giorgio, additional, Nassiri, Isar, additional, Novak, Alex, additional, O'Brien, Darragh P., additional, O'Connor, Daniel, additional, O'Donnell, Denise, additional, Ogg, Graham, additional, Overend, Lauren, additional, Park, Inhye, additional, Pavord, Ian, additional, Peng, Yanchun, additional, Penkava, Frank, additional, Pereira Pinho, Mariana, additional, Perez, Elena, additional, Pollard, Andrew J., additional, Powrie, Fiona, additional, Psaila, Bethan, additional, Quan, T. Phuong, additional, Repapi, Emmanouela, additional, Revale, Santiago, additional, Silva-Reyes, Laura, additional, Richard, Jean-Baptiste, additional, Rich-Griffin, Charlotte, additional, Ritter, Thomas, additional, Rollier, Christine S., additional, Rowland, Matthew, additional, Ruehle, Fabian, additional, Salio, Mariolina, additional, Sansom, Stephen Nicholas, additional, Sanches Peres, Raphael, additional, Santos Delgado, Alberto, additional, Sauka-Spengler, Tatjana, additional, Schwessinger, Ron, additional, Scozzafava, Giuseppe, additional, Screaton, Gavin, additional, Seigal, Anna, additional, Semple, Malcolm G., additional, Sergeant, Martin, additional, Simoglou Karali, Christina, additional, Sims, David, additional, Skelly, Donal, additional, Slawinski, Hubert, additional, Sobrinodiaz, Alberto, additional, Sousos, Nikolaos, additional, Stafford, Lizzie, additional, Stockdale, Lisa, additional, Strickland, Marie, additional, Sumray, Otto, additional, Sun, Bo, additional, Taylor, Chelsea, additional, Taylor, Stephen, additional, Taylor, Adan, additional, Thongjuea, Supat, additional, Thraves, Hannah, additional, Todd, John A., additional, Tomic, Adriana, additional, Tong, Orion, additional, Trebes, Amy, additional, Trzupek, Dominik, additional, Tucci, Felicia Anna, additional, Turtle, Lance, additional, Udalova, Irina, additional, Uhlig, Holm, additional, van Grinsven, Erinke, additional, Vendrell, Iolanda, additional, Verheul, Marije, additional, Voda, Alexandru, additional, Wang, Guanlin, additional, Wang, Lihui, additional, Wang, Dapeng, additional, Watkinson, Peter, additional, Watson, Robert, additional, Weinberger, Michael, additional, Whalley, Justin, additional, Witty, Lorna, additional, Wray, Katherine, additional, Xue, Luzheng, additional, Yeung, Hing Yuen, additional, Yin, Zixi, additional, Young, Rebecca K., additional, Youngs, Jonathan, additional, Zhang, Ping, additional, and Zurke, Yasemin-Xiomara, additional
Published: 2022
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34. The rs429358 Locus in Apolipoprotein E Is Associated With Hepatocellular Carcinoma in Patients With Cirrhosis

Author: Innes, Hamish, Nischalke, Hans Dieter, Guha, Indra Neil, Weiss, Karl Heinz, Irving, Will, Gotthardt, Daniel, Barnes, Eleanor, Fischer, Janett, Ansari, M. Azim, Rosendahl, Jonas, Lin, Shang‐Kuan, Marot, Astrid, Pedergnana, Vincent, Casper, Markus, Benselin, Jennifer, Lammert, Frank, McLauchlan, John, Lutz, Philip L., Hamill, Victoria, Mueller, Sebastian, Morling, Joanne R., Semmler, Georg, Eyer, Florian, von Felden, Johann, Link, Alexander, Vogel, Arndt, Marquardt, Jens U., Sulk, Stefan, Trebicka, Jonel, Valenti, Luca, Datz, Christian, Reiberger, Thomas, Schafmayer, Clemens, Berg, Thomas, Deltenre, Pierre, Hampe, Jochen, Stickel, Felix, Buch, Stephan, UCL - SSS/IREC/MONT - Pôle Mont Godinne, and UCL - (MGD) Service de gastro-entérologie
Subjects: Liver Cirrhosis, Carcinoma, Hepatocellular, Hepatology, Liver Neoplasms, Membrane Proteins, SNP, Genomics, Hepatitis C, Polymorphism, Single Nucleotide, digestive system diseases, ddc, Chronic Liver Disease, Apolipoproteins E, Cirrhosis, Genetics, Humans, Genetic Predisposition to Disease, Liver cancer
Abstract: The host genetic background for hepatocellular carcinoma (HCC) is incompletely understood. We aimed to determine if four germline genetic polymorphisms, rs429358 in apolipoprotein E (APOE), rs2642438 in mitochondrial amidoxime reducing component 1 (MARC1), rs2792751 in glycerol‐3‐phosphate acyltransferase (GPAM), and rs187429064 in transmembrane 6 superfamily member 2 (TM6SF2), previously associated with progressive alcohol‐related and nonalcoholic fatty liver disease, are also associated with HCC. Four HCC case‐control data sets were constructed, including two mixed etiology data sets (UK Biobank and FinnGen); one hepatitis C virus (HCV) cohort (STOP‐HCV), and one alcohol‐related HCC cohort (Dresden HCC). The frequency of each variant was compared between HCC cases and cirrhosis controls (i.e., patients with cirrhosis without HCC). Population controls were also considered. Odds ratios (ORs) associations were calculated using logistic regression, adjusting for age, sex, and principal components of genetic ancestry. Fixed‐effect meta‐analysis was used to determine the pooled effect size across all data sets. Across four case‐control data sets, 2,070 HCC cases, 4,121 cirrhosis controls, and 525,779 population controls were included. The rs429358:C allele (APOE) was significantly less frequent in HCC cases versus cirrhosis controls (OR, 0.71; 95% confidence interval [CI], 0.61‐0.84; P = 2.9 × 10−5). Rs187429064:G (TM6SF2) was significantly more common in HCC cases versus cirrhosis controls and exhibited the strongest effect size (OR, 2.03; 95% CI, 1.45‐2.86; P = 3.1 × 10−6). In contrast, rs2792751:T (GPAM) was not associated with HCC (OR, 1.01; 95% CI, 0.90‐1.13; P = 0.89), whereas rs2642438:A (MARC1) narrowly missed statistical significance (OR, 0.91; 95% CI, 0.84‐1.00; P = 0.043). Conclusion: This study associates carriage of rs429358:C (APOE) with a reduced risk of HCC in patients with cirrhosis. Conversely, carriage of rs187429064:G in TM6SF2 is associated with an increased risk of HCC in patients with cirrhosis.
Published: 2022
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35. Viral genome wide association study identifies novel hepatitis C virus polymorphisms associated with sofosbuvir treatment failure

Author: Smith, David A., Fernandez-Antunez, Carlota, Magri, Andrea, Bowden, Rory, Chaturvedi, Nimisha, Fellay, Jacques, McLauchlan, John, Foster, Graham R., Irving, William L., Simmonds, Peter, Pedergnana, Vincent, Ramirez, Santseharay, Bukh, Jens, Barnes, Eleanor, Ansari, M. Azim, Ball, Jonathan, Brainard, Diana, Burgess, Gary, Cooke, Graham, Dillon, John, Gore, Charles, Guha, Neil, Halford, Rachel, Herath, Cham, Holmes, Chris, Howe, Anita, Hudson, Emma, Irving, William, Khakoo, Salim, Klenerman, Paul, Koletzki, Diana, Martin, Natasha, Massetto, Benedetta, Mbisa, Tamyo, McHutchison, John, McKeating, Jane, Miners, Alec, Murray, Andrea, Shaw, Peter, Spencer, Chris C. A., Targett-Adams, Paul, Thomson, Emma, Vickerman, Peter, Zitzmann, Nicole, Nuffield Department of Medicine [Oxford, UK] (Big Data Institute), University of Oxford, University of Copenhagen = Københavns Universitet (UCPH), The Wellcome Trust Centre for Human Genetics [Oxford], Ecole Polytechnique Fédérale de Lausanne (EPFL), Université de Lausanne = University of Lausanne (UNIL), Swiss Institute of Bioinformatics [Lausanne] (SIB), Centre Hospitalier Universitaire Vaudois [Lausanne] (CHUV), University of Glasgow, Queen Mary University of London (QMUL), University of Nottingham, UK (UON), Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), STOP-HCV Consortium, Ball, J., Brainard, D., Burgess, G., Cooke, G., Dillon, J., Gore, C., Guha, N., Halford, R., Herath, C., Holmes, C., Howe, A., Hudson, E., Irving, W., Khakoo, S., Klenerman, P., Koletzki, D., Martin, N., Massetto, B., Mbisa, T., McHutchison, J., McKeating, J., Miners, A., Murray, A., Shaw, P., Spencer, CCA, Targett-Adams, P., Thomson, E., Vickerman, P., and Zitzmann, N.
Subjects: ns2, Sofosbuvir, [SDV]Life Sciences [q-bio], viruses, General Physics and Astronomy, Genome-wide association study, resistance-associated substitutions, Hepacivirus, Viral Nonstructural Proteins, Chronic liver disease, medicine.disease_cause, chemistry.chemical_compound, 0302 clinical medicine, Treatment Failure, 0303 health sciences, Multidisciplinary, Hepatitis C virus, virus diseases, Viral Load, Antivirals, 3. Good health, Hepatocellular carcinoma, 030211 gastroenterology & hepatology, Viral load, medicine.drug, Genotype, ribavirin, Science, Genome, Viral, Antiviral Agents/therapeutic use, Genome, Viral/genetics, Hepacivirus/drug effects, Hepacivirus/genetics, Hepacivirus/isolation & purification, Hepatitis C, Chronic/drug therapy, Hepatitis C, Chronic/virology, Humans, Polymorphism, Genetic, Sofosbuvir/therapeutic use, Viral Load/drug effects, Viral Load/genetics, Viral Nonstructural Proteins/genetics, Antiviral Agents, General Biochemistry, Genetics and Molecular Biology, Article, Virus, 03 medical and health sciences, medicine, Potency, emergence, 030304 developmental biology, NS3, business.industry, Ribavirin, General Chemistry, biochemical phenomena, metabolism, and nutrition, Hepatitis C, Chronic, medicine.disease, Virology, infection, digestive system diseases, chemistry, Viral infection, protein, business
Abstract: Sofosbuvir is a common therapy in hepatitis C virus infection, which targets the NS5B polymerase. Here, Smith et al. analyze the association between whole genome HCV polymorphisms and sofosbuvir treatment failure and identify three common polymorphisms present in non-targeted NS2 and NS3 proteins associated with reduced treatment response., Persistent hepatitis C virus (HCV) infection is a major cause of chronic liver disease, worldwide. With the development of direct-acting antivirals, treatment of chronically infected patients has become highly effective, although a subset of patients responds less well to therapy. Sofosbuvir is a common component of current de novo or salvage combination therapies, that targets the HCV NS5B polymerase. We use pre-treatment whole-genome sequences of HCV from 507 patients infected with HCV subtype 3a and treated with sofosbuvir containing regimens to detect viral polymorphisms associated with response to treatment. We find three common polymorphisms in non-targeted HCV NS2 and NS3 proteins are associated with reduced treatment response. These polymorphisms are enriched in post-treatment HCV sequences of patients unresponsive to treatment. They are also associated with lower reductions in viral load in the first week of therapy. Using in vitro short-term dose-response assays, these polymorphisms do not cause any reduction in sofosbuvir potency, suggesting an indirect mechanism of action in decreasing sofosbuvir efficacy. The identification of polymorphisms in NS2 and NS3 proteins associated with poor treatment outcomes emphasises the value of systematic genome-wide analyses of viruses in uncovering clinically relevant polymorphisms that impact treatment.
Published: 2021

36. The rs429358 Locus in Apolipoprotein E Is Associated With Hepatocellular Carcinoma in Patients With Cirrhosis

Author: Innes, Hamish, primary, Nischalke, Hans Dieter, additional, Guha, Indra Neil, additional, Weiss, Karl Heinz, additional, Irving, Will, additional, Gotthardt, Daniel, additional, Barnes, Eleanor, additional, Fischer, Janett, additional, Ansari, M. Azim, additional, Rosendahl, Jonas, additional, Lin, Shang‐Kuan, additional, Marot, Astrid, additional, Pedergnana, Vincent, additional, Casper, Markus, additional, Benselin, Jennifer, additional, Lammert, Frank, additional, McLauchlan, John, additional, Lutz, Philip L., additional, Hamill, Victoria, additional, Mueller, Sebastian, additional, Morling, Joanne R., additional, Semmler, Georg, additional, Eyer, Florian, additional, von Felden, Johann, additional, Link, Alexander, additional, Vogel, Arndt, additional, Marquardt, Jens U., additional, Sulk, Stefan, additional, Trebicka, Jonel, additional, Valenti, Luca, additional, Datz, Christian, additional, Reiberger, Thomas, additional, Schafmayer, Clemens, additional, Berg, Thomas, additional, Deltenre, Pierre, additional, Hampe, Jochen, additional, Stickel, Felix, additional, and Buch, Stephan, additional
Published: 2021
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37. An HLA-I signature favouring KIR-educated Natural Killer cells mediates immune control of HIV in children and contrasts with the HLA-B-restricted CD8+ T-cell-mediated immune control in adults

Author: Vieira, Vinicius A., primary, Adland, Emily, additional, Malone, David F. G., additional, Martin, Maureen P., additional, Groll, Andreas, additional, Ansari, M. Azim, additional, Garcia-Guerrero, Maria C., additional, Puertas, Mari C., additional, Muenchhoff, Maximilian, additional, Guash, Claudia Fortuny, additional, Brander, Christian, additional, Martinez-Picado, Javier, additional, Bamford, Alasdair, additional, Tudor-Williams, Gareth, additional, Ndung’u, Thumbi, additional, Walker, Bruce D., additional, Ramsuran, Veron, additional, Frater, John, additional, Jooste, Pieter, additional, Peppa, Dimitra, additional, Carrington, Mary, additional, and Goulder, Philip J. R., additional
Published: 2021
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38. Immunogenicity of standard and extended dosing intervals of BNT162b2 mRNA vaccine

Author: Payne, Rebecca P., primary, Longet, Stephanie, additional, Austin, James A., additional, Skelly, Donal T., additional, Dejnirattisai, Wanwisa, additional, Adele, Sandra, additional, Meardon, Naomi, additional, Faustini, Sian, additional, Al-Taei, Saly, additional, Moore, Shona C., additional, Tipton, Tom, additional, Hering, Luisa M., additional, Angyal, Adrienn, additional, Brown, Rebecca, additional, Nicols, Alexander R., additional, Gillson, Natalie, additional, Dobson, Susan L., additional, Amini, Ali, additional, Supasa, Piyada, additional, Cross, Andrew, additional, Bridges-Webb, Alice, additional, Reyes, Laura Silva, additional, Linder, Aline, additional, Sandhar, Gurjinder, additional, Kilby, Jonathan A., additional, Tyerman, Jessica K., additional, Altmann, Thomas, additional, Hornsby, Hailey, additional, Whitham, Rachel, additional, Phillips, Eloise, additional, Malone, Tom, additional, Hargreaves, Alexander, additional, Shields, Adrian, additional, Saei, Ayoub, additional, Foulkes, Sarah, additional, Stafford, Lizzie, additional, Johnson, Sile, additional, Wootton, Daniel G., additional, Conlon, Christopher P., additional, Jeffery, Katie, additional, Matthews, Philippa C., additional, Frater, John, additional, Deeks, Alexandra S., additional, Pollard, Andrew J., additional, Brown, Anthony, additional, Rowland-Jones, Sarah L., additional, Mongkolsapaya, Juthathip, additional, Barnes, Eleanor, additional, Hopkins, Susan, additional, Hall, Victoria, additional, Dold, Christina, additional, Duncan, Christopher J.A., additional, Richter, Alex, additional, Carroll, Miles, additional, Screaton, Gavin, additional, de Silva, Thushan I., additional, Turtle, Lance, additional, Klenerman, Paul, additional, Dunachie, Susanna, additional, Abuelgasim, Hibatullah, additional, Adland, Emily, additional, Adlou, Syed, additional, Akther, Hossain Delowar, additional, Alhussni, Ahmed, additional, Ali, Mohammad, additional, Ansari, M. Azim, additional, Arancibia-Cárcamo, Carolina V., additional, Bayley, Martin, additional, Brown, Helen, additional, Chalk, Jeremy, additional, Chand, Meera, additional, Chawla, Anu, additional, Chinnakannan, Senthil, additional, Cutteridge, Joseph, additional, de Lara, Catherine, additional, Denly, Lucy, additional, Diffey, Ben, additional, Dimitriadis, Stavros, additional, Drake, Thomas M., additional, Donnison, Timothy, additional, Dupont, Maeva, additional, Eyre, David, additional, Fairman, Alex, additional, Gardiner, Siobhan, additional, Gilbert-Jarmillo, Javier, additional, Goulder, Philip, additional, Hackstein, Carl-Philipp, additional, Hambleton, Sophie, additional, Haniffa, Muzlifah, additional, Haworth, Jenny, additional, Holmes, Jennifer, additional, Horner, Emily, additional, Jämsén, Anni, additional, Jones, Chris, additional, Kasanyinga, Mwila, additional, Kelly, Sinead, additional, Kirk, Rosemary, additional, Knight, Michael L., additional, Lawrie, Allan, additional, Lee, Lian, additional, Lett, Lauren, additional, Lillie, Katy, additional, Lim, Nicholas, additional, Mehta, Hema, additional, Mentzer, Alexander J., additional, O’Donnell, Denise, additional, Ogbe, Ane, additional, Pace, Matthew, additional, Payne, Brendan A.I., additional, Platt, Gareth, additional, Poolan, Sonia, additional, Provine, Nicholas, additional, Ramamurthy, Narayan, additional, Robinson, Nichola, additional, Romaniuk, Leigh, additional, Rongkard, Patpong, additional, Sampson, Oliver L., additional, Simmons, Beatrice, additional, Spegarova, Jarmila S., additional, Stephenson, Emily, additional, Subramaniam, Kris, additional, Thaventhiran, James, additional, Thomas, Sarah, additional, Travis, Simon, additional, Tucker, Stephanie, additional, Turton, Helena, additional, Watson, Adam, additional, Watson, Lisa, additional, Weeks, Esme, additional, Wilson, Robert, additional, Wood, Steven, additional, Wright, Rachel, additional, Xiao, Huiyuan, additional, and Zawia, Amira A.T., additional
Published: 2021
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39. Genetic variation in TERTmodifies the risk of hepatocellular carcinoma in alcohol-related cirrhosis: results from a genome-wide case-control study

Author: Buch, Stephan, Innes, Hamish, Lutz, Philipp Ludwig, Nischalke, Hans Dieter, Marquardt, Jens U, Fischer, Janett, Weiss, Karl Heinz, Rosendahl, Jonas, Marot, Astrid, Krawczyk, Marcin, Casper, Markus, Lammert, Frank, Eyer, Florian, Vogel, Arndt, Marhenke, Silke, von Felden, Johann, Sharma, Rohini, Atkinson, Stephen Rahul, McQuillin, Andrew, Nattermann, Jacob, Schafmayer, Clemens, Franke, Andre, Strassburg, Christian, Rietschel, Marcella, Altmann, Heidi, Sulk, Stefan, Thangapandi, Veera Raghavan, Brosch, Mario, Lackner, Carolin, Stauber, Rudolf E, Canbay, Ali, Link, Alexander, Reiberger, Thomas, Mandorfer, Mattias, Semmler, Georg, Scheiner, Bernhard, Datz, Christian, Romeo, Stefano, Ginanni Corradini, Stefano, Irving, William Lucien, Morling, Joanne R, Guha, Indra Neil, Barnes, Eleanor, Ansari, M Azim, Quistrebert, Jocelyn, Valenti, Luca, Mu¨ller, Sascha A, Morgan, Marsha Yvonne, Dufour, Jean-Francois, Trebicka, Jonel, Berg, Thomas, Deltenre, Pierre, Mueller, Sebastian, Hampe, Jochen, and Stickel, Felix
Abstract: ObjectiveHepatocellular carcinoma (HCC) often develops in patients with alcohol-related cirrhosis at an annual risk of up to 2.5%. Some host genetic risk factors have been identified but do not account for the majority of the variance in occurrence. This study aimed to identify novel susceptibility loci for the development of HCC in people with alcohol related cirrhosis.DesignPatients with alcohol-related cirrhosis and HCC (cases: n=1214) and controls without HCC (n=1866), recruited from Germany, Austria, Switzerland, Italy and the UK, were included in a two-stage genome-wide association study using a case–control design. A validation cohort of 1520 people misusing alcohol but with no evidence of liver disease was included to control for possible association effects with alcohol misuse. Genotyping was performed using the InfiniumGlobal Screening Array (V.24v2, Illumina) and the OmniExpress Array (V.24v1-0a, Illumina).ResultsAssociations with variants rs738409 in PNPLA3and rs58542926 in TM6SF2previously associated with an increased risk of HCC in patients with alcohol-related cirrhosis were confirmed at genome-wide significance. A novel locus rs2242652(A) in TERT(telomerase reverse transcriptase) was also associated with a decreased risk of HCC, in the combined meta-analysis, at genome-wide significance (p=6.41×10−9, OR=0.61 (95% CI 0.52 to 0.70). This protective association remained significant after correction for sex, age, body mass index and type 2 diabetes (p=7.94×10−5, OR=0.63 (95% CI 0.50 to 0.79). Carriage of rs2242652(A) in TERTwas associated with an increased leucocyte telomere length (p=2.12×10−44).ConclusionThis study identifies rs2242652 in TERTas a novel protective factor for HCC in patients with alcohol-related cirrhosis.
Published: 2023
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40. Using host genetics to infer the global spread and evolutionary history of HCV subtype 3a.

Author: Lin, Shang-Kuan, Maio, Nicola De, Pedergnana, Vincent, Wu, Chieh-Hsi, Thézé, Julien, Wilson, Daniel J, Barnes, Eleanor, and Ansari, M Azim
Subjects: GENEALOGY, HEPATITIS C virus, GENETICS, VIRAL transmission
Abstract: Studies have shown that hepatitis C virus subtype 3a (HCV-3a) is likely to have been circulating in South Asia before its global spread. However, the time and route of this dissemination remain unclear. For the first time, we generated host and virus genome-wide data for more than 500 patients infected with HCV-3a from the UK, North America, Australia, and New Zealand. We used the host genomic data to infer the ancestry of the patients and used this information to investigate the epidemic history of HCV-3a. We observed that viruses from hosts of South Asian ancestry clustered together near the root of the tree, irrespective of the sampling country, and that they were more diverse than viruses from other host ancestries. We hypothesized that South Asian hosts are more likely to have been infected in South Asia and used the inferred host ancestries to distinguish between the location where the infection was acquired and where the sample was taken. Next, we inferred that three independent transmission events resulted in the spread of the virus from South Asia to the UK, North America, and Oceania. This initial spread happened during or soon after the end of World War II. This was subsequently followed by many independent transmissions between the UK, North America, and Oceania. Using both host and virus genomic information can be highly informative in studying the virus epidemic history, especially in the context of chronic infections where migration histories need to be accounted for. [ABSTRACT FROM AUTHOR]
Published: 2021
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41. An HLA-I signature favouring KIR-educated Natural Killer cells mediates immune control of HIV in children and contrasts with the HLA-B-restricted CD8+ T-cell-mediated immune control in adults.

Author: Adriano Vieira, Vinicius, Adland, Emily, Malone, David F. G., Martin, Maureen P., Groll, Andreas, Ansari, M. Azim, Garcia-Guerrero, Maria C., Puertas, Mari C., Muenchhoff, Maximilian, Guash, Claudia Fortuny, Brander, Christian, Martinez-Picado, Javier, Bamford, Alasdair, Tudor-Williams, Gareth, Ndung'u, Thumbi, Walker, Bruce D., Ramsuran, Veron, Frater, John, Jooste, Pieter, and Peppa, Dimitra
Subjects: ADULTS, HIV-positive children, CD8 antigen, IMMUNE response, CELL populations, KILLER cells, AGE groups
Abstract: Natural Killer (NK) cells contribute to HIV control in adults, but HLA-B-mediated T-cell activity has a more substantial impact on disease outcome. However, the HLA-B molecules influencing immune control in adults have less impact on paediatric infection. To investigate the contribution NK cells make to immune control, we studied >300 children living with HIV followed over two decades in South Africa. In children, HLA-B alleles associated with adult protection or disease-susceptibility did not have significant effects, whereas Bw4 (p = 0.003) and low HLA-A expression (p = 0.002) alleles were strongly associated with immunological and viral control. In a comparator adult cohort, Bw4 and HLA-A expression contributions to HIV disease outcome were dwarfed by those of protective and disease-susceptible HLA-B molecules. We next investigated the immunophenotype and effector functions of NK cells in a subset of these children using flow cytometry. Slow progression and better plasma viraemic control were also associated with high frequencies of less terminally differentiated NKG2A+NKp46+CD56dim NK cells strongly responsive to cytokine stimulation and linked with the immunogenetic signature identified. Future studies are indicated to determine whether this signature associated with immune control in early life directly facilitates functional cure in children. Author summary: In adults, immune control of HIV is strongly influenced by antiviral CD8+ T-cell responses restricted by 'protective' HLA class I molecules, such as HLA-B*57, and by 'disease-susceptible' HLA class I molecules such as HLA-B*58:02. By contrast, Natural Killer (NK) cells responses make a smaller, albeit significant, contribution. In this study, we evaluate in children living with HIV the contribution of NK cell responses to immune control of HIV, in an age group where HIV-specific CD8+ T-cell responses have less impact on disease outcome. A cohort of >300 therapy-naïve children living with HIV shows that a genetic signature favouring a KIR-education on NK cells is associated with slow progression and better viraemic control. Consistent with this, we observed control of HIV viraemia and lower total HIV DNA levels among children was associated with a less differentiated NKG2A+NKp46+ CD56dim NK cell population that functionally was highly responsive to cytokine stimulation. Thus, the study identifies a signature that can impact future therapeutic strategies to achieve remission in children. [ABSTRACT FROM AUTHOR]
Published: 2021
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42. Genetic variation in TERT modifies the risk of hepatocellular carcinoma in alcohol-related cirrhosis: results from a genome-wide case-control study.

Author: Buch S, Innes H, Lutz PL, Nischalke HD, Marquardt JU, Fischer J, Weiss KH, Rosendahl J, Marot A, Krawczyk M, Casper M, Lammert F, Eyer F, Vogel A, Marhenke S, von Felden J, Sharma R, Atkinson SR, McQuillin A, Nattermann J, Schafmayer C, Franke A, Strassburg C, Rietschel M, Altmann H, Sulk S, Thangapandi VR, Brosch M, Lackner C, Stauber RE, Canbay A, Link A, Reiberger T, Mandorfer M, Semmler G, Scheiner B, Datz C, Romeo S, Ginanni Corradini S, Irving WL, Morling JR, Guha IN, Barnes E, Ansari MA, Quistrebert J, Valenti L, Müller SA, Morgan MY, Dufour JF, Trebicka J, Berg T, Deltenre P, Mueller S, Hampe J, and Stickel F
Subjects: Humans, Case-Control Studies, Diabetes Mellitus, Type 2 complications, Genetic Variation, Genome-Wide Association Study, Polymorphism, Single Nucleotide, Risk Factors, Carcinoma, Hepatocellular etiology, Carcinoma, Hepatocellular genetics, Genetic Predisposition to Disease, Liver Cirrhosis, Alcoholic complications, Liver Cirrhosis, Alcoholic genetics, Liver Neoplasms etiology, Liver Neoplasms genetics, Telomerase genetics
Abstract: Objective: Hepatocellular carcinoma (HCC) often develops in patients with alcohol-related cirrhosis at an annual risk of up to 2.5%. Some host genetic risk factors have been identified but do not account for the majority of the variance in occurrence. This study aimed to identify novel susceptibility loci for the development of HCC in people with alcohol related cirrhosis., Design: Patients with alcohol-related cirrhosis and HCC (cases: n=1214) and controls without HCC (n=1866), recruited from Germany, Austria, Switzerland, Italy and the UK, were included in a two-stage genome-wide association study using a case-control design. A validation cohort of 1520 people misusing alcohol but with no evidence of liver disease was included to control for possible association effects with alcohol misuse. Genotyping was performed using the InfiniumGlobal Screening Array (V.24v2, Illumina) and the OmniExpress Array (V.24v1-0a, Illumina)., Results: Associations with variants rs738409 in PNPLA3 and rs58542926 in TM6SF2 previously associated with an increased risk of HCC in patients with alcohol-related cirrhosis were confirmed at genome-wide significance. A novel locus rs2242652(A) in TERT (telomerase reverse transcriptase) was also associated with a decreased risk of HCC, in the combined meta-analysis, at genome-wide significance (p=6.41×10 -9 , OR=0.61 (95% CI 0.52 to 0.70). This protective association remained significant after correction for sex, age, body mass index and type 2 diabetes (p=7.94×10 -5 , OR=0.63 (95% CI 0.50 to 0.79). Carriage of rs2242652(A) in TERT was associated with an increased leucocyte telomere length (p=2.12×10 -44 )., Conclusion: This study identifies rs2242652 in TERT as a novel protective factor for HCC in patients with alcohol-related cirrhosis., Competing Interests: Competing interests: JT has received speaking and/or consulting fees from Versantis, Gore, Bayer, Alexion, Norgine, Grifols and CSL Behring., (© Author(s) (or their employer(s)) 2023. Re-use permitted under CC BY. Published by BMJ.)
Published: 2023
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