2024

  • Absolute quantitative and base-resolution sequencing reveals comprehensive landscape of pseudouridine across the human transcriptome

    Xu H, Kong L, Cheng J, Moussawi KA, Chen X, Iqbal A, Wing PAC, Harris JM, Tsukuda S, Embare-Buh A, Wei G, Castello A, Kriaucionis S, McKeating JA, and Song CX.

    Nature Methods (2024)

  • An atlas of the human liver diurnal transcriptome and its perturbation by hepatitis C virus infection

    Mukherji A, Jühling F, Simanjuntak Y, Crouchet E, Del Zompo F, Teraoka Y, Haller A, Baltzinger P, Paritala S, Rasha F, Fujiwara N, Gadenne C, Slovic N, Oudot MA, Durand SC, Ponsolles C, Schuster C, Zhuang X, Holmes J, Yeh M-L, Abe-Chayama H, Heikenwälder M, Sangiovanni A, Iavarone M, Colombo M, Foung SKH, McKeating JA, Davidson I, Yu M-L, Chung RT, Hoshida Y, Chayama K, Lupberger J and Baumert TF

    Nature Communications (2024)

  • Characterisation of HBV and co-infection with HDV and HIV through spatial transcriptomics

    Cross A, Harris JM, Arb-Barnes E, Nixon C, Dhairyawan R, Hall A, Quaglia A, Issa F, Kennedy PTF, McKeating JA, Gill US, and Peppa D.

    eGastroenterology (2024)

  • Highlights from the 2023 International Meeting on the Molecular Biology of Hepatitis B Virus

    HBV2023, Allwiess L, Cohen C, Dias J, Fumagalli V, Guo H, Harris M, Hu J, Iannacone M, sogawa M, J WJ, Kim KH, Kramvis A, Li W, Lucifora J, Muramatsu M, Neuveut C, Ploss A, Pollicino T, Protzer U, Tan A, Tanaka Y, Tu T, Tsukuda S, Thimme R, Urban S, Watashi K, Yuan Z, Yeh SH, McKeating JA, and Revill P.

    Journal of General Virology (2024)

  • Hypoxia inducible factors inhibit respiratory syncytial virus infection by modulation of nucleolin expression.

    Zhuang X, Gallo G, Sharma P, Ha J, Magri A, Borrmann H, Harris JM, Tsukuda S, Bentley E, Kirby A, de Neck S, Yang H, Balfe P, Wing PAC, Matthews D, Harris AL, Kipar A, Stewart JP, Bailey D, and McKeating JA

    iScience (2024)

    https://ars.els-cdn.com/content/image/1-s2.0-S2589004223028407-fx1_lrg.jpg
  • The N6-methyladenosine demethylase ALKBH5 regulates the hypoxic HBV transcriptome

    Tsukuda S, Harris JM, Magri A, Balfe P, Wing PAC, Siddiqui A, and McKeating JA.

    PLoS Pathogens (2024)

  • Oxygen-dependent histone lysine demethylase 4 restricts hepatitis B virus replication

    Harris JM, Magri A, Faria AR, Tsukuda S, Balfe P, Wing PAC, and McKeating JA

    Journal of Biological Chemistry (2024)

  • CTCF regulates hepatitis B virus cccDNA chromatin topology

    Dobrica MO, Varghese CS, Harris JM, Ferguson J, Magri A, Arnold R, Varnai C, Parish JL, and McKeating JA. 

    Journal of General Virology (2024)

2023

  • ASSP2 binds to hepatitis C virus NS5A protein via an SH3 domain/PxxP motif-mediated interaction and potentiates infection

    Smirnov A, Magri A, Lotz R, Huan X, Yin C, Harris M, Osterburg O, Dötsch V, McKeating JA and Lu X.

    Journal of General Virology (2023)

  • Hypoxia dampens innate immune signalling at early time points and increases Zika virus replication in iPSC-derived macrophages

    Schilling M, Vaughan-Jackson A, James W, and McKeating JA.

    Journal of General Virology (2023)

  • Inhibition of salt inducible kinases reduces rhythmic HIV-1 replication and reactivation from latency

    Borrmann H, Ismed D, Kliszcak A, Borrow P, Vasudevan S, Jagannath A, Zhuang X, and McKeating JA.

    Journal of General Virology (2023)

  • HLA-E-restricted SARS-CoV-2-specific T cells from convalescent COVID-19 patients suppress virus replication despite HLA class Ia down-regulation

    Yang H, Sun H, Brackenridge S, Zhuang X, Wing PAC, Quastel M, Walters L, Garner L, Wang B, Yao X, Felce SL, Peng Y, Moore S, Peeters BWA, Rei M, Gomes JC, Tomas A, Davidson A, Semple MG, Turtle LCW, Openshaw PJM, Baillie JK, Mentzer A, Klenerman P, ISARIC4C Investigators, Borrow P, Dong T, McKeating JA, Gillespie GM, and McMichael AJ.

    Science Immunology (2023)

  • Molecular components of the circadian clock regulate HIV-1 replication

    Borrmann H, Ulkar G, Kliszczak AE, Ismed D, Schilling M, Magri A, Harris JM, Balfe P, Vasuvedan S, Borrow P, Zhuang X, and McKeating JA.

    iScience (2023)

  • An enrichment protocol and analysis pipeline for long read sequencing of the hepatitis B virus transcriptome

    Ng E, Dobrica M-O, Harris JM, Wu Y, Tsukuda S, Wing PAC, Piazza P, Balfe P, Matthews PC, Ansari MA, and McKeating JA.

    Journal of General Virology (2023)

  • An ACAT inhibitor suppresses SARS-CoV-2 replication and boosts antiviral T cell activity

    Wing PAC, Schmidt NM, Peters R, Erdmann M, Brown R, Wang H, Swadling L, COVIDsortium Investigators, Newman J, Thakur N, Shionya K, Morgan SB, Hinks TSC, Watashi K, Bailey D, Hansen SB, Davidson AD, Maini MK, and McKeating JA.

    PLoS Pathogens (2023)

2022

  • Direct RNA sequencing of respiratory syncytial virus infected human cells generates a detailed overview of RSV polycistronic mRNA and transcript abundance

    Donovan-Banfield I, Milligan R, Hall S, Gao T, Murphy E, Li J, Shawli GT, Hiscox J, Zhuang X, McKeating JA, Fearns R, and Matthews DA.

    PLoS One (2022)

  • Sleep and circadian rhythm disruption alters the lung transcriptome to predispose to viral infection

    Taylor L, Von Lendenfeld F, Ashton A, Sanghani H, Di Pretoro S, Usselmann L, Veretennikova M, Dallman R, McKeating JA, Vasudevan S, and Jagannath A.

    iScience (2022)

  • Hypoxia inducible factors regulate infectious SARS-CoV-2, epithelial damage and respiratory symptoms in a hamster COVID-19 model

    Wing PAC, Prange-Barczynska M, Cross A, Crotta S, Orbegozo Rubio C, Cheng X, Harris JM, Zhuang X, Johnson RL, Ryan KA, Hall Y, Carroll MW, Issa F, Balfe P, Wack A, Bishop T, Salguero FJ, and McKeating JA.

    PLOS Pathogens (2022)

  • Time-of-Day Variation in SARS-CoV-2 RNA Levels during the Second Wave of COVID-19.

    Zhuang X, Wang W, Borrmann H, Balfe P, Matthews PC, Eyre DW, Klerman EB, and McKeating JA.

    Viruses (2022)

  • Inflammatory Gene Expression Associates with Hepatitis B Virus cccDNA- but Not Integrant-Derived Transcripts in HBeAg Negative Disease.

    Magri A, Harris JM, D'Arienzo V, Minisini R, Jühling F, Wing PAC, Rapetti R, Leutner M, Testoni B, Baumert TF, Zoulim F, Balfe P, Pirisi M, McKeating JA.

    Viruses (2022)

  • Hypoxia is more than HIFs

    Harris JM, McKeating JA, and Wing PAC

    Journal of Hepatology (2022)

  • The role of circadian clock pathways in viral replication.

    Zhuang X, Edgar RS, and McKeating JA.

    Seminars in Immunopathology (2022)

  • Absolute quantitation of individual SARS-CoV-2 RNA molecules provides a new paradigm for infection dynamics and variant differences.

    Lee JY, Wing PAC, Gala DS, Noerenberg M, Järvelin AI, Titlow J, Zhuang X, Palmalux N, Iselin L, Thompson MK, Parton RM, Prange-Barczynska M, Wainman A, Salguero FJ, Bishop T, Agranoff D, James W, Castello A, McKeating JA, and Davis I

    eLife (2022)

  • Acute intermittent hypoxia drives hepatic de novo lipogenesis in humans and rodents

    Hazlehurst, JM., Lim, TR., Charlton, C., Miller, JJ., Gathercole, LL., Cornfield, T., Nikolaou, N., Harris, SE., Moolla, A., Othonos, N., Heather,LC., Marjot, T., Tyler, DJ., Carr, C., Hodson, L., Mckeating, JA., and Tomlinson, JW.

    Metabolism Open (2022)

  • The HCV Envelope Glycoprotein Down-Modulates NF-κB Signalling and Associates With Stimulation of the Host Endoplasmic Reticulum Stress Pathway.

    McKay LGA, Thomas J, Albalawi W, Fattaccioli A, Dieu M, Ruggiero A, McKeating JA, Ball JK, Tarr AW, Renard P, Pollakis G, and Paxton WA.

    Frontiers in Immunology (2022)

  • Are the Patterns of Cytomegalovirus Viral Load Seen After Solid Organ Transplantation Affected by Circadian Rhythm?

    Rafferty H, Murray MJ, Tam JCH, Macfarlane A, Smith C, Lumley SF, Atabani S, McKeating JA, Sharma D, Reeves M, Whitmore D, and Griffiths P.

    Journal of Infectious Diseases (2022)

  • Time of Day of Vaccination Affects SARS-CoV-2 Antibody Responses in an Observational Study of Health Care Workers.

    Wang W, Balfe P, Eyre DW, Lumley SF, O'Donnell D, Warren F, Crook DW, Jeffery K, Matthews PC, Klerman EB, and McKeating JA.

    Journal of Biological Rhythms (2022)

2021

  • A Role for B Cells to Transmit Hepatitis C Virus Infection.

    Desombere I, Van Houtte F, Farhoudi A, Verhoye L, Buysschaert C, Gijbels Y, Couvent S, Swinnen W, Van Vlierberghe H, Elewaut A, Magri A, Stamataki Z, Meuleman P, McKeating JA, and Leroux-Roels G.

    Frontiers in Immunology (2021)

  • An immunodominant NP105-113-B*07:02 cytotoxic T cell response controls viral replication and is associated with less severe COVID-19 disease.

    Peng Y, Felce SL, Dong D, Penkava F, Mentzer AJ, Yao X, Liu G, Yin Z, Chen JL, Lu Y, Wellington D, Wing PAC, Dominey-Foy DCC, Jin C, Wang W, Hamid MA, Fernandes RA, Wang B, Fries A, Zhuang X, Ashley N, Rostron T, Waugh C, Sopp P, Hublitz P, Beveridge R, Tan TK, Dold C, Kwok AJ, Rich-Griffin C, Dejnirattisa W, Liu C, Kurupati P, Nassiri I, Watson RA, Tong O, Taylor CA, Kumar Sharma P, Sun B, Curion F, Revale S, Garner LC, Jansen K, Ferreira RC, Attar M, Fry JW, Russell RA; COMBAT Consortium, Stauss HJ, James W, Townsend A, Ho LP, Klenerman P, Mongkolsapaya J, Screaton GR, Dendrou C, Sansom SN, Bashford-Rogers R, Chain B, Smith GL, McKeating JA, Fairfax BP, Bowness P, McMichael AJ, Ogg G, Knight JC, and Dong T.

    Nature Immunology (2021)

  • Viral genome wide association study identifies novel hepatitis C virus polymorphisms associated with sofosbuvir treatment failure.

    Smith DA, Fernandez-Antunez C, Magri A, Bowden R, Chaturvedi N, Fellay J, McLauchlan J, Foster GR, Irving WL; STOP-HCV Consortium, Simmonds P, Pedergnana V, Ramirez S, Bukh J, Barnes E, and Ansari MA.

    Nature Communications (2021)

  • The circadian clock component BMAL1 regulates SARS-CoV-2 entry and replication in lung epithelial cells.

    Zhuang X, Tsukuda S, Wrensch F, Wing PAC, Schilling M, Harris JM, Borrmann H, Morgan SB, Cane JL, Mailly L, Thakur N, Conceicao C, Sanghani H, Heydmann L, Bach C, Ashton A, Walsh S, Tan TK, Schimanski L, Huang KA, Schuster C, Watashi K, Hinks TSC, Jagannath A, Vausdevan SR, Bailey D, Baumert TF, and McKeating JA.

    iScience (2021)

  • Hypoxia-Inducible Factor 1 Alpha-Mediated RelB/APOBEC3B Down-regulation Allows Hepatitis B Virus Persistence.

    Riedl T, Faure-Dupuy S, Rolland M, Schuehle S, Hizir Z, Calderazzo S, Zhuang X, Wettengel J, Lopez MA, Barnault R, Mirakaj V, Prokosch S, Heide D, Leuchtenberger C, Schneider M, Heßling B, Stottmeier B, Wessbecher IM, Schirmacher P, McKeating JA, Protzer U, Durantel D, Lucifora J, Dejardin E, and Heikenwalder M.

    Hepatology (2021)

  • Targeting human Acyl-CoA:cholesterol acyltransferase as a dual viral and T cell metabolic checkpoint.

    Schmidt NM, Wing PAC, Diniz MO, Pallett LJ, Swadling L, Harris JM, Burton AR, Jeffery-Smith A, Zakeri N, Amin OE, Kucykowicz S, Heemskerk MH, Davidson B, Meyer T, Grove J, Stauss HJ, Pineda-Torra I, Jolly C, Jury EC, McKeating JA, and Maini MK.

    Nature Communications (2021)

  • Supramolecular Cylinders Target Bulge Structures in the 5' UTR of the RNA Genome of SARS-CoV-2 and Inhibit Viral Replication*.

    Melidis L, Hill HJ, Coltman NJ, Davies SP, Winczura K, Chauhan T, Craig JS, Garai A, Hooper CAJ, Egan RT, McKeating JA, Hodges NJ, Stamataki Z, Grzechnik P, and Hannon MJ.

    Angewandte Chemie International Edition (2021)

  • Hypoxic and pharmacological activation of HIF inhibits SARS-CoV-2 infection of lung epithelial cells.

    Wing PAC, Keeley TP, Zhuang X, Lee JY, Prange-Barczynska M, Tsukuda S, Morgan SB, Harding AC, Argles ILA, Kurlekar S, Noerenberg M, Thompson CP, Huang KA, Balfe P, Watashi K, Castello A, Hinks TSC, James W, Ratcliffe PJ, Davis I, Hodson EJ, Bishop T, and McKeating JA.

    Cell Reports (2021)

  • Potential anti-COVID-19 agents, cepharanthine and nelfinavir, and their usage for combination treatment.

    Ohashi H, Watashi K, Saso W, Shionoya K, Iwanami S, Hirokawa T, Shirai T, Kanaya S, Ito Y, Kim KS, Nomura T, Suzuki T, Nishioka K, Ando S, Ejima K, Koizumi Y, Tanaka T, Aoki S, Kuramochi K, Suzuki T, Hashiguchi T, Maenaka K, Matano T, Muramatsu M, Saijo M, Aihara K, Iwami S, Takeda M, McKeating JA, and Wakita T.

    iScience (2021)

  • Estimating hepatitis B virus cccDNA persistence in chronic infection.

    Lythgoe KA, Lumley SF, Pellis L, McKeating JA, and Matthews PC.

    Virus Evolution (2021)

  • Circadian control of hepatitis B virus replication.

    Zhuang X, Forde D, Tsukuda S, D'Arienzo V, Mailly L, Harris JM, Wing PAC, Borrmann H, Schilling M, Magri A, Rubio CO, Maidstone RJ, Iqbal M, Garzon M, Minisini R, Pirisi M, Butterworth S, Balfe P, Ray DW, Watashi K, Baumert TF, and McKeating JA.

    Nature Communications (2021)

  • Hypoxia inducible factors regulate hepatitis B virus replication by activating the basal core promoter.

    Wing PAC, Liu PJ, Harris JM, Magri A, Michler T, Zhuang X, Borrmann H, Minisini R, Frampton NR, Wettengel JM, Mailly L, D'Arienzo V, Riedl T, Nobre L, Weekes MP, Pirisi M, Heikenwalder M, Baumert TF, Hammond EM, Mole DR, Protzer U, Balfe P, and McKeating JA.

    Journal of Hepatology (2021)

  • Clocks, Viruses, and Immunity: Lessons for the COVID-19 Pandemic.

    Sengupta S, Ince L, Sartor F, Borrmann H, Zhuang X, Naik A, Curtis A, and McKeating JA.

    Journal of Biological Rhythms (2021)

  • The Circadian Clock and Viral Infections.

    Borrmann H, McKeating JA, and Zhuang X.

    Journal of Biological Rhythms (2021)

  • The CCCTC-binding factor CTCF represses hepatitis B virus enhancer I and regulates viral transcription.

    D'Arienzo V, Ferguson J, Giraud G, Chapus F, Harris JM, Wing PAC, Claydon A, Begum S, Zhuang X, Balfe P, Testoni B, McKeating JA, and Parish JL.

    Cellular Microbiology (2021)

  • A PCR assay to quantify patterns of HBV transcription.

    D'Arienzo V, Magri A, Harris JM, Wing PAC, Ko C, Rubio CO, Revill PA, Protzer U, Balfe P, and McKeating JA.

    Journal of General Virology (2021)

2020

  • Oxygen Sensing and Viral Replication: Implications for Tropism and Pathogenesis.

    Liu PJ, Balfe P, McKeating JA, and Schilling M.

    Viruses (2020)

  • Cholesterol-modifying drugs in COVID-19.

    Schmidt NM, Wing PAC, McKeating JA, and Maini MK.

    Oxford Open Immunology (2020)

  • Hypoxic gene expression in chronic hepatitis B virus infected patients is not observed in state-of-the-art in vitro and mouse infection models.

    Liu PJ, Harris JM, Marchi E, D'Arienzo V, Michler T, Wing PAC, Magri A, Ortega-Prieto AM, van de Klundert M, Wettengel J, Durantel D, Dorner M, Klenerman P, Protzer U, Giotis ES, and McKeating JA.

    Scientific Reports (2020)

  • Synchronised infection identifies early rate-limiting steps in the hepatitis B virus life cycle.

    Chakraborty A, Ko C, Henning C, Lucko A, Harris JM, Chen F, Zhuang X, Wettengel JM, Roessler S, Protzer U, and McKeating JA.

    Cellular Microbiology (2020)

  • Pharmacological activation of the circadian component REV-ERB inhibits HIV-1 replication.

    Borrmann H, Davies R, Dickinson M, Pedroza-Pacheco I, Schilling M, Vaughan-Jackson A, Magri A, James W, Balfe P, Borrow P, McKeating JA, and Zhuang X.

    Scientific Reports (2020)

  • Hypoxic microenvironment shapes HIV-1 replication and latency.

    Zhuang X, Pedroza-Pacheco I, Nawroth I, Kliszczak AE, Magri A, Paes W, Rubio CO, Yang H, Ashcroft M, Mole D, Balfe P, Borrow P, and McKeating JA.

    Communications Biology (2020)

  • Accurate targeted long-read DNA methylation and hydroxymethylation sequencing with TAPS.

    Liu Y, Cheng J, Siejka-Zielińska P, Weldon C, Roberts H, Lopopolo M, Magri A, D'Arienzo V, Harris JM, McKeating JA, and Song CX.

    Genomes Biology (2020)

  • Cost-Effectiveness Analysis of Baseline Testing for Resistance-Associated Polymorphisms to Optimize Treatment Outcome in Genotype 1 Noncirrhotic Treatment-Naïve Patients With Chronic Hepatitis C Virus.

    Fawsitt CG, Vickerman P, Cooke GS; STOP HCV Consortium, and Welton NJ.

    Value in Health (2020)

2019

  • Bacterial flagellin promotes viral entry via an NF-kB and Toll Like Receptor 5 dependent pathway.

    Benedikz EK, Bailey D, Cook CNL, Gonçalves-Carneiro D, Buckner MMC, Blair JMA, Wells TJ, Fletcher NF, Goodall M, Flores-Langarica A, Kingsley RA, Madsen J, Teeling J, Johnston SL, MacLennan CA, Balfe P, Henderson IR, Piddock LJV, Cunningham AF, and McKeating JA.

    Scientific Reports (2019)

  • A dual role for SAMHD1 in regulating HBV cccDNA and RT-dependent particle genesis.

    Wing PA, Davenne T, Wettengel J, Lai AG, Zhuang X, Chakraborty A, D'Arienzo V, Kramer C, Ko C, Harris JM, Schreiner S, Higgs M, Roessler S, Parish JL, Protzer U, Balfe P, Rehwinkel J, and McKeating JA.

    Life Science Alliance (2019)

  • The circadian clock components BMAL1 and REV-ERBα regulate flavivirus replication.

    Zhuang X, Magri A, Hill M, Lai AG, Kumar A, Rambhatla SB, Donald CL, Lopez-Clavijo AF, Rudge S, Pinnick K, Chang WH, Wing PAC, Brown R, Qin X, Simmonds P, Baumert TF, Ray D, Loudon A, Balfe P, Wakelam M, Butterworth S, Kohl A, Jopling CL, Zitzmann N, and McKeating JA.

    Nature Communications (2019)

  • Hepatitis C virus infection is associated with hepatic and adipose tissue insulin resistance that improves after viral cure.

    Lim TR, Hazlehurst JM, Oprescu AI, Armstrong MJ, Abdullah SF, Davies NP, Flintham R, Balfe P, Mutimer DJ, McKeating JA, and Tomlinson JW.

    Clinical Endocrinology (2019)

  • Insights From Deep Sequencing of the HBV Genome-Unique, Tiny, and Misunderstood.

    McNaughton AL, D'Arienzo V, Ansari MA, Lumley SF, Littlejohn M, Revill P, McKeating JA, and Matthews PC.

    Gastroenterology (2019)

2018

  • Glucose and glutamine availability regulate HepG2 transcriptional responses to low oxygen.

    Lai AG, Forde D, Chang WH, Yuan F, Zhuang X, Orbegozo Rubio C, Song CX, and McKeating JA.

    Wellcome Open Research (2018)

  • Daytime variation in hepatitis C virus replication kinetics following liver transplant.

    Zhuang X, Lai AG, McKeating JA, Rowe I, and Balfe P.

    Wellcome Open Research (2019)

  • Metallo supramolecular cylinders inhibit HIV-1 TAR-TAT complex formation and viral replication in cellulo.

    Cardo L, Nawroth I, Cail PJ, McKeating JA, and Hannon MJ.

    Scientific Reports (2019)

  • Hepatitis B virus genome recycling and de novo secondary infection events maintain stable cccDNA levels.

    Ko C, Chakraborty A, Chou WM, Hasreiter J, Wettengel JM, Stadler D, Bester R, Asen T, Zhang K, Wisskirchen K, McKeating JA, Ryu WS, and Protzer U.

    Hepatology (2019)

Key Earlier Publications