Archive Page: Kellam Group | Virus Genomics

Archive Page: Kellam Group | Virus Genomics

Kellam Group

Archive Page - this page is maintained as a historical record and is no longer being updated. It was last edited in 2016.
pmp5882.jpgSanger Institute, Genome Research Limited

Our Research and Approach

Although virus genomes are small they are incredibly diverse and subject to rapid genetic change. In addition, the host organisms viruses infected produce a wide array of defences encoded by genes that are also subjected to accelerated evolution. At the most extreme end of this evolution is the mutation and selection of unique B cells that produce antibodies to counter the diversity of virus proteins and provide immunological memory. The aim of the Virus Genomics team was to understand how genetic changes in viruses and hosts influence the biological properties of viral pathogenesis, persistence and host susceptibility to infection.

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Paul Kellam
Group Leader

Paul was the Senior Group leader of the Virus Genomics Team at the Sanger Institute

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Key Projects, Collaborations, Tools & Data

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  • Nosocomial transmission of influenza: A retrospective cross-sectional study using next generation sequencing at a hospital in England (2012-2014).

    Blackburn RM, Frampton D, Smith CM, Fragaszy EB, Watson SJ et al.

    Influenza and other respiratory viruses 2019;13;6;556-563

  • Genomic analysis of respiratory syncytial virus infections in households and utility in inferring who infects the infant.

    Agoti CN, Phan MVT, Munywoki PK, Githinji G, Medley GF et al.

    Scientific reports 2019;9;1;10076

  • Essential role of inverted repeat in Epstein-Barr virus IR-1 in B cell transformation; geographical variation of the viral genome.

    Bridges R, Correia S, Wegner F, Venturini C, Palser A et al.

    Philosophical transactions of the Royal Society of London. Series B, Biological sciences 2019;374;1773;20180299

  • Heterogeneity of the Epstein-Barr Virus (EBV) Major Internal Repeat Reveals Evolutionary Mechanisms of EBV and a Functional Defect in the Prototype EBV Strain B95-8.

    Ba Abdullah MM, Palermo RD, Palser AL, Grayson NE, Kellam P et al.

    Journal of virology 2017;91;23

  • Role of HIV-specific CD8+ T cells in pediatric HIV cure strategies after widespread early viral escape.

    Leitman EM, Thobakgale CF, Adland E, Ansari MA, Raghwani J et al.

    The Journal of experimental medicine 2017;214;11;3239-3261

  • From clinical sample to complete genome: Comparing methods for the extraction of HIV-1 RNA for high-throughput deep sequencing.

    Cornelissen M, Gall A, Vink M, Zorgdrager F, Binter Š et al.

    Virus research 2017;239;10-16

  • Characterization of Posa and Posa-like virus genomes in fecal samples from humans, pigs, rats, and bats collected from a single location in Vietnam.

    Oude Munnink BB, Phan MVT, VIZIONS Consortium, Simmonds P, Koopmans MPG et al.

    Virus evolution 2017;3;2;vex022

  • Dynamic variation of CD5 surface expression levels within individual chronic lymphocytic leukemia clones.

    Bashford-Rogers RJ, Palser AL, Hodkinson C, Baxter J, Follows GA et al.

    Experimental hematology 2017;46;31-37.e10

  • Optimisation of ex vivo memory B cell expansion/differentiation for interrogation of rare peripheral memory B cell subset responses.

    Muir L, McKay PF, Petrova VN, Klymenko OV, Kratochvil S et al.

    Wellcome open research 2017;2;97

  • Eye on the B-ALL: B-cell receptor repertoires reveal persistence of numerous B-lymphoblastic leukemia subclones from diagnosis to relapse.

    Bashford-Rogers RJ, Nicolaou KA, Bartram J, Goulden NJ, Loizou L et al.

    Leukemia 2016;30;12;2312-2321

  • Resistance of Transmitted Founder HIV-1 to IFITM-Mediated Restriction.

    Foster TL, Wilson H, Iyer SS, Coss K, Doores K et al.

    Cell host & microbe 2016;20;4;429-442

  • Alphavirus Restriction by IFITM Proteins.

    Weston S, Czieso S, White IJ, Smith SE, Wash RS et al.

    Traffic (Copenhagen, Denmark) 2016;17;9;997-1013

  • Ebola virus disease cluster — Northern Sierra Leone, January 2016

    Alpren,C., Sloan,M., Boegler,K.A., Martin,D.W., Ervin,E. et al.

    Morbidity and Mortality Weekly Report 2016;65;26;681-3

  • Human Rhinovirus B and C Genomes from Rural Coastal Kenya.

    Agoti CN, Kiyuka PK, Kamau E, Munywoki PK, Bett A et al.

    Genome announcements 2016;4;4

  • Coalescent Inference Using Serially Sampled, High-Throughput Sequencing Data from Intra-Host HIV Infection.

    Dialdestoro K, Sibbesen JA, Maretty L, Raghwani J, Gall A et al.

    Genetics 2016

  • Complete Genome Characterization of Two Wild-Type Measles Viruses from Vietnamese Infants during the 2014 Outbreak.

    Oude Munnink BB, Phan MV, Kellam P, Cotten M and VIZIONS Consortium

    Genome announcements 2016;4;2

  • Rapid outbreak sequencing of Ebola virus in Sierra Leone identifies transmission chains linked to sporadic cases.

    Arias A, Watson SJ, Asogun D, Tobin EA, Lu J et al.

    Virus evolution 2016;2;1;vew016

  • The Vietnam Initiative on Zoonotic Infections (VIZIONS): A Strategic Approach to Studying Emerging Zoonotic Infectious Diseases.

    Rabaa MA, Tue NT, Phuc TM, Carrique-Mas J, Saylors K et al.

    EcoHealth 2015;12;4;726-35

  • A novel genus in the order Picornavirales detected in human stool.

    Oude Munnink BB, Cotten M, Deijs M, Jebbink MF, Bakker M et al.

    The Journal of general virology 2015;96;11;3440-3443

  • Molecular Epidemiology and Evolution of Influenza Viruses Circulating within European Swine between 2009 and 2013.

    Watson SJ, Langat P, Reid SM, Lam TT, Cotten M et al.

    Journal of virology 2015;89;19;9920-31

  • Lessons from Ebola: Improving infectious disease surveillance to inform outbreak management.

    Woolhouse ME, Rambaut A and Kellam P

    Science translational medicine 2015;7;307;307rv5

  • Dynamics of immunoglobulin sequence diversity in HIV-1 infected individuals.

    Hoehn KB, Gall A, Bashford-Rogers R, Fidler SJ, Kaye S et al.

    Philosophical transactions of the Royal Society of London. Series B, Biological sciences 2015;370;1676

  • Widespread Reassortment Shapes the Evolution and Epidemiology of Bluetongue Virus following European Invasion.

    Nomikou K, Hughes J, Wash R, Kellam P, Breard E et al.

    PLoS pathogens 2015;11;8;e1005056

  • IVA: accurate de novo assembly of RNA virus genomes.

    Hunt M, Gall A, Ong SH, Brener J, Ferns B et al.

    Bioinformatics (Oxford, England) 2015;31;14;2374-6

  • Immediate T-Helper 17 Polarization Upon Triggering CD11b/c on HIV-Exposed Dendritic Cells.

    Wilflingseder D, Schroll A, Hackl H, Gallasch R, Frampton D et al.

    The Journal of infectious diseases 2015;212;1;44-56

  • Disease progression despite protective HLA expression in an HIV-infected transmission pair.

    Brener J, Gall A, Batorsky R, Riddell L, Buus S et al.

    Retrovirology 2015;12;55

  • Discovery of a polyomavirus in European badgers (Meles meles) and the evolution of host range in the family Polyomaviridae.

    Hill SC, Murphy AA, Cotten M, Palser AL, Benson P et al.

    The Journal of general virology 2015;96;Pt 6;1411-22

  • Bat and pig IFN-induced transmembrane protein 3 restrict cell entry by influenza virus and lyssaviruses.

    Benfield CT, Smith SE, Wright E, Wash RS, Ferrara F et al.

    The Journal of general virology 2015;96;Pt 5;991-1005

  • Genome diversity of Epstein-Barr virus from multiple tumor types and normal infection.

    Palser AL, Grayson NE, White RE, Corton C, Correia S et al.

    Journal of virology 2015;89;10;5222-37

  • A novel X-linked trichothiodystrophy associated with a nonsense mutation in RNF113A.

    Corbett MA, Dudding-Byth T, Crock PA, Botta E, Christie LM et al.

    Journal of medical genetics 2015;52;4;269-74

  • Local evolutionary patterns of human respiratory syncytial virus derived from whole-genome sequencing.

    Agoti CN, Otieno JR, Munywoki PK, Mwihuri AG, Cane PA et al.

    Journal of virology 2015;89;7;3444-54

  • Host genetics of Epstein-Barr virus infection, latency and disease.

    Houldcroft CJ and Kellam P

    Reviews in medical virology 2015;25;2;71-84

  • Identification of a novel human rhinovirus C type by antibody capture VIDISCA-454.

    Jazaeri Farsani SM, Oude Munnink BB, Canuti M, Deijs M, Cotten M et al.

    Viruses 2015;7;1;239-51

  • Molecular evolution of broadly neutralizing Llama antibodies to the CD4-binding site of HIV-1.

    McCoy LE, Rutten L, Frampton D, Anderson I, Granger L et al.

    PLoS pathogens 2014;10;12;e1004552

  • Novel porcine-like human G26P[19] rotavirus identified in hospitalized paediatric diarrhoea patients in Ho Chi Minh City, Vietnam.

    My PV, Rabaa MA, Donato C, Cowley D, Phat VV et al.

    The Journal of general virology 2014;95;Pt 12;2727-33

  • Respiratory tract samples, viral load, and genome fraction yield in patients with Middle East respiratory syndrome.

    Memish ZA, Al-Tawfiq JA, Makhdoom HQ, Assiri A, Alhakeem RF et al.

    The Journal of infectious diseases 2014;210;10;1590-4

  • Accumulation of human-adapting mutations during circulation of A(H1N1)pdm09 influenza virus in humans in the United Kingdom.

    Elderfield RA, Watson SJ, Godlee A, Adamson WE, Thompson CI et al.

    Journal of virology 2014;88;22;13269-83

  • Evidence for camel-to-human transmission of MERS coronavirus.

    Madani TA, Azhar EI and Hashem AM

    The New England journal of medicine 2014;371;14;1360

  • Deep sequencing of norovirus genomes defines evolutionary patterns in an urban tropical setting.

    Cotten M, Petrova V, Phan MV, Rabaa MA, Watson SJ et al.

    Journal of virology 2014;88;19;11056-69

  • Phylogenetic studies of transmission dynamics in generalized HIV epidemics: an essential tool where the burden is greatest?

    Dennis AM, Herbeck JT, Brown AL, Kellam P, de Oliveira T et al.

    Journal of acquired immune deficiency syndromes (1999) 2014;67;2;181-95

  • Generation and characterization of influenza A viruses with altered polymerase fidelity.

    Cheung PP, Watson SJ, Choy KT, Fun Sia S, Wong DD et al.

    Nature communications 2014;5;4794

  • Genomic diversity of Epstein-Barr virus genomes isolated from primary nasopharyngeal carcinoma biopsy samples.

    Kwok H, Wu CW, Palser AL, Kellam P, Sham PC et al.

    Journal of virology 2014;88;18;10662-72

  • Capturing needles in haystacks: a comparison of B-cell receptor sequencing methods.

    Bashford-Rogers RJ, Palser AL, Idris SF, Carter L, Epstein M et al.

    BMC immunology 2014;15;29

  • Human immunodeficiency virus Tat associates with a specific set of cellular RNAs.

    Bouwman RD, Palser A, Parry CM, Coulter E, Rasaiyaah J et al.

    Retrovirology 2014;11;53

  • Community case clusters of Middle East respiratory syndrome coronavirus in Hafr Al-Batin, Kingdom of Saudi Arabia: a descriptive genomic study.

    Memish ZA, Cotten M, Watson SJ, Kellam P, Zumla A et al.

    International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases 2014;23;63-8

  • Human infection with MERS coronavirus after exposure to infected camels, Saudi Arabia, 2013.

    Memish ZA, Cotten M, Meyer B, Watson SJ, Alsahafi AJ et al.

    Emerging infectious diseases 2014;20;6;1012-5

  • Spread, circulation, and evolution of the Middle East respiratory syndrome coronavirus.

    Cotten M, Watson SJ, Zumla AI, Makhdoom HQ, Palser AL et al.

    mBio 2014;5;1

  • Complete Genome Sequence of the WHO International Standard for HIV-1 RNA Determined by Deep Sequencing.

    Gall A, Morris C, Kellam P and Berry N

    Genome announcements 2014;2;1

  • IFITM proteins-cellular inhibitors of viral entry.

    Smith S, Weston S, Kellam P and Marsh M

    Current opinion in virology 2014;4;71-7

  • A systematic review of definitions of extreme phenotypes of HIV control and progression.

    Gurdasani D, Iles L, Dillon DG, Young EH, Olson AD et al.

    AIDS (London, England) 2014;28;2;149-62

  • A membrane topology model for human interferon inducible transmembrane protein 1.

    Weston S, Czieso S, White IJ, Smith SE, Kellam P and Marsh M

    PloS one 2014;9;8;e104341

  • European surveillance network for influenza in pigs: surveillance programs, diagnostic tools and Swine influenza virus subtypes identified in 14 European countries from 2010 to 2013.

    Simon G, Larsen LE, Dürrwald R, Foni E, Harder T et al.

    PloS one 2014;9;12;e115815

  • Full genome virus detection in fecal samples using sensitive nucleic acid preparation, deep sequencing, and a novel iterative sequence classification algorithm.

    Cotten M, Oude Munnink B, Canuti M, Deijs M, Watson SJ et al.

    PloS one 2014;9;4;e93269

  • Host genetic variants and gene expression patterns associated with Epstein-Barr virus copy number in lymphoblastoid cell lines.

    Houldcroft CJ, Petrova V, Liu JZ, Frampton D, Anderson CA et al.

    PloS one 2014;9;10;e108384

  • RNA-seq analysis of host and viral gene expression highlights interaction between varicella zoster virus and keratinocyte differentiation.

    Jones M, Dry IR, Frampton D, Singh M, Kanda RK et al.

    PLoS pathogens 2014;10;1;e1003896

  • Transmission and evolution of the Middle East respiratory syndrome coronavirus in Saudi Arabia: a descriptive genomic study.

    Cotten M, Watson SJ, Kellam P, Al-Rabeeah AA, Makhdoom HQ et al.

    Lancet (London, England) 2013;382;9909;1993-2002

  • Chicken interferon-inducible transmembrane protein 3 restricts influenza viruses and lyssaviruses in vitro.

    Smith SE, Gibson MS, Wash RS, Ferrara F, Wright E et al.

    Journal of virology 2013;87;23;12957-66

  • Amphotericin B increases influenza A virus infection by preventing IFITM3-mediated restriction.

    Lin TY, Chin CR, Everitt AR, Clare S, Perreira JM et al.

    Cell reports 2013;5;4;895-908

  • Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations.

    Bashford-Rogers RJ, Palser AL, Huntly BJ, Rance R, Vassiliou GS et al.

    Genome research 2013;23;11;1874-84

  • Persistence of HIV-1 transmitted drug resistance mutations.

    Castro H, Pillay D, Cane P, Asboe D, Cambiano V et al.

    The Journal of infectious diseases 2013;208;9;1459-63

  • Modeling the association of space, time, and host species with variation of the HA, NA, and NS genes of H5N1 highly pathogenic avian influenza viruses isolated from birds in Romania in 2005-2007.

    Alkhamis M, Perez A, Batey N, Howard W, Baillie G et al.

    Avian diseases 2013;57;3;612-21

  • Hospital outbreak of Middle East respiratory syndrome coronavirus.

    Assiri A, McGeer A, Perl TM, Price CS, Al Rabeeah AA et al.

    The New England journal of medicine 2013;369;5;407-16

  • Metagenomic study of the viruses of African straw-coloured fruit bats: detection of a chiropteran poxvirus and isolation of a novel adenovirus.

    Baker KS, Leggett RM, Bexfield NH, Alston M, Daly G et al.

    Virology 2013;441;2;95-106

  • The CD225 domain of IFITM3 is required for both IFITM protein association and inhibition of influenza A virus and dengue virus replication.

    John SP, Chin CR, Perreira JM, Feeley EM, Aker AM et al.

    Journal of virology 2013;87;14;7837-52

  • Activation of the B cell antigen receptor triggers reactivation of latent Kaposi's sarcoma-associated herpesvirus in B cells.

    Kati S, Tsao EH, Günther T, Weidner-Glunde M, Rothämel T et al.

    Journal of virology 2013;87;14;8004-16

  • Population genomics of post-vaccine changes in pneumococcal epidemiology.

    Croucher NJ, Finkelstein JA, Pelton SI, Mitchell PK, Lee GM et al.

    Nature genetics 2013;45;6;656-63

  • Full-genome deep sequencing and phylogenetic analysis of novel human betacoronavirus.

    Cotten M, Lam TT, Watson SJ, Palser AL, Petrova V et al.

    Emerging infectious diseases 2013;19;5;736-42B

  • Evolution of equine influenza virus in vaccinated horses.

    Murcia PR, Baillie GJ, Stack JC, Jervis C, Elton D et al.

    Journal of virology 2013;87;8;4768-71

  • The evolutionary dynamics of influenza A virus adaptation to mammalian hosts.

    Bhatt S, Lam TT, Lycett SJ, Leigh Brown AJ, Bowden TA et al.

    Philosophical transactions of the Royal Society of London. Series B, Biological sciences 2013;368;1614;20120382

  • Viral population analysis and minority-variant detection using short read next-generation sequencing.

    Watson SJ, Welkers MR, Depledge DP, Coulter E, Breuer JM et al.

    Philosophical transactions of the Royal Society of London. Series B, Biological sciences 2013;368;1614;20120205

  • Different patterns of Epstein-Barr virus latency in endemic Burkitt lymphoma (BL) lead to distinct variants within the BL-associated gene expression signature.

    Kelly GL, Stylianou J, Rasaiyaah J, Wei W, Thomas W et al.

    Journal of virology 2013;87;5;2882-94

  • Restriction of V3 region sequence divergence in the HIV-1 envelope gene during antiretroviral treatment in a cohort of recent seroconverters.

    Gall A, Kaye S, Hué S, Bonsall D, Rance R et al.

    Retrovirology 2013;10;8

  • Autologous antibody capture to enrich immunogenic viruses for viral discovery.

    Oude Munnink BB, Jazaeri Farsani SM, Deijs M, Jonkers J, Verhoeven JT et al.

    PloS one 2013;8;11;e78454

  • Defining the range of pathogens susceptible to Ifitm3 restriction using a knockout mouse model.

    Everitt AR, Clare S, McDonald JU, Kane L, Harcourt K et al.

    PloS one 2013;8;11;e80723

  • Interferon-induced transmembrane protein-3 genetic variant rs12252-C is associated with severe influenza in Chinese individuals.

    Zhang YH, Zhao Y, Li N, Peng YC, Giannoulatou E et al.

    Nature communications 2013;4;1418

  • Universal amplification, next-generation sequencing, and assembly of HIV-1 genomes.

    Gall A, Ferns B, Morris C, Watson S, Cotten M et al.

    Journal of clinical microbiology 2012;50;12;3838-44

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

    Lycett SJ, Baillie G, Coulter E, Bhatt S, Kellam P et al.

    The Journal of general virology 2012;93;Pt 11;2326-36

  • Permissive and restricted virus infection of murine embryonic stem cells.

    Wash R, Calabressi S, Franz S, Griffiths SJ, Goulding D et al.

    The Journal of general virology 2012;93;Pt 10;2118-30

  • IFITM3 restricts the morbidity and mortality associated with influenza.

    Everitt AR, Clare S, Pertel T, John SP, Wash RS et al.

    Nature 2012;484;7395;519-23

  • Analysis of high-depth sequence data for studying viral diversity: a comparison of next generation sequencing platforms using Segminator II.

    Archer J, Baillie G, Watson SJ, Kellam P, Rambaut A and Robertson DL

    BMC bioinformatics 2012;13;47

  • Evolution of an Eurasian avian-like influenza virus in naïve and vaccinated pigs.

    Murcia PR, Hughes J, Battista P, Lloyd L, Baillie GJ et al.

    PLoS pathogens 2012;8;5;e1002730

  • Evolutionary dynamics of local pandemic H1N1/2009 influenza virus lineages revealed by whole-genome analysis.

    Baillie GJ, Galiano M, Agapow PM, Myers R, Chiam R et al.

    Journal of virology 2012;86;1;11-8

  • Metagenomics and the molecular identification of novel viruses.

    Bexfield N and Kellam P

    Veterinary journal (London, England : 1997) 2011;190;2;191-8

  • Disease-associated XMRV sequences are consistent with laboratory contamination.

    Hué S, Gray ER, Gall A, Katzourakis A, Tan CP et al.

    Retrovirology 2010;7;1;111

  • The RING-CH ligase K5 antagonizes restriction of KSHV and HIV-1 particle release by mediating ubiquitin-dependent endosomal degradation of tetherin.

    Pardieu C, Vigan R, Wilson SJ, Calvi A, Zang T et al.

    PLoS pathogens 2010;6;4;e1000843

  • Regulation of the Epstein-Barr virus Zp promoter in B lymphocytes during reactivation from latency.

    McDonald C, Karstegl CE, Kellam P and Farrell PJ

    The Journal of general virology 2010;91;Pt 3;622-9

  • KSHV-encoded miRNAs target MAF to induce endothelial cell reprogramming.

    Hansen A, Henderson S, Lagos D, Nikitenko L, Coulter E et al.

    Genes & development 2010;24;2;195-205

  • X-box binding protein 1 contributes to induction of the Kaposi's sarcoma-associated herpesvirus lytic cycle under hypoxic conditions.

    Dalton-Griffin L, Wilson SJ and Kellam P

    Journal of virology 2009;83;14;7202-9

  • Genome-wide innate immune responses in HIV-1-infected macrophages are preserved despite attenuation of the NF-kappa B activation pathway.

    Noursadeghi M, Tsang J, Miller RF, Straschewski S, Kellam P et al.

    Journal of immunology (Baltimore, Md. : 1950) 2009;182;1;319-28

  • Computational inference of replication and transcription activator regulator activity in herpesvirus from gene expression data.

    Recchia A, Wit E, Vinciotti V and Kellam P

    IET systems biology 2008;2;6;385-96

  • X box binding protein XBP-1s transactivates the Kaposi's sarcoma-associated herpesvirus (KSHV) ORF50 promoter, linking plasma cell differentiation to KSHV reactivation from latency.

    Wilson SJ, Tsao EH, Webb BL, Ye H, Dalton-Griffin L et al.

    Journal of virology 2007;81;24;13578-86

  • A statistical model for HIV-1 sequence classification using the subtype analyser (STAR).

    Myers RE, Gale CV, Harrison A, Takeuchi Y and Kellam P

    Bioinformatics (Oxford, England) 2005;21;17;3535-40

  • Consensus clustering and functional interpretation of gene-expression data.

    Swift S, Tucker A, Vinciotti V, Martin N, Orengo C et al.

    Genome biology 2004;5;11;R94

  • Kaposi's sarcoma-associated herpesvirus-infected primary effusion lymphoma has a plasma cell gene expression profile.

    Jenner RG, Maillard K, Cattini N, Weiss RA, Boshoff C et al.

    Proceedings of the National Academy of Sciences of the United States of America 2003;100;18;10399-404