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Archive Page - this page is maintained as a historical record and is no longer being updated.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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People

Paul Kellam
Group Leader

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

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Alumni

Key Projects, Collaborations, Tools & Data

COMPARE

COllaborative Management Platform for detection and Analyses of (Re-) emerging and foodborne outbreaks in Europe

COMPARE is a large EU project with the intention to speed up the detection of and response to disease outbreaks among humans and animals worldwide through the use of new genome technology.

ICONIC

Infection response through virus genomics (ICONIC)

ICONIC uses pathogen (virus) genome sequence to inform evidence based infection control health care levels, outbreak/pandemic preparedness and stratified patient management with current, future and experimental treatments.

PANGEA

PHYLOGENETICS AND NETWORKS FOR GENERALISED HIV EPIDEMICS IN AFRICA

The PANGEA_HIV project aims to adapt modern molecular epidemiology and phylodynamics of HIV sequence data to generate new insights into HIV transmission dynamics in generalized epidemics in Africa, and to provide a potential new approach for the evaluation of transmission interventions.

QUASR

QUASR is a lightweight pipeline written to process and analyse next-generation sequencing (NGS) data from Illumina, 454, and Ion Torrent platforms. Although originally written for viral data, it is generic enough to work on any NGS dataset.

WT-VIZIONS

Wellcome Trust-Viet Nam Initiative on Zoonotic Infections (VIZIONS)

VIZIONS aims to understand the nature, public health importance and origins of the large number of undiagnosed infectious disease cases that occur in Vietnam, as in most other countries in the world. VIZIONS is testing the hypothesis that a significant number of these infections are zoonotic and that some will be caused by currently unrecognized and possibly newly emerging agents. VIZIONS is generating new insights into the diversity of human pathogens (especially viruses) and into the biological and behavioural processes involved in the emergence of novel pathogens.

Partners and Funders

Internal Partners
Pathogen Informatics

The Pathogen Informatics team develop and maintain software applications and systems to support the research activities of the Parasites and Microbes programme. We develop and maintain scalable and robust automated tools for sequence and annotation tracking and analysis and provide ad-hoc informatics support and training to the researchers in the programme.

Publications

  • 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

    PUBMED: 31536169; DOI: 10.1111/irv.12679

  • 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

    PUBMED: 31296922; PMC: 6624209; DOI: 10.1038/s41598-019-46509-w; URL:

  • 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

    PUBMED: 30955492; PMC: 6501908; DOI: 10.1098/rstb.2018.0299; URL:

  • 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

    PUBMED: 28983013; PMC: 5679167; DOI: 10.1084/jem.20162123

  • Heterogeneity of the Epstein-Barr virus major internal repeat reveals evolutionary mechanisms of EBV and a functional defect in the prototype EBV strain B95-8.

    Ba Abdullah M, Palermo R, Palser A, Grayson NE, Kellam P et al.

    Journal of virology 2017

    PUBMED: 28904201; DOI: 10.1128/JVI.00920-17

  • 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

    PUBMED: 27497916; DOI: 10.1016/j.virusres.2016.08.004

  • 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

    PUBMED: 28948041; PMC: 5597861; DOI: 10.1093/ve/vex022

  • 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

    PUBMED: 29588920; PMC: 5843844; DOI: 10.12688/wellcomeopenres.11386.2

  • 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

    PUBMED: 27211266; PMC: 5155029; DOI: 10.1038/leu.2016.142

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

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

    Experimental hematology 2016

    PUBMED: 27693386; DOI: 10.1016/j.exphem.2016.09.010

  • 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

    PUBMED: 27640936; DOI: 10.1016/j.chom.2016.08.006

  • 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

    PUBMED: 27219333; PMC: 5025721; DOI: 10.1111/tra.12416

  • 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

    DOI: 10.15585/mmwr.mm6526a4; URL: http://dx.doi.org/10.15585/mm...wr.mm6526a4.

  • 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

    PUBMED: 27469941; PMC: 4966474; DOI: 10.1128/genomeA.00751-16

  • 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

    PUBMED: 26857628; DOI: 10.1534/genetics.115.177931

  • 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

    PUBMED: 27081130; DOI: 10.1128/genomeA.00250-16

  • 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

    PUBMED: 28694998; PMC: 5499387; DOI: 10.1093/ve/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

    PUBMED: 26403795; PMC: 4700077; DOI: 10.1007/s10393-015-1061-0

  • 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;3440-3

    PUBMED: 26354795; DOI: 10.1099/jgv.0.000279

  • 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

    PUBMED: 26202246; PMC: 4577897; DOI: 10.1128/JVI.00840-15

  • 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

    PUBMED: 26424572; PMC: 5819730; DOI: 10.1126/scitranslmed.aab0191

  • 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

    PUBMED: 26194755; PMC: 4528418; DOI: 10.1098/rstb.2014.0241

  • 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

    PUBMED: 26252219; PMC: 4529188; DOI: 10.1371/journal.ppat.1005056

  • 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

    PUBMED: 25725497; PMC: 4495290; DOI: 10.1093/bioinformatics/btv120

  • 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

    PUBMED: 25583169; DOI: 10.1093/infdis/jiv014

  • 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

    PUBMED: 26123575; PMC: 4487201; DOI: 10.1186/s12977-015-0179-z

  • 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

    PUBMED: 25626684; PMC: 4635489; DOI: 10.1099/vir.0.000071

  • 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

    PUBMED: 25614588; PMC: 4631062; DOI: 10.1099/vir.0.000058

  • 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

    PUBMED: 25787276; PMC: 4442510; DOI: 10.1128/JVI.03614-14

  • 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

    PUBMED: 25612912; DOI: 10.1136/jmedgenet-2014-102418

  • 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

    PUBMED: 25609811; PMC: 4403408; DOI: 10.1128/JVI.03391-14

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

    Houldcroft CJ and Kellam P

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

    PUBMED: 25430668; PMC: 4407908; DOI: 10.1002/rmv.1816

  • 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

    PUBMED: 25606972; PMC: 4306836; DOI: 10.3390/v7010239

  • 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

    PUBMED: 25522326; PMC: 4270772; DOI: 10.1371/journal.ppat.1004552

  • 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

    PUBMED: 25121549; PMC: 4233630; DOI: 10.1099/vir.0.068403-0

  • 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

    PUBMED: 24837403; DOI: 10.1093/infdis/jiu292

  • 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

    PUBMED: 25210166; PMC: 4249111; DOI: 10.1128/JVI.01636-14

  • 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

    PUBMED: 25271614; DOI: 10.1056/NEJMc1409847

  • 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

    PUBMED: 25056894; PMC: 4178781; DOI: 10.1128/JVI.01333-14

  • 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

    PUBMED: 24977473; PMC: 4304655; DOI: 10.1097/QAI.0000000000000271

  • 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

    PUBMED: 25183443; PMC: 4155405; DOI: 10.1038/ncomms5794

  • 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

    PUBMED: 24991008; PMC: 4178900; DOI: 10.1128/JVI.01665-14

  • 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

    PUBMED: 25189176; PMC: 4243823; DOI: 10.1186/s12865-014-0029-0

  • 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

    PUBMED: 24990269; PMC: 4086691; DOI: 10.1186/1742-4690-11-53

  • 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

    PUBMED: 24699184; PMC: 4441753; DOI: 10.1016/j.ijid.2014.03.1372

  • 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

    PUBMED: 24857749; PMC: 4036761; DOI: 10.3201/eid2006.140402

  • 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

    PUBMED: 24549846; PMC: 3944817; DOI: 10.1128/mBio.01062-13

  • 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

    PUBMED: 24503998; PMC: 3916492; DOI: 10.1128/genomeA.01254-13

  • IFITM proteins-cellular inhibitors of viral entry.

    Smith S, Weston S, Kellam P and Marsh M

    Current opinion in virology 2014;4;71-7

    PUBMED: 24480526; DOI: 10.1016/j.coviro.2013.11.004

  • 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

    PUBMED: 24149086; PMC: 3882304; DOI: 10.1097/QAD.0000000000000049

  • 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

    PUBMED: 25105503; PMC: 4126714; DOI: 10.1371/journal.pone.0104341

  • 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

    PUBMED: 25542013; PMC: 4277368; DOI: 10.1371/journal.pone.0115815

  • 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

    PUBMED: 24695106; PMC: 3973683; DOI: 10.1371/journal.pone.0093269

  • 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

    PUBMED: 25290448; PMC: 4188571; DOI: 10.1371/journal.pone.0108384

  • 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

    PUBMED: 24497829; PMC: 3907375; DOI: 10.1371/journal.ppat.1003896

  • 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

    PUBMED: 24055451; PMC: 3898949; DOI: 10.1016/S0140-6736(13)61887-5

  • 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

    PUBMED: 24067955; PMC: 3838109; DOI: 10.1128/JVI.01443-13

  • 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

    PUBMED: 24268777; PMC: 3898084; DOI: 10.1016/j.celrep.2013.10.033

  • 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

    PUBMED: 23742949; PMC: 3814887; DOI: 10.1101/gr.154815.113

  • 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

    PUBMED: 23904291; PMC: 3789571; DOI: 10.1093/infdis/jit345

  • 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

    PUBMED: 24283126; PMC: 3980047; DOI: 10.1637/10494-011713-Reg.1

  • 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

    PUBMED: 23782161; PMC: 4029105; DOI: 10.1056/NEJMoa1306742

  • 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

    PUBMED: 23562481; PMC: 3667569; DOI: 10.1016/j.virol.2013.03.014

  • 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

    PUBMED: 23658454; PMC: 3700195; DOI: 10.1128/JVI.00481-13

  • 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

    PUBMED: 23678173; PMC: 3700181; DOI: 10.1128/JVI.00506-13

  • 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

    PUBMED: 23644493; PMC: 3725542; DOI: 10.1038/ng.2625

  • 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

    PUBMED: 23693015; PMC: 3647518; DOI: 10.3201/eid1905.130057

  • 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

    PUBMED: 23388708; PMC: 3624384; DOI: 10.1128/JVI.03379-12

  • 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

    PUBMED: 23382435; PMC: 3678336; DOI: 10.1098/rstb.2012.0382

  • 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

    PUBMED: 23382427; PMC: 3678329; DOI: 10.1098/rstb.2012.0205

  • 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

    PUBMED: 23269792; PMC: 3571367; DOI: 10.1128/JVI.03003-12

  • 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

    PUBMED: 23331949; PMC: 3605130; DOI: 10.1186/1742-4690-10-8

  • 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

    PUBMED: 24223808; PMC: 3817278; DOI: 10.1371/journal.pone.0078454

  • 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

    PUBMED: 24278312; PMC: 3836756; DOI: 10.1371/journal.pone.0080723

  • 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

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