Dr Matthew Cotten | Senior Staff Scientist

This person is a member of Sanger Institute Alumni.

Matthew Cotten describes the evolution of medically important viruses. He is developing high throughput methods for generating and analysing virus genomic sequences from clinical samples. He recently assisted with efforts to sequence Ebolavirus locally in Sierra Leone and he has led the group's work on MERS-Coronavirus.

Current work
1. Outbreak sequencing (Ebolavirus, MERS-Coronavirus)
2. Agnostic sequencing for discovering novel virus variants and for assessing zoonotic risks
4. Special application algorithms for virus genome analysis
5. Large scale sequencing projects including Norovirus, RSV, Hepatitis C Virus

Previous work
1. HIV-2 evolution, Viral diagnostics and viral load measurements in African setting
2. Drug discovery, identifying novel targets for antiviral drugs
3. Mechanisms of virus entry into mammalian cells
4. Creation of synthetic viruses for gene delivery applications
5. Virus activation of host inflammatory and apoptotic responses
6. Small nuclear RNA molecules involved in mRNA processing
7. Mechanisms of chromatin assembly, how is newly synthesized mammalian DNA packaged into chromatin?
8. The role of histone acetylation in activating gene expression

Publications

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • Exploiting features of adenovirus replication to support mammalian kinase production.

    Cotten M, Stegmueller K, Eickhoff J, Hanke M, Herzberger K et al.

    Nucleic acids research 2003;31;21;e128

  • Activation of heat-shock response by an adenovirus is essential for virus replication.

    Glotzer JB, Saltik M, Chiocca S, Michou AI, Moseley P and Cotten M

    Nature 2000;407;6801;207-11

  • Histone deacetylase 1 inactivation by an adenovirus early gene product.

    Chiocca S, Kurtev V, Colombo R, Boggio R, Sciurpi MT et al.

    Current biology : CB 2002;12;7;594-8

  • Taking forward a 'One Health' approach for turning the tide against the Middle East respiratory syndrome coronavirus and other zoonotic pathogens with epidemic potential.

    Zumla A, Dar O, Kock R, Muturi M, Ntoumi F et al.

    International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases 2016

  • Zika virus outbreak and the case for building effective and sustainable rapid diagnostics laboratory capacity globally.

    Zumla A, Goodfellow I, Kasolo F, Ntoumi F, Buchy P et al.

    International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases 2016;45;92-4

  • 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;3440-3

  • 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

  • The presence of prolines in the flanking region of an immunodominant HIV-2 gag epitope influences the quality and quantity of the epitope generated.

    Jallow S, Leligdowicz A, Kramer HB, Onyango C, Cotten M et al.

    European journal of immunology 2015;45;8;2232-42

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • Unexplained diarrhoea in HIV-1 infected individuals.

    Oude Munnink BB, Canuti M, Deijs M, de Vries M, Jebbink MF et al.

    BMC infectious diseases 2014;14;22

  • 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

  • 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

  • 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

  • Population dynamics of HIV-2 in rural West Africa: comparison with HIV-1 and ongoing transmission at the heart of the epidemic.

    de Silva TI, van Tienen C, Onyango C, Jabang A, Vincent T et al.

    AIDS (London, England) 2013;27;1;125-34

  • 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

  • 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

  • Maternal proviral load and vertical transmission of human T cell lymphotropic virus type 1 in Guinea-Bissau.

    van Tienen C, McConkey SJ, de Silva TI, Cotten M, Kaye S et al.

    AIDS research and human retroviruses 2012;28;6;584-90

  • An international collaboration to standardize HIV-2 viral load assays: results from the 2009 ACHI(E)V(2E) quality control study.

    Damond F, Benard A, Balotta C, Böni J, Cotten M et al.

    Journal of clinical microbiology 2011;49;10;3491-7

  • Highly avid, oligoclonal, early-differentiated antigen-specific CD8+ T cells in chronic HIV-2 infection.

    Leligdowicz A, Onyango C, Yindom LM, Peng Y, Cotten M et al.

    European journal of immunology 2010;40;7;1963-72

  • HIV-2 capsids distinguish high and low virus load patients in a West African community cohort.

    Onyango CO, Leligdowicz A, Yokoyama M, Sato H, Song H et al.

    Vaccine 2010;28 Suppl 2;B60-7

  • Direct relationship between virus load and systemic immune activation in HIV-2 infection.

    Leligdowicz A, Feldmann J, Jaye A, Cotten M, Dong T et al.

    The Journal of infectious diseases 2010;201;1;114-22

  • Declining trend of serological syphilis among genitourinary medicine patients in the Gambia, West Africa.

    Hontelez JA, van der Loeff MF, Peterson I, Peterson K, Ahadzie B et al.

    Sexually transmitted diseases 2009;36;12;745-9

  • Virological response to highly active antiretroviral therapy in patients infected with human immunodeficiency virus type 2 (HIV-2) and in patients dually infected with HIV-1 and HIV-2 in the Gambia and emergence of drug-resistant variants.

    Jallow S, Alabi A, Sarge-Njie R, Peterson K, Whittle H et al.

    Journal of clinical microbiology 2009;47;7;2200-8

  • Comprehensive analysis of HIV Gag-specific IFN-gamma response in HIV-1- and HIV-2-infected asymptomatic patients from a clinical cohort in The Gambia.

    Ondondo BO, Rowland-Jones SL, Dorrell L, Peterson K, Cotten M et al.

    European journal of immunology 2008;38;12;3549-60

  • HIV-2: the forgotten AIDS virus.

    de Silva TI, Cotten M and Rowland-Jones SL

    Trends in microbiology 2008;16;12;588-95

  • Application of a novel, rapid, and sensitive oligonucleotide ligation assay for detection of cancer-predicting mutations in the precore and basal core promoter of hepatitis B virus.

    Mendy ME, Kaye S, Le Roux E, Kirk GD, Jeng-Barry A et al.

    Journal of clinical microbiology 2008;46;8;2723-30

  • Quality control assessment of human immunodeficiency virus type 2 (HIV-2) viral load quantification assays: results from an international collaboration on HIV-2 infection in 2006.

    Damond F, Benard A, Ruelle J, Alabi A, Kupfer B et al.

    Journal of clinical microbiology 2008;46;6;2088-91

  • The role of RIP2 in p38 MAPK activation in the stressed heart.

    Jacquet S, Nishino Y, Kumphune S, Sicard P, Clark JE et al.

    The Journal of biological chemistry 2008;283;18;11964-71

  • Robust Gag-specific T cell responses characterize viremia control in HIV-2 infection.

    Leligdowicz A, Yindom LM, Onyango C, Sarge-Njie R, Alabi A et al.

    The Journal of clinical investigation 2007;117;10;3067-74

  • Proteomic characterization of the angiogenesis inhibitor SU6668 reveals multiple impacts on cellular kinase signaling.

    Godl K, Gruss OJ, Eickhoff J, Wissing J, Blencke S et al.

    Cancer research 2005;65;15;6919-26

  • NF-kappaB activation can mediate inhibition of human cytomegalovirus replication.

    Eickhoff JE and Cotten M

    The Journal of general virology 2005;86;Pt 2;285-95

  • Cellular targets of gefitinib.

    Brehmer D, Greff Z, Godl K, Blencke S, Kurtenbach A et al.

    Cancer research 2005;65;2;379-82

  • Chemical proteomic analysis reveals alternative modes of action for pyrido[2,3-d]pyrimidine kinase inhibitors.

    Wissing J, Godl K, Brehmer D, Blencke S, Weber M et al.

    Molecular & cellular proteomics : MCP 2004;3;12;1181-93

  • RNA-containing adenovirus/polyethylenimine transfer complexes effectively transduce dendritic cells and induce antigen-specific T cell responses.

    Gust TC, Diebold SS, Cotten M and Zenke M

    The journal of gene medicine 2004;6;4;464-70

  • RICK activates a NF-kappaB-dependent anti-human cytomegalovirus response.

    Eickhoff J, Hanke M, Stein-Gerlach M, Kiang TP, Herzberger K et al.

    The Journal of biological chemistry 2004;279;10;9642-52

  • An efficient proteomics method to identify the cellular targets of protein kinase inhibitors.

    Godl K, Wissing J, Kurtenbach A, Habenberger P, Blencke S et al.

    Proceedings of the National Academy of Sciences of the United States of America 2003;100;26;15434-9

  • Exploiting features of adenovirus replication to support mammalian kinase production.

    Cotten M, Stegmueller K, Eickhoff J, Hanke M, Herzberger K et al.

    Nucleic acids research 2003;31;21;e128

  • Induction of short interspersed nuclear repeat-containing transcripts in epithelial cells upon infection with a chicken adenovirus.

    Wick N, Luedemann S, Vietor I, Cotten M, Wildpaner M et al.

    Journal of molecular biology 2003;328;4;779-90

  • Identification and characterization of amphiphysin II as a novel cellular interaction partner of the hepatitis C virus NS5A protein.

    Zech B, Kurtenbach A, Krieger N, Strand D, Blencke S et al.

    The Journal of general virology 2003;84;Pt 3;555-60

  • Mannose receptor-mediated gene delivery into antigen presenting dendritic cells.

    Diebold SS, Plank C, Cotten M, Wagner E and Zenke M

    Somatic cell and molecular genetics 2002;27;1-6;65-74

  • TIS7 interacts with the mammalian SIN3 histone deacetylase complex in epithelial cells.

    Vietor I, Vadivelu SK, Wick N, Hoffman R, Cotten M et al.

    The EMBO journal 2002;21;17;4621-31

  • Identification of SRPK1 and SRPK2 as the major cellular protein kinases phosphorylating hepatitis B virus core protein.

    Daub H, Blencke S, Habenberger P, Kurtenbach A, Dennenmoser J et al.

    Journal of virology 2002;76;16;8124-37

  • Histone deacetylase 1 inactivation by an adenovirus early gene product.

    Chiocca S, Kurtev V, Colombo R, Boggio R, Sciurpi MT et al.

    Current biology : CB 2002;12;7;594-8

  • Defining CAR as a cellular receptor for the avian adenovirus CELO using a genetic analysis of the two viral fibre proteins.

    Tan PK, Michou AI, Bergelson JM and Cotten M

    The Journal of general virology 2001;82;Pt 6;1465-72

  • Preparation of adenovirus-polylysine-DNA complexes.

    Cotten M, Baker A, Birnstiel ML, Zatloukal K and Wagner E

    Current protocols in human genetics / editorial board, Jonathan L. Haines ... [et al.] 2001;Chapter 12;Unit 12.3

  • Mammalian sprouty-1 and -2 are membrane-anchored phosphoprotein inhibitors of growth factor signaling in endothelial cells.

    Impagnatiello MA, Weitzer S, Gannon G, Compagni A, Cotten M and Christofori G

    The Journal of cell biology 2001;152;5;1087-98

  • MHC class II presentation of endogenously expressed antigens by transfected dendritic cells.

    Diebold SS, Cotten M, Koch N and Zenke M

    Gene therapy 2001;8;6;487-93

  • Microtubule-independent motility and nuclear targeting of adenoviruses with fluorescently labeled genomes.

    Glotzer JB, Michou AI, Baker A, Saltik M and Cotten M

    Journal of virology 2001;75;5;2421-34

  • Fibroblast growth factors are required for efficient tumor angiogenesis.

    Compagni A, Wilgenbus P, Impagnatiello MA, Cotten M and Christofori G

    Cancer research 2000;60;24;7163-9

  • Activation of heat-shock response by an adenovirus is essential for virus replication.

    Glotzer JB, Saltik M, Chiocca S, Michou AI, Moseley P and Cotten M

    Nature 2000;407;6801;207-11

  • Cell cycle dependence of gene transfer by lipoplex, polyplex and recombinant adenovirus.

    Brunner S, Sauer T, Carotta S, Cotten M, Saltik M and Wagner E

    Gene therapy 2000;7;5;401-7

  • Characterization of CELO virus proteins that modulate the pRb/E2F pathway.

    Lehrmann H and Cotten M

    Journal of virology 1999;73;8;6517-25

  • Mannose polyethylenimine conjugates for targeted DNA delivery into dendritic cells.

    Diebold SS, Kursa M, Wagner E, Cotten M and Zenke M

    The Journal of biological chemistry 1999;274;27;19087-94

  • Efficient gene delivery into human dendritic cells by adenovirus polyethylenimine and mannose polyethylenimine transfection.

    Diebold SS, Lehrmann H, Kursa M, Wagner E, Cotten M and Zenke M

    Human gene therapy 1999;10;5;775-86

  • Mutational analysis of the avian adenovirus CELO, which provides a basis for gene delivery vectors.

    Michou AI, Lehrmann H, Saltik M and Cotten M

    Journal of virology 1999;73;2;1399-410

  • Transient transfection of mammary epithelial cells with a PEI/DNA/adenovirus system.

    Bischof J, Vietor I, Cotten M and Huber LA

    Biological chemistry 1999;380;2;269-73

  • A rapid, quantitative and inexpensive method for detecting apoptosis by flow cytometry in transiently transfected cells.

    Lamm GM, Steinlein P, Cotten M and Christofori G

    Nucleic acids research 1997;25;23;4855-7

  • Stabilization of gene delivery systems by freeze-drying.

    Talsma H, Cherng J, Lehrmann H, Kursa M, Ogris M et al.

    International journal of pharmaceutics 1997;157;2;233-238

  • Polyethylenimine (PEI) is a simple, inexpensive and effective reagent for condensing and linking plasmid DNA to adenovirus for gene delivery.

    Baker A, Saltik M, Lehrmann H, Killisch I, Mautner V et al.

    Gene therapy 1997;4;8;773-82

  • Delivery of bacterial artificial chromosomes into mammalian cells with psoralen-inactivated adenovirus carrier.

    Baker A and Cotten M

    Nucleic acids research 1997;25;10;1950-6

  • Permeabilization of mammalian cells to proteins: poliovirus 2A(pro) as a probe to analyze entry of proteins into cells.

    Novoa I, Benavente J, Cotten M and Carrasco L

    Experimental cell research 1997;232;1;186-90

  • Identification of a novel antiapoptotic protein, GAM-1, encoded by the CELO adenovirus.

    Chiocca S, Baker A and Cotten M

    Journal of virology 1997;71;4;3168-77

  • Intracellular delivery of lipopolysaccharide during DNA transfection activates a lipid A-dependent cell death response that can be prevented by polymyxin B.

    Cotten M and Saltik M

    Human gene therapy 1997;8;5;555-61

Cotten, Matthew
Follow Matthew Online
Matthew's Timeline
2010

Joined the Sanger Institute

2005

Research Scientist, MRC Gambia

2000

Group Leader, Axxima Pharmaceutical, Munich, Germany

1992

Group Leader, Institute for Molecular Pathology, Vienna Austria

1988

Postdoc, Institute for Molecular Pathology, Vienna Austria

1987

Postdoc, Vanderbilt University

1986

PhD University of Iowa