Publications by authors named "Matthew Cotten"

79Publications

Automated download and clean-up of family specific databases for kmer-based virus identification.

Bioinformatics 2020 Oct 8. Epub 2020 Oct 8.

Department of Viroscience, Erasmus University Medical Centre, CA Rotterdam, PO Box 2040, the Netherlands.

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http://dx.doi.org/10.1093/bioinformatics/btaa857DOI Listing
October 2020

Entamoeba and Giardia parasites implicated as hosts of CRESS viruses.

Nat Commun 2020 09 15;11(1):4620. Epub 2020 Sep 15.

Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1038/s41467-020-18474-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7493932PMC
September 2020

Increased resolution of African swine fever virus genome patterns based on profile HMMs of protein domains.

Virus Evol 2020 Jul 19;6(2):veaa044. Epub 2020 Jun 19.

Viral Genomics, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK.

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http://dx.doi.org/10.1093/ve/veaa044DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7474929PMC
July 2020

Nosocomial outbreak of the Middle East Respiratory Syndrome coronavirus: A phylogenetic, epidemiological, clinical and infection control analysis.

Travel Med Infect Dis 2020 Sep - Oct;37:101807. Epub 2020 Jun 27.

Senior Infectious Diseases Consultant & Director Research & Innovation Center, King Saud Medical City, Ministry of Health, Riyadh, Saudi Arabia; Faculty of Medicine, Alfaisal University, Riyadh, Saudi Arabia; Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA. Electronic address:

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http://dx.doi.org/10.1016/j.tmaid.2020.101807DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7319941PMC
October 2020

Characterization of Norovirus and Other Human Enteric Viruses in Sewage and Stool Samples Through Next-Generation Sequencing.

Food Environ Virol 2019 12 24;11(4):400-409. Epub 2019 Aug 24.

Ifremer, Laboratoire de Microbiologie, LSEM-SG2M, BP 21105, 44311, Nantes Cedex 3, France.

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http://dx.doi.org/10.1007/s12560-019-09402-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6848244PMC
December 2019

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

Sci Rep 2019 07 11;9(1):10076. Epub 2019 Jul 11.

Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Epidemiology and Demography Department, Kilifi, Kenya.

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http://dx.doi.org/10.1038/s41598-019-46509-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6624209PMC
July 2019

Identification and characterization of Coronaviridae genomes from Vietnamese bats and rats based on conserved protein domains.

Virus Evol 2018 Jul 15;4(2):vey035. Epub 2018 Dec 15.

Virus Genomics, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK.

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http://dx.doi.org/10.1093/ve/vey035DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6295324PMC
July 2018

Evaluating the performance of tools used to call minority variants from whole genome short-read data.

Wellcome Open Res 2018 13;3:21. Epub 2018 Sep 13.

KEMRI-Wellcome Trust Research Programme, KEMRI Centre for Geographic Medicine Research - Coast, Kilifi, Kenya.

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https://wellcomeopenresearch.org/articles/3-21/v2
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http://dx.doi.org/10.12688/wellcomeopenres.13538.2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6234735PMC
September 2018

Virus discovery reveals frequent infection by diverse novel members of the Flaviviridae in wild lemurs.

Arch Virol 2019 Feb 20;164(2):509-522. Epub 2018 Nov 20.

Laboratory of Experimental Virology, Department of Medical Microbiology, Academic Medical Center of the University of Amsterdam, Meibergdreef 15, 1105 AZ, Amsterdam, Netherlands.

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http://dx.doi.org/10.1007/s00705-018-4099-9DOI Listing
February 2019

Complete Genome Sequences of Six Measles Virus Strains.

Genome Announc 2018 Mar 29;6(13). Epub 2018 Mar 29.

Department of Viroscience, Erasmus MC, Rotterdam, The Netherlands

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http://dx.doi.org/10.1128/genomeA.00184-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5876482PMC
March 2018

Next-generation sequencing and norovirus.

Future Virol 2016 Nov 11;11(11):719-722. Epub 2016 Nov 11.

Virosciences Department, Erasmus Medical Center, Rotterdam, The Netherlands.

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https://www.futuremedicine.com/doi/10.2217/fvl-2016-0099
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http://dx.doi.org/10.2217/fvl-2016-0099DOI Listing
November 2016

Transmission patterns and evolution of respiratory syncytial virus in a community outbreak identified by genomic analysis.

Virus Evol 2017 Jan 11;3(1):vex006. Epub 2017 Mar 11.

Epidemiology and Demography Department, Kenya Medical Research Institute (KEMRI) - Wellcome Trust Research Collaborative Programme, Kilifi, Kenya.

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http://dx.doi.org/10.1093/ve/vex006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5399923PMC
January 2017

Virus genomes reveal factors that spread and sustained the Ebola epidemic.

Nature 2017 04 12;544(7650):309-315. Epub 2017 Apr 12.

Institute of Evolutionary Biology, University of Edinburgh, King's Buildings, Edinburgh EH9 3FL, UK.

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http://dx.doi.org/10.1038/nature22040DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5712493PMC
April 2017

Genome Sequences of a Novel Vietnamese Bat Bunyavirus.

Genome Announc 2016 Dec 22;4(6). Epub 2016 Dec 22.

Wellcome Trust Sanger Institute, Hinxton, England.

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http://dx.doi.org/10.1128/genomeA.01366-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5180378PMC
December 2016

A Novel Astrovirus-Like RNA Virus Detected in Human Stool.

Virus Evol 2016 Jan 2;2(1):vew005. Epub 2016 Mar 2.

Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, 1105 AZ Amsterdam, the Netherlands.

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http://dx.doi.org/10.1093/ve/vew005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4989881PMC
January 2016

Infectious diseases epidemic threats and mass gatherings: refocusing global attention on the continuing spread of the Middle East Respiratory syndrome coronavirus (MERS-CoV).

BMC Med 2016 09 7;14(1):132. Epub 2016 Sep 7.

Special Infectious Agents Unit, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia.

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http://dx.doi.org/10.1186/s12916-016-0686-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5015245PMC
September 2016

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

J Gen Virol 2015 Nov;96(11):3440-3443

Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands.

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http://www.microbiologyresearch.org/content/journal/jgv/10.1
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http://dx.doi.org/10.1099/jgv.0.000279DOI Listing
November 2015

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

Viruses 2015 Jan 19;7(1):239-51. Epub 2015 Jan 19.

Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, Amsterdam 1105 AZ, the Netherlands.

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http://dx.doi.org/10.3390/v7010239DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4306836PMC
January 2015

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

J Virol 2014 Oct 23;88(19):11056-69. Epub 2014 Jul 23.

Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam The London School of Hygiene and Tropical Medicine, London, United Kingdom Centre for Tropical Medicine, University of Oxford, Oxford, United Kingdom.

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http://dx.doi.org/10.1128/JVI.01333-14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4178781PMC
October 2014

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

J Infect Dis 2014 Nov 15;210(10):1590-4. Epub 2014 May 15.

Global Centre for Mass Gatherings Medicine and Ministry of Health, Riyadh, Kingdom of Saudi Arabia and College of Medicine, Alfaisal University, Division of Infection and Immunity, University College London (UCL), and UCL Hospitals National Health Service Foundation Trust, United Kingdom.

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http://dx.doi.org/10.1093/infdis/jiu292DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7107391PMC
November 2014

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

Int J Infect Dis 2014 Jun 31;23:63-8. Epub 2014 Mar 31.

Saudi Aramco Medical Services Organization, Saudi Aramco, Dhahran, Kingdom of Saudi Arabia and Indiana University School of Medicine, Indianapolis, IN (USA).

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https://linkinghub.elsevier.com/retrieve/pii/S12019712140145
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http://dx.doi.org/10.1016/j.ijid.2014.03.1372DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4441753PMC
June 2014

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

PLoS One 2014 2;9(4):e93269. Epub 2014 Apr 2.

Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0093269PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3973683PMC
January 2015

Unexplained diarrhoea in HIV-1 infected individuals.

BMC Infect Dis 2014 Jan 13;14:22. Epub 2014 Jan 13.

Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1186/1471-2334-14-22DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3925291PMC
January 2014

Autologous antibody capture to enrich immunogenic viruses for viral discovery.

PLoS One 2013 4;8(11):e78454. Epub 2013 Nov 4.

Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0078454PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3817278PMC
August 2014

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

J Clin Microbiol 2012 Dec 19;50(12):3838-44. Epub 2012 Sep 19.

Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom.

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http://jcm.asm.org/cgi/doi/10.1128/JCM.01516-12
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http://dx.doi.org/10.1128/JCM.01516-12DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3502977PMC
December 2012

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

AIDS Res Hum Retroviruses 2012 Jun 9;28(6):584-90. Epub 2012 Mar 9.

Viral Diseases Program, Medical Research Council, Fajara, The Gambia and Erasmus Medical Centre, Medical Microbiology and Infectious Diseases, Rotterdam, The Netherlands.

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http://dx.doi.org/10.1089/AID.2011.0219DOI Listing
June 2012

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

Eur J Immunol 2010 Jul;40(7):1963-72

Weatherall Institute of Molecular Medicine, Medical Research Council Human Immunology Unit, John Radcliffe Hospital, Oxford, UK.

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http://dx.doi.org/10.1002/eji.200940295DOI Listing
July 2010

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

J Infect Dis 2010 Jan;201(1):114-22

Weatherall Institute of Molecular Medicine, Medical Research Council Human Immunology Unit, John Radcliffe Hospital, Oxford, UK.

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http://dx.doi.org/10.1086/648733DOI Listing
January 2010

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.

Eur J Immunol 2008 Dec;38(12):3549-60

MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford, UK.

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http://dx.doi.org/10.1002/eji.200838759DOI Listing
December 2008

HIV-2: the forgotten AIDS virus.

Trends Microbiol 2008 Dec 27;16(12):588-95. Epub 2008 Oct 27.

Medical Research Council Laboratories, Atlantic Road, PO Box 273, Fajara, The Gambia, West Africa.

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http://dx.doi.org/10.1016/j.tim.2008.09.003DOI Listing
December 2008