Imperial College London

ProfessorChristopheFraser

Faculty of MedicineSchool of Public Health

Visiting Professor
 
 
 
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Contact

 

+44 (0)20 7594 3397c.fraser Website

 
 
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Location

 

G28Norfolk PlaceSt Mary's Campus

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Summary

 

Publications

Publication Type
Year
to

153 results found

Blanquart F, Lehtinen S, Fraser C, 2017, An evolutionary model to predict the frequency of antibiotic resistance under seasonal antibiotic use, and an application to Streptococcus pneumoniae, PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, Vol: 284, ISSN: 0962-8452

JOURNAL ARTICLE

Blanquart F, Wymant C, Cornelissen M, Gall A, Bakker M, Bezemer D, Hall M, Hillebregt M, Ong SH, Albert J, Bannert N, Fellay J, Fransen K, Gourlay AJ, Grabowski MK, Gunsenheimer-Bartmeyer B, Guenthard HF, Kivela P, Kouyos R, Laeyendecker O, Liitsola K, Meyer L, Porter K, Ristola M, van Sighem A, Vanham G, Berkhout B, Kellam P, Reiss P, Fraser Cet al., 2017, Viral genetic variation accounts for a third of variability in HIV-1 set-point viral load in Europe, PLOS BIOLOGY, Vol: 15, ISSN: 1545-7885

JOURNAL ARTICLE

Cori A, Donnelly CA, Dorigatti I, Ferguson NM, Fraser C, Garske T, Jombart T, Nedjati-Gilani G, Nouvellet P, Riley S, Van Kerkhove MD, Mills HL, Blake IMet al., 2017, Key data for outbreak evaluation: building on the Ebola experience, PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, Vol: 372, ISSN: 0962-8436

JOURNAL ARTICLE

Cornelissen M, Gall A, Vink M, Zorgdrager F, Binter Š, Edwards S, Jurriaans S, Bakker M, Ong SH, Gras L, van Sighem A, Bezemer D, de Wolf F, Reiss P, Kellam P, Berkhout B, Fraser C, van der Kuyl AC, BEEHIVE Consortiumet al., 2017, From clinical sample to complete genome: Comparing methods for the extraction of HIV-1 RNA for high-throughput deep sequencing., Virus Res, Vol: 239, Pages: 10-16

The BEEHIVE (Bridging the Evolution and Epidemiology of HIV in Europe) project aims to analyse nearly-complete viral genomes from >3000 HIV-1 infected Europeans using high-throughput deep sequencing techniques to investigate the virus genetic contribution to virulence. Following the development of a computational pipeline, including a new de novo assembler for RNA virus genomes, to generate larger contiguous sequences (contigs) from the abundance of short sequence reads that characterise the data, another area that determines genome sequencing success is the quality and quantity of the input RNA. A pilot experiment with 125 patient plasma samples was performed to investigate the optimal method for isolation of HIV-1 viral RNA for long amplicon genome sequencing. Manual isolation with the QIAamp Viral RNA Mini Kit (Qiagen) was superior over robotically extracted RNA using either the QIAcube robotic system, the mSample Preparation Systems RNA kit with automated extraction by the m2000sp system (Abbott Molecular), or the MagNA Pure 96 System in combination with the MagNA Pure 96 Instrument (Roche Diagnostics). We scored amplification of a set of four HIV-1 amplicons of ∼1.9, 3.6, 3.0 and 3.5kb, and subsequent recovery of near-complete viral genomes. Subsequently, 616 BEEHIVE patient samples were analysed to determine factors that influence successful amplification of the genome in four overlapping amplicons using the QIAamp Viral RNA Kit for viral RNA isolation. Both low plasma viral load and high sample age (stored before 1999) negatively influenced the amplification of viral amplicons >3kb. A plasma viral load of >100,000 copies/ml resulted in successful amplification of all four amplicons for 86% of the samples, this value dropped to only 46% for samples with viral loads of <20,000 copies/ml.

JOURNAL ARTICLE

Didelot X, Fraser C, Gardy J, Colijn Cet al., 2017, Genomic Infectious Disease Epidemiology in Partially Sampled and Ongoing Outbreaks, MOLECULAR BIOLOGY AND EVOLUTION, Vol: 34, Pages: 997-1007, ISSN: 0737-4038

JOURNAL ARTICLE

Doekes HM, Fraser C, Lythgoe KA, 2017, Effect of the Latent Reservoir on the Evolution of HIV at the Within- and Between-Host Levels, PLOS COMPUTATIONAL BIOLOGY, Vol: 13, ISSN: 1553-734X

JOURNAL ARTICLE

Dudas G, Carvalho LM, Bedford T, Tatem AJ, Baele G, Faria NR, Park DJ, Ladner JT, Arias A, Asogun D, Bielejec F, Caddy SL, Cotten M, D'Ambrozio J, Dellicour S, Di Caro A, Diclaro JW, Duraffour S, Elmore MJ, Iii LSF, Faye O, Gilbert ML, Gevao SM, Gire S, Gladden-Young A, Gnirke A, Goba A, Grant DS, Haagmans BL, Hiscox JA, Jah U, Kugelman JR, Liu D, Lu J, Malboeuf CM, Mate S, Matthews DA, Matranga CB, Meredith LW, Qu J, Quick J, Pas SD, Phan MVT, Pollakis G, Reusken CB, Sanchez-Lockhart M, Schaffner SF, Schieffelin JS, Sealfon RS, Simon-Loriere E, Smits SL, Stoecker K, Thorne L, Tobin EA, Vandi MA, Watson SJ, West K, Whitmer S, Wiley MR, Winnicki SM, Wohl S, Wolfel R, Yozwiak NL, Andersen KG, Blyden SO, Bolay F, Carroll MW, Dahn B, Diallo B, Formenty P, Fraser C, Gao GF, Garry RF, Goodfellow I, Gnther S, Happi CT, Holmes EC, Kargbo B, Keita S, Kellam P, Koopmans MPG, Kuhn JH, Loman NJ, Magassouba N, Naidoo D, Nichol ST, Nyenswah T, Palacios G, Pybus OG, Sabeti PC, Sall A, Stroher U, Wurie I, Suchard MA, Lemey P, Rambaut Aet al., 2017, Virus genomes reveal factors that spread and sustained the Ebola epidemic, NATURE, Vol: 544, Pages: 309-+, ISSN: 0028-0836

JOURNAL ARTICLE

Garske T, Cori A, Ariyarajah A, Blake IM, Dorigatti I, Eckmanns T, Fraser C, Hinsley W, Jombart T, Mills HL, Nedjati-Gilani G, Newton E, Nouvellet P, Perkins D, Riley S, Schumacher D, Shah A, Van Kerkhove MD, Dye C, Ferguson NM, Donnelly CAet al., 2017, Heterogeneities in the case fatality ratio in the West African Ebola outbreak 2013-2016, PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, Vol: 372, ISSN: 0962-8436

JOURNAL ARTICLE

Lehtinen S, Blanquart F, Croucher NJ, Turner P, Lipsitch M, Fraser Cet al., 2017, Evolution of antibiotic resistance is linked to any genetic mechanism affecting bacterial duration of carriage, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, Vol: 114, Pages: 1075-1080, ISSN: 0027-8424

JOURNAL ARTICLE

Mostowy RJ, Croucher NJ, De Maio N, Chewapreecha C, Salter SJ, Turner P, Aanensen DM, Bentley SD, Didelot X, Fraser Cet al., 2017, Pneumococcal Capsule Synthesis Locus cps as Evolutionary Hotspot with Potential to Generate Novel Serotypes by Recombination, MOLECULAR BIOLOGY AND EVOLUTION, Vol: 34, Pages: 2537-2554, ISSN: 0737-4038

JOURNAL ARTICLE

Ratmann O, Hodcroft EB, Pickles M, Cori A, Hall M, Lycett S, Colijn C, Dearlove B, Didelot X, Frost S, Hossain ASMM, Joy JB, Kendall M, Kuhnert D, Leventhal GE, Liang R, Plazzotta G, Poon AFY, Rasmussen DA, Stadler T, Volz E, Weis C, Brown AJL, Fraser Cet al., 2017, Phylogenetic Tools for Generalized HIV-1 Epidemics: Findings from the PANGEA-HIV Methods Comparison, MOLECULAR BIOLOGY AND EVOLUTION, Vol: 34, Pages: 185-203, ISSN: 0737-4038

JOURNAL ARTICLE

Rutstein SE, Ananworanich J, Fidler S, Johnson C, Sanders EJ, Sued O, Saez-Cirion A, Pilcher CD, Fraser C, Cohen MS, Vitoria M, Doherty M, Tucker JDet al., 2017, Clinical and public health implications of acute and early HIV detection and treatment: a scoping review, JOURNAL OF THE INTERNATIONAL AIDS SOCIETY, Vol: 20, ISSN: 1758-2652

JOURNAL ARTICLE

Agua-Agum J, Allegranzi B, Ariyarajah A, Aylward RB, Blake IM, Barboza P, Bausch D, Brennan RJ, Clement P, Coffey P, Cori A, Donnelly CA, Dorigatti I, Drury P, Durski K, Dye C, Eckmanns T, Ferguson NM, Fraser C, Garcia E, Garske T, Gasasira A, Gurry C, Gutierrez GJ, Hamblion E, Hinsley W, Holden R, Holmes D, Hugonnet S, Jombart T, Kelley E, Santhana R, Mahmoud N, Mills HL, Mohamed Y, Musa E, Naidoo D, Nedjati-Gilani G, Newton E, Norton I, Nouvellet P, Perkins D, Perkins M, Riley S, Schumacher D, Shah A, Minh T, Varsaneux O, Van Kerkhove MDet al., 2016, After Ebola in West Africa - Unpredictable Risks, Preventable Epidemics, NEW ENGLAND JOURNAL OF MEDICINE, Vol: 375, Pages: 587-596, ISSN: 0028-4793

JOURNAL ARTICLE

Agua-Agum J, Ariyarajah A, Aylward B, Bawo L, Bilivogui P, Blake IM, Brennan RJ, Cawthorne A, Cleary E, Clement P, Conteh R, Cori A, Dafae F, Dahl B, Dangou J-M, Diallo B, Donnelly CA, Dorigatti I, Dye C, Eckmanns T, Fallah M, Ferguson NM, Fiebig L, Fraser C, Garske T, Gonzalez L, Hamblion E, Hamid N, Hersey S, Hinsley W, Jambei A, Jombart T, Kargbo D, Keita S, Kinzer M, George FK, Godefroy B, Gutierrez G, Kannangarage N, Mills HL, Moller T, Meijers S, Mohamed Y, Morgan O, Nedjati-Gilani G, Newton E, Nouvellet P, Nyenswah T, Perea W, Perkins D, Riley S, Rodier G, Rondy M, Sagrado M, Savulescu C, Schafer IJ, Schumacher D, Seyler T, Shah A, Van Kerkhove MD, Wesseh CS, Yoti Zet al., 2016, Exposure Patterns Driving Ebola Transmission in West Africa: A Retrospective Observational Study, PLOS MEDICINE, Vol: 13, ISSN: 1549-1676

JOURNAL ARTICLE

Agua-Agum J, Ariyarajah A, Blake IM, Cori A, Donnelly CA, Dorigatti I, Dye C, Eck-Manns T, Ferguson NM, Fraser C, Garske T, Hinsley W, Jombart T, Mills HL, Nedjati-Gilani G, Newton E, Nouvellet P, Perkins D, Riley S, Schumacher D, Shah A, Thomas LJ, Van Kerkhove MDet al., 2016, Ebola Virus Disease among Male and Female Persons in West Africa, NEW ENGLAND JOURNAL OF MEDICINE, Vol: 374, Pages: 96-98, ISSN: 0028-4793

JOURNAL ARTICLE

Blanquart F, Grabowski MK, Herbeck J, Nalugoda F, Serwadda D, Eller MA, Robb ML, Gray R, Kigozi G, Laeyendecker O, Lythgoe KA, Nakigozi G, Quinn TC, Reynolds SJ, Wawer MJ, Fraser Cet al., 2016, A transmission-virulence evolutionary trade-off explains attenuation of HIV-1 in Uganda, ELIFE, Vol: 5, ISSN: 2050-084X

JOURNAL ARTICLE

Cauchemez S, Nouvellet P, Cori A, Jombart T, Garske T, Clapham H, Moore S, Mills HL, Salje H, Collins C, Rodriquez-Barraquer I, Riley S, Truelove S, Algarni H, Alhakeem R, AlHarbi K, Turkistani A, Aguas RJ, Cummings DAT, Van Kerkhove MD, Donnelly CA, Lessler J, Fraser C, Al-Barrak A, Ferguson NMet al., 2016, Unraveling the drivers of MERS-CoV transmission, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, Vol: 113, Pages: 9081-9086, ISSN: 0027-8424

JOURNAL ARTICLE

Croucher NJ, Mostowy R, Wymant C, Turner P, Bentley SD, Fraser Cet al., 2016, Horizontal DNA Transfer Mechanisms of Bacteria as Weapons of Intragenomic Conflict, PLOS BIOLOGY, Vol: 14, ISSN: 1545-7885

JOURNAL ARTICLE

Heffernan A, Barber E, Thomas R, Fraser C, Pickles M, Cori Aet al., 2016, Impact and Cost-Effectiveness of Point-Of-Care CD4 Testing on the HIV Epidemic in South Africa, PLOS ONE, Vol: 11, ISSN: 1932-6203

JOURNAL ARTICLE

Herbeck JT, Mittler JE, Gottlieb GS, Goodreau SM, Murphy JT, Cori A, Pickles M, Fraser Cet al., 2016, Evolution of HIV virulence in response to widespread scale up of antiretroviral therapy: a modeling study, VIRUS EVOLUTION, Vol: 2, ISSN: 2057-1577

JOURNAL ARTICLE

Lamers SL, Barbier AE, Ratmann O, Fraser C, Rose R, Laeyendecker O, Grabowski MKet al., 2016, HIV-1 Sequence Data Coverage in Central East Africa from 1959 to 2013, AIDS RESEARCH AND HUMAN RETROVIRUSES, Vol: 32, Pages: 904-908, ISSN: 0889-2229

JOURNAL ARTICLE

Lessler J, Salje H, Van Kerkhove MD, Ferguson NM, Cauchemez S, Rodriquez-Barraquer I, Hakeem R, Jombart T, Aguas R, Al-Barrak A, Cummings DATet al., 2016, Estimating the Severity and Subclinical Burden of Middle East Respiratory Syndrome Coronavirus Infection in the Kingdom of Saudi Arabia, AMERICAN JOURNAL OF EPIDEMIOLOGY, Vol: 183, Pages: 657-663, ISSN: 0002-9262

JOURNAL ARTICLE

Lythgoe KA, Blanquart F, Pellis L, Fraser Cet al., 2016, Large Variations in HIV-1 Viral Load Explained by Shifting-Mosaic Metapopulation Dynamics, PLOS BIOLOGY, Vol: 14, ISSN: 1545-7885

JOURNAL ARTICLE

Pinsent A, Fraser C, Ferguson NM, Riley Set al., 2016, A systematic review of reported reassortant viral lineages of influenza A, BMC INFECTIOUS DISEASES, Vol: 16, ISSN: 1471-2334

JOURNAL ARTICLE

Ratmann O, van Sighem A, Bezemer D, Gavryushkina A, Jurriaans S, Wensing A, de Wolf F, Reiss P, Fraser Cet al., 2016, Sources of HIV infection among men having sex with men and implications for prevention, SCIENCE TRANSLATIONAL MEDICINE, Vol: 8, ISSN: 1946-6234

JOURNAL ARTICLE

Agua-Agum J, Ariyarajah A, Blake IM, Cori A, Donnelly CA, Dorigatti I, Dye C, Eckmanns T, Ferguson NM, Fowler RA, Fraser C, Garske T, Hinsley W, Jombart T, Mills HL, Murthy S, Nedjati-Gilani G, Nouvellet P, Pelletier L, Riley S, Schumacher D, Shah A, Van Kerkhove MDet al., 2015, Ebola Virus Disease among Children in West Africa, NEW ENGLAND JOURNAL OF MEDICINE, Vol: 372, Pages: 1274-1277, ISSN: 0028-4793

JOURNAL ARTICLE

Bezemer D, Cori A, Ratmann O, van Sighem A, Hermanides HS, Dutilh BE, Gras L, Faria NR, van den Hengel R, Duits AJ, Reiss P, de Wolf F, Fraser Cet al., 2015, Dispersion of the HIV-1 Epidemic in Men Who Have Sex with Men in the Netherlands: A Combined Mathematical Model and Phylogenetic Analysis, PLOS MEDICINE, Vol: 12, ISSN: 1549-1676

JOURNAL ARTICLE

Bonhoeffer S, Fraser C, Leventhal GE, 2015, High Heritability Is Compatible with the Broad Distribution of Set Point Viral Load in HIV Carriers, PLOS PATHOGENS, Vol: 11, ISSN: 1553-7366

JOURNAL ARTICLE

Cori A, Pickles M, van Sighem A, Gras L, Bezemer D, Reiss P, Fraser Cet al., 2015, CD4(+) cell dynamics in untreated HIV-1 infection: overall rates, and effects of age, viral load, sex and calendar time, AIDS, Vol: 29, Pages: 2435-2446, ISSN: 0269-9370

JOURNAL ARTICLE

Eaton JW, Bacaer N, Bershteyn A, Cambiano V, Cori A, Dorrington RE, Fraser C, Gopalappa C, Hontelez JAC, Johnson LF, Klein DJ, Phillips AN, Pretorius C, Stover J, Rehle TM, Hallett TBet al., 2015, Assessment of epidemic projections using recent HIV survey data in South Africa: a validation analysis of ten mathematical models of HIV epidemiology in the antiretroviral therapy era, LANCET GLOBAL HEALTH, Vol: 3, Pages: E598-E608, ISSN: 2214-109X

JOURNAL ARTICLE

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