PETER SIMMONDS, BM, Phd, Frcpath, FRS(E)

CURRICULUM VITAE

PETER SIMMONDS, BM, PhD, FRCPath, FRS(E)

Date26th September, 2016

Contact information

Nuffield Department of Experimental Medicine

University of Oxford

Peter Medawar Building

South Parks Road

Oxford, OX1 3SY

Tel.01865 281 233

Qualifications

Batchelor of Medicine (BM), University of Southampton, July, 1982

General Medical Council Registration (GMC no. 2571014) - August, 1993

PhD, University of Edinburgh, July, 1988

MRCPath in Virology (by Exam), July, 1994

Current Appointments

Virology, University of Oxford (since April, 2016)

Research Interests and Career highlights

My main current research programme is in the investigation of the evolutionary and functional basis for the pervasive suppression of CpG and UpA dinucleotides in RNA viruses. Modelling evidence I obtained for selection against them in cytoplasmically-expressed RNA sequences demanded functional investigations. The discovery that viruses with high frequencies of CpG/UpA are recognised and suppressed by as yet uncharacterised intrinsic defence mechanisms suddenly opens exciting, new areas of enquiry into innate immunity in mammalian cells. Conversely, accelerated replication of viruses with suppressed frequencies confronts us with a seeming evolutionary paradox which we will investigate through experimental investigations of relationships between disease processes and transmission dynamics. Enhanced expression of genes with low CpG and UpA frequencies can be exploited as a generic technology in vaccine and vector design.

Other ongoing and recent research has been focussed on the characterisation of RNA secondary structure in viruses, and its effect on virus evolution. Discovery of large scale RNA structure in many families of positive-stranded RNA viruses followed the development of large-scale bioinformatic methods to quantify and characterise RNA secondary structure formation in viral genomes. The association of genome-scale organised RNA structure (GORS) with host persistence, and the finding that their genomes are structured in a fundamentally different way from those causing acute infections has been the subject of ongoing investigations of the nature of virus interactions with host cell defences modulated by double-stranded RNA, the physical structure of the predicted RNA structures and the influence of RNA structure as a sequence constraint on the evolution of persistent viruses. This area of research has also initiated a series of functional studies of the role of RNA secondary structure elements in the replication of HCV (Professor David Evans, University of Warwick), caliciviruses (Dr Ian Goodfellow, Imperial College, London) and hepatitis A virus (Professor S. Lemon, University of Texas Medical Branch).

A second area of research focuses on the molecular epidemiology, evolution and emergence of a wide range of human pathogenic viruses. This includes aetiological investigations of the role of known and recently discovered viruses in respiratory, enteric and neurological disease. I am closely involved in an active ongoing programme of research in clinical virology in its broadest sense with investigations ranging from basic science molecular epidemiology, evolutionary and pathogenicity studies through to investigations of the impact and newly discovered and emerging viruses in human health, and the development of diagnostics for patient screening and monitoring.

Collectively, these investigations fit into a broader theme of research work in the nature of evolutionary process in RNA viruses, how it differs from that of their mammalian hosts, how this and recombination shapes their molecular epidemiology and clinical manifestations.

PUBLICATIONS

Publications

453 authored papers listed on Medline

28 book chapters

Citations

Google Scholar

h-index = 99

37,624 citations

Selected recent published papers

2016

Thomson E, Ip CL, Badhan A, Christiansen MT, Adamson W, Ansari MA, Bibby D, Breuer J, Brown A, Bowden R, Bryant J, Bonsall D, Da Silva Filipe A, Hinds C, Hudson E, Klenerman P, Lythgow K, Mbisa JL, McLauchlan J, Myers R, Piazza P, Roy S, Trebes A, Sreenu VB, Witteveldt J, Barnes E, Simmonds P. 2016. Comparison of Next-Generation Sequencing Technologies for Comprehensive Assessment of Full-Length Hepatitis C Viral Genomes. J Clin Microbiol 54:2470-2484.

Magri A, Ozerov AA, Tunitskaya VL, Valuev-Elliston VT, Wahid A, Pirisi M, Simmonds P, Ivanov AV, Novikov MS, Patel AH. 2016. Exploration of acetanilide derivatives of 1-(omega-phenoxyalkyl)uracils as novel inhibitors of Hepatitis C Virus replication. Sci Rep 6:29487.

Salmona M, Caporossi A, Simmonds P, Thelu MA, Fusillier K, Delarue SM, De Castro N, LeGoff J, Chaix ML, Francois O, Simon F, Morand P, Larrat S, Maylin S. 2016. First NGS full genome characterization of a hepatitis C virus genotype 7 divergent subtype. Clin Microbiol Infect doi:10.1016/j.cmi.2016.07.032.

Brown A, Halliday JS, Swadling L, Madden R, Bendall R, Hunter JG, Maggs J, Simmonds P, Smith DB, Vine L, McLaughlin C, Collier J, Bonsall D, Jeffery K, Dunachie SJ, Klenerman P, Izopet J, Kamar N, Dalton HR, Barnes E. 2016. Characterisation of the specificity, functionality and durability of host T-cell responses against the full-length hepatitis E virus. Hepatology doi:10.1002/hep.28819.

Adams MJ, Lefkowitz EJ, King AM, Harrach B, Harrison RL, Knowles NJ, Kropinski AM, Krupovic M, Kuhn JH, Mushegian AR, Nibert M, Sabanadzovic S, Sanfacon H, Siddell SG, Simmonds P, Varsani A, Zerbini FM, Gorbalenya AE, Davison AJ. 2016. Ratification vote on taxonomic proposals to the International Committee on Taxonomy of Viruses (2016). Arch Virol doi:10.1007/s00705-016-2977-6.

Smith DB, Gaunt ER, Digard P, Templeton K, Simmonds P. 2016. Detection of influenza C virus but not influenza D virus in Scottish respiratory samples. J Clin Virol 74:50-53.

Gaunt E, Wise HM, Zhang H, Lee LN, Atkinson NJ, Nicol MQ, Highton AJ, Klenerman P, Beard PM, Dutia BM, Digard P, Simmonds P. 2016. Elevation of CpG frequencies in influenza A genome attenuates pathogenicity but enhances host response to infection. Elife 5:e12735.

Smith DB, Gaunt ER, Digard P, Templeton K, Simmonds P. 2016. Detection of influenza C virus but not influenza D virus in Scottish respiratory samples. J Clin Virol 74:50-53.

Bonsall D, Gregory WF, Ip CL, Donfield S, Iles J, Ansari MA, Piazza P, Trebes A, Brown A, Frater J, Pybus OG, Goulder P, Klenerman P, Bowden R, Gomperts ED, Barnes E, Kapoor A, Sharp CP, Simmonds P. 2016. Evaluation of Viremia Frequencies of a Novel Human Pegivirus by Using Bioinformatic Screening and PCR. Emerg Infect Dis 22:671-678.

Witteveldt J, Martin-Gans M, Simmonds P. 2016. Enhancement of the Replication of Hepatitis C Virus Replicons of Genotypes 1 to 4 by Manipulation of CpG and UpA Dinucleotide Frequencies and Use of Cell Lines Expressing SECL14L2 for Antiviral Resistance Testing. Antimicrob Agents Chemother 60:2981-2992.

Kokki I, Smith D, Simmonds P, Ramalingam S, Wellington L, Willocks L, Johannessen I, Harvala H. 2016. Hepatitis E virus is the leading cause of acute viral hepatitis in Lothian, Scotland. New Microbes New Infect 10:6-12.

Smith DB, Simmonds P, Izopet J, Oliveira-Filho EF, Ulrich RG, Johne R, Koenig M, Jameel S, Harrison TJ, Meng XJ, Okamoto H, Van der Poel WH, Purdy MA. 2016. Proposed reference sequences for hepatitis E virus subtypes. J Gen Virol 97:537-542.

Smith DB, Paddy JO, Simmonds P. 2016. The use of human sewage screening for community surveillance of hepatitis E virus in the UK. J Med Virol 88:915-918.

2015

Adams MJ, Lefkowitz EJ, King AM, Bamford DH, Breitbart M, Davison AJ, Ghabrial SA, Gorbalenya AE, Knowles NJ, Krell P, Lavigne R, Prangishvili D, Sanfacon H, Siddell SG, Simmonds P, Carstens EB. 2015. Ratification vote on taxonomic proposals to the International Committee on Taxonomy of Viruses (2015). Arch Virol 160:1837-1850.

Boros, A., P. Pankovics, P. Simmonds, E. Pollak, R. Matics, T. G. Phan, E. Delwart, and G. Reuter. 2015. Genome analysis of a novel, highly divergent picornavirus from common kestrel (Falco tinnunculus): The first non-enteroviral picornavirus with type-I-like IRES. Infect. Genet. Evol. 32:425-431.

Gaunt, E., H. Harvala, R. Osterback, S. Vattipally, E. Thomson, M. Waris, and P. Simmonds. 2015. Genetic characterisation of Coxsackievirus A6 variants associated with atypical hand, foot and mouth disease; a potential role of recombination in emergence and pathogenicity. J. Gen. Virol. 96:1067-1079

Kapoor A, Kumar A, Simmonds P, Bhuva N, Singh Chauhan L, Lee B, Sall AA, Jin Z, Morse SS, Shaz B, Burbelo PD, Lipkin WI. 2015. Virome Analysis of Transfusion Recipients Reveals a Novel Human Virus That Shares Genomic Features with Hepaciviruses and Pegiviruses. MBio 6:e01466-01415.

Matthews, P. C., C. P. Sharp, A. Malik, W. F. Gregory, E. Adland, P. Jooste, P. J. Goulder, P. Simmonds, and P. Klenerman. 2015. Human Parvovirus 4 Infection among Mothers and Children in South Africa. Emerg. Infect. Dis. 21:713-715.

Scheel, T. K., P. Simmonds, and A. Kapoor. 2015. Surveying the global virome: Identification and characterization of HCV-related animal hepaciviruses. Antiviral Res. 115C:83-93.

Shah A, Connelly M, Whitaker P, McIntyre C, Etherington C, Denton M, Hale A, Harvala H, Simmonds P, Peckham DG. 2015. Pathogenicity of individual rhinovirus species during exacerbations of cystic fibrosis. Eur Respir J 45:1748-1751.

Simmonds, P., F. Tulloch, D. J. Evans, and M. D. Ryan. 2015. Attenuation of dengue (and other RNA viruses) with codon pair recoding can be explained by increased CpG/UpA dinucleotide frequencies. Proc. Natl. Acad. Sci. U. S. A. 112:E3633-E3634

Simmonds, P. 2015. Methods for virus classification and the challenge of incorporating metagenomic sequence data. J. Gen. Virol. 96:1193-1206

Smith, D. B., S. Ijaz, R. Tedder, B. Hogema, H. Zaaijer, J. Izopet, A. Bradley-Stewart, R. Gunson, H. Harvala, I. Kokki, and P. Simmonds. 2015. Variability and pathogenicity of Hepatitis E virus genotype 3 variants. J. Gen. Virol.10

Smith DB, Ijaz S, Tedder RS, Hogema B, Zaaijer HL, Izopet J, Bradley-Stewart A, Gunson R, Harvala H, Kokki I, Simmonds P. 2015. Variability and pathogenicity of hepatitis E virus genotype 3 variants. J Gen Virol 96:3255-3264.

Toppinen M, Perdomo MF, Palo JU, Simmonds P, Lycett SJ, Soderlund-Venermo M, Sajantila A, Hedman K. 2015. Bones hold the key to DNA virus history and epidemiology. Sci Rep 5:17226.

Smith DB, Paddy JO, Simmonds P. 2016. The use of human sewage screening for community surveillance of hepatitis E virus in the UK. J Med Virol 88:915-918.

2014

Atkinson, N. J., D. J. Evans, and P. Simmonds. 2014. The influence of CpG and UpA dinucleotide frequencies on RNA virus replication and characterisation of the innate cellular pathways underlying virus attenuation and enhanced replication. Nucleic Acids Res. 42:4527-4545

Cabrerizo, M., G. Trallero, and P. Simmonds. 2014. Recombination and evolutionary dynamics of human echovirus 6. J Med Virol. 86:857-864

Firth, C., M. Bhat, M. A. Firth, S. H. Williams, M. J. Frye, P. Simmonds, J. M. Conte, J. Ng, J. Garcia, N. P. Bhuva, B. Lee, X. Che, P. L. Quan, and W. I. Lipkin. 2014. Detection of Zoonotic Pathogens and Characterization of Novel Viruses Carried by Commensal Rattus norvegicus in New York City. MBio. 5:e01933-14.

Harvala, H., D. Smith, K. Salvatierra, R. Gunson, B. von Wissmann, A. Reynolds, C. Frew, A. MacLean, A. Hunt, D. Yirrell, P. Simmonds, J. McMenamin, and K. Templeton. 2014. Burden of influenza B virus infections in Scotland in 2012/13 and epidemiological investigations between 2000 and 2012. Euro. Surveill. 19:20903.

Harvala, H., J. Calvert, D. Van Nguyen, L. Clasper, N. Gadsby, P. Molyneaux, K. Templeton, L. C. McWilliams, and P. Simmonds. 2014. Comparison of diagnostic clinical samples and environmental sampling for enterovirus and parechovirus surveillance in Scotland, 2010 to 2012. Euro. Surveill. 19:20772.

Harvala, H., D. Van Nguyen, C. McIntyre, S. Ahuka-Mundeke, N. E. Mpoudi, E. Delaporte, M. Peeters, and P. Simmonds. 2014. Co-circulation of enteroviruses between apes and humans. J Gen Virol. 95:403-407

Harvala, H., V. Wong, P. Simmonds, I. Johannessen, and S. Ramalingam. 2014. Acute viral hepatitis - Should the current screening strategy be modified? J Clin Virol. 59:18410-187

Harvala, H., M. Griffiths, T. Solomon, and P. Simmonds. 2014. Distinct systemic and central nervous system disease patterns in enterovirus and parechovirus infected children. J Infect. 69:69-74

Iles, J. C., J. Raghwani, G. L. Harrison, J. Pepin, C. F. Djoko, U. Tamoufe, M. Lebreton, B. S. Schneider, J. N. Fair, F. M. Tshala, P. K. Kayembe, J. J. Muyembe, S. Edidi-Basepeo, N. D. Wolfe, P. Simmonds, P. Klenerman, and O. G. Pybus. 2014. Phylogeography and epidemic history of hepatitis C virus genotype 4 in Africa. Virology. 464-465: 233-243

Lyons, S., A. Kapoor, B. S. Schneider, N. D. Wolfe, G. Culshaw, B. Corcoran, A. E. Durham, F. Burden, B. C. McGorum, and P. Simmonds. 2014. Viraemic frequencies and seroprevalence of non-primate hepacivirus and equine pegiviruses in horses and other mammalian species. J Gen Virol. 95: 1701-1711.

Matthews PC, Malik A, Simmons R, Sharp C, Simmonds P, Klenerman P. 2014. PARV4: an emerging tetraparvovirus. PLoS Pathog 10:e1004036.

Nguyen, D. V., A. H. Pham, C. V. Nguyen, H. T. Ngo, J. Carrique-Mas, H. B. Vo, J. Campbell, S. Baker, J. Farrar, M. E. Woolhouse, J. E. Bryant, and P. Simmonds. 2014. Prevalence, genetic diversity and recombination of species G enteroviruses infecting pigs in Vietnam. J Gen Virol. 95:549-556

Nishiyama, S., B. M. Dutia, J. P. Stewart, A. L. Meredith, D. J. Shaw, P. Simmonds, and C. P. Sharp. 2014. The identification of novel anelloviruses with broad diversity in UK rodents. J Gen Virol. 95: 1544-1553.

Servant-Delmas, A., S. Laperche, F. Lionnet, C. Sharp, P. Simmonds, and J. J. Lefrere. 2014. Human parvovirus 4 infection in low- and high-risk French individuals. Transfusion. 54:744-745

Siebrasse, E. A., N. L. Nguyen, C. Smith, P. Simmonds, and D. Wang. 2014. Immunohistochemical detection of KI polyomavirus in lung and spleen. Virology. 468-470 :178-184

Simmonds, P. 2014. Methods for virus classification and the challenge of incorporating metagenomic sequence data. J. Gen. Virol. Dec 11 [Epub ahead of print].

Sinclair, C., E. Gaunt, P. Simmonds, D. Broomfield, N. Nwafor, L. Wellington, K. Templeton, L. Willocks, O. Schofield, and H. Harvala. 2014. Atypical hand, foot, and mouth disease associated with coxsackievirus A6 infection, Edinburgh, United Kingdom, January to February 2014. Euro. Surveill. 19:20745

Smith, D. B., P. Simmonds, and J. E. Bell. 2014. Brain viral burden, neuroinflammation and neurodegeneration in HAART-treated HIV positive injecting drug users. J Neurovirol. 20:28-38

Smith, D. B., J. Bukh, C. Kuiken, A. S. Muerhoff, C. M. Rice, J. T. Stapleton, and P. Simmonds. 2014. Expanded classification of hepatitis C Virus into 7 genotypes and 67 Subtypes: updated criteria and assignment web resource. Hepatology. 59:318-327

Smith, D. B. and P. Simmonds. 2014. Hepatitis E virus and fulminant hepatitis-a virus or host-specific pathology? Liver Int.10

Smith, D. B., P. Simmonds, S. Jameel, S. U. Emerson, T. J. Harrison, X. J. Meng, H. Okamoto, W. H. Van der Poel, and M. A. Purdy. 2014. Consensus proposals for the classification of the family Hepeviridae. J. Gen. Virol. 95: 2223-2232.

Tulloch, F., N. J. Atkinson, D. J. Evans, M. D. Ryan, and P. Simmonds. 2014. RNA virus attenuation by codon pair deoptimisation is an artefact of increases in CpG/UpA dinucleotide frequencies. eLife 3: e04531.

Van Nguyen, D., H. Harvala, E. M. Ngole, E. Delaporte, M. E. Woolhouse, M. Peeters, and P. Simmonds. 2014. High rates of infection with novel enterovirus variants in wild populations of mandrills and other Old World Monkey species. J Virol. 88:5967-5976

Witteveldt, J., R. J. Blundell, J. Maarleveldt, N. McFadden, D. J. Evans, and P. Simmonds. 2014. The influence of viral RNA secondary structure on interactions with innate host cell defences. Nucleic Acids Res. 42:3314-3329

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