Oliver Pybus

Oliver Pybus

Professor of Evolution & Infectious Disease

Room C31

Department of Zoology

University of Oxford

South Parks Road

Oxford, OX1 3PS, UK

I investigate the evolutionary and ecological dynamics of infectious diseases, particularly pathogenic RNA viruses. My current research concerns (i) the molecular epidemiology and epidemic history of HIV and the hepatitis C virus, (ii) viral adaptation and natural selection, (iii) the evolutionary behaviour of influenza, (iv) the evolution of endogenous retroviruses, and (v) phylogenetic and population genetic methods of gene sequence analysis. More generally, I am interested in topics at the interface between ecology and evolution including adaptive radiation, speciation, and molecular ecology.

Research Interests

Other Information

I am an editor of PLOS Pathogens, Molecular Biology & Evolution, and Methods in Ecology & Evolution.

I have been awarded the Scientific Medal of the Zoological Society of London and the Daiwa Adrian Prize for my research.

I am a Fellow of New College, Oxford.

2013

Bhatt S, Lam TT, Lycett SJ, Leigh Brown AJ, Bowden TA, Holmes EC, Wood JLN, Brown IH, Kellam P, COSI consortium, Pybus OG (2013). Rapid adaptation of swine influenza virus after cross-species transmission from birds. Philosophical Transactions of the Royal Society Series B 368:20120382

Pybus OG, Fraser C, Rambaut A (2013) Evolutionary epidemiology: preparing for an age of genomic plenty. Philosophical Transactions of the Royal Society Series B 368:20120193

[front cover] [link]

Iles JC, Harrison GLA, Lyons S, Djoko CF, Tamoufe U, Lebreton M, Schneider BS, Fair JN, Tshala FM, Kayembe PK, Muyembe JJ, Edidi-Basepeo S, Wolfe ND, Klenerman P, Simmonds P, Pybus OG (2013) Hepatitis C virus infections in the Democratic Republic of Congo exhibit a cohort effect. Infection, Genetics & Evolution In press

Lam TT, Lui W, Bowden TA, Cui N, Zhuang L, Liu K, Zhang YY, Cao WC, Pybus OG (2013) Evolutionary and molecular analysis of the emergent severe fever with thrombocytopenia syndrome virus. Epidemics 5:1-10

Cotton M, Lam TT, Watson SJ, Palser AL, Petrova V, Grant P, Pybus OG, Rambaut A, Guan Y, Pillay D, Kellam P, Nastouli E (2013) Full genome deep sequencing and phylogenetic analysis of a novel human betacoronavirus. Emerging Infectious Diseases In press

[news coverage] [link]

Wang H, Yuan Z, Barnes E, Yuan M, Li C, Fu Y, Xia X, Li G, Newton P, Vongsouvath M, Klenerman P, Pybus OG, Murphy D, Abe K, Lu L (2013) Eight novel hepatitis C virus genomes reveal the changing taxonomic structure of genotype 6. Journal of General Virology 94:76-80

Lam TT, Chong YL, Shi M, Hon CC, Li J, Martin DP, Tang JWT, Mok CK, Shih SR, Yip CW, Jiang J, Hui RKH, Pybus OG, Holmes EC, Leung FCC (2013) Systematic phylogenetic analysis of influenza A virus reveals many novel mosaic genome segments. Infection, Genetics & Evolution In press

Magiorkinis G, Sypsa V, Magiorkinis E, Paraskevis D, Katsoulidou A, Belshaw R, Fraser C, Pybus OG, Hatzakis A (2013) Integrating phylodynamics and epidemiology to estimate transmission diversity in viral epidemics. PLOS Computational Biology 9:e1002876

[news coverage] [pdf]

2012

Pybus OG*, Suchard M*, Lemey P*, Bernardin F, Rambaut A, Crawford FW, Gray RR, Arinaminpathy N, Stramer S, Busch MP, Delwart E (2012) Unifying the spatial epidemiology and molecular evolution of emerging epidemics. Proceedings of the National Academy of Sciences USA 109:15066-71

[Science Editors’ Choice] [pdf]

Pybus OG*, Perrins CM*, Manvell RJ*, Schulenburg B, Sheldon B, Brown IH (2012) The ecology and age structure of a highly pathogenic avian influenza virus outbreak in wild mute swans. Parasitology 139:1914-23

[front cover] [link]

Pybus OG (2012) A pandemic made less surprising. The Lancet 379:702

Farci P, Wollenberg K, Diaz G, Engle RE, Lai ME, Klenerman P, Purcell RH, Pybus OG, Alter HJ (2012) Profibrogenic chemokines and viral evolution predict rapid progression of hepatitis C to cirrhosis. Proceedings of the National Academy of Sciences USA 109:14562-7

[commentary] [link]

Gray RR, Salemi M, Klenerman P, Pybus OG (2012) A new evolutionary model for hepatitis C virus chronic infection. PLOS Pathogens 8:e1002656

Raghwani J, Thomas XV, Koekkoek SM, Schinkel J, Molenkamp R, van de Laar TJ, Takebe Y, Tanaka Y, Mizokami M, Rambaut A, Pybus OG (2012) The origin and evolution of the unique hepatitis C virus circulating recombinant form 2k/1b. Journal of Virology 86:2212-20

Lam TTY, Zhu H, Smith DK, Guan Y, Holmes EC, Pybus OG (2012) The recombinant origin of emerging human norovirus GII.4/2008: intra-genotypic exchange of the capsid P2 domain. Journal of General Virology 93:817-22

Markov PV, van de Laar TJ, Thomas XV, Aronson SJ, Weegink CJ, van den Berk GE, Prins M, Pybus OG*, Schinkel J* (2012) Colonial history and contemporary transmission shape the genetic diversity of hepatitis C genotype 2 in Amsterdam. Journal of Virology 86:7677-87

Baille GJ, Galiano M, Agapow PM, Myers R, Chiam R, Gall A, Palser AL, Watson SJ, Hedge J, Underwood A, Platt S, Mclean E, Pebody RG, Rambaut A, Green J, Daniels R, Pybus OG*, Kellam P*, Zambon M* (2012) Evolutionary dynamics of local pandemic H1N1/09 influenza lineages revealed by whole genome analysis. Journal of Virology 86:11-8

Gray RR, Strickland S, Veras NM, Goodenow MM, Pybus OG, Lemon S, Fried M, Nelson DR, Salemi M (2012) Unexpected maintenance of hepatitis C virus diversity following liver transplantation. Journal of Virology 86:8432-9

Allicock OM, Lemey P, Tatum AJ, Pybus OG, Bennett SN, Mueller BA, Suchard MA, Foster JE, Rambaut A, Carrington CVF (2012) Phylogeography and population dynamics of Dengue viruses in the Americas. Molecular Biology & Evolution 29:1533-43

Coyne KP, Christley RM, Pybus OG, Dawson S, Gaskell RM, Radford AD (2012) Large scale spatial and temporal genetic diversity of feline calicivirus. Journal of Virology 86:11356-67

Lam TTY, Hon CC, Lemey P, Pybus OG, Shi M, Tun HM, Li J, Jiang J, Holmes EC, Leung FC (2012) Phylodynamics of H5N1 avian influenza virus in Indonesia. Molecular Ecology 21:3062-77

Lycett SJ, Baillie G, Coulter E, Bhatt S, Kellam P, McCauley JW, Brown IH, Pybus OG, Wood JLN, Leigh Brown AJ, COSI consortium (2012) Estimating reassortment rates in co-circulating Eurasian swine influenza strains. Journal of General Virology 93:2326-36

Nakano T, Takahashi K, Pybus OG, Hashimoto N, Kato H, Okano H, Kobayashi M, Fujita N, Shiraki K, Takei Y, Ayada M, Arai M, Okamoto H, Mishiro S (2012) New findings regarding the epidemic history and population dynamics of Japan-indigenous genotype 3 hepatitis E virus inferred by molecular evolution. Liver International 32:675-88

Lavoie M, Sharp CP, Pépin J, Pennington C, Foupouapouognigni Y, Pybus OG, Njouom R, Simmonds P (2012) Human parvovirus 4 infection, Cameroon. Emerging Infectious Diseases 18:680-3

2011

Vijaykrishna D*, Smith GJD*, Pybus OG*, Zhu H, Bhatt S, Poon LLM, Riley S, Bahl J, Ma SK, Cheung CL, Perera RAP, Chen H, Shortridge KF, Webby RJ, Webster RG, Guan Y, Peiris J (2011) Long-term evolution and transmission dynamics of swine influenza A virus. Nature 473:519-222

[news coverage] [link]

Bhatt S, Holmes EC, Pybus OG (2011) The genomic rate of molecular adaptation of the human influenza A virus. Molecular Biology & Evolution 28:2443-51

[software] [F1000 must read] [pdf]

Gray RR, Parker J, Lemey P, Salemi M, Katzourakis A, Pybus OG (2011) The mode and tempo of hepatitis C virus evolution within and among hosts. BMC Evolutionary Biology 11:131

Barnes I, Duda A, Pybus OG, Thomas MG (2011) Ancient urbanisation predicts genetic resistance to tuberculosis. Evolution 65:842-8

[news coverage] [link]

Belshaw R, Sanjuan R, Pybus OG (2011) Viral mutation and substitution: units and levels. Current Opinion in Virology 1:430-5

Gray RR, Tatem AJ, Johnson JA, Alexseyenko AV, Pybus OG, Suchard MA, Salemi M (2011) Testing spatiotemporal hypotheses of bacterial evolution using methicillin-resistant Staphylococcus aureus ST239 genome-wide data within a Bayesian framework. Molecular Biology & Evolution 28:1593-603

Shapiro B, Ho SYW, Drummond AJ, Suchard MA, Pybus OG, Rambaut A (2011) A Bayesian phylogenetic method to estimate unknown sequence ages. Molecular Biology & Evolution 28:879-87

Gray RR, Pybus OG, Salemi M (2011) Measuring the temporal structure in serially-sampled phylogenies. Methods in Ecology & Evolution 2:437-45

Fu Y, Wang Y, Xia W, Pybus OG, Qin W, Lu L, Nelson K (2011) New trends of HCV infection in China revealed by genetic analysis of viral sequences determined from first-time volunteer blood donors. Journal of Viral Hepatitis 18:42-52

2010

Tee KK, Lam TT, Chan Y, Bible JM, Tong W, Kamarulzaman A, Takebe Y, Pybus OG (2010) Evolutionary genetics of human enterovirus 71: origin, population dynamics, natural selection and periodicity of the VP1 gene. Journal of Virology 84:3339-50

Bhatt S, Katzourakis A, Pybus OG (2010) Detecting natural selection in RNA virus populations using sequence summary statistics. Infection, Genetics & Evolution 10:421-30

Hué S, Gray ER, Gall A, Katzourakis A, Tan CP, Houldcroft C, McLaren S, Pillay D, Futreal A, Garson J, Pybus OG, Kellam P, Towers GJ (2010) Disease-associated XMRV sequences are consistent with laboratory contamination. Retrovirology 7:111

[F1000 recommended] [news coverage] [commentary] [more commentary] [pdf]

Auguste AJ, Lemey P, Pybus OG, Suchard MA, Salas RA, Adesiyun AA, Barrett AD, Tesh RB, Weaver SC, Carrington CVF (2010) Yellow fever virus maintenance in Trinidad and its dispersal throughout the Americas. Journal of Virology 84:9967-77

Pépin J, Lavoie M, Pybus OG, Pouillot R, Foupouapouognigni Y, Rousset D, Labbé AC, Njouom R (2010) Risk factors for hepatitis C virus transmission in colonial Cameroon. Clinical Infectious Diseases 51:768-76

[news coverage] [commentary] [link]

Bennett SN, Drummond AJ, Kapan DD, Suchard MA, Muñoz-Jordan JL, Pybus OG, Holmes EC, Gubler DJ (2010) Epidemic dynamics revealed in dengue evolution. Molecular Biology & Evolution 27:811-8

Sharp CP, LeBreton M, Kantola K, Nana A, Diffo JL, Djoko CF, Tamoufe U, Kiyang JA, Babila TG, Ngole EM, Pybus OG, Delwart E, Delaporte E, Peeters M, Soderlund-Venermo M, Hedman K, Wolfe ND, Simmonds P (2010) Widespread infection with homologues of human parvoviruses B19, PARV4, and human bocavirus of chimpanzees and gorillas in the wild. Journal of Virology 84:10289-96

Huang KH, Bonsall D, Katzourakis A, Thomson EC, Fidler SJ, Main J, Muir D, Weber JN, Frater AJ, Phillips RE, Pybus OG, Goulder PJ, McClure MO, Cooke GS, Klenerman P (2010) B cell depletion reveals a role for antibodies in the control of chronic HIV-1 infection. Nature Communications 1:102

[F1000 must read] [pdf]

Sharp CP, Vermeulen M, Nébié Y, Djoko CK, LeBreton M, Tamoufe U, Rimoin AW, Kayembe PK, Carr JK, Servant-Delmas A, Laperche S, Harrison GL, Pybus OG, Delwart E, Wolfe ND, Saville A, Lefrère JJ, Simmonds P (2010) Epidemiology of human parvovirus 4 infection in sub-Saharan Africa. Emerging Infectious Diseases 16:1605-07

Sahin GO, Bowles EJ, Parker J, Uchtenhagen H, Sheik-Khalil E, Taylor S, Pybus OG, Mäkitalo B, Walther-Jallow L, Spangberg M, Thorstensson R, Achour A, Fenyo EM, Stewart-Jones GB, Spetz AL (2010) Generation of neutralizing antibodies and divergence of SIVmac239 in Cynomolgus macaques following short-term early antiretroviral therapy. PLOS Pathogens 6:e1001084

Jones R, Brown D, Nelson M, Low E, Bhagani S, Atkins M, Danta M, Dusheiko G, Pybus O, Asboe D (2010) Re-emergent hepatitis C viremia after apparent clearance in HIV-positive men who have sex with men: reinfection or late recurrence? Journal of Acquired Immune Deficiency Syndromes 53:547-50

Li Y, Uenishi R, Hase S, Liao H, Li XJ, Takayo T, Tee KK, Pybus OG, Takebe Y (2010) Explosive HIV-1 subtype B' epidemics in Asia driven by geographic and risk group founder events. Virology 402:223-7

Fu Y, Xia W, Wang Y, Tian L, Pybus OG, Lu L, Nelson K (2010) The seroprevalence of hepatitis C virus among 559,890 first-time volunteer blood donors in China reflects regional heterogeneity in HCV prevalence and changes in blood donor recruitment models Transfusion 50:1505-11

Li Y, Tee KK, Liao H, Hase S, Uenishi R, Li XJ, Tsuchiura T, Yang R, Govindasamy S, Yong YK, Tan HY, Pybus OG, Kamarulzaman A, Takebe Y (2010) Identification of a novel second-generation circulating recombinant form (CRF48_01B) in Malaysia: a descendant of the previously identified CRF33_01B. Journal of Acquired Immune Deficiency Syndromes 54:129-36

2009

Katzourakis A, Gifford RJ, Tristem M, Gilbert MTP, Pybus OG (2009) Macroevolution of complex retroviruses. Science 325:1512

[news coverage] [pdf]

Fraser C, Donnelly CA, Cauchemez S, Hanage WP, Van Kerkhove MD, Hollingsworth TD, Griffin J, Baggaley RF, Jenkins HE, Lyons EJ, Jombart T, Hinsley WR, Grassly NC, Balloux F, Ghani AC, Ferguson NM, Rambaut A, Pybus OG, Lopez-Gatell H, Apluche- Aranda CM, Chapela IB, Zavala EP, Guevara DMA, Checchi F, Fitzner J, Garcia E, Hugonnet S, Roth C (2009) Pandemic potential of a novel strain of influenza A (H1N1): early findings. Science 324:1557-61

[front cover] [F1000 must read] [news coverage] [pdf]

Smith GJD*, Vijaykrishna D*, Bahl J*, Lycett SJ*, Worobey M*, Pybus OG*, Ma SK, Cheung CM, Raghwani J, Bhatt S, Peiris JS, Guan Y, Rambaut A (2009) Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic. Nature 459:1122-5

[F1000 must read] [news coverage] [pdf]

Kawashima Y, Pfafferott K, Frater J, Matthews P, Payne R, Addo M, Gatanaga H, Fujiwara M, Hachiya A, Koizumi H, Kuse N, Oka S, Duda A, Prendergast A, Crawford H, Leslie A, Brumme Z, Brumme C, Allen T, Brander C, Kaslow R, Tang J, Hunter E, Allen S, Mulenga J, Branch S, Roach T, John M, Mallal S, Ogwu A, Shapiro R, Prado J, Fidler S, Weber J, Pybus OG, Klenerman P, Ndung’u T, Phillips R, Heckerman D, Harrigan PR, Walker BD, Takiguchi M, Goulder P (2009) Adaptation of HIV-1 to human leukocyte antigen class I. Nature 458:641-5

[F1000 recommended] [news coverage] [link]

Pybus OG*, Barnes E*, Taggart R, Lemey P, Markov PV, Rasachak B, Syhavong B, Rattanaphone P, Sheridan I, Humphreys IS, Lu L, Newton P, Klenerman P (2009) The genetic history of the hepatitis C virus in East Asia. Journal of Virology 83:1071-82

Pybus OG, Rambaut A (2009) Evolutionary analysis of the dynamics of viral infectious disease. Nature Reviews Genetics 10:540-50

Pybus OG, Shapiro B (2009) Natural selection and adaptation of molecular sequences. In The Phylogenetic Handbook, 2nd Edition (P Lemey, M Salemi, A Vandamme, editors) pp.407-418. Cambridge University Press

Penman BS, Pybus OG, Weatherall DJ, Gupta S (2009) Epistatic interactions between genetic disorders of hemoglobin can explain why the sickle cell gene in uncommon in the Mediterranean. Proceedings of the National Academy of Sciences USA 106:21242-6

[Science Editors’ Choice] [pdf]

Markov PV, Pepin J, Frost E, Deslandes S, Labbé AC, Pybus OG (2009) The phylogeography and molecular epidemiology of hepatitis C virus genotype 2 in Africa. Journal of General Virology 90:2086-96

Tee KK*, Pybus OG*, Parker J, Ng KP, Kamarulzaman A, Takebe Y (2009) Estimating the date of origin of an HIV-1 circulating recombinant form. Virology 387:229-34

Humphreys I, Fleming V, Fabris P, Parker J, Schulenberg B, Brown A, Demetriou C, Gaudieri S, Pfafferott K, Lucas M, Collier J, Huang KH, Pybus OG, Klenerman P, Barnes E (2009) Full-length characterisation of the hepatitis C virus subtype 3a reveals novel hypervariable regions under positive selection during acute infection. Journal of Virology 83:11456-66

[software] [pdf]

Magiorkinis G, Magiorkinis E, Paraskevis D, Ho S, Shapiro B, Pybus OG, Allain JP, Hatzakis A (2009) The global spread of hepatitis C virus 1a and 1b: a phylodynamic and phylogeographic analysis. PLOS Medicine 6:e1000198

Paraskevis D, Pybus O, Magiorkinis G, Hatzakis A, Wensing A, van de Vijver D, Albert J, Angarano G, Asjo B, Balotta C, Boeri E, Camacho R, Chaix M, Coughlan S, Costagliola D et al. (2009) Tracing the HIV-1 subtype B mobility in Europe: a phylogeographic approach. Retrovirology 6:49

[news coverage] [pdf]

Liao H, Tee KK, Hase S, Uenishi R, Li XJ, Kusagawa S, Thang PH, Hien NT, Pybus OG, Takebe Y (2009) Phylodynamic analysis of the dissemination of HIV-1 CRF01_AE in Vietnam. Virology 391:51-6

Alcantara LC, Cassol S, Libin P, Deforche K, Pybus OG, Van Ranst M, Galvão-Castro B, Vandamme AM, de Oliveira T (2009) A standardized framework for accurate high-throughput genotyping of recombinant and non-recombinant viral sequences. Nucleic Acids Research 37:W634-42

[software] [pdf]

van de Laar T, Pybus O, Bruisten S, Brown D, Nelson M, Bhagani S, Vogel M, Baumgarten A, Chaix ML, Fisher M, Gotz H, Matthews G, Neifer S, White P, Rawlinson W, Pol S, Rockstroh J, Coutinho R, Dore G, Dusheiko G, Danta M (2009) Evidence of a large international HCV transmission network in HIV-positive men who have sex with men (MSM). Gastroenterology 136:1609-17

[F1000 recommended] [link]

Matthews PC, Leslie A, Katzourakis A, Pfafferott K, Power K, Kelleher AD, Carlson J, Heckerman D, Walker BD, Allen TM, Pybus OG, Goulder PJR (2009) HLA footprints in HIV-1 gag are associated with phylogenetic clustering and clade-specific amino acid polymorphism. Journal of Virology 83:4605-15

Auguste AJ, Pybus OG, Carrington CVF (2009) Evolution and dispersal of St. Louis encephalitis virus in the Americas. Infection, Genetics & Evolution 9:709-15

2008

Rambaut A, Pybus OG, Nelson MI, Viboud C, Taubenberger JK, Holmes EC (2008) The genomic and epidemiological dynamics of human influenza A virus. Nature 453:615-9

[F1000 recommended] [news coverage] [pdf]

Gifford, RJ, Katzourakis A, Tristem M, Pybus OG, Winters M, Shafer RW (2008) A transitional endogenous lentivirus from the genome of a basal primate and implications for lentivirus evolution. Proceedings of the National Academy of Sciences USA 105:20362-7

[news coverage] [commentary] [pdf]

Belshaw R, Gardner A, Rambaut A, Pybus OG (2008) Pacing a small cage: mutation and RNA viruses. Trends in Ecology & Evolution 23:188-93

Parker P, Rambaut A, Pybus OG (2008) Correlating viral phenotypes with phylogeny: accounting for phylogenetic uncertainty. Infection, Genetics and Evolution 8:239-46

[software] [pdf]

Tee KK, Pybus OG, Li XJ, Han X, Shang H, Kamarulzaman A, Takebe Y (2008) Temporal and spatial dynamics of the HIV-1 circulating recombinant forms 08_BC and 07_BC in Asia. Journal of Virology 82:9206-15

Danta M, Semmo N, Fabris P, Brown D, Pybus OG, Sabin CA, Bhagani S, Emery VC, Dusheiko GM, Klenerman P (2008) Impact of HIV on host-viral interactions during early hepatitis C virus infection. Journal of Infectious Diseases 197:1558-66

Tee KK, Pybus OG, Liao H, Uenishi R, Hase S, Kamarulzaman A, Li X-J, Takebe Y (2008) Chronology of the HIV-1 CRF07_BC expansion in East Asia. AIDS 22:156-8

Kelly, CK, Bowler, MG, Pybus O, Harvey PH (2008) Phylogeny, niches and relative abundance in natural communities. Ecology 89:962-70

[commentary] [pdf]

Lam TT, Hon CC, Pybus OG, Kosakovsky Pond SL, Wong R, Yip C, Zeng F, Leung FC (2008) Evolutionary and transmission dynamics of reassortant H5N1 influenza virus in Indonesia. PLOS Pathogens 4:e1000130

Neumann-Haefelin C, Frick DN, Wang JJ, Pybus OG, Salloum S, Narula GS, Eckart A, Biezynski A, Eiermann T, Klenerman P, Viazov S, Roggendorf M, Thimme R, Reiser M, Timm J (2008) Analysis of the evolutionary forces in an immunodominant CD8 epitope in the hepatitis C virus at a population level. Journal of Virology 82:3438-51

Xia X, Zhao W, Tee KK, Feng Y, Takebe Y, Li Q, Pybus OG, Lu L (2008) Complete genome sequencing and phylogenetic analysis of HCV isolates from China reveals a new subtype, designated 6u. Journal of Medical Virology 80:1740-6

Pouillot R, Lachenal G, Pybus OG, Rousset D, Njouom R (2008) Variable epidemic histories of hepatitis C virus genotype 2 infection in West Africa and Cameroon. Infection, Genetics & Evolution 8:676-81

Ndong-Atome GR, Makuwa M, Ouwe-Missi-Oukem-Boyer O, Pybus OG, Branger M, Le Hello S, Boye-Cheik SB, Brun-Vezinet F, Kazanji M, Roques P, Bisser S (2008) High prevalence of hepatitis C virus infection and predominance of genotype 4 in rural Gabon. Journal of Medical Virology 80:1581-7

2007

Pybus OG, Rambaut A, Belshaw R, Freckleton RP, Drummond AJ, Holmes EC (2007) Phylogenetic estimation of deleterious mutation load in RNA viruses and its contribution to viral evolution. Molecular Biology & Evolution 24:845-52

Pybus OG*, Markov P*, Wu A, Tatem AJ (2007) Investigating the endemic transmission of the hepatitis C Virus. International Journal of Parasitology 37:839-49

Recker M*, Pybus OG*, Nee S, Gupta S (2007) The generation of influenza outbreaks by a network of host immune responses against a limited set of antigenic types. Proceedings of the National Academy of Sciences USA 104:7711-6

[Science Editors’ Choice] [pdf]

Katzourakis A, Tristem M, Pybus OG, Gifford RJ (2007) Discovery and analysis of the first endogenous lentivirus. Proceedings of the National Academy of Sciences USA 104:6261-5

[F1000 recommended] [news coverage] [commentary] [pdf]

Gifford RJ, de Oliveira T, Rambaut A, Pybus OG, Dunn D, Vandamme AM, Kellam P, Pillay D (2007) Phylogenetic surveillance of viral genetic diversity and the evolving molecular epidemiology of HIV-1. Journal of Virology 81:13050-6

Belshaw R, Pybus OG, Rambaut A (2007) The evolution of genome compression and genomic novelty in RNA viruses. Genome Research 17:1496-504

Paraskevis D, Magiorkinis E, Magiorkinis G, Sypsa V, Paparizos V, Lazanas M, Gargalianos P, Antoniadou A, Panos G, Chrysos G, Sambatakou H, Karafoulidou A, Skoutelis A, Kordossis T, Koratzanis I, Theodoridou M, Daikos GL, Nikolopoulos G, Pybus OG, Hatzakis A (2007) Increasing prevalence of HIV-1 subtype A in Greece: estimating epidemic history and origin. Journal of Infectious Diseases 196:1167-76

[commentary] [pdf]

Lu L, Li C, Fu Y, Thaikruea L, Thongswat S, Maneekarn N, Apichartpiyakul C, Hotta H, Okamoto H, Netski D, Pybus OG, Murphy D, Hagedorn CH, Nelson KE (2007) Complete genomes for hepatitis C virus subtypes 6f, 6i, 6j, and 6m: viral genetic diversity among Thai blood donors and infected spouses. Journal of General Virology 88:1505-18

Lu L, Li C, Fu Y, Gao F, Pybus OG, Abe K, Okamoto H, Hagedorn CH, Murphy D (2007) Complete genomes of hepatitis C virus (HCV) subtypes 6c, 6l, 6o, 6p and 6q: completion of a full panel of genomes for HCV genotype 6. Journal of General Virology 88:1519-25

Danta M, Brown D, Bhagani S, Pybus OG, Sabin CA, Nelson M, Fisher M, Johnson AM, Dusheiko GM (2007) Recent epidemic of acute hepatitis C virus in HIV-positive men who have sex with men linked to high-risk sexual behaviours. AIDS 21:983-91

[F1000 recommended] [commentary] [link]

Lemey P, Kosakovsky Pond S, Drummond AJ, Pybus OG, Shapiro B, Taveira N, Rambaut A (2007) Synonymous substitution rates predict HIV disease progression as a result of underlying replication dynamics. PLOS Computational Biology 3:282-92

Saarma U, Ho SY, Pybus OG, Kaljuste M, Tumanov IL, Kojola I, Vorobiev AA, Markov NI, Saveljev AP, Valdmann H, Lyapunova EA, Abramov AV, Mannil P, Korsten M, Vulla E, Pazetnov SV, Pazetnov VS, Putchkovskiy SV, Rokov AM (2007) Mitogenetic structure of brown bears (Ursus arctos L.) in northeastern Europe and a new time frame for the formation of European brown bear lineages. Molecular Ecology 16:401-413

2006

de Oliveira T*, Pybus OG*, Rambaut A*, Salemi M, Cassol S, Ciccozzi M, Rezza G, Gattinara GC, D'Arrigo R, Amicosante M, Perrin L, Colizzi V, Perno CF, Benghazi Study Group (2006) Molecular epidemiology: HIV-1 and HCV sequences from Libyan outbreak. Nature 444:836-7

[news coverage] [commentary] [pdf]

Pybus OG (2006) Model selection and the molecular clock. PLOS Biology 4:686-8

Nakano T, Lu L, He Y, Fu Y, Robertson BH, Pybus OG (2006) Population genetic history of hepatitis C virus 1b infection in China. Journal of General Virology 87:73-82

Lemey P, Rambaut A, Pybus OG (2006) HIV evolutionary dynamics within and among hosts. AIDS Reviews 8:125-40

Shackelton LA, Rambaut A, Pybus OG, Holmes EC (2006) JC virus evolution and its association with human populations. Journal of Virology 80:9928-33

Edwards CTT, Holmes EC, Pybus OG, Wilson DJ, Viscidi RP, Abrams EJ, Phillips RE, Drummond AJ (2006) Evolution of the human immunodeficiency virus envelope gene evolution is dominated by purifying selection. Genetics 174:1441-53

Shapiro B, Rambaut A, Pybus OG, Holmes EC (2006) A phylogenetic method for detecting positive epistasis in gene sequences and its application to RNA virus evolution. Molecular Biology & Evolution 23:1724-30

Verbeeck J, Maes P, Lemey P, Pybus OG, Wollants E, Song E, Nevens F, Fevery J, Delport W, Van der Merwe S, Van Ranst M (2006) Investigating the origin and spread of hepatitis C virus genotype 5a. Journal of Virology 80:4220-6

Alcantara L, de Oliveira T, Gordon M, Pybus O, Mascarenhas RE, Seixas M, Goncalves M, Hlela C, Cassol S, Galvao-Castro B (2006) Tracing the origins of Brazilian HTLV-I as determined by analysis of host and viral genes. AIDS 20:780-2

Neumann-Haefelin C, McKiernan S, Ward S, Viazov S, Spangenberg H, Killinger T, Baumert TF, Nazarova N, Sheridan I, Pybus O, von Weizsacker F, Roggendorf M, Kelleher D, Klenerman P, Blum H, Thimme R (2006) Dominant influence of an HLA-B27 restricted virus-specific CD8+ T cell response mediating HCV clearance and evolution. Hepatology 43:563-72

Komatsu H, Lauer G, Pybus OG, Ouchi K, Wong D, Ward S, Walker B, Klenerman P (2006) Do antiviral CD8+ T cells select hepatitis C virus escape mutants? Analysis in diverse epitopes targeted by human intrahepatic CD8+ T lymphocytes. Journal of Viral Hepatitis 13:121-30

2005

Hué S, Pillay D, Clewley J, Pybus OG (2005) Genetic analysis reveals the complex structure of HIV-1 transmission within defined risk groups. Proceedings of the National Academy of Sciences USA 102:4425-9

[news coverage] [pdf]

Drummond AJ, Rambaut A, Shapiro B, Pybus OG (2005) Bayesian coalescent inference of past population dynamics from molecular sequences. Molecular Biology & Evolution 22:1185-92

[citation classic] [pdf]

Pybus OG*, Cochrane A*, Holmes EC, Simmonds P (2005) The hepatitis C virus epidemic among injecting drug users. Infection, Genetics & Evolution 5:131-9

Katzourakis A, Rambaut A, Pybus OG (2005) The evolutionary dynamics of endogenous retroviruses. Trends in Microbiology 13:463-8

Carrington CV, Foster JE, Pybus OG, Bennett SN, Holmes EC (2005) Invasion and maintenance of dengue virus type 2 and type 4 in the Americas. Journal of Virology 79:14680-7

Mu J, Joy DA, Duan J, Huang Y, Carlton J, Walker J, Barnwell J, Beerli P, Charleston MA, Pybus OG, Su XZ (2005) Host switch leads to emergence of Plasmodium vivax malaria in humans. Molecular Biology & Evolution 22:1686-93

Walker PR, Pybus OG, Rambaut A, Holmes EC (2005) Comparative population dynamics of HIV-1 subtypes B and C: subtype-specific differences in patterns of epidemic growth. Infection, Genetics & Evolution 5:199-208

Salemi M, de Oliveira T, Soares MA, Pybus O, Dumans AT, Vandamme AM, Tanuri A, Cassol S, Fitch WM (2005) Different epidemic potentials of the HIV-1 B and C subtypes. Journal of Molecular Evolution 60:598-605

Lemey P, Pybus OG, Van Dooren S, Vandamme AM (2005) A Bayesian statistical analysis of human T-cell lymphotropic virus evolutionary rates. Infection, Genetics & Evolution 5:291-8

2004

Grenfell BT, Pybus OG, Gog JR, Wood JL, Daly JM, Mumford JA, Holmes EC (2004) Unifying the epidemiological and evolutionary dynamics of pathogens. Science 303:327-32

Shapiro B, Drummond AJ, Rambaut A, Wilson MC, Matheus PE, Sher AV, Pybus OG, Gilbert MT, Barnes I, Binladen J, Willerslev E, Hansen AJ, Baryshnikov GF, Burns JA, Davydov S, Driver JC, Froese DG, Harington CR, Keddie G, Kosintsev P, Kunz ML, Martin LD, Stephenson RO, Storer J, Tedford R, Zimov S, Cooper A (2004) Rise and fall of the Beringian steppe bison. Science 306:1561-5

[news coverage] [commentary] [pdf]

Nakano T, Lu L, Liu P, Pybus OG (2004) Viral gene sequences reveal the variable history of hepatitis C virus infection among countries. Journal of Infectious Disease 190:1098-108

Flanagan NS, Tobler A, Davidson A, Pybus OG, Kapan DD, Planas S, Linares M, Heckel D, McMillan WO (2004) Historical demography of Müllerian mimicry in the neotropical Heliconius butterflies. Proceedings of the National Academy of Sciences USA 101:9704-9

Lemey P, Pybus OG, Rambaut A, Drummond AJ, Roques P, Worobey M, Vandamme AM (2004) The molecular population genetics of HIV-1 group O. Genetics 167:1059-68

[F1000 recommended] [pdf]

Sheridan I, Pybus OG, Holmes EC, Klenerman P (2004) High resolution phylogenetic analysis of hepatitis C virus adaptation and its relationship to disease progression. Journal of Virology 78:3447-54

Van Dooren S, Pybus OG, Salemi M, Liu HF, Goubau P, Remondegui C, Talarmin A, Gotuzzo E, Alcantara LC, Galvao-Castro B, Vandamme AM (2004) The low evolutionary rate of human T-cell lymphotropic virus type-1 confirmed by analysis of vertical transmission chains. Molecular Biology & Evolution 21:603-11

Le Goff-Vitry MC, Pybus OG, Rogers AD (2004) Genetic structure of the deep-sea coral Lophelia pertusa in the northeast Atlantic revealed by microsatellites and internal transcribed spacer sequences. Molecular Ecology 13:537-49

2003

Pybus OG, Drummond AJ, Nakano T, Robertson BH, Rambaut A (2003) The epidemiology and iatrogenic transmission of hepatitis C virus in Egypt: a Bayesian coalescent approach. Molecular Biology & Evolution 20:381-7

Walker P, Worobey M, Rambaut A, Holmes EC, Pybus OG (2003) Sexual transmission of HIV in Africa. Nature 422:679

[news coverage] [commentary] [pdf]

Lemey P, Pybus OG, Wang B, Saksena NK, Salemi M, Vandamme AM (2003) Tracing the origin and history of the HIV-2 epidemic. Proceedings of the National Academy of Sciences USA 100:6588-92

[news coverage] [pdf]

Drummond AJ, Pybus OG, Rambaut A (2003) Inference of viral evolutionary rates from molecular sequences. Advances in Parasitology 54:331-58

Ndjomou J, Pybus OG, Matz, B (2003) Phylogenetic analysis of hepatitis C virus (HCV) isolates indicates a unique pattern of endemic infection in Cameroon. Journal of General Virology 84:2333-41

Drummond AJ, Pybus OG, Rambaut A, Forsberg R, Rodrigo A (2003) Measurably evolving populations. Trends in Ecology & Evolution 18:481-8

Twiddy SS, Pybus OG, Holmes EC (2003) Comparative population dynamics of the mosquito-borne flaviviruses. Infection, Genetics & Evolution 3:87-95

[F1000 recommended] [pdf]

Robbins KE, Lemey P, Pybus OG, Jaffe HW, Youngpairoj AS, Brown TM, Salemi M, Vandamme AM, Kalish ML (2003) U.S. human immunodeficiency virus type 1 epidemic: date of origin, population history, & characterization of early strains. Journal of Virology 77:6359-66

[news coverage] [pdf]

2002

Pybus OG, Rambaut A, Holmes EC, Harvey PH (2002) New inferences from tree shape: numbers of missing taxa and population growth rates. Systematic Biology 51:881-8

Pybus OG, Rambaut. A (2002) GENIE: Estimating demographic history from molecular phylogenies. Bioinformatics 18:1404-5

[software] [pdf]

Worobey M, Rambaut A, Pybus OG, Robertson DL (2002) Questioning the evidence for genetic recombination in the 1918 “Spanish Flu” virus. Science 296:211a

Stumpf MPH, Pybus OG (2002) Genetic diversity and models of viral evolution for the hepatitis C virus. FEMS Microbiology Letters 214:143-52

Jenkins GM, Rambaut A, Pybus OG, Holmes EC (2002) Rates of molecular evolution in RNA viruses: a quantitative phylogenetic analysis. Journal of Molecular Evolution 54:152-61

Woelk CH, Pybus OG, Jin L, Brown DWG, Holmes EC (2002) Increased positive selection pressure in persistent (SSPE) versus acute measles virus infections. Journal of General Virology 83:1419-30

2001

Pybus OG, Charleston MA, Gupta S, Rambaut A, Holmes EC, Harvey PH (2001) The epidemic behaviour of the hepatitis C virus. Science 292:2323-5

Rambaut A, Robertson DL, Pybus OG, Peeters M, Holmes EC (2001) Phylogeny and the origin of HIV-1. Nature 410:1047-8

[news coverage] [commentary] [pdf]

Strimmer K, Pybus OG (2001) Exploring the demographic history of DNA sequences using the generalised skyline plot. Molecular Biology & Evolution 18:2298-305

Yusim K, Peeters M, Pybus OG, Bhattacharya T, Delaporte E, Mulanga C, Muldoon M, Theiler J, Korber B (2001) Using HIV-1 sequences to infer historical features of the AIDS epidemic and HIV evolution. Philosophical Transactions of the Royal Society Series B 356:855-66

2000

Pybus OG, Rambaut A, Harvey PH (2000) An integrated framework for the inference of viral population history from reconstructed genealogies. Genetics 155:1429-37

Pybus OG, Harvey PH (2000) Testing macro-evolutionary models using incomplete molecular phylogenies. Proceedings of the Royal Society Series B 267:2267-72

Beerli P, Grassly N, Kuhner MK, Nickle D, Pybus OG, Rain M, Rambaut A, Rodrigo AG, Wang Y (2000) Population genetics of HIV: parameter estimation using genealogy-based methods. In Computational & Evolutionary Analysis of HIV Molecular Sequences (AG Rodrigo & GH Learn, editors) pp. 217-52. Kluwer Academic Publishers

Pybus OG (2000) Praxis makes perfect? Diversity & Distributions 6:327-8

1999

Pybus OG, Holmes EC, Harvey PH (1999) The mid-depth method and HIV-1: a practical approach for testing hypotheses of viral epidemic history. Molecular Biology & Evolution 16:953-9

Holmes EC, Pybus OG, Harvey PH (1999) The molecular population dynamics of HIV-1. In The Evolution of HIV (KA Crandall, editor) pp. 177-207. John Hopkins University Press

Publications

* denotes equal contributions