Author
Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.
17 papers
Recent·Most cited
B. Li, J. Raghwani, S. C. Hill, S. Francois, N. Lefrancq, Y. Liang, Z. Wang, L. Dong, P. Lemey, O. G. Pybus, H. Tian
This study examines how poultry vaccination affects H5 avian influenza virus transmission and evolution, finding increased nonsynonymous divergence in vaccinated poultry lineages.
bioRxiv · Dec 20, 2023Evolutionary Biology
Y. Li, M. Ghafari, A. J. Holbrook, I. Boonen, N. M. S. Amor, S. Catalano, J. P. Webster, Y. Li, H. Li, V. Vergote, P. Maes, Y. L. Chong, A. Laudisoit, P. Baelo, S. Ngoy, , P. Lemey
This study identifies novel rodent hosts of hepaciviruses, documents their diversity, and estimates the origin of the genus to be about 22 million years ago.
bioRxiv · Jun 30, 2023 · PreprintMicrobiology
S. Francois, S. Nazki, S. H. Vickers, G. Fournie, C. M. Perrins, A. J. Broadbent, O. G. Pybus, S. C. Hill
The paper characterizes a gammacoronavirus in waterbirds, revealing its genetic diversity, recombination origin, and cross-species transmission potential.
bioRxiv · Jun 8, 2023Ecology
Q. Yang, B. Wang, P. Lemey, L. Dong, T. Mu, R. A. Wiebe, F. Guo, N. S. Trovao, S. W. Park, N. Lewis, J. Tsui, S. Bajaj, Y. Cheng, L. Yang, Y. Haba, , B. T. Grenfell
The paper uses phylodynamic analyses to link bird migration patterns with the global spread of HPAIV H5 clade 2.3.4.4, identifying vulnerable bird orders and highlighting Suliformes and Ciconiiformes as important in virus dispersal.
bioRxiv · May 22, 2023Ecology
Y. Li, M. Bletsa, Z. Zisi, I. Boonen, S. Gryseels, L. Kafetzopoulou, J. P. Webster, S. Catalano, O. G. Pybus, F. Van de Perre, H. Li, Y. Li, Y. Li, A. Abramov, P. Lymberakis, , S. Lequime
The paper identifies Flaviviridae-derived endogenous viral elements in shrew genomes, revealing an ancient origin of pestiviruses and their potential role as natural reservoirs.
bioRxiv · Feb 11, 2022Microbiology
J. Raghwani, C. L. Faust, S. Francois, D. Nguyen, K. Marsh, A. Raulo, S. C. Hill, K. V. Parag, P. Simmonds, S. C. L. Knowles, O. G. Pybus
This study examines seasonal changes in the virome of wild rodents, finding that many viruses are seasonally transient and linked to host and environmental factors.
bioRxiv · Feb 9, 2022Ecology
M. Wille, C. Tolf, N. Latorre-Margalef, R. A. M. Fouchier, R. A. Halpin, D. E. Wentworth, J. Ragwani, O. G. Pybus, B. Olsen, J. Waldenstrom
This study investigates the evolutionary dynamics of avian influenza A virus in waterfowl, finding lineage replacement and reassortment across multiple viral segments over time.
bioRxiv · Nov 24, 2021Evolutionary Biology
M. Escalera-Zamudio, S. L. Kosakovsky Pond, N. Martinez de la Vina, B. Gutierrez, R. P. D. Inward, J. Theze, L. van Dorp, H. G. Castelan, T. A. Bowden, O. G. Pybus, R. J. G. Hulswit
The paper identifies site-specific evolutionary trajectories shared across human betacoronaviruses by analyzing mutations and positive selection in four viruses.
bioRxiv · May 24, 2021 · PreprintEvolutionary Biology
K. B. Hoehn, J. S. Turner, F. I. Miller, R. Jiang, O. G. Pybus, A. H. Ellebedy, S. H. Kleinstein
The paper shows that influenza vaccination leads to measurable evolution in B cell lineages engaged by germinal centers, but not in blood lineages.
bioRxiv · Jan 6, 2021Immunology
J. Mokaya, T. I. Vasylyeva, E. Barnes, M. A. Ansari, O. G. Pybus, P. C. Matthews
This study analyzes the global prevalence and phylogeny of HBV drug and vaccine resistance mutations, finding high prevalence in genotype C and evidence of independent emergence of resistance mutations.
bioRxiv · Oct 7, 2020Evolutionary Biology
S. Dellicour, S. Lequime, B. Vrancken, M. S. Gill, P. Bastide, K. Gangavarapu, N. L. Matteson, Y. Tan, L. du Plessis, A. A. Fisher, M. I. Nelson, M. Gilbert, M. A. Suchard, K. G. Andersen, N. D. Grubaugh, , P. Lemey
This study uses phylogeographic and phylodynamic methods to test hypotheses about West Nile virus dispersal and genetic diversity, finding temperature influences on spread and no strong evidence for migratory bird flyway restriction.
bioRxiv · Sep 19, 2020 · PreprintEvolutionary Biology
K. B. Hoehn, O. G. Pybus, S. H. Kleinstein
The paper develops three summary statistics to infer migration, differentiation, and isotype switching in B cells using BCR sequence data and applies them to HIV and food allergy datasets.
bioRxiv · May 30, 2020Immunology
M. Escalera-Zamudio, M. Golden, B. Gutierrez, J. Theze, J. Russell Keown, L. Carrique, T. A. Bowden, O. G. Pybus
This study identifies parallel mutations in avian influenza viruses associated with high pathogenicity using phylogenetic and statistical methods.
bioRxiv · Aug 22, 2019Evolutionary Biology
B. Gutierrez, E. Wise, S. Pullan, C. Logue, T. A. A. Bowden, G. Trueba, M. Nunes, N. R. Faria, O. G. Pybus
This study analyzes the evolutionary dynamics of Oropouche Virus in South America using genomic data to identify evolutionary processes and structural features.
bioRxiv · Jun 26, 2019 · PreprintEvolutionary Biology
K. B. Hoehn, J. A. Vander Heiden, J. Q. Zhou, G. Lunter, O. G. Pybus, S. H. Kleinstein
This study introduces a hierarchical phylogenetic framework to analyze B cell repertoires, revealing age-related changes in SHM motifs and a link between tree length and negative selection.
bioRxiv · Feb 25, 2019Immunology
J. Raghwani, C.-H. Wu, C. K. Ho, M. de Jong, R. Molenkamp, J. Schinkel, O. G. Pybus, K. A. Lythgoe
This study analyzes within-host HCV evolution in HIV-coinfected individuals, finding population structure, regional variation in mutation rates, and a low recombination rate.
bioRxiv · Aug 28, 2018Evolutionary Biology
J. Lu, J. Raghwani, J. Wu, R. Pryce, T. A. Bowden, J. Theze, S. Huang, Y. Song, L. Zou, L. Liang, R. Bai, Y. Jin, P. Zhou, M. Kang, L. Yi, , C. Ke
The paper analyzes the evolution and adaptation of H7N9 influenza viruses in China, identifying lineage-specific mutations and high-pathogenicity strains.
bioRxiv · Jun 25, 2017Evolutionary Biology