Author
Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.
8 papers
Recent·Most cited
M. Ghafari, M. Somera, C. Sarmiento, A. Niehl, E. Hebrard, T. Tsoleridis, J. Ball, B. Moury, P. Lemey, A. Katzourakis, D. Fargette
This study applies a mechanistic model to correct for time-dependent rate phenomena in plant viruses, revealing an ancient origin for sobemoviruses over four million years ago.
bioRxiv · Sep 29, 2023Evolutionary Biology
J. E. Pekar, S. Lytras, M. Ghafari, A. F. Magee, E. Parker, J. L. Havens, A. Katzourakis, T. I. Vasylyeva, M. A. Suchard, A. C. Hughes, J. Hughes, D. L. Robertson, S. Dellicour, M. Worobey, J. O. Wertheim, P. Lemey
The paper identifies the recent origin and geographical distribution of bat viruses ancestral to SARS-CoV and SARS-CoV-2, showing they circulated in Asia before spilling over into humans.
bioRxiv · Jul 12, 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
M. Ghafari, P. Simmonds, A. Katzourakis
This paper reconstructs the evolutionary history of SIVs and pSIVs across timescales using a time-dependent rate model, finding the most recent common ancestor of extant SIVs dates to ~1 million years ago.
bioRxiv · Jun 28, 2023Evolutionary Biology
M. Ghafari, Q. Liu, A. Dhillon, A. Katzourakis, D. Weissman
This study investigates the evolutionary origins of the first three SARS-CoV-2 variants of concern, finding that they likely evolved within long-term infections in single individuals through multiple mutations.
bioRxiv · May 9, 2022Evolutionary Biology
M. Ghafari, P. Simmonds, O. Pybus, A. Katzourakis
The paper introduces a mechanistic model explaining time-dependent substitution rate decay in viruses, showing it applies across virus types and revises evolutionary timescales for HCV and sarbecoviruses.
bioRxiv · Feb 9, 2021Evolutionary Biology
M. Ghafari, C. K. Lumby, D. Weissman, C. J. R. Illingworth
This paper introduces a novel haplotype reconstruction method to infer viral transmission bottleneck size from sequence data, finding that most influenza A transmission events involve 1-13 viral particles.
bioRxiv · Jan 3, 2020Evolutionary Biology