Evolution of pathogens

Recent publications

• 1. MS Fiori*, L Ferretti*, A Di Nardo, L Zhao et al, “A naturally occurring microhomology-mediated deletion of three genes in African Swine Fever Virus isolated from two Sardinian wild boars”, Viruses 14(11), 2524 (2022).

  2. L Zhao, M Hall, M de Cesare, G MacIntyre-Cockett, K Lythgoe, C Fraser, D Bonsall, T Golubchik, COVID-19 Genomics UK (COG-UK) Consortium and L Ferretti, “The mutational spectrum of SARS- CoV-2 genomic and antigenomic RNA”, Proceedings of the Royal Society B 289:20221747 (2022).

  3. MS Fiori*, L Ferretti*, M Floris, F Loi, A D Nardo, A M Sechi, A Ladu, G Puggioni, D Sanna, F Scarpa, ML Sanna, MP Madrau, C Torresi, R Sirica, E Evangelista, A Oggiano and S Dei Giudici, “First genomic evidence of dual African Swine Fever Virus infection: case report from recent and historical outbreaks in Sardinia”, Viruses 13 2145 (2021).

  4. MS Fiori, D Sanna, F Scarpa, M Floris, A Di Nardo, L Ferretti, F Loi, S Cappai, AM Sechi, PP Angioi, S Zinellu, R Sirica, E Evangelista, M Casu, G Franzoni, A Oggiano and S Dei Giudici, “A deeper insight into evolutionary patterns and phylogenetic history of ASFV epidemics in Sardinia (Italy) through extensive genomic sequencing”, Viruses 13 1994 (2021).

  5. A Di Nardo, L Ferretti, J Wadsworth, V Mioulet, B Gelman, S Karniely, A Scherbakov, G Ziay, F O ̈zyo ̈ru ̈k, U ̈ Parlak, P Tunceraˆ-Go ̈ktuna, R Hassanzadeh, M Khalaj, SM Dastoor, D Abdollahi, E Khan, M Afzal, M Hussain, NJ Knowles and DP King, “Evolutionary and ecological drivers shape the emergence and extinction of Foot-and-Mouth Disease Virus lineages”, Molecular Biology and Evolution 38 4346–4361 (2021).

  6. K A Lythgoe*, M Hall*, L Ferretti, M de Cesare, G MacIntyre-Cockett, A Trebes, M Andersson, N Otecko, E L Wise, N Moore, J Lynch, S Kidd, N Cortes, M Mori, R Williams, G Vernet, A Justice, A Green, SM Nicholls, M Azim Ansari, L Abeler-Do ̈rner, CE Moore, TEA Peto, DW Eyre, R Shaw, P Simmonds, D Buck, JA Todd, Oxford Virus Sequencing Analysis Group (OVSG), TR Connor, S Ashraf, A da Silva Filipe, J Shepherd, EC Thomson, COVID-19 Genomics UK (COG-UK) Consortium, D Bonsall, C Fraser and T Golubchik, “SARS-CoV-2 within-host diversity and transmission”, Science 372 eabg0821 (2021).

  7. A Jadhav*, L Zhao*, W Liu, C Ding, V Nair, S E Ramos-Onsins* and L Ferretti* “Genomic diversity and evolution of quasispecies in Newcastle Disease Virus infections”, Viruses 12 1305 (2020).

Intra-host genetic diversity and evolution

• We found that FMDV infections in buffaloes often present a peculiar pattern of genetic diversity, corresponding to a multi-swarm/quasi-species structure. This unusual diversity structure allowed us to detect within-host selection, pervasive recombination and epistasis at the intra-host level [1,2,3]. Our results suggest that the evolutionary dynamics of FMDV is considerably more complex than previously thought, with intra-host evolutionary forces playing a major role in it.

  1. Ferretti L, Di Nardo A, Singer B, Lasecka-Dykes L, Logan G, Wright CF, Pérez-Martín E, King DP, Tuthill TJ and Ribeca P, “Within-host recombination in the Foot-and-Mouth Disease Virus genome”, Viruses, 10(5)221 (2018). 

  2. Cortey M, Ferretti L, Pérez-Martín E, Zhang F, de Klerk-Lorist LM, Scott K, Freimanis G, Seago J, Ribeca P, van Schalkwyk L, Juleff ND, Maree FF and Charleston B, Persistent Infection of African Buffalo (Syncerus caffer) with Foot-and-Mouth Disease Virus: Limited Viral Evolution and No Evidence of Antibody Neutralization Escape, J Virol, 93(15) (2019).

  3. Ferretti L, Pérez-Martín E, Zhang F,  Maree F, Charleston B and Ribeca P, "Pervasive within-host recombination and epistasis as major determinants of the molecular evolution of the Foot-and-Mouth Disease Virus capsid", PLoS Pathogens (2020).