Complete Genome Analyses of Foot-and-Mouth Disease Viruses Belonging to Serotypes O, A and SAT 2 in East, West and North Africa
Résumé
Foot-and-mouth disease is generally considered to be endemic in Egypt, but only to occur sporadically in other North African countries. FMD has always been endemic in East and West Africa, with the two regions having their own FMD virus (FMDV) pools (named Pool 4 and Pool 5, respectively). To examine the origin, evolution and interaction of FMD viruses in these three areas, we have sequenced the near-complete genomes of 66 O/EA-3, 35 A/AFRICA/G-IV and 39 SAT2/VII viruses from East, West and North Africa, and compared them with previously published sequences. Phylogenetic analyses of different genome regions revealed that, while the outer capsid-coding regions (VP2, VP3 and VP1) show serotype-specific phylogenies, the non-structural coding and untranslated regions do not, suggesting the possibility of extensive recombination. Recombination analyses further identified at least 25 events of both inter- and intra-typic recombination outside the outer capsid-coding region. Phylogenetic analyses indicate that both FMDV types O and A have spread from East Africa to West Africa and Egypt, independently. Spread of these two serotypes into the Maghreb countries occurred from West Africa in 2017 and 2018. FMDV serotype SAT2 also spread in Egypt on at least three occasions possibly from East Africa twice and West Africa once. The building of new trans-Saharan highways along with changes in the political situation in the region have probably led to increased legal and illegal trade between North Africa and both East and West African countries leading to the expansion of FMDV lineages from their traditional pools.