National Strategic Research Institute at the University of Nebraska


Date of this Version


Document Type



Emerging Infectious Diseases • • Vol. 24, No. 4, April 2018


We analyzed whole-genome sequences of 8 enterovirus A71 isolates (EV-A71). We confirm the circulation of genogroup C and the new genogroup E in West Africa. Our analysis demonstrates wide geographic circulation and describes genetic exchanges between EV-A71 and autochthonous EV-A that might contribute to the emergence of pathogenic lineages.

Genogroup E was previously identified and characterized only on the basis of VP1 analysis (3). This study confirms the circulation in West and Central Africa of EV-A71 isolates belonging to the new genogroup E on the basis of the characterization of whole genomes. The divergence among isolates indicates that this genogroup has been extensively circulating in Africa. We also suggest that the common ancestor of EV-A71-C2 strains in West Africa has undergone recombination with >1 EV-A circulating in Africa. Genogroup E and recombinant C2 appear to be indigenous to Africa; they have not yet been detected elsewhere. Further exploration of environmental or clinical samples using deep sequencing technology would be of interest to determine the extent of EV-A71 circulation in Africa in the absence of AFP cases. Systematic surveillance based on full-genome sequencing could also serve to monitor these viruses for potential recombinations and to study their role in the emergence of new EV-A71 variants in Africa.