Genetic Characterization of Enterovirus A71 Circulating in Africa

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  Figure 1. Phylogenetic relationships of the Africa enterovirus EV-A71 study strains based on A) P1 and B) P3 coding regions. An expanded version based on P1, P2, and P3 coding regions is online (LINK). Apart from the studied sequences, subgenomic datasets included their best nucleotide sequence matches identified by NCBI BLAST search (http://www.ncbi.nlm.nih.gov/BLAST) as well as representative sequences of different EV-A71 genogroups and subgenogroups originating worldwide. Trees were constructed from the nucleotide sequence alignment using MEGA 5.0. software (http://megasoftware.net/) with the neighbor-joining method. Distances were computed using the Kimura 2-parameter model. The robustness of the nodes was tested by 1,000 bootstrap replications. Bootstrap support values >75 are shown in nodes and indicate a strong support for the tree topology. For clarity, CV-A10, CV-A5, and EV-A71 subgenogroups C3, C4, and C5 have been collapsed. Study strains are indicated by laboratory code, country of origin, and year of isolation; previously published strains are indicated by GenBank accession number, isolate code, country of origin, and year of isolation. Black triangles indicate EV-A71 strains…

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  Figure 2. Identification of recombinant sequences in the genome of EV-A71 C2 isolates from patients with acute flaccid paralysis in Africa (14-157, 14-250, 13-365, 15-355) by similarity plot against potential parent genomes (CV-A14 strain 14-254; EV-A71 genogroup E strains 13-194, 08-146, and 03-008) and from GenBank (CV-A10, CV-A5, EV-A120). Similarity plot analysis was performed using SimPlot version 3.5.1 (http://sray.med.som.jhmi.edu/SCRoftware/simplot) on the basis of full-length genomes. For the analysis, we used a window of 600 nt moving in 20-nt steps. Approximate nt positions in the enterovirus genome are indicated. The enterovirus genetic map is shown in the top panel. We used the genome of EV-A71 study strain 14-157 as a query sequence. UTR, untranslated region.