Figure 3 | Scientific Reports

Figure 3

From: Amplification and next generation sequencing of near full-length human enteroviruses for identification and characterisation from clinical samples

Figure 3

Phylogenetic analysis of the near full-length EV genomes (n = 70) from 58 clinical VIGR stool samples from VIGR children with six previously sequenced prototype strains (CVB1 clone (M16560), CVB3 ATCC Nancy (M33854), CVB4 cultured J.V.B (X05690), CVB5 ATCC Faulkner (AF114383), CVB6 cultured Schmitt (AF039205), ECHO18 cultured Metcalf (AF081331)), a CVB1 lab-cultured strain and an EV71 clinical isolate. The unrooted phylogenetic tree was constructed using the HKY genetic distance model and the Neighbour-Joining method (1000 bootstrap replicates) and displayed as rooted with PV3 outgroup selected, implemented in Geneious software package version 9 (Biomatters). Samples named in the format “sampleID/year of collection (for VIGR isolates)/top BLAST hit”. Scale bar indicates genetic distance (substitutions per nucleotide). Sample clustering into EV species A-C is also depicted. Multiple infections indicated by A and B isolates for samples V13, V35, V38 and V47.

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