Diversity of Human Enterovirus Co-Circulations in Five Kindergartens in Bangkok between July 2019 and January 2020

Figures

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  Figure 1. The phylogenetic tree on panel (A) was reconstructed based on 6,919 bases of 116 reference complete enterovirus genomes, while the tree on panel (B) was reconstructed based on 410 bases of the 5′-UTR region from 41 clinical specimens (18 index cases and 14 case contacts) in this cohort study and reference sequences from trimmed complete genomes. The maximum likelihood method and General Time-Reversible model were used to estimate genetic relatedness. The percentage of trees (over 50%) in which the associated taxa clustered together is shown above the branches. The scale bars show substitutions per site: (A) 30% and (B) 5%. The enterovirus genotype clusters were compared between two trees. The EV-A71 genotypes B and C were separated into two and four clusters on the 5′-UTR tree, respectively. The CVA4 genotypes were divided into two clusters on the 5′-UTR tree: CVA4 and CVA4/16.

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  Figure 2. The phylogenetic tree was reconstructed based on 410 bases of the 5′-UTR region from 41 clinical specimens of the selected 18 index cases and 14 case contacts in this cohort study and 13 trimmed complete genome sequences using the maximum likelihood method and General Time-Reversible model. The percentage of trees in which the associated taxa clustered together is shown above the branches. The scale bar indicates 5% mutations per site, equal to a 20.5 single-nucleotide polymorphisms’ distance. The right panel next to the tree shows Event No., followed by Kindergarten No., Identification No., Visiting No., and type of specimens. The boxes showing Visiting No. were filled with orange when specimens belonged to index cases (symptomatic cases) and with pink when specimens belonged to case contacts (asymptomatic cases). The white letter “T” on the blue background represents the throat swab, the black letter “Bl” on the grey background represents the blister swab, and the white letter “St” on the black background represents the stool sample.

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  Figure 3. The selected 18 HFMD index cases (symptomatic infections) and 14 case contacts (asymptomatic infections) with confirmed infections via real-time RT-PCR and high-quality 5′-UTR sequences used in this study. A total of 15 infection events were assigned corresponding to index case notifications in each classroom and kindergarten. Each of the five compartments shows the index cases and case contacts in the kindergartens. Dot lines separate participants between classrooms. Each kindergarten’s total number of index cases and case contacts are shown at the bottom of each compartment. Child face characters present infection status. Sad faces with rash (red dots) present symptomatic human enterovirus infections, while happy faces represent asymptomatic infections. The texts above the characters show enterovirus genotypes based on the 5′-UTR sequences. The texts beneath the characters indicate each kindergarten’s participant identification numbers and the date of the first visit.