High Diversity of Human Non-Polio Enterovirus Serotypes Identified in Contaminated Water in Nigeria

Figures

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  Figure 1. Enteroviruses (EV) serotypes identified in water samples from Nigeria. Filtered next generation sequencing (NGS) reads from RT-PCR products from the water concentrates were mapped to consensus sequences obtained for each sample. The proportions of reads mapping to each EV serotype in each sample are shown with different colors as indicated at the bottom of the figure.

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  Figure 2. Overall prevalence of EV serotypes in water samples from Nigeria. Filtered NGS reads from RT-PCR products from the water concentrates were mapped to consensus sequences obtained for each sample. The proportions of NGS reads mapping to each EV serotype are shown. The sample source is shown in different colors as indicated at the bottom of the figure.

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  Figure 3. Phylogenetic analysis of VP1 sequences of EV strains from species (A–D) (panels A–D in the figure) identified in water samples from Nigeria. Phylogenetic relationships between EV sequences were inferred by using the Maximum Likelihood method and Tamura-Nei model using MEGA X software [29]. Initial tree(s) for the heuristic search were obtained automatically by applying Neighbor-Join and BioNJ algorithms to a matrix of pairwise distances estimated using the Maximum Composite Likelihood (MCL) approach, and then selecting the topology with superior log likelihood value. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) are shown next to the branches. VP1 sequences from Nigerian strains in this study are shown in blue text. Abbreviations for country names are shown in the Abbreviations section at the bottom of the manuscript.

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  Figure 4. Genome coverage of EV-D94-14.534 strain from the Republic of Niger (orange line) and EV-D111-KAT-1263 strain from Nigeria (blue line) by NGS analysis. Filtered reads were mapped to the final consensus sequences generated by de novo assembly. The number of sequence reads at each nucleotide position is shown. The location of viral genes is indicated.

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  Figure 5. Recombination analysis of EV-D94-14-534 strain from Niger. Plot of similarity (A) and bootscanning analysis (B) using EV D whole-genome sequences from the NCBI sequence database. The EV genetic map is shown in the top panel. The analyses were conducted using SimPlot version 3.5.1 with the Kimura distance method and a sliding window of 700 base pairs moving in steps of 70 nucleotides. The genome of EV-D94-14-534 strain served as a query sequence.