Direct detection of canine picornavirus complete coding sequence in wastewater using long-range reverse-transcriptase polymerase chain reaction and long-read sequencing

Figures

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  Fig. 1.. Similarity plot using cCDS of the four contigs sequenced in this study and the ten CanPV sequences with cCDS publicly available in GenBank as at September 8, 2023. The red dashed lines denote demarcation between L, P1, P2 and P3 genomic regions. S1_contig1 was used as query sequence. This analysis was done using the Kimura (2-parameter) model in SimPlot version 3.5.1 with a sliding window of 200 base pairs moving in steps of 20 nucleotides.

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  Fig. 2.. Maximum-Likelihood (ML) tree of CanPV cCDS, P1, P2 and P3 described in this study alongside the ten cCDS present in GenBank as of September 8, 2023. The ML trees were inferred using IQ-Tree 1.6.12. with the best substitution model for each analysis determined using ModelFinder. Please note the best substitution model for cCDS (ORF), P2 and P3 was TIM2 + F + G4 and that for P1 was TIM2 + F + I + G4.

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  Fig. 3.. Pairwise identity analysis of P1 genomic region nucleotides (A) and amino acid (B). The analysis was done in SDT using P1 genomic region of CanPV contigs described in this study alongside the ten cCDS present in GenBank as of September 8, 2023. The sequences described in this study are noted with black circles. Red lines demarcate the different clusters.