High levels of unreported intraspecific diversity among RNA viruses in faeces of neonatal piglets with diarrhoea

Figures

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  Fig. 1. The box-and-whisker plots show, for the 47 samples from diarrhoeic animals, the distribution of the proportion of reads for a given mammalian viral species over the total number of mammalian viral reads (viral reads in a sample/total viral reads). Minimum, maximum, median, 25 and 75 quartiles are shown. Only virus showing read proportions larger than 0.001 are represented. Virus abbreviations: Rotavirus A, RVA; Rotavirus B, RVB; Rotavirus C, RVC; Kobuvirus, KobuV; Sapovirus, SAV; Astrovirus 3, AstV3

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  Fig. 2. Scatter plot graph representing the number of viral reads indexed per virus and per sample (X-axis), versus the proportion that those viral reads represents over the total number of mammalian virus reads indexed (Y-axis) in each one of the 47 diarrhoeic animals analysed. Only Rotavirus A, B and C, KobuV and SAV were considered

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  Fig. 3. Neighbor-joining phylogenetic tree based on the p-distance among the nucleotide sequences of the complete genomes for Kobuvirus. Along the branches, percentage of bootstrap values based on 10,000 replicates. Only values equal or larger than 80% are shown. The dataset contains the 51 complete Kobuvirus genomes available in GenBank plus the 17 genomes – marked in green and with a circle – reported in this work

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  Fig. 4. Neighbor-joining phylogenetic tree based on the p-distance among the nucleotide sequences of the VP7 segment for Rotavirus A. Along the branches, percentage of bootstrap values based on 10,000 replicates. Only values equal or larger than 80% are shown. The dataset contains 41 reference sequences representing RVA strains isolated in different species, included for comparison purposes, plus the 23 sequences – marked in green and with a circle – reported in this work. The division of genotypes is based on the 80% nucleotide cut-off values proposed by the RotaC 2.0 genotyping tool [23], and the RVA genotype determination tool of Virus Pathogen Resource [24]

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  Fig. 5. Neighbor-joining phylogenetic tree based on the p-distance among the nucleotide sequences of the VP7 segment for Rotavirus B. Along the branches, percentage of bootstrap values based on 10,000 replicates. Only values equal or larger than 80% are shown. The dataset contains 58 reference sequences representing the 26 RVB VP7 genotypes described plus the 8 sequences – marked with a circle – reported in this work. The division of genotypes is based on the 80% nucleotide cut-off value proposed by [25]; accordingly, two new genotypes (labelled as GX1 and GX2 in the Figure) are tentatively proposed

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  Fig. 6. Neighbor-joining phylogenetic tree based on the p-distance among the nucleotide sequences of the VP7 segment for Rotavirus C. Along the branches, percentage of bootstrap values based on 10,000 replicates. Only values equal or larger than 80% are shown. The dataset contains 34 reference sequences representing the 11 RVC VP7 genotypes described plus the 17 sequences – marked with a circle – reported in this work. The division of genotypes is based on the 85–86% nucleotide cut-off value proposed by [26]; accordingly, two new genotypes (labelled as GX1 and GX2 in the Figure) are tentatively proposed

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  Fig. 7. Neighbor-joining phylogenetic tree based on the p-distance among the nucleotide sequences of the complete genomes of Porcine Sapovirus. Along the branches, percentage of bootstrap values based on 10,000 replicates. Only values equal or larger than 80% are shown. The dataset contains 37 reference genomes representing the 8 Sapovirus genogroups described so far in swine plus the 4 complete sequences – marked with a circle – reported in this work. The division of genotypes is based on the classification proposed by [27]

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  Fig. 8. Neighbor-joining phylogenetic tree based on the p-distance among the nucleotide sequences of the complete genomes of Porcine Astrovirus 3. Along the branches, percentage of bootstrap values based on 10,000 replicates. Only values equal or larger than 80% are shown. The dataset contains the 11 complete genomes available so far in swine plus the 2 complete sequences – marked with a circle – reported in this work