Fig. 3: Environmental contigs cover the majority of virus genes in poultry with a high sequence similarity. | Nature Communications

Fig. 3: Environmental contigs cover the majority of virus genes in poultry with a high sequence similarity.

From: Environmental metagenomics enhances detection of circulating viruses from live poultry markets in Cambodia

Fig. 3: Environmental contigs cover the majority of virus genes in poultry with a high sequence similarity.

A Presents a heatmap of detection rates for over 4,000 poultry virus reference genes (identified using DIAMOND blastx) in poultry swabs versus environmental samples. Red indicates that genes were found in both groups at the same timepoint, pale yellow represents detections only in poultry swabs, and blue for genes detected only in the environment. Rows correspond to individual virus genes annotated by genus (shown in the lower-right corner) and major clusters are labelled on the right. B For each gene (x axis) the difference in percent identity (PID) between poultry and environmental contigs is shown. C shows the number of poultry environment contig pairs at specified PID thresholds. D Distribution of percent identity (PID) values for environmental contigs aligning to the same reference genes as those detected in poultry. Boxplot displays the median (centre line), interquartile range (box), and whiskers extending to 1.5× the interquartile range; points represent individual samples. E Differences in percent coverage between poultry and environmental contigs are shown for each environmental sample type. Poultry samples comprised chicken oropharyngeal (n = 15), chicken cloacal (n = 15), duck oropharyngeal (n = 14), and duck cloacal (n = 15) swabs. Environmental samples were collected from air (holding area, n = 13; slaughter area, n = 14; outside, n = 10), wash water (n = 19), drinking water (n = 9), and cage swabs (n = 17). Each group represents independent biological samples. F For contig pairs aligned to the same gene(s), this plot displays the relative proportions of the major virus genera within each sample group. G For contigs that aligned uniquely to a single gene (unpaired), this plot shows the relative proportion contributed by each gene. Statistics were calculated using a Kruskal-Wallis with Dunns post-hoc test. All P values obtained were corrected for false-discovery rate (FDR) using the Benjamini-Hochberg method.

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