Deep sequencing of HK PRRSV strains.

<p>Shown from the periphery to the centre of the figure for each strain is strain ID, genome ideogram (blue for type 1; red for type 2), sequencing depth across the genome, minor variants detected across the genome with at least 1% frequency (<10% in green, > = 10% in yellow, > = 30% in red), amino acid comparisons (green for type 1; blue for type 2) with reference strains (LV for type 1; ATCC VR2332 for type 2) for individual ORFs across the genome (non-conformity represented by white streaks), and pairwise aligned amino acid differences between sequenced strains for individual ORFs (non-structural ones in light shade; structural ones in dark shade) across the genome (blue for type 1; red for type 2).</p

Predicted effect of minor nonsynonymous variants on the protein structure of different PRRSV ORFs.

<p>Predicted effects were classified as being either neutral (<b>○</b>) or non-neutral (•) only when such effects were independently confirmed by PROVEAN and SNAP tools. Variants which had differing predicted effects by the two software tools were excluded. For PROVEAN, “neutral” designation was assigned when a score higher than −2.5 was obtained and “non-neutral” when lower. Confidence of predictions made by SNAP is indicated by the expected accuracy score generated by the tool. Results are summarized based on individual ORFs (first eight panels) and viral strains (color legend, panel 8). The distribution of consensus predictions (out of total predictions) by the two programs across ORFs of different strains is summarized in the last panel as boxplots (bottom right).</p

Summary of sample information, assembly-related statistics, and genomic features of sequenced PRRSV strains.

#<p>: cell culture supernatant (CCS); swine lung tissue (SLT).</p>∧<p>: coverage estimated using prototype isolates for type 1 (LV) and type 2 (ATCC VR2332) PRRSV as references.</p><p>*: positions of amino acid deletions given are based on the Nsp2 protein from prototype isolates of type 1 (LV) and type 2 (ATCC VR2332) PRRSV.</p>+<p>: number obtained after quality filtering procedures detailed in the methods section.</p>//<p>: depth calculation takes into account duplicate reads as well.</p

Summary on the nature, incidence, and impact on codons of minor variants across consensus genomes of HK PRRSV strains.

<p>*: percentage of codons (out of the total number of codons) in the coding region with at least one minor variant.</p>+<p>: percentage of minor variants (out of the total number of variants) capable of causing an amino acid change in their respective consensus codons.</p>∧<p>: percentage of codons with variants (out of the total number of codons with variants) capable of causing an amino acid change in their respective consensus codons.</p><p><i>Sn</i>: Shannon entropy.</p

Summary features of deletions detected in minor variants of a subset of HK PRRSV strains.

<p>*: Deletion falls in the overlapping region of adjacent ORFs affecting both.</p