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. 2016 Jun 13;13:98. doi: 10.1186/s12985-016-0554-y

Table 3.

Pairwise sequence comparison of Segment S1 of selected PRV strains showing Genotypes I (sub-genotypes Ia and Ib) and II1

Genotype Ia Ib II
PRV isolate 2 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 Ia
KT456503 - 99.9 99.8 99.8 99.6 99.6 99.6 99.6 99.6 99.5 99.3 99.3 99.2 99.0 98.7 96.0 96.0 96.0 96.0 96.0 96.0 95.9 95.8 80.7 80.5 nd
KU131593 a 100 - 99.6 99.6 99.5 99.5 99.5 99.5 99.5 99.4 99.2 99.2 99.0 98.9 98.6 95.9 95.9 95.9 95.9 95.9 95.9 95.8 95.7 80.9 80.3 nd
KU131594 a 100 100 - 99.5 99.6 99.4 99.4 99.4 99.4 99.3 99.0 99.0 98.9 98.9 98.4 95.8 95.8 95.8 95.8 95.8 95.8 95.7 95.5 80.6 80.4 nd
KC473454 99.3 99.3 99.3 - 99.4 99.4 99.4 99.4 99.4 99.3 99.0 99.0 98.9 98.8 98.4 95.8 95.8 95.8 95.8 95.8 95.8 95.7 95.5 80.5 80.3 nd
KU131591 a 100 100 100 99.3 - 99.3 99.3 99.3 99.3 99.2 98.9 98.9 98.8 98.8 98.3 95.7 95.7 95.7 95.7 95.7 95.7 95.5 95.4 80.7 80.5 nd
KR872636 99.6 99.6 99.6 98.9 99.6 - 99.3 99.5 99.5 99.6 99.4 99.4 99.0 99.2 98.6 95.9 95.9 95.9 95.9 95.9 95.9 95.8 95.7 80.6 80.4 nd
KT456500b 98.9 98.9 98.9 98.2 98.9 98.6 - 99.3 99.3 99.2 98.9 99.2 98.8 98.7 98.3 95.7 95.7 95.7 95.7 95.7 95.7 95.5 95.4 80.4 80.2 nd
JN991006 100 100 100 99.3 100 99.6 98.9 - 99.8 99.4 99.2 99.2 99.3 98.9 98.8 96.3 96.3 96.3 96.3 96.3 96.3 96.1 96.0 80.6 80.4 nd
HG329868 100 100 100 99.3 100 99.6 98.9 100 - 99.4 99.2 99.2 99.5 98.9 99.0 96.4 96.4 96.4 96.4 96.4 96.4 96.3 96.1 80.9 80.6 nd
KU160514 99.6 99.6 99.6 98.9 99.6 99.3 98.6 99.6 99.6 - 99.3 99.5 98.9 99.3 98.4 95.8 95.8 95.8 95.8 95.8 95.8 95.7 95.5 80.2 80.3 nd
KT456501 98.6 98.6 98.6 97.8 98.6 98.2 97.5 98.6 98.6 98.2 - 99.0 98.7 98.9 98.2 95.5 95.5 95.5 95.5 95.5 95.5 95.4 95.3 80.5 80.3 nd
KC473453 99.6 99.6 99.6 98.9 99.6 99.3 99.3 99.6 99.6 99.3 99.3 - 98.7 99.0 98.2 95.5 95.5 95.5 95.5 95.5 95.5 95.4 95.3 80.3 80.0 nd
KT456505 98.6 98.6 98.6 97.8 98.6 98.2 97.5 98.6 98.6 98.2 97.1 98.2 - 98.4 98.6 96.1 96.1 96.1 96.1 96.1 96.1 96.0 95.9 80.9 80.7 nd
KU160513 98.9 98.9 98.9 98.2 98.9 98.6 97.8 98.9 98.9 98.6 97.5 98.6 97.5 - 98.0 95.3 95.3 95.3 95.3 95.3 95.3 95.2 95.1 80.2 79.9 nd
HG329848 100 100 100 99.3 100 99.6 98.9 100 100 99.6 98.6 99.6 98.6 98.9 - 96.4 96.4 96.4 96.4 96.4 96.4 96.3 96.1 80.9 80.7 nd
KU131597 96.4 96.4 96.4 95.7 96.4 96.0 95.3 96.4 96.4 96.0 95.3 96.0 95.3 95.3 96.4 - 100 100 100 100 100 99.9 99.8 79.2 79.0 nd Ib
HG329897c 96.4 96.4 96.4 95.7 96.4 96.0 95.3 96.4 96.4 96.0 95.3 96.0 95.3 95.3 96.4 100 - 100 100 100 100 99.9 99.8 79.2 79.0 nd
KU131602 96.4 96.4 96.4 95.7 96.4 96.0 95.3 96.4 96.4 96.0 95.3 96.0 95.3 95.3 96.4 100 100 - 100 100 100 99.9 99.8 79.2 79.0 nd
KC795571 96.4 96.4 96.4 95.7 96.4 96.0 95.3 96.4 96.4 96.0 95.3 96.0 95.3 95.3 96.4 100 100 100 - 100 100 99.9 99.8 79.2 79.0 nd
KU131604 a 96.4 96.4 96.4 95.7 96.4 96.0 95.3 96.4 96.4 96.0 95.3 96.0 95.3 95.3 96.4 100 100 100 100 - 100 99.9 99.8 79.2 79.0 nd
GU994022 96.4 96.4 96.4 95.7 96.4 96.0 95.3 96.4 96.4 96.0 95.3 96.0 95.3 95.3 96.4 100 100 100 100 100 - 99.9 99.8 79.2 79.0 nd
KU131603 96.0 96.0 96.0 95.3 96.0 95.7 94.9 96.0 96.0 95.7 94.9 95.7 94.9 94.9 96.0 99.6 99.6 99.6 99.6 99.6 99.6 - 99.6 79.1 78.8 nd
KU131598 a 95.7 95.7 95.7 94.9 95.7 95.3 94.6 95.7 95.7 95.3 94.6 95.3 94.6 94.6 95.7 99.3 99.3 99.3 99.3 99.3 99.3 98.9 - 79.0 78.7 nd
KU131595 a 79.0 79.0 79.0 78.3 79.0 79.0 78.3 79.0 79.0 79.0 78.3 79.0 79.0 78.3 79.0 78.3 78.3 78.3 78.3 78.3 78.3 77.9 77.5 - 99.5 nd II
KU131596 a 78.6 78.6 78.6 77.9 78.6 78.6 77.9 78.6 78.6 78.6 77.9 78.6 78.6 77.9 78.6 77.9 77.9 77.9 77.9 77.9 77.9 77.5 77.2 99.3 - nd
LN680851d nd nd Nd nd nd Nd nd nd nd Nd nd nd nd nd nd nd nd nd nd nd nd nd nd nd nd -

1Pairwise sequence comparision was done with EMBOSS Water on-line program using default settings [52]; values above the diagonal are nucleotide sequence identities (%) in 830 nt overlap; values below the diagonal are deduced amino acid sequence identities of Outer clamp (σ3) protein (%) in 276 aa overlap. Bold text denotes new Chilean PRV sequences generated in this study

2PRV isolates identified in vertical column by GenBank Accession Numbers and on the top horizontal row by order of listing in the vertical column

3nd denotes not done because LN680851 available sequence is only 561 nt or 187 aa. aDenotes PRV “isolates” from coho salmon; bDenotes PRV “isolate” from Chinook salmon; cDenotes PRV “isolate” from sea trout. dDenotes PRV “isolate” from rainbow trout