Table 1. Summary of sequenced genome segments (λ1, λ2, λ3, μ2, μ1, μNS, σ3, σ2, σNS and σ1) of the virus detected in S. trutta (PRV Ger) and genetic similarity to piscine virus sequences detected in S. salar, O. mykiss and O. kisutch from Norway, Canada, Japan and Chile grouped in genotype cluster Ia, Ib, II and PRV2 according to Takano et al. [40] with additional information from GenBank entries (PRV3); Segment (Seg.), name of the segment (Name), fragment length in base pairs of the segments sequenced in this study (Seq. (bp)), segment function, sequence coverage of segments (in percent) (Ref. Seq.), and pairwise identity of sequenced fragment and corresponding reference sequence (P.I.).
Segment IDs were assigned according to the nomenclature used by Palacios et al. (2010) [37]. (Accession numbers of reference segments are given in S2 Table).
| Seg. | Name | Seq. (bp) |
Function | PRV Ger vs. Genotype Ia (n = 2) |
PRV Ger vs. Genotype Ib (n = 3) |
PRV Ger vs. PRV2 (n = 1) |
PRV Ger vs. PRV3 Chile (Genotype II) (n = 1) |
PRV Ger vs. PRV3 Nor (Genotype II) (n = 1) |
||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Ref. Seq (%) |
P.I. (%) |
Ref. Seq. (%) |
P.I. (%) |
Ref. Seq. (%) |
P.I. (%) |
Ref. Seq. (%) |
P.I. (%) |
Ref. Seq. (%) |
P.I. (%) |
|||||||
| L1 | λ1 (Core shell) |
1514 | Helicase | 38.85 | 78.35 | 38.93 | 78.43 | 38.80 | 75.80 | 38.20 | 98.40 | 39.40 | 97.30 | |||
| L2 | λ2 (Core turret) |
800 | Guanylyl-transferase | 20.35 | 81.40 | 20.37 | 81.13 | 20.30 | 74.00 | 20.20 | 99.50 | 20.70 | 97.40 | |||
| L3 | λ3 (Core RdRp) |
2636 | RNA-dependent RNA polymerase | 67.45 | 79.35 | 67.33 | 79.70 | 67.30 | 76.20 | 65.70 | 99.40 | 68.30 | 97.70 | |||
| M1 | μ2 (Core NTPase) |
1220 | Minor inner capsid protein | 51.30 | 79.45 | 51.53 | 78.50 | 51.20 | 72.70 | 51.40 | 99.80 | 53.40 | 97.00 | |||
| M2 | μ1 (Outer shell) |
1228 | Outer capsid protein. membrane penetration | 56.70 | 81.00 | 56.77 | 80.93 | 56.40 | 75.90 | 56.10 | 99.20 | 58.00 | 97.20 | |||
| M3 | μNS (NS factory) |
629 | Non-structural protein | 26.25 | 81.90 | 26.37 | 82.30 | 26.20 | 65.80 | 25.70 | 98.60 | 27.80 | 98.40 | |||
| S1 | σ3 (Outer clamp) |
767 | Outer capsid protein. zinc metalloprotein | 71.25 | 81.90 | 72.07 | 80.67 | 71.00 | 73.30 | 68.20 | 99.50 | 77.20 | 96.60 | |||
| S2 | σ2 (Core clamp) |
1172 | Inner capsid protein | 88.60 | 79.60 | 89.10 | 79.93 | 88.10 | 69.60 | 87.00 | 99.50 | 92.90 | 99.50 | |||
| S3 | σNS (NS RNA) |
699 | Nonstructural protein | 61.45 | 87.90 | 62.07 | 87.97 | 61.20 | 78.00 | 61.60 | 99.70 | 65.60 | 97.90 | |||
| S4 | σ1 (Outer fiber) |
301 | Virus attachment protein | 29.10 | 90.00 | 29.40 | 89.80 | 29.00 | 71.80 | 28.60 | 100.0 | 30.50 | 99.70 | |||
| Mean | 51.13 | 82.09 | 51.39 | 81.94 | 50.95 | 73.31 | 50.27 | 99.36 | 53.38 | 97.87 | ||||||