In “Piscine Reovirus: Genomic and Molecular Phylogenetic Analysis from Farmed and Wild Salmonids Collected on the Canada/US Pacific Coast,” by Siah et al. [1], clarifications were needed in regards to the following: (a) the sampling population used in this paper versus that of Kibenge et al. [2] and; (b) the discussion of work by Kibenge et al. [2]. Additionally, there was an error in Fig 6 and Table 2. Here, the authors would like to provide some additional information about the methods used in the PLOS ONE article, clarify the discussion, and correct the aforementioned Figure and Table.
Comparison of the sampling population used in this article versus that of Kibenge et al. [2]
The authors would like to clarify the differences in the sampling population used in Siah et al. [1] versus Kibenge et al. [2], since such differences may contribute to the different conclusions reached in these articles:
In the present study [1], the samples were selected from extensive PRV surveys performed on the west coast of Canada and the US. Salmonids archived paraffin blocks from 1974 to 2008 (n = 363), fresh-frozen samples from 2013–2014 (n = 1,838) from wild and farmed fish collected in British Columbia, fresh-frozen samples from fish collected in Alaska (n = 295) and fresh or RNA-later preserved samples from fish collected in Washington State (n = 724) were analyzed with real-time RT-PCR [3]. Only samples (n = 71) with Ct values lower than 30 and from which the authors were able to amplify a PCR product were used for this study. Our work extended our knowledge of PRV sequence diversity across a larger geographical range. Additionally, the authors found that partial segment S1 sequence types derived from archived Atlantic and Chinook salmon samples collected in 2001 and 2005 were identical to some PRV sequence types obtained from samples collected in 2013–2014. The phylogenetic analysis of partial PRV S1 sequences from North American Pacific Coast indicated high genetic homogeneity, forming a subgroup within Group II. Little genetic differentiation was observed among sequence types since 2001.
In Kibenge et al. [2], the authors examined PRV segment S1 sequences variation within British Columbia salmon and trout samples (14 samples in total from western Canada) recently collected in 2012.
Correction to the Discussion, regarding work by Kibenge et al. [2]
In the last paragraph of the current study [1], Siah et al. conclude, "This suggests that the circulating virus sequence types are relatively stable in western North American Pacific waters and rules out a recent introduction of PRV into the western North Pacific as suggested by Kibenge et al [10]." The work by Kibenge et al. was instead done in the eastern north Pacific (off the western coast of Canada), not the western north Pacific. In addition, after careful reconsideration, the authors feel this conclusion is overstated. The authors would like to correct these two issues with the following revision to the final paragraph:
In previous study performed by Kibenge et al [10], the authors examined PRV segment S1 sequences variation within British Columbia salmon and trout samples recently collected in 2012. In the present study, we analyzed PRV sequences obtained from samples of wild and farmed salmonids collected across an expanded geographic range from Alaska to Washington State over 13 year period. The phylogenetic analysis of partial PRV S1 sequences from western North America Pacific Region indicated high genetic homogeneity and they form a subgroup within Group II. In addition, the results presented here suggest that salmonids from western North America Pacific waters carried PRV RNA sequences for at least 13 years with little genetic differentiation among sequence types in selected samples spanning 2001 to 2014. However, the mechanisms by which the virus is globally distributed, as well as transmission pathways remain to be elucidated.
Please see the correct Fig 6 here.
Fig 6. Amino acid alignment of open reading frame consensus sequences encoding the Piscine reovirus σ3 and μ1 protein.
Secondary structure and transmembrane domains were predicted using EMBOSS 6.6.7 (Geneious software v6.1). Predicted secondary structure of alpha helix, beta strand, coil and turn are presented in purple cylinders, yellow arrows, grey sinusoids and blue curved arrow. Sequences are identified using the GenBank accession numbers. A/ represents ORF sequences encoding PRV σ3 amino acid alignment. Red stars are conserved Zn-finger motifs. B/ represents ORF sequences encoding PRV μ1 amino acid alignment. Red cross is myristoylation site in the MRV protein and green line is post-translational cleavage site in MRV and ARV [7].
Please see the correct Table 2 here.
Table 2. Information on partial segment S1 sequenced from fish samples collected in Alaska, British Columbia and Washington State.
Ten types of identical sequences have been identified and grouped in five clusters.
| Clusters | Types | GenBank ID | Name | Host species (common name) | Collection Date | Tissue | Location (State, Country) |
|---|---|---|---|---|---|---|---|
| Cluster 1 (C1) | BCJ31915 | KR558677 | BC131_13 | Farmed Salmo salar (Atlantic salmon) | May-13 | Heart | DFO area 12 (British Columbia, Canada) |
| KR781117 | BC1310_13 | Farmed Salmo salar (Atlantic salmon) | May-13 | Heart | DFO area 12 (British Columbia, Canada) | ||
| KR781118 | BC1311_13 | Farmed Salmo salar (Atlantic salmon) | May-13 | Heart | DFO area 12 (British Columbia, Canada) | ||
| KR558678 | BC132_13 | Farmed Salmo salar (Atlantic salmon) | May-13 | Heart | DFO area 12 (British Columbia, Canada) | ||
| KR558679 | BC133_13 | Farmed Salmo salar (Atlantic salmon) | May-13 | Heart | DFO area 12 (British Columbia, Canada) | ||
| KR558680 | BC134_13 | Farmed Salmo salar (Atlantic salmon) | May-13 | Heart | DFO area 12 (British Columbia, Canada) | ||
| KR558681 | BC135_13 | Farmed Salmo salar (Atlantic salmon) | May-13 | Heart | DFO area 12 (British Columbia, Canada) | ||
| KR558682 | BC136_13 | Farmed Salmo salar (Atlantic salmon) | May-13 | Heart | DFO area 12 (British Columbia, Canada) | ||
| KR558683 | BC137_13 | Farmed Salmo salar (Atlantic salmon) | May-13 | Heart | DFO area 12 (British Columbia, Canada) | ||
| KR558684 | BC138_13 | Farmed Salmo salar (Atlantic salmon) | May-13 | Heart | DFO area 12 (British Columbia, Canada) | ||
| KR558685 | BC139_13 | Farmed Salmo salar (Atlantic salmon) | May-13 | Heart | DFO area 12 (British Columbia, Canada) | ||
| KR872637 | BC361_14 | Farmed Salmo salar (Atlantic salmon) | May-14 | Heart | Hatchery (British Columbia, Canada) | ||
| BC362_14 | Farmed Salmo salar (Atlantic salmon) | May-14 | Heart | Hatchery (British Columbia, Canada) | |||
| BC363_14 | Farmed Salmo salar (Atlantic salmon) | May-14 | Heart | Hatchery (British Columbia, Canada) | |||
| BC364_14 | Farmed Salmo salar (Atlantic salmon) | May-14 | Heart | Hatchery (British Columbia, Canada) | |||
| BC365_14 | Farmed Salmo salar (Atlantic salmon) | May-14 | Heart | Hatchery (British Columbia, Canada) | |||
| BC366_14 | Farmed Salmo salar (Atlantic salmon) | May-14 | Heart | Hatchery (British Columbia, Canada) | |||
| BC367_14 | Farmed Salmo salar (Atlantic salmon) | May-14 | Heart | Hatchery (British Columbia, Canada) | |||
| BC368_14 | Farmed Salmo salar (Atlantic salmon) | May-14 | Heart | Hatchery (British Columbia, Canada) | |||
| KR347084 | BCJ24201_13 | Farmed Salmo salar (Atlantic salmon) | Sep-13 | Heart | DFO area 12 (British Columbia, Canada) | ||
| KR347085 | BCJ28529_13 | Farmed Salmo salar (Atlantic salmon) | Apr-13 | Heart | DFO area 7 (British Columbia, Canada) | ||
| KR347086 | BCJ28537_13 | Farmed Salmo salar (Atlantic salmon) | Apr-13 | Heart | DFO area 7 (British Columbia, Canada) | ||
| KR347087 | BCJ28545_13 | Farmed Salmo salar (Atlantic salmon) | Apr-13 | Heart | DFO area 7 (British Columbia, Canada) | ||
| KR347088 | BCJ31910_13 | Farmed Salmo salar (Atlantic salmon) | Oct-13 | Heart | Hatchery (British Columbia, Canada) | ||
| KR347089 | BCJ31914_13 | Farmed Salmo salar (Atlantic salmon) | Oct-13 | Heart | Hatchery (British Columbia, Canada) | ||
| KR347090 | BCJ31915_13 | Farmed Salmo salar (Atlantic salmon) | Oct-13 | Heart | Hatchery (British Columbia, Canada) | ||
| KR347091 | BCJ31916_13 | Farmed Salmo salar (Atlantic salmon) | Oct-13 | Heart | Hatchery (British Columbia, Canada) | ||
| KR347092 | BCJ31920_13 | Farmed Salmo salar (Atlantic salmon) | Oct-13 | Heart | Hatchery (British Columbia, Canada) | ||
| KR347094 | BCJ35240_13 | Farmed Salmo salar (Atlantic salmon) | Nov-13 | Heart | Hatchery (British Columbia, Canada) | ||
| KR347096 | BCJ35249_13 | Farmed Salmo salar (Atlantic salmon) | Nov-13 | Heart | Hatchery (British Columbia, Canada) | ||
| KR347098 | BCJ35256_13 | Farmed Salmo salar (Atlantic salmon) | Nov-13 | Heart | Hatchery (British Columbia, Canada) | ||
| KR347095 | BCJ35246_13 | Farmed Salmo salar (Atlantic salmon) | Nov-13 | Heart | Hatchery (British Columbia, Canada) | ||
| KR347097 | BCJ35255_13 | Farmed Salmo salar (Atlantic salmon) | Nov-13 | Heart | Hatchery (British Columbia, Canada) | ||
| KR347100 | BCJ40723_13 | Farmed Salmo salar (Atlantic salmon) | Nov-13 | Heart | Hatchery (British Columbia, Canada) | ||
| KR347102 | BCJ40740_13 | Farmed Salmo salar (Atlantic salmon) | Nov-13 | Heart | Hatchery (British Columbia, Canada) | ||
| KR347101 | BCJ40731_13 | Farmed Salmo salar (Atlantic salmon) | Nov-13 | Heart | Hatchery (British Columbia, Canada) | ||
| KR347105 | BCJ402256_13 | Wild Oncorhynchus kisutch (Coho salmon) | Nov-13 | Heart | Quinsam Hatchery (British Columbia, Canada) | ||
| KR347112 | BCK14114_14 | Farmed Salmo salar (Atlantic salmon) | Apr-14 | Heart | DFO area 27 (British Columbia, Canada) | ||
| KR347113 | BCK14120_14 | Farmed Salmo salar (Atlantic salmon) | Apr-14 | Heart | DFO area 27 (British Columbia, Canada) | ||
| KR347106 | BCJ402276_13 | Wild Oncorhynchus kisutch (Coho salmon) | Nov-13 | Heart | Quinsam Hatchery (British Columbia, Canada) | ||
| Cluster 2 (C2) | BCJ18824 | KR347081 | BCJ18824_13 | Wild Oncorhynchus tshawytscha (Chinook salmon) | Aug-13 | Heart | DFO area 127 (British Columbia, Canada) |
| KR347083 | BCJ19943_13 | Wild Oncorhynchus kisutch (Coho salmon) | Aug-13 | Heart | DFO area 127 (British Columbia, Canada) | ||
| KR347093 | BCJ34056_13 | Wild Oncorhynchus kisutch (Coho salmon) | Oct-13 | Heart | Quinsam Hatchery (British Columbia, Canada) | ||
| KR347103 | BCJ378151_13 | Wild Oncorhynchus kisutch (Coho salmon) | Nov-13 | Heart | Quinsam Hatchery (British Columbia, Canada) | ||
| Cluster 3 (C3) | BCJ19323 | KR347082 | BCJ19323_13 | Wild Oncorhynchus kisutch (Coho salmon) | Aug-13 | Heart | DFO area 7 (British Columbia, Canada) |
| KR347104 | BCJ378241_13 | Wild Oncorhynchus kisutch (Coho salmon) | Nov-13 | Heart | Quinsam Hatchery (British Columbia, Canada) | ||
| KR347099 | BCJ37896_13 | Wild Oncorhynchus kisutch (Coho salmon) | Nov-13 | Heart | Quinsam Hatchery (British Columbia, Canada) | ||
| KR347110 | BCK1562_14 | Wild Oncorhynchus kisutch (Coho salmon) | May-14 | Heart | Quinsam Hatchery (British Columbia, Canada) | ||
| KR347115 | BCK15625_14 | Wild Oncorhynchus kisutch (Coho salmon) | May-14 | Heart | Quinsam Hatchery (British Columbia, Canada) | ||
| KR347111 | BCK1566_14 | Wild Oncorhynchus kisutch (Coho salmon) | May-14 | Heart | Quinsam Hatchery (British Columbia, Canada) | ||
| KR478634 | WS1209_12 | Wild Oncorhynchus tshawytscha (Chinook salmon) | Sep-12 | Pool of gill, heart and kidney | Columbia River (Washington State, US) | ||
| KR478637 | WSKFH11_14 | Wild Oncorhynchus kisutch (Coho salmon) | Mar-14 | Blood | Columbia River (Washington State, US) | ||
| KR478639 | WSKFH13_14 | Wild Oncorhynchus kisutch (Coho salmon) | Mar-14 | Blood | Columbia River (Washington State, US) | ||
| KR478636 | WSKFH2_14 | Wild Oncorhynchus kisutch (Coho salmon) | Mar-14 | Blood | Columbia River (Washington State, US) | ||
| KR478633 | WS1207_12 | Wild Oncorhynchus tshawytscha (Chinook salmon) | Sep-12 | Pool of gill, heart and kidney | Columbia River (Washington State, US) | ||
| Cluster 4 (C4) | BCA1338 | KR478642 | BCA1338_01 | Wild Oncorhynchus tshawytscha (Chinook salmon) | May-01 | Multiple Organs | DFO Area 13 (British Columbia, Canada) |
| KR478643 | BCA1846_01 | Farmed Salmo salar (Atlantic salmon) | Aug-01 | Multiple Organs | DFO Area 18 (British Columbia, Canada) | ||
| KR478644 | BCA1848_01 | Farmed Salmo salar (Atlantic salmon) | Aug-01 | Multiple Organs | DFO Area 18 (British Columbia, Canada) | ||
| KR347078 | BCA1849_01 | Farmed Salmo salar (Atlantic salmon) | Aug-01 | Multiple Organs | DFO Area 18 (British Columbia, Canada) | ||
| KR347079 | BCA1850_01 | Farmed Salmo salar (Atlantic salmon) | Aug-01 | Multiple Organs | DFO Area 18 (British Columbia, Canada) | ||
| KR347080 | BCA1854_05 | Farmed Salmo salar (Atlantic salmon) | Mar-05 | Head kidney, trunk kidney, liver and spleen | DFO Area 18 (British Columbia, Canada) | ||
| KR347107 | BCJ402334_13 | Wild Oncorhynchus kisutch (Coho salmon) | Nov-13 | Heart | Quinsam Hatchery (British Columbia, Canada) | ||
| KR347109 | BCK1436_14 | Salmo salar (Atlantic salmon) | Apr-14 | Heart | DFO area 12 (British Columbia, Canada) | ||
| Cluster (C5) | AKJ20115 | KR478640 | AKJ20115_13 | Wild Oncorhynchus kisutch (Coho salmon) | Aug-13 | Heart | Copper River (Alaska, US) |
| KR478641 | AKJ20120_13 | Wild Oncorhynchus kisutch (Coho salmon) | Aug-13 | Heart | Copper River (Alaska, US) | ||
| KR872635 | BCINOC3_13 | Wild Oncorhynchus tshawytscha (Chinook salmon) | May-13 | DFO area 124 (British Columbia, Canada) | |||
| KR478635 | WSKFH1_14 | Wild Oncorhynchus kisutch (Coho salmon) | Mar-14 | Blood | Columbia River (Washington State, US) | ||
| KR478638 | WSKFH12_14 | Wild Oncorhynchus kisutch (Coho salmon) | Mar-14 | Blood | Columbia River (Washington State, US) | ||
| KR347108 | BCK1435_14 | Farmed Salmo salar (Atlantic salmon) | Apr-14 | Heart | DFO area 12 (British Columbia, Canada) | ||
| KR347114 | BCK14310_14 | Farmed Salmo salar (Atlantic salmon) | Apr-14 | Heart | DFO area 12 (British Columbia, Canada) | ||
| KR872636 | BCINOC12_13 | Wild Oncorhynchus tshawytscha (Chinook salmon) | May-13 | DFO area 124 (British Columbia, Canada) |
References
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