First description of clinical presentation of piscine orthoreovirus (PRV) infections in salmonid aquaculture in Chile and identification of a second genotype (Genotype II) of PRV

Godoy, Marcos G.; Kibenge, Molly J. T.; Wang, Yingwei; Suarez, Rudy; Leiva, Camila; Vallejos, Francisco; Kibenge, Frederick S. B.

doi:10.1186/s12985-016-0554-y

Virology Journal

Table 3 Pairwise sequence comparison of Segment S1 of selected PRV strains showing Genotypes I (sub-genotypes Ia and Ib) and II¹

From: First description of clinical presentation of piscine orthoreovirus (PRV) infections in salmonid aquaculture in Chile and identification of a second genotype (Genotype II) of PRV

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
KT456500^b	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
HG329897^c	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
LN680851^d	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

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ISSN: 1743-422X

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