Genus

Locus

Characteristic PNS markers

V1

Absence in position 22―size of V1 21 bp (exception U);

C C bulge in position 11;

A-U in position 10 (exceptions A C, U U, G A and G G bulges);

Y:G (U*G or C-G) in position 8 (exceptions U-A, G*U, C A, C C, A G and G G bulges, insertion A in correspondence of 8r);

U-A in position 7 (exception G:Y, U*G, G A and A A bulges, insertion A in correspondence of 7r);

A in position 6 (exception G);

Y:G in position 5;

U in position 5 right nucleotide (exceptions U-A, C, U C and U U bulges, insertion A in correspondence of 5r);

G:Y in position 4 (exception G A and A C bulges)

V2

GGGGY loop (V2 positions 10-12: V2/10 G:Y; V2/11 GG; V2/12 G) (exceptions V2/12: GG-GGGGGGG-insertion G in V2 loop, absence-GGGY-deletion of G in V2 loop; V2/11: CG-GCGGY; V2/10: GG-GGGGG, AG-AGGGG, UU-UGGGU);

Y:G in position 8 (exception A G and C A bulges, insertion A)

Species

Locus

Characteristic PNS markers

BVDV-1

V1

V1/21 Absence; U-A in position 15 (exception Y:G-U*G or C-G, A A, C A and U U bulges)

V2

G:Y in position 5 (exceptions A-U, U-A)

V3

G:Y in position 5 (exception Y:G, G A bulge)

A in position 10 (exceptions G, U, A-U, U-A, G:Y, C-G or A C, A A, G A, U U, C C and G G bulges or absence)

BVDV-2

V1

A-U or A C bulge in position 20 (exceptions G:Y, C C or A A bulges, absence); A, G or U in position 21 (exception G G, absence); absence in V1/20 and 21 is limited to strain A3-118/US is not considered in software parameters due to confusion with BVDV1 definition

V2

U-A or Y:G in position 6 (exception C A bulge)

V3

A-U or A C bulge in position 7 (exception G:Y and AA bulge Chinese strains)

BVDV-3

(HoBi group)

V1

U-A in position 15 (exception CA BGD/ZS1 and BGD/ZS5)

V3

G-C or G*U in position 3 (exception A-U or GA bulge BGDZS1); A-U in position 7 (exception G-C or A G, C U, U U and U C bulges); A in position 10 (exception UA, G)

BDV

V1

C-G or U*G in position 13; A-U in position 14 (exceptions U-A, G:Y and A A bulge); G:Y or A-U in position 15 (exceptions C U and A C bulges)

V2

U-A, Y:G or A-U in position 5

V3

U C and U U bulges or Y:G in position 7 (exceptions A-U, U-A, G:Y and C C, A C, C U and C A bulges)

BDV-2 (Italian ovine isolates) tentative species

V1

C-G or U*G in position 13; U-A or C A bulge in position 15

V3

G:Y or G G bulge in position 8

Pestivirus I

V1

C-G or U*G in position 13; C-G in position 14; G:Y or A-U in position 15 (exceptions C U and A C bulges)

V2

G:Y in position 5

V3

Y:G in position 7; U Uor C U bulge in position 10