Introduction
ISAV-HPR0 designation | Country or Region | Description | Source |
---|---|---|---|
PR European consensus | (In silico description) | PR groups; PR variant | Mjaaland et al.[13] |
HPR0 | Scotland | Novel variant of the highly polymorphic region | Cunningham et al.[14] |
HPR0 | North America | HPR0-like variant in North America European-like HPR0 variants | Cook-Versloot et al.[15] |
HPR0 | Norway | ISAV from wild salmon in Scotland, Scot-w | Nylund et al.[16] |
HPR0 | Norway | Non-pathogenic wild type, wild type | Nylund et al.[17] |
HPR0 | Chile | Non-pathogenic viruses | Kibenge et al.[8] |
HPR0 | Norway | Low- or avirulent HPR0 genotype | Markunsen et al.[18] |
HPR0 | Scotland | HPR0 ISAV variant | McBeath et al.[11] |
HPR0 | Iceland | Low/none pathogen ISAv (HPR0) (prevalance in farmed Atlantic salmon stock was approx. 0.6% in 2011 & approx. 0.5% in first half of 2012) | MAST1, 2009 (Dr. Marcos Godoy Personal communication) |
HPR0 | Denmark | HPR0 in 1/9 samples of Atlantic salmon broodstock (August 2010 surveillance sample) | Skall [10] |
HPR0 | Norway | HPR0 genotypes | Lyngstad et al.[19] |
HPR0 | Faroe Island | Low-pathogenic variant of infectious salmon anemia virus (ISAV-HPR0) | Christiansen et al.[12] |
SAV-HPR0 | Norway | Low virulent infectious salmon anaemia virus (ISAV-HPR0) | Lyngstad et al.[20] |
HPR0 ISA | Norway | Avirulent (HPR0) viruses HPR0 ISA viruses (avirulent viruses) | Plarre et al.[21] |
Results and discussion
Emergence of low pathogenic ISAV (ISAV-HPR0) in Chile
The cycle threshold (Ct) values of the ISAV-HPR0 cases and 2013 ISAV-HPR∆ cases in Chile show two distinct patterns
Spatial and temporal analysis of ISAV-HPR0 cases shows relationship to 2013 ISAV-HPR∆ cases in Chile
Alignment of ISAV segments 5 and 6 sequences reveals presence of only one ISAV-HPR0 in Chile and is related to the 2013 ISAV-HPR∆ (HPR3 and HPR14)
Group | ISAV (GenBank Acc. No) | Predicted amino acid sequence1 | aa deleted |
---|---|---|---|
HPRO | Canada 980712 (AY46060) | TDV-JIRDAIPPQTFNTFNQPSTSVLSNIFISM-GVA | 0 |
HPRO | U. K. NWM10 (FJ178189) | TDV-KIRDAIPPQLNQTFNTNQPSTSVLSNIFISM-GVA | 0 |
HPRO | USA USA2004 (AY973194) | TDV-KIRVDAIPPQLNQTFNTNQVEQPSTSVLSNIFISM-GVA | 0 |
HPRO | Faroe Island FO/03/06 (HQ664993) | TDV-KIRVDAIPPQLNQTFNTNQVEQPSTSVLSNIFISM-GVA | 0 |
HPRO | Faroe Island FO/03b/07 (HQ664997) | TDV-KIRVDAIPPQLNQTFNTNQVEQPSTSVLSNIFISM-GVA | 0 |
HPRO | Faroe Island FO/08/07 (HQ664998) | TDV-KIRVDAIPPQLNQTFNTNQVEQPSTSVLSNIFISM-GVA | 0 |
HPRO | Faroe Island FO/01/06 (HQ664992) | TDV-KIRVDAIPPQLNQTFNTNQVEQPANSVLSNIFISM-GVA | 0 |
HPRO | Faroe Island FO/01/08 (HQ664999) | TDV-KIRVDAIPPQLNQTFNTNQVEQPANSVLSNIFISM-GVA | 0 |
HPRO | Faroe Island FO/01a/08 (HQ664994) | TDV-KIRVDAIPPQLNQTFNTNQVEQPANSVLSNIFISM-GVA | 0 |
HPRO | Faroe Island FO/01b/07 (HQ664995) | TDV-KIRVDAIPPQLNQTFNTNQVEQPANSVLSNIFISM-GVA | 0 |
HPRO | Scotland 1703/01/86 (AJ440971) | TDV-KIRVDAIPPQLNQTFNTNQVEQPANSVLSNIFISM-GVA | 0 |
HPRO | Norway FM173/11 (JN711060) | TDV-KIRVDAIPPQLNQTFNTNQVEQPANSVLSNIFISM-GVA | 0 |
HPRO | Norway H97/04 (DQ108604) | TDV-KIRVDAIPPQLNQTFNTNQVEQPATSVLSNIFISM-GVA | 0 |
HPRO | Norway H138/08 (JN711063) | TDV-KIRVDAIPPQLNQTFNTNQVEQPATSVLSNIFISM-GVA | 0 |
HPRO | Chile CGA/1059 (KC414113) | TDV-KIRVDAIPPQLNQTFNTNQVEQPATSVLSNIFISM-GVA | 0 |
HPRO | Chile CGA/ID758 (KF019742) | TDV-KIRVDAIPPQLNQTFNTNQVEQPATSVLSNIFISM-GVA | 0 |
HPRO | Scotland Scot157/08 (JN711096) | TDV-KIRVDAIPPQLNQTFNTNQVEQPATSVLSNIFISM-GVA | 0 |
HPRO | Canada EF6-6 (AY646058) | TDV-KIRVDAIPPQLNQTFNTNQVEQPATSVLSNIFISM-GVA | 0 |
Group | ISAV isolate (GenBank Acc. No.) | Predicted amino acid sequence1 | aa deleted | ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
HPRO | United Kingdom NWM10 (FJ178189) | T | D | V | K | I | R | V | D | A | I | P | P | Q | L | N | Q | T | F | N | T | N | Q | V | E | Q |
P
|
S
|
T
| S | V | L | S | N | I | F | I | S | M | G | V | A | 0 |
HPRO | Scotland 1703/01/86 (AJ440971) | T | D | V | K | I | R | V | D | A | I | P | P | Q | L | N | Q | T | F | N | T | N | Q | V | E | Q |
P
|
A
|
N
| S | V | L | S | N | I | F | I | S | M | G | V | A | 0 |
HPRO | Chile CH29/o8 (JN711094) | T | D | V | K | I | R | V | D | A | I | P | P | Q | L | N | Q | T | F | N | T | N | Q | V | E | Q |
P
|
A
|
T
| S | V | L | S | N | I | F | I | S | M | G | V | A | 0 |
HPR20 | Canada RPC/NB 98-0280-2 (AF294870) | T | D | V | K | I | R | V | D | A | I | - | - | - | L | - | - | - | - | G | V | N | Q | V | E | Q |
P
|
S
|
T
| S | V | L | S | N | I | F | I | S | M | G | V | A | 7 |
HPR36 | Norway Vir22 (DQ785258) | T | D | V | K | I | R | V | D | A | - | - | - | - | - | - | - | - | F | N | T | N | Q | V | E | Q |
P
|
A
|
T
| S | V | L | S | N | I | F | I | S | M | G | V | A | 8 |
HPR6 | Norway MR60/01 (AY127876) | T | D | V | K | I | R | V | D | A | I | - | - | - | - | - | - | - | - | - | - | - | Q | V | E | Q |
P
|
A
|
T
| S | V | L | S | N | I | F | I | S | M | G | V | A | 11 |
HPR14 | Norway ST21/96 (AF364886) | T | D | V | K | I | R | V | D | A | - | - | - | - | - | - | - | - | - | - | - | N | Q | V | E | Q |
P
|
A
|
T
| S | V | L | S | N | I | F | I | S | M | G | V | A | 11 |
HPR33 | Norway N127/07 (JN711066) | T | D | V | K | I | R | V | D | - | - | - | - | - | - | - | - | - | - | - | D | N | - | V | E | Q |
P
|
A
|
T
| S | V | L | S | N | I | F | I | S | M | G | V | A | 12 |
HPR17 | Norway MR103/05 (DQ108606) | T | D | V | K | I | R | - | - | - | - | - | - | - | L | - | - | - | - | - | - | - | E | V | E | Q |
P
|
A
|
T
| S | V | L | S | N | I | F | I | S | M | G | V | A | 14 |
HPR9b | Chile 2006B-13364 (FJ594284) | T | D | V | K | I | R | V | D | A | I | P | P | Q | L | N | Q | T | F | N | T | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | I | S | M | G | V | A | 15 |
HPR12 | Norway N5/89 (AY127882) | T | D | V | K | I | R | V | D | A | I | P | P | Q | L | N | Q | T | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | N | I | F | I | S | M | G | V | A | 15 |
HPR21 | Chile 7833–1 (AF294879) | T | D | V | K | I | R | V | D | A | I | P | P | Q | L | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | S | N | I | F | I | S | M | G | V | A | 17 |
HPR3 | Norway ST110/05 (DQ108598) | T | D | V | K | I | R | V | D | A | I | P | P | Q | L | N | Q | T | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | F | I | S | M | G | V | A | 17 |
HPR4 | Norway Gullesfjord/94 (AF302801) | T | D | V | K | I | R | V | D | A | I | P | P | Q | L | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | S | N | I | F | I | S | M | G | V | A | 17 |
HPR4c | Chile 26560–10 (EU625666) | T | D | V | K | I | R | V | D | A | I | P | P | Q | L | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | N | I | F | I | S | M | G | V | A | 18 |
HPR9 | Norway FM116/06 (JN711058) | T | D | V | K | I | R | V | D | A | I | P | P | Q | L | N | Q | T | F | N | T | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | G | V | A | 18 |
HPR10 | Norway MR52/00 (AF364892) | T | D | V | K | I | R | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | Q |
P
|
A
|
T
| S | V | L | S | N | I | F | I | S | M | G | V | A | 18 |
HPR12a | Norway ISAV3 (DQ785247) | T | D | V | K | I | R | V | D | A | I | P | P | Q | L | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | N | I | F | I | S | M | G | V | A | 18 |
HPR31 | Norway T126/07 (JN711076) | T | D | V | K | I | R | V | D | A | I | P | P | Q | L | N | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | I | F | I | S | M | G | V | A | 18 |
HPR11 | Norway SF57/00 (AF364890) | T | D | V | K | I | R | V | D | A | I | P | P | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | R | N | I | F | I | S | M | G | V | A | 19 |
HPR13 | Faroe Island 1173/01/12 (AJ440970) | T | D | V | K | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | E | Q |
P
|
A
|
N
| S | V | L | S | N | I | F | I | S | M | G | V | A | 19 |
HPR16 | Norway T90/04 (AY971666) | T | D | V | K | I | R | V | D | A | I | P | P | Q | L | N | Q | T | F | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | M | G | V | A | 19 |
HPR21b | Canada NB1330-2 (AY646063) | T | D | V | K | I | R | V | D | A | I | P | P | Q | L | N | Q | T | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | M | G | V | A | 20 |
HPR35 | Norway NT156/09 (JN711072) | T | D | V | K | I | R | V | D | A | I | P | P | Q | L | N | Q | T | F | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | G | V | A | 20 |
HPR2 | Norway T131/07 (JN711078) | T | D | V | K | I | R | V | D | A | I | P | P | Q | L | N | Q | T | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | M | G | V | A | 20 |
HPR19 | Norway SF18/96 (AF364869) | T | D | V | K | I | R | V | D | A | I | P | P | Q | L | N | Q | T | - | - | - | - | - | - | - | - | - | - | - | - | - | L | - | - | - | - | - | - | - | G | V | A | 20 |
HPR1 | Norway FM86/04 (AY971659) | T | D | V | K | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
P
|
A
|
T
| S | V | L | S | N | I | F | I | S | M | G | V | A | 21 |
HPR5 | Norway T152/09 (JN711086) | T | D | V | K | I | R | V | D | A | I | P | P | Q | L | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | I | S | M | G | V | A | 21 |
HPR34 | Norway NT134/08 (JN711069) | T | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | Q |
P
|
A
|
T
| S | V | L | S | N | I | F | I | S | M | G | V | A | 21 |
HPR1c | Chile 31606-H (FJ594281) | T | D | V | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | A | T | S | V | L | S | N | I | F | I | S | M | G | V | A | 23 |
HPR7b | Chile 31991-3N (FJ786983) | T | D | V | K | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | T | S | V | L | S | N | I | F | I | S | M | G | V | A | 23 |
HPR15 | Norway H56/00 (AF364880) | T | D | V | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | E | - | - | - | T | S | V | L | S | N | I | F | I | S | M | G | V | A | 23 |
HPR15c | Chile 901 (GU830908) | T | D | V | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | A | T | S | V | L | S | N | I | F | I | S | M | G | V | A | 23 |
HPR15e | 32246 (FJ86988) | T | D | V | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | T | - | - | - | - | - | - | - | T | S | V | L | S | N | I | F | I | S | M | G | V | A | 23 |
HPR8 | Norway MR46/99 (AF364896) | T | D | V | K | I | R | V | D | A | I | P | P | Q | L | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | G | V | A | 24 |
HPR15b | cHILE 31150–3 (FJ786985) | T | D | V | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | T | S | V | L | S | N | I | F | I | S | M | G | V | A | 24 |