Background
Results and discussion
RT-PCR, gene sequencing and analysis
Phylogenetic analysis of combined ISAV F and HE glycoprotein genes is a better approximation of genetic relatedness between ISAV isolates
More detailed analysis of the new Chile ISAV isolates identifies 7 distinct strains
ISAV Clade | 2.2.2.1.2.1 | 2.2.2.1.2.2 | 2.2.2.1.2.3 | 2.2.2.1.2.4 | 2.2.2.1.2.5 | 2.2.2.1.2.6 | 2.2.2.1.2.7 |
---|---|---|---|---|---|---|---|
31682-10 | 31687-5 | 30290-5 | 31667-3GH | 31648-5GH | 32232-2044 | 26905-1t | |
31592-2 | 31687-3 | 30740-3 | 31667-5GH | 31647-8GH | 32232-2032 | 26905-10 | |
31592-4 | 32089-P1 | 30741-8 | 31648-3GH | 31591-6 | 26829-2 | ||
31606H | 31689-1 | 30290-2 | PM-4165/8 | 31590-20 | U24636 | ||
31682-5 | 31689-4 | 31905-7cCz | 31647-3GH | 26830 | |||
26936-2 | 1508-6 | 31905-9Cz | 31685-1 | ||||
26936-1t | 1508-7 | PM-4165/11 | 31685-3 | ||||
2006B13364 | 31790-3GH | 26572-6 | |||||
31790-9GH | 31591-7 | ||||||
CH01/08 | 31590-18 | ||||||
31587-8 | |||||||
30942/943 |
Estimation of branching times of ISAV isolates shows new Chile ISAV strains diverged from Norway ISAV isolates around 1996
11-amino acid insert in F protein unique to new Chile ISAV strains
Multiple HPR groups in ISA outbreak is manifestation of ISAV quasispecies
HPR group | No. of isolates sequenced1 | Percent of total |
---|---|---|
HPR 7b
| 192 | 79.7% |
HPR 7c
| 1 | 0.4% |
HPR 7e
| 1 | 0.4% |
HPR 7f
| 3 | 1.2% |
HPR 7g
| 1 | 0.4% |
HPR 7h
| 1 | 0.4% |
HPR 7i
| 2 (1 was mixed with HPR 7b) | 0.8% |
HPR 1b
| 1 | 0.4% |
HPR 1c
| 7 | 2.9% |
HPR 2
| 10 | 4.1% |
HPR 2c
| 1 (mixed with HPR 2) | 0.4% |
HPR 2d
| 1 | 0.4% |
HPR 3
| 6 | 2.5% |
HPR 3a
| 1 | 0.4% |
HPR 4c
| 3 (2 were mixed with HPR 7b) | 1.2% |
HPR 5
| 2 | 0.8% |
HPR 5c
| 1 | 0.4% |
HPR 9b
| 2 | 0.8% |
HPR 15
| 1 | 0.4% |
HPR 15b
| 1 | 0.4% |
HPR 15c
| 1 (mixed with HPR 7b) | 0.4% |
HPR 15d
| 1 | 0.4% |
HPR 15e
| 1 | 0.4% |
New HPR (12-aa deletion)
| 5 | 2.1% |
HPR0
| 1 (mixed with HPR 7b) | 0.4% |