|
Outbreak
|
Genotype
|
Primersa
|
Fragment length (bases)
|
Identical/sequencedb
|
|---|
|
1
|
GGII4
|
Ni/E3, Mon 381/383
|
357
|
4/4
|
|
2
|
GGII4
|
Ni/E3, Mon 381/383
|
357
|
4/4
|
|
3
|
GGII4
|
Ni/E3, Mon 381/383
|
357
|
4/5
|
|
4
|
GGI
|
SG1/D1
|
109
|
57/60
|
|
5
|
GGIIr
|
Ni/E3
|
76
|
9/9
|
|
6
|
GGII4
|
Ni/E3
|
76
|
7/7
|
|
7
|
GGII1
|
Ni/E3
|
76
|
8/8
|
|
8
|
GGII4
|
Ni/E3
|
76
|
2/2
|
|
9
|
GGII4
|
Ni/E3
|
76
|
2/2
|
|
10
|
GI2
|
SG1/D1
|
109
|
2/2
|
|
11
|
GGII4
|
Ni/E3
|
76
|
2/2
|
|
12
|
GGII1
|
Ni/E3
|
76
|
4/4
|
|
13
|
GGII3
|
Ni/E3
|
76
|
3/3
|
|
14
|
GGI1
|
SG1/D1
|
109
|
2/3
|
|
15
|
GGII1
|
Ni/E3
|
76
|
4/4
|
|
16
|
GGI1
|
SG1/D1
|
109
|
2/2
|
|
17
|
GGII4
|
Ni/E3
|
76
|
2/2
|
|
18
|
GGI1
|
Ni/E3
|
76
|
2/2
|
|
19
|
GGII4
|
Ni/E3
|
76
|
2/2
|
|
20
|
GGII4
|
Ni/E3
|
76
|
3/3
|
|
21
|
GGII4
|
Ni/E3
|
76
|
2/2
|
|
22
|
GGII4
|
Ni/E3
|
76
|
4/4
|
|
23
|
GGII4
|
Ni/E3
|
76
|
2/2
|
|
24
|
GGI3
|
Ni/E3
|
76
|
2/2
|
|
25
|
GGII4
|
Ni/E3
|
76
|
2/2
|
|
26
|
GGII4
|
Ni/E3
|
76
|
2/2
|
|
27
|
GGII4
|
Ni/E3
|
76
|
1/2
|
|
28
|
GGII7
|
SG1/D1
|
109
|
1/2
|
|
29
|
GGI6
|
Ni/E3
|
76
|
2/2
|
|
30
|
GGII4
|
Ni/E3
|
76
|
2/2
|
|
31
|
GGI3
|
SG1/D1
|
109
|
2/2
|
|
32
|
GGII8
|
Ni/E3
|
76
|
2/2
|
|
33
|
GGII8
|
Ni/E3
|
76
|
4/4
|
|
34
|
GGII4
|
Ni/E3
|
76
|
1/2
|
|
35
|
GGI6
|
SG1/D1
|
109
|
1/2
|
|
36
|
GGII4
|
Ni/E3
|
76
|
2/2
|
|
Total
| | |
18678
|
157/166
|
-
aNi/E3 and SG1/DI amplify the pol (ORF 1) region. Mon 381/383 amplify the cap (ORF2) region.
-
b'Non-identical' variants all differed by a single point mutation
-
r Recombinant
- *Short sequences within the RdRp can be used to differentiate between strains but genotyping relies on sequencing a region of the gene encoding the capsid. Also, sequencing regions of either the capsid or the RdRp will not identify recombinant strains. In this study, the characterisation of the genes encoding the RdRp and capsid was confirmed by sequencing a region spanning the ORF1/ORF2 junction, a common recombination site (data not shown).
