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Table 2 Studies that analysed within-outbreak sequence variation (not including mixed outbreaks caused by multiple genotypes), includes the present study (n = 3) and various other studies (n = 33) conducted by the Enteric Virus Unit, 2002–04*

From: Linking healthcare associated norovirus outbreaks: a molecular epidemiologic method for investigating transmission

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
  1. aNi/E3 and SG1/DI amplify the pol (ORF 1) region. Mon 381/383 amplify the cap (ORF2) region.
  2. b'Non-identical' variants all differed by a single point mutation
  3. r Recombinant
  4. *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).
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