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

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*

Outbreak	Genotype	Primers^a	Fragment length (bases)	Identical/sequenced^b
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	GGII^r	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).

ISSN: 1471-2334