Genetic variability in the region encompassing reiteration VII of herpes simplex virus type 1, including deletions and multiplications related to recombination between direct repeats

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Table 2 Pattern no. of nucleotide sequences of the region encompassing reiteration VII

Pattern no. ^a (No. of isolates)	Nucleotide no. of base substitutions ^b											Deletion ^c	Multiplication ^d
Pattern no. ^a (No. of isolates)	12082	12098	12102	12106	12110	12173	12174	12185	12193	12221	12234	Deletion ^c	Multiplication ^d
Strain 17 as the standard	C	T	C	G	T	C	C	C	G	A	G
1 (12)	+	+	+	+	+	+	+	+	+	+	+	4
2 (1)	+	+	+	+	+	+	+	+	+	+	np	3
3 (1)	+	+	+	C	+	+	+	+	+	np	np	6
4 (10)	+	C	G	C	+	+	+	+	+	G	+	1
5 (9)	+	C	G	C	+	+	+	+	+	np	np	2	2
6 (1)	+	C	G	C	+	+	+	+	+	np	np	2	3
7 (2)	+	+	G	C	G	+	+	+	+	np	np	2
8 (1)	+	+	G	C	G	+	+	+	+	np	np	2	2
9 (1)	+	+	G	C	G	+	+	+	+	np	np	2	4
10 (10)	+	C	G	C	+	+	+	T	+	G	+	1
11 (1)	+	C	G	C	+	+	+	T	+	np	np	2	1
12 (1)	+	C	G	C	+	+	+	T	+	np	np	2
13 (4)	+	C	G	C	G	+	+	+	+	np	np	2	2
14 (1)	+	C	G	C	+	T	+	+	+	G	A	1
15 (1)	+	C	G	C	+	T	+	+	+	G	+	5
16 (1)	+	C	G	C	+	+	T	+	+	np	np	2	2
17 (1)	T	C	G	C	+	+	+	+	+	np	np	2	2
18 (2)	+	C	G	C	+	+	+	T	C	G	+	1
19 (1)	T	C	G	C	+	+	+	T	+	G	+	1
20 (1)	+	C	G	C	G	+	+	T	+	np	np	2

^aThe nucleotide sequences of the region encompassing reiteration VII were classified into twenty groups, named pattern no. 1 (PN-1) to 20 (PN-20), and indicated as 1 to 20, respectively. The nucleotide sequences of strain 17 were used as the standard (McGeoch et al. 1985). “+” indicates “the same as that of strain 17”. “np” indicates “not present” due to deletions.
^bThe nucleotide numbering system used was a short unique region of HSV-1 strain 17 (McGeoch et al. 1985).
^cSix kinds of deletions were found, named del-1 to del-6 (Table 3), and indicated as 1 to 6, respectively.
^dFour kinds of multiplications were found, named mul-1 to mul-4 (Table 3), and indicated as 1 to 4, respectively.