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Table 3 Sequence differences between HSV-2 HG52 and clinical isolates of HSV-2 in the database

From: Stability of glycoprotein gene sequences of herpes simplex virus type 2 from primary to recurrent human infection, and diversity of the sequences among patients attending an STD clinic

Gene

UL27/gB (2715nt)

US4/gG (2100nt)

US7/gI (1119nt)

US8/gE (1638nt)

Total no. of isolates

69

64

49

48

Nucleotide diversity (%) affecting:

1 isolate

1.14

2.24

1.70

1.40

≥2 isolates

0.81

1.52

0.80

0.55

 

Position

No. of isolates

Substitutions, comments

Position

No. of isolates

Substitutions, comments

Position

No. of isolates

Substitutions, comments

Position

No. of isolates

Substitutions, comments

 

19

21

A G

104

58

G A

39

5

C T

131

46

ins. GGC CGG AGG

 

64-72 or 76-84*

66

del. GCC CCG GCG or GCG GCC CCG

274

26

T C

338

2

A G

341

2

G T

 

104

2

G A

329

17

G A

530

2

C T

392

11

T G

 

106

2

G A

405

8

C T

618

3

A G

605

6

C A

 

117

6

C G

432

22

G C

642

2

A C

1146

8

A G

 

146

48

G A

611

10

C T

643

13

C T

1211

14

A C

 

179

13

A G

635

13

G A

644

6

C T

1245

2

C T

 

210

8

C T

872

3

A G

716

45

T G

1293

2

C T

 

211

13

A G

878-880

16

del. TCG

717

11

A C

1621

44**

C T

 

850

2

C T

891

4

G A

      
 

989

16

G A

930

50

C T

      
 

1186

35

G C

982

2

G A

      
 

2247

47

A C

993

2

G T

      

Specification of substitutions affecting ≥2 isolates

2533

29

G C

1045

19

G A

      
   

1048

64

A G

      
   

1116

64

A G

      
   

1125

2

C A

      
   

1268

37

T C

      
   

1282-1285 or 1284-1286*

63

del.GCG or GGC

      
   

1324

7

T C

      
   

1419

2

A G

      
   

1470

7

G A

      
   

1510

3

A G

      
   

1722

2

G T

      
   

1758

2

T C

      
   

1761

7

G C

      
   

1853

4

G A

      
   

1994

2

T G

      
  1. *Alternative alignments. **Lacking sequences in the 3′- end of a few isolates. Nt nucleotides, Del Deletion, Ins insertion. Positions are numbered from the first nucleotide in the start codon.