TABLE 3.

Nucleotide and amino acid diversity of HSV-2 strains in open reading frames

ORF	Protein functiona	Orientationb	Length (bp) (nucleic acid reference sequence)	% Diversity (SE)		dN/dS	No. of variable sites
				Nucleotide	Amino acid
UL1	Glycoprotein L	F	675	0.1 (0.0)	0.2 (0.1)	1.00	10
UL2	Uracil-DNA glycosylase	F	1,005	0.2 (0.0)	0.2 (0.1)	0.25	20
UL3	Nuclear phosphoprotein	F	702	0.1 (0.0)	0.0 (0.0)	0.00	7
UL4	Nuclear protein	R	606	0.3 (0.2)	0.3 (0.2)	0.17	13
UL5	Component of DNA helicase-primase	R	2,646	0.2 (0.0)	0.1 (0.1)	0.25	28
UL6	Minor capsid protein	F	2,043	0.2 (0.0)	0.3 (0.1)	0.33	33
UL7	Virion egress protein	F	891	0.4 (0.1)	0.4 (0.2)	0.20	16
UL8	Component of DNA helicase-primase	R	2,259	0.3 (0.1)	0.3 (0.1)	0.40	47
UL9	Ori binding protein	R	2,608	0.2 (0.0)	0.1 (0.1)	0.20	42
UL10	Glycoprotein M	F	1,404	0.2 (0.1)	0.2 (0.1)	0.14	26
UL11	Myristylated tegument protein	R	291	0.1 (0.1)	0.3 (0.2)	1.00	4
UL12	DNase	R	1,863	0.2 (0.0)	0.3 (0.1)	0.33	31
UL13	Protein kinase; tegument protein	R	1,496	0.2 (0.0)	0.1 (0.0)	0.00	19
UL14	Tegument protein	R	660	0.0 (0.0)	0.0 (0.0)	0.00	4
UL15	Role in DNA packaging	F	5,862	0.1 (0.0)	0.2 (0.0)	0.50	70
UL16	Proposed initiator CTG codon	R	1,119	0.1 (0.1)	0.2 (0.1)	0.50	12
UL17	Tegument protein; DNA packaging	R	2,118	0.2 (0.0)	0.3 (0.1)	0.67	29
UL18	Capsid protein	R	957	0.1 (0.0)	0.0 (0.0)	0.00	6
UL19	Major capsid protein	R	4,125	0.1 (0.0)	0.1 (0.0)	0.50	45
UL20	Virion membrane protein	R	669	0.2 (0.1)	0.6 (0.3)	3.00	6
UL21	Tegument protein	F	1,599	0.0 (0.0)	0.0 (0.0)	0.00	6
UL22	Glycoprotein H	R	2,517	0.3 (0.1)	0.3 (0.1)	0.17	39
UL23	Thymidine kinase [2 possible poly(A) sites]	R	1,131	0.2 (0.1)	0.3 (0.1)	1.00	16
UL24	Nuclear protein	F	846	0.4 (0.1)	0.4 (0.2)	0.22	21
UL25	Virion protein	F	1,758	0.1 (0.0)	0.1 (0.0)	0.00	20
UL26	Capsid maturation protease	F	1,923	0.3 (0.1)	0.4 (0.1)	0.29	55
UL26.5	Capsid assembly protein	F	990	0.4 (0.1)	0.6 (0.2)	0.38	39
UL27	Glycoprotein B	R	2,718	0.2 (0.0)	0.5 (0.1)	0.67	45
UL28	Role in DNA packaging	R	2,358	0.2 (0.0)	0.2 (0.1)	0.17	36
UL29	Single-stranded DNA binding protein	R	3,609	0.2 (0.0)	0.2 (0.1)	0.14	61
UL30	DNA polymerase catalytic subunit	F	3,723	0.1 (0.0)	0.1 (0.0)	0.50	32
UL31	Virion egress protein	R	918	0.1 (0.0)	0.0 (0.0)	0.00	11
UL32	Role in DNA packaging	R	1,797	0.2 (0.1)	0.3 (0.1)	0.17	29
UL33	Role in DNA packaging	F	393	0.2 (0.1)	0.1 (0.1)	0.00	4
UL34	Membrane-associated phosphoprotein	F	831	0.1 (0.1)	0.2 (0.2)	0.50	7
UL35	Capsid protein	F	339	0.1 (0.0)	0.1 (0.1)	0.00	4
UL36	Very large tegument protein	R	9,412	0.2 (0.0)	0.2 (0.0)	0.25	160
UL37	Tegument protein	R	3,345	0.1 (0.0)	0.2 (0.1)	0.50	43
UL38	Capsid protein	F	1,401	0.4 (0.1)	0.4 (0.1)	0.22	36
UL39	Ribonucleotide reductase large subunit	F	3,441	0.4 (0.1)	0.5 (0.1)	0.18	97
UL40	Ribonucleotide reductase small subunit	F	1,014	0.1 (0.0)	0.0 (0.0)	0.00	11
UL41	Tegument protein; host shutoff factor	R	1,479	0.1 (0.0)	0.1 (0.1)	0.00	14
UL42	DNA polymerase subunit	F	1,413	0.2 (0.1)	0.4 (0.1)	1.00	18
UL43	Probable membrane protein	F	1,245	0.3 (0.1)	0.4 (0.1)	0.40	22
UL44	Glycoprotein C	F	1,443	0.4 (0.1)	0.7 (0.2)	0.80	24
UL45	Tegument/envelope protein	F	519	0.1 (0.0)	0.1 (0.1)	1.00	5
UL46	Tegument protein	R	2,169	0.3 (0.1)	0.4 (0.1)	0.33	40
UL47	Tegument protein	R	2,091	0.1 (0.0)	0.3 (0.1)	1.00	26
UL48	Tegument protein; transactivator of immediate-early genes	R	1,473	0.2 (0.1)	0.1 (0.1)	0.00	17
UL49	Tegument protein	R	912	0.5 (0.1)	0.8 (0.3)	0.40	26
UL49A	Probable virion membrane protein	R	264	0.4 (0.2)	0.2 (0.1)	0.07	7
UL50	Deoxyuridine triphosphatase	F	1,110	0.2 (0.1)	0.3 (0.1)	0.25	23
UL51	Tegument protein	R	735	0.1 (0.1)	0.0 (0.0)	0.00	5
UL52	Component of DNA helicase-primase	F	3,204	0.2 (0.0)	0.3 (0.1)	0.25	49
UL53	Glycoprotein K	F	1,017	0.4 (0.1)	0.7 (0.2)	0.50	27
UL54	ICP27 immediate-early regulatory protein	F	1,539	0.1 (0.0)	0.2 (0.1)	0.50	22
UL55	Nuclear protein	F	561	0.1 (0.0)	0.2 (0.1)	0.50	7
UL56	Membrane protein	R	708	0.2 (0.1)	0.4 (0.2)	0.50	13
US1	ICP4 immediate-early transactivator	F	1,239	0.4 (0.1)	0.4 (0.2)	0.38	32
US2	Virion protein	F	873	0.2 (0.1)	0.4 (0.2)	0.50	11
US3	Protein kinase	F	1,443	0.2 (0.1)	0.3 (0.1)	0.25	22
US4	Glycoprotein G	F	2,097	0.4 (0.1)	0.7 (0.1)	1.00	61
US5	Glycoprotein J	F	276	0.2 (0.1)	0.2 (0.1)	0.17	9
US6	Glycoprotein D	F	1,179	0.2 (0.0)	0.3 (0.1)	0.25	17
US7	Glycoprotein I	F	1,116	0.3 (0.1)	0.6 (0.2)	0.75	24
US8	Glycoprotein E	F	1,635	0.2 (0.0)	0.4 (0.1)	1.00	29
US9	Tegument protein	F	267	0.4 (0.2)	0.2 (0.1)	0.08	6
US10	Virion protein	R	906	0.3 (0.1)	0.4 (0.2)	0.40	16
US11	RNA binding protein	R	453	0.2 (0.1)	0.5 (0.3)	1.00	7
US12	Immediate-early inhibitor of antigen presentation	R	258	0.2 (0.1)	0.0 (0.0)	0.00	2

^aReference 1.

^bF, forward; R, reverse.