TABLE 2.

Comparison of the divergence between PTLV strains^a

Strain	Gene	% nt difference from corresponding gene of:
		HTLV-2b NRA	HTLV-2c KAY1	HTLV-2d Efe2	STLV-2 PP1664	HTLV-1a ATK1	STLV-L PH969
HTLV-2a Mo	LTR	7.4	5.0	10.7	31.6	42.1	44.6
	gag	4.1		6.6	23.3	30.6	31.9
	pol	4.9		6.7	23.3	34.5	34.8
	env	4.4	1.0	6.5	23.8	34.6	32.0
	tax/rex	2.2	0.4	3.3	10.7	21.4	22.6
HTLV-2b NRA	LTR		6.0	7.2	29.8	42.6	44.2
	gag			6.7	23.1	30.0	31.5
	pol			6.5	22.6	35.0	34.6
	env		3.9	6.9	23.6	34.3	32.4
	tax/rex		2.2	2.4	10.4	22.0	22.3
HTLV-2c KAY1	LTR			10.0	32.0	42.0	44.0
	gag
	pol
	env			5.7	20.0	32.8	28.1
	tax/rex			3.3	12.3	21.4	22.1
HTLV-2d Efe2	LTR				29.2	43.1	43.4
	gag				22.8	30.2	40.0
	pol				22.4	34.6	34.7
	env				22.9	33.5	31.8
	tax/rex				11.5	22.5	22.4
STLV-2 PP1664	LTR					43.3	44.5
	gag					30.6	30.2
	pol					35.5	34.5
	env					36.1	33.1
	tax/rex					21.9	22.9
HTLV-Ia ATK1	LTR						42.3
	gag						30.7
	pol						36.6
	env						34.7
	tax/rex						21.1

^aTransitions and transversions are scored equally. For details of the strains, see Materials and Methods. LTR, entire LTR (except for HTLV-2c, for which only 479 nt is available); gag, entire gag ORF; pol, entire pol ORF without protease, starting from the protease cleavage site at the C terminus from the protease; env, entire env ORF (except for HTLV-c, for which only 610 nt, including the entire gp21-coding sequence, is available); tax/rex, entire second ORF of rex, overlapping with part of the tax ORF (the ATK1 and PH969 rex second ORFs are 60 and 36 nt longer, respectively; this extension compared with HTLV-2 was excluded from the comparison). The distances between HTLV-2d genes and those of the other PTLV types and HTLV-2 subtypes are in boldface.