Table 2.

Subtyping of All Seven New South African HIV-1 Non-Subtype C Strains

Sequence name	REGA 3.0	jpHMM	SimPlot	ML-tree	Subtype assigned	GenBank accession
TV016	B	B/K	B	B	B	KJ948656
TV047	B	B	B	B	B	KJ948657
TV096	A1	A1	A1	A1	A1	KJ948658
TV101	A1/D	A1/D	A1/D	A1	URF A1/D	KJ948659
TV218	A1/C	A1/C	A1/C	C outlier	URF A1/C	KJ948661
TV546	G	G	G	G	G	KJ948662
TV1057	B	B	B	B	B	KJ948660

ML, maximum likelihood; jpHMM, jumping profile hidden Markov model.