Subtype-specific sequence variation of the HIV type 1 long terminal repeat and primer-binding site.
We studied sequence differences in regulatory elements of the long terminal repeat (LTR) and primer-binding site (PBS) among various human immunodeficiency virus type 1 (HIV-1) subtypes. Phylogenetic sequence analysis of a fragment of 729 base pairs (bp) covering the Gag-coding region for half of p24 and all of p17 revealed the gag subtype of all 60 viruses included in the study: A (n = 20), B (n = 12), C (n = 7), D (n = 10), E (n = 3), F (n = 4), G (n = 3), and H (n = 1). The subtype was also determined by analysis of a 689-bp fragment comprising the LTR and the PBS motif. Comparison of the LTR versus gag sequences showed a mosaic genome for seven isolates. After analysis of all sequences, we could describe subtype-specific differences in sequences encompassing the regulatory elements of the LTR and the PBS motif.
De Baar
M P
MP
Department of Human Retrovirology, Academic Medical Center, University of Amsterdam, The Netherlands. m.p.debaar@amc.uva.nl
De Ronde
A
A
Berkhout
B
B
Cornelissen
M
M
Van Der Horn
K H
KH
Van Der Schoot
A M
AM
De Wolf
F
F
Lukashov
V V
VV
Goudsmit
J
J
D001483:Base Sequence; D001665:Binding Sites / Q000235:genetics; D016384:Consensus Sequence; D005814:Genes, Viral / Q000235:genetics; D015750:Genes, gag / Q000235:genetics; D015658:HIV Infections / Q000821:virology*; D015497:HIV-1 / Q000737:chemistry / Q000235:genetics*; D006801:Humans; D008969:Molecular Sequence Data; D010802:Phylogeny; D016415:Sequence Alignment; D020079:Terminal Repeat Sequences / Q000235:genetics