Rapid full-length genomic sequencing of two cytopathically heterogeneous Australian primary HIV-1 isolates.
Two Australian HIV-1 isolates, derived from patient blood (HIV(MBC200)) and cerebrospinal fluid (HIV(MBC925)), were characterized after in vitro culture in peripheral blood mononuclear cells (PBMC). Although virus replication was similar, as measured by cell-free reverse transcriptase activity, only one of the two isolates (HIV-1(MCB200)) consistently induced cell syncytia and depleted the PBMC population of CD4+ cells by cell killing. A novel technique, devised for rapidly obtaining high-quality viral sequence data and the full-length genomic sequence of these two isolates, is presented. Analysis of the predicted sequence of the viral Env proteins provides correlates of the observed phenotypes. Phylogenetic analysis derived using near full-length sequence of these and other HIV-1 subtype B genomic sequences (including two other Australian isolates) shows a star-shaped phylogeny with each member having a similar genetic diversity. These data expand the database of genomic sequence available from well-characterized primary clinical isolates of HIV-1 using a novel rapid technique.
Oelrichs
R B
RB
AIDS, Molecular, Macfarlane Burnet Centre for Medical Research, Fairfield, Australia. oelrichs@loxinfo.co.th
Lawson
V A
VA
Coates
K M
KM
Chatfield
C
C
Deacon
N J
NJ
McPhee
D A
DA
D000163:Acquired Immunodeficiency Syndrome / Q000821:virology; D000595:Amino Acid Sequence; D015704:CD4 Antigens / Q000502:physiology; D003588:Cytopathogenic Effect, Viral; D019143:Evolution, Molecular; D015686:Gene Products, env / Q000737:chemistry; D016679:Genome, Viral; D015497:HIV-1 / Q000235:genetics* / Q000302:isolation & purification / Q000502:physiology; D006801:Humans; D008969:Molecular Sequence Data; D009517:New South Wales; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D019718:Receptors, CXCR4 / Q000502:physiology; D016415:Sequence Alignment; D017423:Sequence Analysis, RNA / Q000379:methods*; D017386:Sequence Homology, Amino Acid; D014739:Victoria; D014779:Virus Replication
D015704:CD4 Antigens; D015686:Gene Products, env; D019718:Receptors, CXCR4