HIV-1 origin and subtypes
There are two viruses that cause AIDS in humans, namely HIV-1 (human immunodeficiency virus type 1) and HIV-2. Both viruses have isogenic counterparts in chimpanzee and sooty mangabey (simian immunodeficiency viruses SIVcpz and SIVsm, respectively), and probably at least two cross-species transmissions of different retroviruses occurred from monkey in man. Most HIV-1 isolates identified to date in the pandemic belong to a group designated M for major. This group has spread worldwide within the last two decades. There are at least two additional HIV-1 groups that are confined to a more restricted geographical area in Africa. Several AIDS patients from West Central Africa have viruses from a distinct group designated O (outlier group). More recently, one member of a third group designated N (new group) was isolated from a Cameroon AIDS patient. It is suspected that each group originated from a different SIVcpz transmission from monkey into human. There is no evidence to suggest that the O and N group viruses are less virulent or defective in transmission, and the worldwide spread of group M viruses may just result from a stochastic or chance process.

The group M viruses that comprise the current global pandemic have diversified during their worldwide spread. These isolates have been grouped based on the genomic sequences, and can be divided into at least ten distinct subtypes or clades termed A through J. Isolates from different subtypes may differ by 30-40% in the amino acid sequence of the Env protein, whereas variation ranges from 5-20% within a subtype. Subtypes are no stable entities because recombinants, even intergroup recombinants, with mosaic genomes are known to occur at an appreciable frequency. The different subtypes are not distributed evenly throughout the world. For example, subtype B predominates in Northern America and Europe and subtype E [CRF-AE(CM240)] predominates in northern Thailand. There is at present no evidence for subtype-specific variation in virulence or transmission, and their diverse geographical distribution is likely to result from stochastic founder effects. Nevertheless, the possibility that the subtypes differ in their biological properties cannot be excluded, and this may affect their pathogenic potential. For instance, it has been suggested that subtype E viruses are particularly virulent and that they replicate more efficiently than other subtypes in Langerhans cells, which are potential target cells in heterosexual transmission, although follow-up studies could not confirm these results. The relationship between virus subtype, biological properties and pathogenicity is unknown, in part, because virus replication studies have been performed almost exclusively with subtype B viruses.

The HIV-1 promoter
The HIV-1 long terminal repeat (LTR) encodes the transcriptional promoter. The LTR of subtypes A through G was cloned and analyzed to test if there are subtype-specific differences in gene expression. Sequence analysis demonstrated a unique LTR enhancer/promoter configuration for each subtype.

Enlarged view

Detail of the subtype B LTR region. Schematic of the LTR region from -356 to +55 showing the binding sites for cellular transcription factors that have been described to interact with the prototype subtype B. The transcription start site is at +1.The enhancer contains two NFkB motifs, the core promoter encompasses the three Sp1 sites and the TATA box.

Enlarged view

LTR promoter organization of HIV-1 subtypes A through G. Most experimental evidence for protein binding sites has been provided for the LTR of HIV-1 subtype B. Furthermore, recent evidence supports the conversion of the upstream NF-kB site of subtype E into a GABP binding site. The box placed at -28 represents the TAAAA variant of the TATA canonical box present in subtype E. RBEIII, NFkB, Sp1, AP-1 and GABP motifs are shown. The hatched boxes represent overlapping motifs.

Transcription assays with luciferase reporter constructs showed that all subtype LTRs are functional promoters with a low basal transcriptional activity and a high activity in the presence of the viral Tat transcriptional activator protein. All subtype LTRs responded equally well to the Tat trans-activator protein of subtype B. This result suggests that there are no major differences in the mechanism of Tat-mediated trans-activation among the subtypes. Nevertheless, subtype-specific differences in the activity of the basal LTR promoter were measured in different cell types. Furthermore, we measured a differential response to TNF-alpha, and the induction level correlated with the number of NF-kB sites in the respective LTRs, which varies from one (subtype E) to three (subtype C). In general, subtype E was found to encode the most potent LTR, and we therefore inserted the core promoter elements of subtype E in the infectious molecular clone of the LAI isolate (subtype B). This recombinant LAI-E virus exhibited a profound replication advantage compared with the original LAI virus in the SupT1 T-cell line, indicating that subtle differences in LTR promoter activity can have a significant impact on viral replication kinetics. These results suggest that there may be considerable biological differences among the HIV-1 subtypes.

We have recently constructed the complete set of LAI-subtype B molecular clones with the LTR promoter of subtypes A to G. Replication in different host cell types and the effect of different cell stimuli are currently being studied.

Relevant publications

Jeeninga R, Hoogenkamp M, Armand-Ugon M, de Baar M, Verhoef K and Berkhout B. 2000. Functional differences between the LTR transcriptional promoters of HIV-1 subtypes A through G. Journal of Virology 74, 3740-3751.

Verhoef K, Sanders RW, Fontaine V, Kitajima S, Berkhout B. 1999. Evolution of the HIV-1 LTR promoter by conversion of an NF-kB enhancer element into a GABP binding site. Journal of Virology 73, 1331-1340.

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