Nucleotide sequence of a Guinea-Bissau-derived human immunodeficiency virus type 2 proviral clone (HIV-2CAM2)

Structure of the zinc finger domain encompassing residues 13-51 of the nucleocapsid protein from simian immunodeficiency virus

The NCps (nucleocapsid proteins) of HIV-1 (HIV type 1), HIV-2 and SIV (simian immunodeficiency virus) are small highly basic proteins, characterized by the presence of two CCHC ZF (zinc finger) domains. NCps, closely associated with the dimeric RNA genome in the core of the virus particle, were shown to promote the specific encapsidation of the viral RNA and are implicated in reverse transcription. Solution structure of the HIV-1 NCp7 and complexes of NCp7 with RNA or DNA showed the critical relationships between the structure and its various functions. HIV-1 and HIV-2 have resulted respectively from transmissions of SIV from chimpanzees and sooty mangabeys. It has been shown that the SIVlhoest (SIV from l'Hoest monkeys) also has the potential to infect human populations. Since monkeys are of great interest for clinical studies of antiviral drugs, the structure of (13-51)NCp8 (zinc finger domain of NCp8, encompassing residues 13-51) from SIVlhoest was determined by NMR to appraise the influence of major differences in the sequence, since Glu21, Gly43 and Met46 in NCp7 are replaced by Pro, Glu and Phe respectively in this particular NCp8. The structure of (13-51)NCp8 is very well defined, and surprisingly the structure of each ZF is similar in NCp7 and NCp8. Moreover, contrary to NCp7, the two ZFs are strongly locked to each other in this NCp8. This first reported structure of a simian NCp8 compared with that of NCp7 shows that the main structural differences occur at the flexible linker between the two ZFs but the essential residues responsible for the interaction with oligonucleotides adopt the same orientation in the two proteins.

Human retroviruses in leukaemia and AIDS: reflections on their discovery, biology and epidemiology

The study of retroviruses has had a profound impact by unveiling an unusual form of viral replication: the multiplication of RNA viruses via a proviral DNA, for which Jan Svoboda provided the experimental model over forty years ago. In 1970 Temin, Mizutani and Baltimore discovered that this group of viruses contains a unique enzyme catalysing the synthesis of a DNA copy of the viral RNA: reverse transcriptase (RT). The discovery of RT has itself had an enormous impact on molecular biology in general, but also stimulated many premature claims of its detection in human disease. Claims by Gallo's laboratory that the cytoplasm of human leukaemia cells contained RT proved to be unfounded, as did his report in collaboration with Weiss that myeloid leukaemia contained HL23 virus, this organism proving not to be human but a laboratory contaminant of three monkey viruses. Conclusive demonstration of a retroviral involvement in human leukaemia was first provided in 1981 by Hinuma and his associates, showing that adult T-cell leukaemia (ATL), a rare form of leukaemia endemic to south-west Japan, is caused by a new retrovirus (ATLV). Other publications in December 1980 and through 1981 claimed the discovery of a new human T-cell leukaemia virus involved in mycosis fungoides (MF) and Sézary's syndrome (SS). This virus was termed HTLV by Gallo. The nucleotide sequence of ATLV is strongly conserved, that of my 1983 isolate from a black British ATL patient being practically identical with the Japanese virus isolates. After AIDS was recognised in 1981 by Gottlieb and coworkers as a new human disease, several papers were published by Gallo and his associates during 1983-4, invoking the oncovirus responsible for adult T-cell leukaemia as the cause of AIDS. In 1983 the French scientist Barré-Sinoussi and her colleagues succeeded in isolating a new agent in the disease, a lentivirus, which they named LAV. The French immunologist Klatzmann and his colleagues discovered that LAV killed CD4+ T-cells, furnishing an explanation for the pathogenesis of AIDS and providing a mechanism for how AIDS developed. For some time Gallo continued to suggest leukaemia virus involvement, claiming that his independent isolate of the AIDS virus, termed HTLV-III, was closely related to HTLV-I (the Japanese ATLV). Although this created considerable confusion among researchers for a period, the relationship was eventually disproved. Unlike ATLV, whose nucleic acid sequence is very stable, the AIDS virus (now termed HIV by international agreement) is extraordinarily unstable, the sequences of independent HIV isolates being quite unique: this made it possible to establish conclusively that both HTLV-III and another independent isolate CBL-1, from Weiss' laboratory, were actually LAV isolates from the French laboratory. It has been shown by Hayami and his associates that only African primates are infected with similar lentiviruses to HIV which explains why AIDS started in Africa. Further research has clarified the origin of HIV-1 to be a chimpanzee lentivirus and HIV-2 to be the sooty mangabey lentivirus, which began to spread in humans perhaps no more than fifty years ago. The infection has spread rapidly, primarily through sexual intercourse, but also by transmission through blood and its products as well as contaminated needles and syringes. Sexual intercourse has now spread the virus around the World; and there are probably some 70 million infected. 90% of those infected with HIV develop the deadly disease of AIDS within ten years of infection: the death toll from the disease has been enormous. By contrast, HTLV-1 has been infecting man in isolated areas probably for hundreds of years; but it has not spread widely. HTLV causes leukaemia in only less than 1% of those infected. The prime mode of transmission of HTLV-1 is between mother and neonate; infections can be reduced by stopping breast-feeding by infected mothers. The isolation of HIV enabled screening tests to be developed for contaminated blood. However, due to the peculiar biology of HIV infection, unfortunately all efforts to develop an effective vaccine have so far failed.

Fast analysis of genomic homologies: primate immunodeficiency virus

We have recently published a new probabilistic algorithm which performs genomic comparisons on a huge scale. In the present paper it was applied to immunodeficiency viral sequences extracted from international gene databanks. During global sequence analysis of human (HIV1 and HIV2) and simian viruses by means of dot-matrix representation, series of homology were obtained which permitted the definition of families of viruses overlapping the species divisions. Sequences of interest were characterized to the lexical base sentence through successive zoomings. Strain-to-strain comparison confirmed subfamily classifications and led, for example, to the identification of divergent LTR sequences. By way of example, we described the application of the algorithm to the ANT70C and MVP5180 HIV1-O viruses, for which the observed differences were shown to correspond to a deletion in the U3 region, situated between the LEF and NF-kappaB sites. It was of interest to consider these data in a tentative phylogenetic interpretation.

Biological phenotype of HIV type 2 isolates correlates with V3 genotype

The biological phenotype of HIV-2 isolates can be divided into two groups, rapid/high and slow/low, based on the ability to infect CD4+ tumor cell lines. Similar differences in the biological phenotype of HIV-1 isolates are largely determined by the charge of two specific amino acids in the V3 loop of the envelope protein gp120. In this study we have sequenced the V3 loop and flanking regions of 14 HIV-2 isolates from Guinea-Bissau and the Ivory Coast and correlated the results to the biological phenotype of the isolates. The sequences were obtained by PCR amplification of DNA from peripheral blood mononuclear cells infected with the different isolates, followed by direct sequencing of the amplified products. Eleven other HIV-2 isolates with known V3 sequence and biological phenotype were also included. Thirteen of the 14 new isolates were classified as subtype A of HIV-2 and one as subtype B. The V3 loop of rapid/high HIV-2 isolates differed significantly from slow/low isolates in that it was more heterogeneous in sequence and had higher net charge. Mutations at two specific amino acid positions (313 and 314), often to positively charged amino acids, were also significantly associated with the rapid/high phenotype. There were no sequence differences between rapid/high and slow/low isolates in the regions that flank the V3 loop. Our findings indicate that there may be a high degree of similarity in the molecular features that underlie the biological phenotypes of HIV-1 and HIV-2 isolates.

Genetic diversity of human immunodeficiency virus type 2: evidence for distinct sequence subtypes with differences in virus biology

The virulence properties of human immunodeficiency virus type 2 (HIV-2) are known to vary significantly and to range from relative attenuation in certain individuals to high-level pathogenicity in others. These differences in clinical manifestations may, at least in part, be determined by genetic differences among infecting virus strains. Evaluation of the full spectrum of HIV-2 genetic diversity is thus a necessary first step towards understanding its molecular epidemiology, natural history of infection, and biological diversity. In this study, we have used nested PCR techniques to amplify viral sequences from the DNA of uncultured peripheral blood mononuclear cells from 12 patients with HIV-2 seroreactivity. Sequence analysis of four nonoverlapping genomic regions allowed a comprehensive analysis of HIV-2 phylogeny. The results revealed (i) the existence of five distinct and roughly equidistant evolutionary lineages of HIV-2 which, by analogy with HIV-1, have been termed sequence subtypes A to E; (ii) evidence for a mosaic HIV-2 genome, indicating that coinfection with genetically divergent strains and recombination can occur in HIV-2-infected individuals; and (iii) evidence supporting the conclusion that some of the HIV-2 subtypes may have arisen from independent introductions of genetically diverse sooty mangabey viruses into the human population. Importantly, only a subset of HIV-2 strains replicated in culture: all subtype A viruses grew to high titers, but attempts to isolate representatives of subtypes C, D, and E, as well as the majority of subtype B viruses, remained unsuccessful. Infection with all five viral subtypes was detectable by commercially available serological (Western immunoblot) assays, despite intersubtype sequence differences of up to 25% in the gag, pol, and env regions. These results indicate that the genetic and biological diversity of HIV-2 is far greater than previously appreciated and suggest that there may be subtype-specific differences in virus biology. Systematic natural history studies are needed to determine whether this heterogeneity has clinical relevance and whether the various HIV-2 subtypes differ in their in vivo pathogenicity.

Molecular and biological characteristics of a novel HIV-2 isolate, HIV-2HOM

In 1991 a new HIV-2 isolate (HIV-2HOM) was isolated first from a German individual most likely infected in West Africa in the beginning of the 1970s. The virus was isolated from both, the plasma and the peripheral blood lymphocytes of the patient by using OKT-3-stimulated cord blood lymphocytes. The recovered viruses could be further propagated on Jurkat cells and exhibited a broad cell tropism. Biochemical and antigenic properties of HIV-2HOM were examined by radioimmunoprecipitations. For a more detailed molecular characterization, a 1520 bp DNA fragment from the env gene and a 722 bp DNA fragment from the pol gene were amplified by polymerase chain reactions, cloned and sequenced. A comparison of both sequences to prototypic HIV-2 and SIV isolates revealed a close relationship to HIV-2ST. This strain originated from an asymptomatic Senegalese individual and is supposed to be of reduced pathogenicity. Taking into account genetic data, it may be assumed that HIV-2HOM and HIV-2ST are closely related strains with different growth characteristics and pathogenic features.

Subcloning of HIV-2 nef genes in E. coli and immunological reactivity of expressed fusion proteins

The nef gene located in the 3' region of the HIV-2 genome encodes an N-terminally myristylated protein of 27-35 kD, likely to be involved in the regulation of viral transcription. The nef genes of HIV-2 isolates GH-1, ROD, ST, BEN, and D194.17 were inserted into E. coli pEX vectors and expression of Nef beta-galactosidase fusion proteins was detected in stained gels. All fusion proteins specifically reacted with a rabbit serum raised against bacterially expressed Nef from HIV-2D194.17. Sera from monkeys inoculated with HIV-2BEN or SIVMAC251 recognized the Nef proteins of only certain HIV-2 isolates. No cross-reactivity of these sera with HIV-1 Nef and of a rabbit anti-HIV-1-Nef serum with the described HIV-2 Nef fusion proteins was observed.