Michael M. Thomson

IL-7 is a potent and proviral strain–specific inducer of latent HIV-1 cellular reservoirs of infected individuals on virally suppressive HAART

The persistence of HIV-1 in virally suppressed infected individuals on highly active antiretroviral therapy (HAART) remains a major therapeutic problem. The use of cytokines has been envisioned as an additional therapeutic strategy to stimulate latent proviruses in these individuals. Immune activation therapy using IL-2 has shown some promise. In the present study, we found that IL-7 was significantly more effective at enhancing HIV-1 proviral reactivation than either IL-2 alone or IL-2 combined with phytohemagglutinin (PHA) in CD8-depleted PBMCs. IL-7 also showed a positive trend for inducing proviral reactivation from resting CD4(+) T lymphocytes from HIV-1-infected patients on suppressive HAART. Moreover, the phylogenetic analyses of viral envelope gp120 genes from induced viruses indicated that distinct proviral quasispecies had been activated by IL-7, as compared with those activated by the PHA/IL-2 treatment. These studies thus demonstrate that different activators of proviral latency may perturb and potentially deplete only selected, specific portions of the proviral archive in virally suppressed individuals. The known immunomodulatory effects of IL-7 could be combined with its ability to stimulate HIV-1 replication from resting CD4(+) T lymphocytes, in addition to other moieties, to potentially deplete HIV-1 reservoirs and lead to the rational design of immune-antiretroviral approaches.

Molecular epidemiology of HIV-1 genetic forms and its significance for vaccine development and therapy

Since their initial expansion in human beings roughly seven decades ago in central Africa, the HIV-1 pandemic strains have diversified extensively through mutation and recombination. 24 circulating genetic forms of the main HIV-1 group are presently recognised, including 11 subtypes or sub-subtypes and 13 circulating recombinant forms. New genetic forms are being introduced in different areas of the world, changing the molecular epidemiology of the infection. It is generally agreed that the control of the HIV-1 pandemic requires the development of vaccines that efficiently protect against the range of HIV-1 genetic forms. The introduction of effective antiretroviral therapies in areas of high HIV-1 prevalence may also contribute to the control of the pandemic, as has been documented in developed countries. Efficient targeting of the extensive genetic diversity of HIV-1 constitutes one of the major challenges in present efforts against the pandemic, although the significance of HIV-1 genetic forms for vaccine development and therapy remains to be defined.

Travel and the Introduction of Human Immunodeficiency Virus Type 1 Non-B Subtype Genetic Forms into Western Countries

Both high mutation rates and recombination contribute to the genetic diversity of human immunodeficiency virus type 1 (HIV-1). Among viruses of the main group, which are responsible for the HIV-1 pandemic, 21 circulating genetic forms have been reported, 11 of which are recombinant between > or = 2 subtypes. In Western Europe and the Americas, the HIV-1 epidemic is largely dominated by B subtype viruses; however, infections with diverse non-B subtype genetic forms are increasingly being recognized. In Western Europe and North America, most of them have been identified in immigrants or travelers returning from areas with high HIV-1 prevalence, mainly from sub-Saharan Africa and Southeast Asia, where non-B subtype genetic forms predominate, but propagation within other groups has been reported in some Western countries. This may have implications for prophylactic and therapeutic strategies and, by bringing in contact different genetic forms, may favor the generation of novel recombinant viruses. Travelers from different categories--including immigrants, military personnel, seamen, tourists, expatriates, diplomats, and businessmen--may be at risk of transporting HIV non-B subtype genetic forms to Western countries.

Identification of a newly characterized HIV-1 BG intersubtype circulating recombinant form in Galicia, Spain, which exhibits a pseudotype-like virion structure

Summary: We recently reported the finding of phylogenetically related HIV‐1 BG intersubtype recombinant and G subtype nonrecombinant viruses circulating among injecting drug users in the region of Galicia in northwestern Spain. Here, we report the characterization of near full‐length genome sequences of nine of these viruses (seven BG recombinant and two of nonrecombinant G subtype), obtained from epidemiologically unlinked individuals. Bootscan analysis reveals that six recombinant viruses share an identical mosaic structure, with two intersubtype breakpoints delimiting a B subtype segment comprising most of Env gp120 and the external portion of Env gp41, with the remaining portions of the genome being of subtype G, thus mimicking a pseudotype virion structure. The seventh BG recombinant virus exhibits breakpoints in env coincident with the other BG viruses but contains additional B subtype segments in gag and pol. In phylogenetic trees of complete genomes and of the B subtype segment of env, all seven BG viruses group in a monophyletic cluster. G subtype portions of the BG viruses group uniformly with the newly derived nonrecombinant G subtype viruses of Galicia in bootscan analysis, which points to the locally circulating G subtype strain as parental of the recombinants. These results allow us to define a new HIV‐1 circulating recombinant form (CRFI4_BG), the first reported to originate in Western Europe.

HIV-1 genetic diversity in Galicia Spain: BG intersubtype recombinant viruses circulating among injecting drug users.

BackgroundThe HIV-1 epidemics in Western Europe are dominated by B subtype viruses. Non-B subtype is largely restricted to individuals infected outside of Europe and to their direct contacts and is generally acquired by the heterosexual route. MethodsProtease and a segment of reverse transcriptase were amplified and sequenced from plasma RNA in 451 individuals from seven cities of Galicia, north-western Spain. Subtype sequence homologies were determined using the BLAST algorithm. Non-B sequences were examined by phylogenetic analysis and intersubtype recombination by bootscanning. The env V3 region was analysed in all non-B and in 38 B subtype viruses. ResultsTen different non-B genetic forms were identified in 20 (4.4%) individuals. Subtypes were concordant between pol and V3 in five viruses; 14 (70%) infections were with intersubtype recombinant viruses, and one individual had a dual B+G infection. Seven recombinant viruses were phylogenetically related to five reported recombinant forms. Three non-recombinant G and six recombinant BG viruses formed a monophyletic cluster for pol. All but three individuals with non-B infections were native Spanish. Only 6 of 16 individuals referred to sexual contacts with sub-Saharan Africans. Twelve (60%) non-B subtype infections, including all with G and BG viruses, were in injecting drug users (IDU). ConclusionsNon-B subtype viruses were identified in 4.4%, with a high diversity of genetic forms, including 70% infections with intersubtype recombinant viruses. The majority of individuals with non-B infections were IDU, most of them without known contacts with non-European sources, and among whom BG recombinant viruses are circulating.

High HIV-1 genetic diversity in Cuba.

BackgroundHIV-1 subtype B is largely predominant in the Caribbean, although other subtypes have been recently identified in Cuba. ObjectivesTo examine HIV-1 genetic diversity in Cuba. MethodsThe study enrolled 105 HIV-1-infected individuals, 93 of whom had acquired the infection in Cuba. DNA from peripheral blood mononuclear cells was used for polymerase chain reaction amplification and sequencing of pol (protease–reverse transcriptase) and env (V3 region) segments. Phylogenetic trees were constructed using the neighbour-joining method. Intersubtype recombination was analysed by bootscanning. ResultsOf the samples, 50 (48%) were of subtype B and 55 (52%) of diverse non-B subtypes and recombinant forms. Among non-B viruses, 12 were non-recombinant, belonging to six subtypes (C, D, F1, G, H and J), the most frequent of which was subtype G (n = 5). The remaining 43 (78%) non-B viruses were recombinant, with 14 different forms, the two most common of which were Dpol/Aenv (n = 21) and U(unknown)pol/Henv (n = 7), which grouped in respective monophyletic clusters. Twelve recombinant viruses were mosaics of different genetic forms circulating in Cuba. Overall, 21 genetic forms were identified, with all known HIV-1 group M subtypes present in Cuba, either as non-recombinant viruses or as segments of recombinant forms. Non-B subtype viruses were predominant among heterosexuals (72%) and B subtype viruses among homo- or bisexuals (63%). ConclusionAn extraordinarily high diversity of HIV-1 genetic forms, unparalleled in the Americas and comparable to that found in Central Africa, is present in Cuba.

Identification of a novel HIV-1 complex circulating recombinant form (CRF18_cpx) of Central African origin in Cuba.

Background:Analysis of partial pol and env sequences have indicated a high diversity of HIV-1 genetic forms in Cuba, including two potential novel circulating recombinant forms (CRF): Upol/Henv and Dpol/Aenv. Objectives:To determine whether Upol/Henv recombinant viruses from Cuba, detected in 7% of samples, represent a novel HIV-1 CRF, and to identify non-Cuban viruses related to this recombinant form. Methods:Near full-length genome amplification was carried out by nested polymerase chain reaction in four overlapping DNA segments of two epidemiologically unlinked viruses in uncultured peripheral blood mononuclear cells. The sequences were analysed phylogenetically. Recombinant structures and phylogenetic relationships were analysed by bootscanning and by maximum likelihood. Searches for related viruses in databases were initially based on sequence homology and sharing of signature nucleotides. Results:Both Cuban viruses clustered uniformly in bootscans all along the genome with each other and with a virus from Cameroon, CM53379, indicating that all three represent the same recombinant form. Their genome comprised multiple segments clustering with subtypes A1, F, G, H and K, as well as segments failing to cluster with recognized subtypes. The newly defined CRF, designated CRF18_cpx, was phylogenetically related in partial segments to CRF13_cpx, CRF04_cpx and 36 additional viruses, most of them from Central Africa. One of the viruses from Cameroon, sequenced in the near full-length genome, was a CRF18_cpx/subtype G secondary recombinant. Conclusions:A novel HIV-1 complex circulating recombinant form (CRF18_cpx) has been identified that is circulating in Cuba and Central Africa.

IMPACT OF CLADE, GEOGRAPHY AND AGE OF THE EPIDEMIC ON HIV-1 NEUTRALIZATION BY ANTIBODIES

ABSTRACT Neutralizing antibodies (nAbs) are a high priority for vaccines that aim to prevent the acquisition of HIV-1 infection. Vaccine effectiveness will depend on the extent to which induced antibodies neutralize the global diversity of circulating HIV-1 variants. Using large panels of genetically and geographically diverse HIV-1 Env-pseudotyped viruses and chronic infection plasma samples, we unambiguously show that cross-clade nAb responses are commonly induced in response to infection by any virus clade. Nonetheless, neutralization was significantly greater when the plasma clade matched the clade of the virus being tested. This within-clade advantage was diminished in older, more-diverse epidemics in southern Africa, the United States, and Europe compared to more recent epidemics in Asia. It was most pronounced for circulating recombinant form (CRF) 07_BC, which is common in China and is the least-divergent lineage studied; this was followed by the slightly more diverse Asian CRF01_AE. We found no evidence that transmitted/founder viruses are generally more susceptible to neutralization and are therefore easier targets for vaccination than chronic viruses. Features of the gp120 V1V2 loop, in particular, length, net charge, and number of N-linked glycans, were associated with Env susceptibility and plasma neutralization potency in a manner consistent with neutralization escape being a force that drives viral diversification and plasma neutralization breadth. The overall susceptibility of Envs and potencies of plasma samples were highly predictive of the neutralization outcome of any single virus-plasma combination. These findings highlight important considerations for the design and testing of candidate HIV-1 vaccines that aim to elicit effective nAbs. IMPORTANCE An effective HIV-1 vaccine will need to overcome the extraordinary variability of the virus, which is most pronounced in the envelope glycoproteins (Env), which are the sole targets for neutralizing antibodies (nAbs). Distinct genetic lineages, or clades, of HIV-1 occur in different locales that may require special consideration when designing and testing vaccines candidates. We show that nAb responses to HIV-1 infection are generally active across clades but are most potent within clades. Because effective vaccine-induced nAbs are likely to share these properties, optimal coverage of a particular clade or combination of clades may require clade-matched immunogens. Optimal within-clade coverage might be easier to achieve in regions such as China and Thailand, where the epidemic is more recent and the virus less diverse than in southern Africa, the United States, and Europe. Finally, features of the first and second hypervariable regions of gp120 (V1V2) may be critical for optimal vaccine design.

High prevalence of unique recombinant forms of HIV-1 in Ghana: molecular epidemiology from an antiretroviral resistance study

Background:In Ghana, programs to expand antiretroviral access are being implemented. In this context, the dynamic genetic evolution of HIV-1 requires continuous surveillance, particularly when diverse genetic forms co-circulate. Methods:Phylogenetic and antiretroviral resistance analyses of HIV-1 partial pol sequences from plasma RNA samples from 207 Ghanaian individuals were performed. Results:66% of infections were CRF02_AG, whereas 25% were unique recombinant forms (URFs). All 52 URFs were characterized by bootscanning. CRF02_AG was parental strain in 87% of URFs, forming recombinants with genetic forms circulating in minor proportions: CRF06_cpx, sub-subtype A3, CRF09_cpx and subtypes G and D. Two triple recombinants (CRF02_AG/A3/CRF06_cpx and CRF02_AG/A3/CRF09_cpx) were identified. Antiretroviral resistance analyses revealed that six individuals, five of which were antiretroviral drug-experienced, harbored mutations conferring high level of resistance to reverse transcriptase inhibitors. No major resistance mutations were identified in the protease, although insertions of one and three amino acids were detected. Conclusions:The high frequency of URFs detected probably reflects a significant incidence of coinfections or superinfections with diverse viral strains, which increases the genetic complexity of the HIV-1 epidemic in West Africa. Monitoring of HIV-1 drug resistance might provide data on the implications of intersubtype recombination in response to antiretrovirals.

Increasing HIV-1 Genetic Diversity in Europe

ferred from the epidemiological features of the incipient epidemic in western Europe, with most AIDS cases being diagnosed among homosexual men, who frequently referred to traveling to the United States in previous years [1, 2], and from the initial association in this population between HIV-1 seropositivity and recent visits to the United States [3]. Consistent with these epidemiological data, European homosexual men are almost uniformlyinfected with subtype B [4, 5], first introduced among homosexual men in the United States, with phylogenetic trees supporting multiple introductions in western Europe [6]. The subtype B epidemic subsequently spread to injection drug users (IDUs) in western Europe, either from local epidemics among homosexual men or, in some countries, possibly from a variant originating among North American IDUs [4, 5, 7]. In addition, HIV-1 African dclades were also introduced early in the epidemic in some countries by African immigrants or European natives who had traveled to or lived in sub-Saharan Africa and were infected via heterosexual contact, with most of the earliest cases reported in Belgium and France in patients linked to Central Africa [2, 8-10]. In contrast to subtype B, in most western European countries propagation of African dclades has been limited to persons with close epidemiological links to Africa (with some exceptions, discussed below) [11-15]. In the former Soviet Union and in the republics that emerged from its disintegration in 1991, the initial propagation of HIV-1 was much more limited than in western Europe, affecting children in southern Russia (Elista and Rostov-onDon) who were infected during nosocomial outbreaks caused by a subtype G strain in 1988-1989 [16, 17], homosexual men infected with subtype B viruses [1719], and individuals infected via heterosexual contact harboring diverse African clades, mainly immigrants from sub-Saharan Africa or individuals epidemiologically linked to this area [16, 18]. The epidemiological picture of the former Soviet Union epidemic started to change dramatically in 1995 with the occurrence of successive outbreaks among IDUs, first in southern Ukraine [20], then in some areas of Russia [21, 22] and Belarus [23], and subsequently in other areas. The HIV-1 epidemic among IDUs in the former Soviet Union is largely dominated by a subtype A variant of monophyletic origin (variously designated as IDU-A, FSU-A, or AFSU) that is distinct from the major African variants [21, 23-26]; it was first introduced in the Ukrainian city of Odessa [27, 28], on the Black Sea, and has spread widely among IDUs to virtually all former Soviet Union countries, with a more recent secondary spread via heterosexual transmission [26, 29, 30]. Therefore, 2 clades dominate the HIV1 epidemic in Europe, subtype B and the Ansu variant, which, according to their geographical spread, divide Europe in 2 major areas: the subtype B area, extending from western Europe to the borders of the former Soviet Union, and the AFsU area, comprising former Soviet Union countries. However, there are exceptions to this division (figure 1). Thus, in former Soviet Union countries, subtype B is the major clade among homosexual men [25, 26, 29] and predominates in the Ukrainian city of Nikolayev on the Black Sea [31], where a subtype B variant was introduced among