Virtually full-length subtype F and F/D recombinant HIV-1 from Africa and South America

Tracing the relationship among HIV-1 sub-subtype F1 strains: a phylodynamic perspective

BACKGROUND

The human immunodeficiency virus type 1, F1 sub-subtype (HIV-1 F1) circulates in three continents: Africa, Europe, and South America. In Brazil, this sub-subtype co-circulates with subtypes B and C and several recombinant forms, mainly BF1 variants.

OBJECTIVES

This study aimed to reconstruct the dynamic history of HIV-1 F1 in Brazil.

METHODS

HIV-1 near full-length genome and pol gene nucleotide sequences available in public databases were assembled in two datasets (POL671 and NFLG53) to cover the largest number of F1 sub-subtype sequences. Phylodynamic and temporal analyses were performed.

FINDINGS

Two main strains of the F1 sub-subtype are circulating worldwide. The first (F1.I) was found among Brazilian samples (75%) and the second (F1.II) among Romanian (62%) and other European and African isolates. The F1 subtype epidemic in Brazil originated from a single entry into the country around 1970. This ancestral sample is related to samples isolated in European countries (France, Finland, and Belgium), which are possibly of African origin. Moreover, further migration (1998 CI: 1994-2003) of strains from Brazil to Europe (Spain and the UK) was observed. Interestingly, all different recombinant BF patterns found, even those from outside Brazil, present the same F1 lineage (F1.I) as an ancestor, which could be related to the acquisition of adaptive advantages for the recombinant progenies.

MAIN CONCLUSIONS

These findings are important for the understanding of the origin and dynamics of the F1 sub-subtype and a consequent better and greater understanding of the HIV-1 F1 and BF epidemic that still spreads from Brazil to other countries.

Impact of genotypic diversity on selection of subtype-specific drug resistance profiles during raltegravir-based therapy in individuals infected with B and BF recombinant HIV-1 strains

BACKGROUND

Current knowledge on HIV-1 resistance to integrase inhibitors (INIs) is based mostly on subtype B strains. This contrasts with the increasing use of INIs in low- and middle-income countries, where non-B subtypes predominate.

MATERIALS AND METHODS

HIV-1 drug resistance genotyping was performed in 30 HIV-1-infected individuals undergoing virological failure to raltegravir. Drug resistance mutations (DRMs) and HIV-1 subtype were characterized using Stanford HIVdb and phylogenetic analyses.

RESULTS

Of the 30 integrase (IN) sequences, 14 were characterized as subtype F (47%), 8 as subtype B (27%), 7 as BF recombinants (23%) and 1 as a putative CRF05_DF (3%). In 25 cases (83%), protease and reverse transcriptase (PR-RT) sequences from the same individuals confirmed the presence of different BF recombinants. Stanford HIVdb genotyping was concordant with phylogenetic inference in 70% of IN and 60% of PR-RT sequences. INI DRMs differed between B and F IN subtypes, with Q148K/R/H, G140S and E138K/A being more prevalent in subtype B (63% versus 0%, P = 0.0021; 50% versus 0%, P = 0.0096; and 50% versus 0%, P = 0.0096, respectively). These differences were independent of the time on raltegravir therapy or viral load at the time of genotyping. INI DRMs in subtype F IN genomes predicted a lower level of resistance to raltegravir and no cross-resistance to second-generation INIs.

CONCLUSIONS

Alternative resistance pathways to raltegravir develop in subtypes B and F IN genomes, with implications for clinical practice. Evaluating the role of HIV-1 subtype in development and persistence of mutations that confer resistance to INIs will be important to improve algorithms for resistance testing and optimize the use of INIs.

Defective HIV-1 proviruses produce novel protein-coding RNA species in HIV-infected patients on combination antiretroviral therapy

Despite years of plasma HIV-RNA levels <40 copies per milliliter during combination antiretroviral therapy (cART), the majority of HIV-infected patients exhibit persistent seropositivity to HIV-1 and evidence of immune activation. These patients also show persistence of proviruses of HIV-1 in circulating peripheral blood mononuclear cells. Many of these proviruses have been characterized as defective and thus thought to contribute little to HIV-1 pathogenesis. By combining 5'LTR-to-3'LTR single-genome amplification and direct amplicon sequencing, we have identified the presence of "defective" proviruses capable of transcribing novel unspliced HIV-RNA (usHIV-RNA) species in patients at all stages of HIV-1 infection. Although these novel usHIV-RNA transcripts had exon structures that were different from those of the known spliced HIV-RNA variants, they maintained translationally competent ORFs, involving elements of gag, pol, env, rev, and nef to encode a series of novel HIV-1 chimeric proteins. These novel usHIV-RNAs were detected in five of five patients, including four of four patients with prolonged viral suppression of HIV-RNA levels <40 copies per milliliter for more than 6 y. Our findings suggest that the persistent defective proviruses of HIV-1 are not "silent," but rather may contribute to HIV-1 pathogenesis by stimulating host-defense pathways that target foreign nucleic acids and proteins.

Close phylogenetic relationship between Angolan and Romanian HIV-1 subtype F1 isolates

BACKGROUND

Here, we investigated the phylogenetic relationships of the HIV-1 subtype F1 circulating in Angola with subtype F1 strains sampled worldwide and reconstructed the evolutionary history of this subtype in Central Africa.

METHODS

Forty-six HIV-1-positive samples were collected in Angola in 2006 and subtyped at the env-gp41 region. Partial env-gp120 and pol-RT sequences and near full-length genomes from those env-gp41 subtype F1 samples were further generated. Phylogenetic analyses of partial and full-length subtype F1 strains isolated worldwide were carried out. The onset date of the subtype F1 epidemic in Central Africa was estimated using a Bayesian Markov chain Monte Carlo approach.

RESULTS

Nine Angolan samples were classified as subtype F1 based on the analysis of the env-gp41 region. All nine Angolan sequences were also classified as subtype F1 in both env-gp120 and pol-RT genomic regions, and near full-length genome analysis of four of these samples confirmed their classification as "pure" subtype F1. Phylogenetic analyses of subtype F1 strains isolated worldwide revealed that isolates from the Democratic Republic of Congo (DRC) were the earliest branching lineages within the subtype F1 phylogeny. Most strains from Angola segregated in a monophyletic group together with Romanian sequences; whereas South American F1 sequences emerged as an independent cluster. The origin of the subtype F1 epidemic in Central African was estimated at 1958 (1934-1971).

CONCLUSION

"Pure" subtype F1 strains are common in Angola and seem to be the result of a single founder event. Subtype F1 sequences from Angola are closely related to those described in Romania, and only distantly related to the subtype F1 lineage circulating in South America. Original diversification of subtype F1 probably occurred within the DRC around the late 1950s.

Different sliding window sizes and inappropriate subtype references result in discordant mosaic maps and breakpoint locations of HIV-1 CRFs

Different sliding window sizes and inappropriate subtype references are often selected for identifying HIV-1 recombination, which results in discordant recombination maps even for the same HIV-1 recombinant and affects the tracking of the epidemic of HIV-1 recombinants. Here, we re-analyzed 11 previously characterized HIV-1 CRFs using SimPlot software (version 3.5) with several sliding window sizes (200, 250, 300, 350 and 400 nt), moving in a step of 10 nt, respectively. We found that the crossovers determined under 250 and 350 nt windows, especially under 300 nt window are significantly closer to hypothetical breakpoint than crossovers obtained under 200 and 400 nt windows (P < 0.01). These suggest that 300 nt window is a preferential selection for HIV-1 recombination analysis. In addition, instead of one bootscan analysis, three bootscanning plots with sliding window sizes of 250, 300 and 350 nt are also recommended. The comparison between crossovers determined under different moving steps showed that a small moving step (e.g. 10 nt) is better than a larger step (e.g. 50 nt) (P < 0.05), suggesting that a small moving step should be used in bootscan analysis. Moreover, we found that inappropriate usage of subtype references in bootscan analysis resulted in misleading recombination maps. HIV-1 strains prevailing in the same geographic areas with HIV-1 inter-subtype recombinants are believed to have chance to participate in recombination events. When HIV-1 reference strains from recombinant-prevailing areas were applied, identified recombination patterns were well supported by phylogenetic analyses. So, in bootscan analysis, HIV-1 subtype references should be selected from recombinant-prevailing areas.

Description of the first full-length HIV type 1 subtype F1 strain in Argentina: implications for the origin and dispersion of this subtype in South America

HIV-1 subtype F1 in South America is mainly found as part of diverse BF1 recombinant forms and only five full-length "pure" F1 strains from Brazil were characterized to date. In the present study we describe the first near full-length sequence of a nonrecombinant F1 HIV-1 strain from Argentina, and explore the epidemiological history of this subtype in South America. Three separate phylogenetic analyses were carried out: with all available F1 full-length sequences, with concatenated F1 sequences contained in F1 and BF1 strains, and with partial F1 env sequences derived from worldwide strains. All analyses were consistent in showing a local origin of the newly reported Argentine subtype F1 strain, and a common ancestry of the South American subtype F1 sequences, present either in pure or recombinant genomes. By coalescent analysis, the onset date of the HIV-1 subtype F1 epidemic in South America was estimated to be around the late 1970s. The results indicate for the first time that nonrecombinant F1 HIV-1 strains are present in Argentina, and suggest that the subtype F1 epidemic in South America was initiated by the introduction of a very small group of genetically related viruses during late 1970s.

Circulating and unique recombinant forms of HIV type 1 containing subsubtype A2

HIV-1 strains containing subsubtype A2 are relatively rare in the pandemic but have been repeatedly identified in Kenya, where candidate vaccines based in part on subtype A, but not A2 strains, may be evaluated. Among the most recent is CRF16_A2D, a circulating recombinant form (CRF) whose prototypes are complete or partial HIV-1 sequences from Kenya, Korea, and Argentina. Using samples from blood bank discards in Kenya and complete genome sequencing, this report further documents CRF16_A2D and related recombinants and identifies a second CRF, CRF21_A2D. The two A2-containing CRFs, and two recombinants related to CRF16_A2D, share common structural elements but appear to have been independently derived. Concerted selection may have influenced the emergence and spread of certain A2-containing strains in Kenya. The second complete subtype C sequence from Kenya is also reported here. Monitoring of A2-containing recombinants and subtype C strains, both relatively rare in Kenya, may be informative in the course of cohort development and evaluation of candidate vaccines.

Worldwide molecular epidemiology of HIV

Human immunodeficiency virus (HIV) is the worldwide disseminated causative agent of acquired immunodeficiency syndrome (AIDS). HIV is a member of the Lentivirus genus of Retroviridae family and is grouped in two types named HIV-1 and HIV-2. These viruses have a notable ability to mutate and adapt to the new conditions of human environment. A large incidence of errors at the transcriptional level results in changes on the genetic bases during the reproductive cycle. The elevated genomic variability of HIV has carried important implications for the diagnosis, treatment and prevention as well as epidemiologic investigations. The present review describes important definitions and geographical distribution of subtypes, circulating recombinant forms and other genomic variations of HIV. The present study aimed at leading students of Biomedical Sciences and public health laboratory staff guidance to general and specific knowledge about the genomic variability of the HIV.

Readily acquired secondary infections of human and simian immunodeficiency viruses following single intravenous exposure in non-human primates

Accumulating evidence suggests that exposed individuals may acquire multiple human immunodeficiency virus (HIV) infections more frequently than originally believed. As a result, circulating recombinant forms of HIV are emerging that are of particular concern in the AIDS epidemic and HIV vaccine development efforts. The aim of this study was to determine under what conditions secondary or superinfections of HIV or simian immunodeficiency virus (SIV) may be acquired under controlled settings in well-defined, non-human primate models. Retrospective analysis of macaques that had acquired apparent immunity upon infection with a defined attenuated SIV(mac) strain revealed that eight out of eight animals that were secondarily exposed to a new virus variant became infected with the new virus strain, but at low levels. Interestingly, similarly high frequencies of secondary infections were observed after early (4 months), as well as late (5 years), exposure following primary infection. As possible causes of susceptibility to secondary infections, perturbations in the immune system associated with exacerbated infections were then investigated prospectively. Results revealed that short-term immune-suppression therapy did not increase susceptibility to secondary infections. Taken together, data suggested that neither early- nor late-exposure immune-suppressive events following primary infection accounted for the observed high incidence of secondary infections. With HIV-1, the question of whether secondary infections with very closely related viral variants could occur in the chimpanzee model was addressed. In both animal models, secondary infections were confirmed, notably with relatively closely related SIV(mac) or HIV-1 strains, following a single exposure to the secondary virus strain. These findings reveal that secondary lentiviral infections may be acquired readily during different stages of primary infection, in contrast to co-infections, which are acquired at the moment of initial infection.

Molecular-based methods for quantifying HIV viral load

Viral load quantitation has become the major prognostic marker for disease prognosis and outcome of antiretroviral therapy in the treatment of HIV-infected individuals. The three major methodologies for viral load quantitation: the reverse transcriptase-polymerase chain reaction (RT-PCR; Amplicor HIV-1 Monitor Test, Roche Diagnostic Systems, Pleasanton, CA), the nucleic acid sequence-based amplification (NASBA; NucliSens HIV-1 QT Test, Organon Teknika, Bostel, The Netherlands); and a signal amplification methodology termed branchedchain DNA (bDNA) technique (Quantiplex HIV-1 RNA test, Bayer Diagnostics, Emeryville, CA) are briefly reviewed here.

Human immunodeficiency virus type 1 superinfection was not detected following 215 years of injection drug user exposure

Evidence for human immunodeficiency virus type 1 (HIV-1) superinfection was sought among 37 HIV-1-positive street-recruited active injection drug users (IDUs) from the San Francisco Bay area. HIV-1 sequences from pairs of samples collected 1 to 12 years apart, spanning a total of 215 years of exposure, were generated at p17 gag, the V3-V5 region of env, and/or the first exon of tat and phylogenetically analyzed. No evidence of HIV-1 superinfection was detected in which a highly divergent HIV-1 variant emerged at a frequency >20% of the serum viral quasispecies. Based on the reported risk behavior of the IDUs and the HIV-1 incidence in uninfected subjects in the same cohort, a total of 3.4 new infections would have been expected if existing infection conferred no protection from superinfection. Adjusted for risk behaviors, the estimated relative risk of superinfection compared with initial infection was therefore 0.0 (95% confidence interval, 0.00, 0.79; P = 0.02), indicating that existing infection conferred a statistically significant level of protection against superinfection with an HIV-1 strain of the same subtype, which was between 21 and 100%.

Evolution and diversity of HIV-1 in Africa--a review

The HIV/AIDS pandemic represents a major development crisis for the African continent, which is the worst affected region in the world. Currently, almost 30 of the 42 million people infected with HIV worldwide live in Africa. AIDS in humans is caused by two lentiviruses, HIV-1 and HIV-2, which entered the human population by zoonotic transmissions from at least two different African primate species. Extensive phylogenetic analyses of partial and full-length genome sequences have helped to gain insights into the evolutionary biology and population dynamics of HIV. One of the major characteristics of HIV is its rapid evolution, which has resulted in substantial genetic diversity amongst different isolates, the majority of which are represented in Africa. Genetic variability of HIV and any consequent phenotypic variation poses a significant challenge to disease control and surveillance in different geographic regions of Africa. This review focuses on the origins and evolution of HIV, current classification and diversity of HIV isolates in Africa and provides an extensive account of the geographic distribution of HIV types, groups, and subtypes in each of the 49 African countries. Numerous epidemiological studies have provided a picture of HIV distribution patterns in most countries in Africa, and these show increasing evidence of the importance of HIV-1 recombinants. In particular, this review highlights that our current understanding of HIV distribution in Africa is incomplete and inadequately represents the diversity of the virus, and underscores the need for ongoing surveillance.

Near full-length genome characterization of an HIV type 1 CRF05_DF virus from Spain

We report the near full-length sequence characterization of a HIV-1 DF intersubtype recombinant virus from Spain, X492, directly amplified from peripheral blood mononuclear cells' DNA. This isolate shares an identical mosaic structure and exhibits consistent phylogenetic clustering along the genome with VI961, a previously characterized DF recombinant virus. By contrast, VI1310, which may represent the same recombinant form as VI961 (CRF05_DF), is only partially homologous to VI961 and X492. Of three additional DF recombinant viruses previously characterized in gag-pol, only one, VI1267, clusters uniformly with VI961 and X492; the other two branch separately in a segment of pol. These results allow us to define an HIV-1 circulating recombinant form (CRF05_DF), characterized in near full-length genomes of two isolates (VI961 and X492) and in partial gag-pol sequences of a third virus (VI1267). Three other reported DF recombinant viruses, including the fully sequenced VI1310, exhibit incomplete homology to VI961 and X492.

Identification of two CRF11-cpx genomes and two preliminary representatives of a new circulating recombinant form (CRF13-cpx) of HIV type 1 in Cameroon

Recombination is an efficient mechanism of HIV-1 to generate genetic variability. Some of the recombinant forms of HIV-1 that have been described are of epidemic importance, and they are referred to as circulating recombinant forms (CRFs). In this study, we characterized four HIV-1 isolates from Cameroon that had previously been classified as subtype J in the protease gene and as subtype A in the env C2-V5 region. Analyses of the nearly complete genomes revealed that two of the samples (95CM-1816 and 96CM-4496) had the same recombinant structure as CRF11-cpx. The two remaining samples (96CM-1849 and 96CM-4164) constituted a new recombinant virus variant with genomic regions identified as subtypes A, G, J, and CRF01-AE. This mosaic virus structure was found in two individuals who had no direct epidemiological relationship, and may thus represent a new CRF. The fragments that were classified as subtype J in the new recombinant form were more related to subtype J regions of the CRF11-cpx sequences than to the reference strains of subtype J. The complex structures of CRF11-cpx and our new recombinant form, which are both the result of at least four recombination events, exemplify the coming difficulties in characterizing the internal relationships and origins of future recombinant HIV-1 strains. The new recombinant structure has been designated CRF13-cpx in the Los Alamos HIV Sequence Database.

Prevalence and origin of HIV-1 group M subtypes among patients attending a Belgian hospital in 1999

HIV-1 group M strains are usually subtyped based on gag and/or env gene sequences. In our lab, part of the pol gene sequence was available in order to determine the genotypic anti-HIV drug resistance profile. To estimate the prevalence of the different HIV-1 subtypes in patients visiting the University Hospitals in Leuven in 1999 and for whom a genotypic drug resistance test was needed, we tried to use the pol sequence for subtyping. Recombination was investigated by similarity plots and bootscanning and subtyping was performed by phylogenetic analysis. The overall region spanning the entire protease and 747 nucleotides of the reverse transcriptase proved very suitable for subtyping, although there was a low phylogenetic signal at the beginning of the reverse transcriptase (nucleotides 0-250), as we demonstrated by likelihood mapping. Of the 41 samples analyzed, 21 belonged to subtype B. Of the other 20 non-B strains, 9 belonged to subtype C, 2 to subtype D and 1 to subtype A, G, H and J, respectively, 3 were CRF_02 (Circulating Recombinant Form), 1 was recombinant with a novel breakpoint and 1 sample was untypable. Although subtype B is still the most prevalent subtype in Belgium, it seems to be responsible for only half of the infections in this study. We could also document that the prevalence of subtype C is high in the Belgian native patients, especially among the heterosexually infected population. This could possibly be an indication for an epidemic spread of HIV-1 subtype C in Belgium, as for one third of these patients, no link to an endemic region could be found. The other non-B subtypes and the recombinants are mainly introduced by immigrants or by Belgian citizens traveling abroad.

CRF06-cpx: a new circulating recombinant form of HIV-1 in West Africa involving subtypes A, G, K, and J

Phylogenetic analysis of numerous strains of HIV-1 isolated from diverse geographic origins has revealed three distinct groups of HIV-1: groups M, N, and O. Within group M, subtypes, sub-subtypes and circulating recombinant forms (CRFs) exist. Recently, two near-full-length genomes of similar complex mosaic viruses containing fragments of subtypes A, G, I, and J were described in patients from Burkina Faso (BFP-90) and Mali (95ML-84). Here, we report on the characterization of two additional full-length genome sequences with similar mosaic structure in epidemiologically unlinked individuals from Senegal (97SE-1078) and Mali (95ML-127). Phylogenetic and recombinant analysis confirmed that the previously described strains, BFP-90 and 95ML-84, were indeed a new CRF of HIV-1, which we can now designate as CRF06-cpx. This new CRF fits the complex (cpx) designation, because four different subtypes (A, G, K, and J) were involved in the mosaic genome structure. The fragment in the pol gene, which was initially characterized as unknown in the BFP-90 strain and subsequently as subtype I in the 95ML-84 strain, is now, with the recent description of the new K subtype, clearly identified as subtype K. CRF06-cpx circulates in Senegal, Mali, Burkina Faso, Ivory Coast, and Nigeria, although the exact prevalence remains to be determined. Importantly, this new variant has also been documented on other continents (Europe [France] and Australia), showing that these viruses are spreading not only locally but globally.

Comparative analysis of HIV-1 viral load assays on subtype quantification: Bayer Versant HIV-1 RNA 3.0 versus Roche Amplicor HIV-1 Monitor version 1.5

Quantification of HIV-1 subtypes is essential for appropriate clinical management. Whereas viral load assays were initially developed to accurately quantify subtype B, the recent worldwide spread of non-B subtypes and the introduction of treatment programs in regions with non-B subtypes have prompted adaptations of these assays. The Bayer Versant HIV-1 RNA 3.0 Assay (branched DNA [bDNA] 3.0) and the Roche Amplicor HIV-1 Monitor version 1.5 (Amplicor 1.5) assays are reported to quantify all subtypes in group M; however, evaluation of performance characteristics remains limited. In this study, we evaluated the accuracy and reliability of bDNA 3.0 and Amplicor 1.5 on multiple serially diluted viral isolates from HIV-1 group M, subtypes A through F. Testing was conducted on both assay systems in two independent laboratories. Comparative pansubtype quantification from regression analysis showed that quantification by bDNA 3.0 was approximately 0.3 log-fold lower than that by Amplicor 1.5. Comparative pansubtype accuracy analysis showed data points more closely distributed about their respective regression lines and thus showing greater reliability by bDNA 3.0 than by Amplicor 1.5.

Human immunodeficiency virus type 1 reverse-transcriptase and protease subtypes: classification, amino acid mutation patterns, and prevalence in a northern California clinic-based population

Phylogenetic analysis of the reverse transcriptase (RT) and protease of 117 published complete human immunodeficiency virus (HIV) type 1 genome sequences demonstrated that these genes cluster into distinct subtypes. There was a slightly higher proportion of informative sites in the RT (40.4%) than in the protease (34.8%; P= .03). Although most variation between subtypes was due to synonymous nucleotide substitutions, several subtype-specific amino acid patterns were observed. In the protease, the subtype-specific variants included 7 positions associated with drug resistance. Variants at positions 10, 20, 36, and 82 were more common in non-B isolates, whereas variants at positions 63, 77, and 93 were more common in subtype B isolates. In the RT, the subtype-specific mutations did not include positions associated with anti-retroviral drug resistance. RT and protease sequences from 2246 HIV-infected persons in northern California were also examined: 99.4% of the sequences clustered with subtype B, whereas 0.6% clustered with subtype A, C, or D.

Evidence of two distinct subsubtypes within the HIV-1 subtype A radiation

Members of HIV-1 group M are responsible for the vast majority of AIDS cases worldwide and have been classified on the basis of their phylogenetic relationships into nine roughly equidistant clades, termed subtypes. Although there are no known phenotypic correlates for these genotypes, the disproportionate spread of certain of these lineages has been taken to indicate that subtype-specific biological differences may exist. The subtype nomenclature thus remains an important molecular epidemiological tool with which to track the course of the group M pandemic. In this study, we have characterized HIV-1 strains described previously as unusual subtype A variants on the basis of partial sequence analysis. Six such strains from Cyprus (CY), South Korea (KR), and the Democratic Republic of Congo (CD) were PCR amplified from infected cell culture or patient PBMC DNA, cloned, and sequences in their entirety (94CY017, 97KR004, 97CDKTB48, and 97CDKP58) or as half genomes (97CDKS10 and 97CDKFE4). Distance and phylogenetic analyses showed that four of these viruses (94CY017, 97CDKTB48, 97CDKFE4, and 97CDKS10) were closely related to each other, but quite divergent from all other HIV-1 strains, except for subtype A viruses, which represented their closest relatives. In phylogenetic trees from gag, pol, env, and nef regions, the four newly characterized HIV-1 strains formed a distinct sister clade to subtype A, which was as closely related to subtype A as subsubtypes F1 and F2 are to each other. According to current nomenclature rules, this defines a subsubtype, which we have tentatively termed A2. The two other viruses, 97KR004 and 97CDKP58, as well as a full-length HIV-1 sequence from the sequence database (ZAM184), were found to represent complex A2/D, A2/G, and A2/C recombinants, respectively. These results indicate that HIV-1 subtype A is composed of two subsubtypes (A1 and A2), both of which appear to have a widespread geographic distribution. The A2 viruses described here represent the first reference reagents for this new group M lineage.

A complex human immunodeficiency virus type 1 A/G/J recombinant virus isolated from a seronegative patient with AIDS from Benin, West Africa

A human immunodeficiency virus type 1 (HIV-1(B76)) originating from Benin (West Africa) was isolated and characterized. The patient had severe clinical AIDS and presented an unusual serological profile. Only one out of five different detection assays was able to demonstrate the presence of antibodies to HIV, whereas confirmatory assays remained indeterminate. In contrast, both plasma viral load and p24 antigen level were unusually high. HIV-1 infection was proved by viral RNA and proviral DNA amplification. HIV-1(B76) partially purified lysate reacted strongly with all anti-HIV-1-positive sera from the region but B76 plasma did not react with subtype A control viral antigen. This patient is likely to have had severe acquired immune dysfunction explaining her lack of immunological reactivity. Phylogenetic analysis of the genome identified a complex HIV-1 A/G/J recombinant. The gag and pol genes, and the majority of nef,are characteristic of subtype A; the gag/pol junction, the 3' end of pol, vpu and env genes were characteristic of subtype G; vif, vpr and the 5' end of nef were subtype J. In addition, part of the HIV-1(B76) genome had considerable sequence similarity with the previously described CRF06 cpx (BFP90) isolate. HIV-1(B76) did not exhibit any remarkable replication properties or cell tropism in vitro.

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

BACKGROUND

The 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.

METHODS

Protease 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.

RESULTS

Ten 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).

CONCLUSIONS

Non-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.

Evolutionary dynamics of the SGM transposon family in the Drosophila obscura species group

SGM (Drosophila subobscura, Drosophila guanche, and Drosophila madeirensis) transposons are a family of transposable elements (TEs) in Drosophila with some functional and structural similarities to miniature inverted-repeat transposable elements (MITEs). These elements were recently active in D. subobscura and D. madeirensis (1-2 MYA), but in D. guanche (3-4 MYA), they gave rise to a species-specifically amplified satellite DNA making up approximately 10% of its genome. SGM elements were already active in the common ancestor of all three species, giving rise to the A-type specific promoter section of the P:-related neogene cluster. SGM sequences are similar to elements found in other obscura group species, such as the ISY elements in D. miranda and the ISamb elements in Drosophila ambigua. SGM elements are composed of different sequence modules, and some of them, i.e., LS and LS-core, are found throughout the Drosophila and Sophophora radiation with similarity to more distantly related TEs. The LS-core module is highly enriched in the noncoding sections of the Drosophila melanogaster genome, suggesting potential regulatory host gene functions. The SGM elements can be considered as a model system elucidating the evolutionary dynamics of mobile elements in their arms race with host-directed silencing mechanisms and their evolutionary impact on the structure and composition of their respective host genomes.