Los Alamos HIV Sequence Database Research Articles

Universal Tre (uTre) recombinase specifically targets the majority of HIV-1 isolates.

Current drugs against HIV can suppress the progression to AIDS but cannot clear the patient from the virus. Because of potential side effects of these drugs and the possible development of drug resistance, finding a cure for HIV infection remains a high priority of HIV/AIDS research. We recently generated a recombinase (termed Tre) tailored to efficiently eradicate the provirus from the host genome of HIV-1 infected cells by specifically targeting a sequence that is present in the long terminal repeats (LTRs) of the viral DNA [1]. In vivo analyses in HIV-infected humanized mice demonstrated highly significant antiviral effects of Tre recombinase [2]. However, the fact that Tre recognizes a particular HIV-1 subtype A strain may limit its broad therapeutic application. To advance our Tre-based strategy towards a universally efficient cure, we have engineered a new, universal recombinase (uTre) applicable to the majority of HIV-1 infections by the various virus strains and subtypes. We employed the search tool SeLOX [3] in order to find a well-conserved HIV-1 proviral sequence that could serve as target site for a universal Tre from sequences compiled in the Los Alamos HIV Sequence Database. We selected a candidate (termed loxLTRu) with a mean conservation rate of 94% throughout the major HIV-1 subtype groups A, B and C. We applied loxLTRu as substrate in our established substrate-linked protein evolution (SLiPE) process [4] and evolved the uTre recombinase in 142 evolution cycles. Highly specific enzymatic activity on loxLTRu is demonstrated for uTre in both Escherichia coli and human cells. Naturally occurring viral variants with single mutations within the loxLTRu sequence are also shown to be efficiently targeted by uTre, further increasing the range of applicability of the recombinase. Potential off-target sites in the human genome are not recombined by uTre. Furthermore, uTre expression in primary human T cells shows no obvious Tre-related cytopathic or genotoxic effects. Finally, uTre expressing mice show no undesired phenotypes during their normal lifespan. We have developed a broad-range HIV-1 LTR specific recombinase that has the potential to be effective against the vast majority of HIV-1 strains and to cure HIV-1 infected cells from the infection. These results strongly encouraged us in our confidence that a Tre recombinase-mediated HIV eradication strategy may become a valuable component of a future therapy for HIV-infected patients.

Intercontinental dispersal of HIV-1 subtype B associated with transmission among men who have sex with men in Japan.

Transmission clusters of HIV-1 subtype B uniquely associated with the epidemic among men who have sex with men (MSM) in East Asia have recently been identified. Using the Los Alamos HIV sequence database and the UK HIV drug resistance database, we explored possible links between HIV MSM epidemics in East Asia and the rest of the world by using phylogenetic and molecular clock analyses. We found that JP.MSM.B-1, a subtype B MSM variant that accounts for approximately one-third of the infections among Japanese MSM, was detected worldwide, in the United Kingdom (n=13), mainland China (n=3), the United States, Germany, Canada, and Taiwan (n=1 each). Interestingly, 10 United Kingdom samples plus two from Germany and the United States formed a distinct monophyletic subgroup within JP.MSM.B-1. The estimated divergence times of JP.MSM.B-1 and the latter subgroup were ∼1989 and ∼1999, respectively. These dates suggest that JP.MSM.B-1 was circulating for many years in Japan among MSM before disseminating to other countries, most likely through global MSM networks. A significant number of other Asian MSM HIV lineages were also detected in the UK HIV drug resistance database. Our study provides insight into the regional and global dispersal of Asian MSM HIV lineages. Further study of these strains is warranted to elucidate viral migration and the interrelationship of HIV epidemics on a global scale. We previously identified several transmission clusters of HIV-1 subtype B uniquely associated with the epidemic among men who have sex with men (MSM) in East Asia. Using the Los Alamos HIV sequence database and the UK HIV drug resistance database, we explored the possible interplay of HIV MSM epidemics in the different geographic regions and found previously unrecognized interrelationships among the HIV-1 epidemics in East Asia, the United Kingdom, and the rest of the world. Our study provides insight into the regional and global dispersal of Asian MSM HIV lineages and highlights the importance of strengthening HIV monitoring efforts and the need for implementing effective control measures to reduce HIV transmission on a global scale.

Reconstituting the epidemic history of mono lineage of HIV-1 CRF01_AE in Guizhou province, Southern China

Guizhou province, located between border provinces and Central province of China, plays a crucial role in the transmission of HIV-1, implying it is important to monitor the epidemic of HIV-1 in this region. Available HIV-1 infected patients’ plasma (n=78) were collected from Tongren city, Eastern Guizhou. Full-length gag, partial pol and env gene sequences were amplified and analyzed using phylogenetic, recombinant and Bayesian molecular clock approaches. Phylogenetic and recombinant analyses showed that CRF01_AE predominated among injecting drug users and heterosexuals in Tongren city with 85.9% proportion, it was followed by B′ (5.1%), CRF07_BC (3.8%), CRF08_BC (3.8%), and B (1.3%). Moreover, 98.5% of CRF01_AE strains belonged to the distinct lineage CRF01_AE-v previously found in Guangxi province. To infer the most probable origin of CRF01_AE-v in Guizhou province, we download all available full length of CRF01_AE gag, pol and env gene region sequences from China in Los Alamos HIV sequence database. Phylodynamic and phylogeographic analyses revealed that the expanding CRF01_AE-v epidemic in Guizhou province was the result of local epidemic driven by multiple independent introductions of CRF01_AE-v strains from Guangxi province in early 2000s. High prevalence of CRF01_AE in Guizhou province may bridge the epidemic to Central China. It provides a new insight for the understanding of HIV-1 epidemic in Guizhou province and makes the evolutionary history of CRF01_AE in China more intact.

HIV gp120 H375 Is Unique to HIV-1 Subtype CRF01_AE and Confers Strong Resistance to the Entry Inhibitor BMS-599793, a Candidate Microbicide Drug

BMS-599793 is a small molecule entry inhibitor that binds to human immunodeficiency virus type 1 (HIV-1) gp120, resulting in the inhibition of CD4-dependent entry into cells. Since BMS-599793 is currently considered a candidate microbicide drug, we evaluated its efficacy against a number of primary patient HIV isolates from different subtypes and circulating recombinant forms (CRFs) and showed that activity varied between ∼3 ρM and 7 μM at 50% effective concentrations (EC(50)s). Interestingly, CRF01_AE HIV-1 isolates consistently demonstrated natural resistance against this compound. Genotypic analysis of >1,600 sequences (Los Alamos HIV sequence database) indicated that a single amino acid polymorphism in Env, H375, may account for the observed BMS-599793 resistance in CRF01_AE HIV-1. Results of site-directed mutagenesis experiments confirmed this hypothesis, and in silico drug docking simulations identified a drug resistance mechanism at the molecular level. In addition, CRF01_AE viruses were shown to be resistant to multiple broadly neutralizing monoclonal antibodies. Thus, our results not only provide insight into how Env polymorphisms may contribute to entry inhibitor resistance but also may help to elucidate how HIV can evade some broadly neutralizing antibodies. Furthermore, the high frequency of H375 in CRF01_AE HIV-1, and its apparent nonoccurrence in other subtypes, could serve as a means for rapid identification of CRF01_AE infections.

Identification of a Novel HIV Type 1 Circulating Recombinant Form (CRF52_01B) in Southeast Asia

Thirty HIV-1 URF_01AE/ B' complete or nearly full-length genome sequences sampled within Southeast Asia were obtained from the Los Alamos HIV Sequence Database. Phylogenetic and recombinant analyses revealed that three sequences indeed displayed the identical recombinant structure. Of note, the three subjects, harboring novel CRF01_AE/B recombinants, did not have apparent epidemiological linkage. They fulfilled the criteria for the designation of a new circulating recombinant form (CRF) and constituted the 52nd CRF identified in the worldwide HIV-1 pandemic. In this chimera, two short subtype B segments were inserted into a backbone of CRF_01AE. The breakpoints corresponded to HXB2 nucleotide positions 2930, 3251, 8521, and 9004 approximately. This CRF is the first one identified by neatening and analyzing the sequences already presented in the Los Alamos HIV Sequence Database. This indicates that we should pay attention not only to explicit subtype sequences but also to those classified as a unique recombinant form (URF) so far.

Low prevalence of transmitted K65R and other tenofovir resistance mutations across different HIV‐1 subtypes: implications for pre‐exposure prophylaxis

IntroductionTenofovir-containing regimens have demonstrated potential efficacy as pre-exposure prophylaxis (PrEP) in preventing HIV-1 infection. Transmitted drug resistance mutations associated with tenofovir, specifically the reverse transcriptase (RT) mutation K65R, may impact the effectiveness of PrEP. The worldwide prevalence of transmitted tenofovir resistance in different HIV-1 subtypes is unknown.MethodsSequences from treatment-naïve studies and databases were aggregated and analyzed by Stanford Database tools and as per the International AIDS Society (IAS-USA) resistance criteria. RT sequences were collected from GenBank, the Stanford HIV Sequence Database and the Los Alamos HIV Sequence Database. Sequences underwent rigorous quality control measures. Tenofovir-associated resistance mutations included K65R, K70E, T69-insertion and ≥3 thymidine analogue mutations (TAMs), inclusive of M41L or L210W.ResultsA total of 19,823 sequences were evaluated across diverse HIV-1 subtypes (Subtype A: 1549 sequences, B: 9783, C: 3198, D: 483, F: 372, G: 594, H: 41, J: 69, K: 239, CRF01_AE: 1797 and CRF02_AG: 1698). Overall, tenofovir resistance prevalence was 0.4% (n=77/19,823, 95% confidence interval or CI: 0.3 to 0.5). K65R was found in 20 sequences (0.1%, 95% CI: 0.06 to 0.15). Differences in the prevalence of K65R between HIV-1 subtypes were not statistically significant. K70E and ≥3 TAMs were found in 0.015% (95% CI: 0.004 to 0.04) and 0.27% (95% CI: 0.2 to 0.4) of sequences, respectively.ConclusionsPrevalence of transmitted K65R and other tenofovir resistance mutations across diverse HIV-1 subtypes and recombinants is low, suggesting minimal effect on tenofovir-containing PrEP regimens.

Rapid Expansion of a HIV-1 Subtype F Cluster of Recent Origin Among Men Who Have Sex With Men in Galicia, Spain

Rapid Expansion of a HIV-1 Subtype F Cluster of Recent Origin Among Men Who Have Sex With Men in Galicia, Spain

Genetic Analysis of a UNAIDS HIV Type 1 from Brazil Revealed an Unexpected Recombination Pattern

Genetic Analysis of a UNAIDS HIV Type 1 from Brazil Revealed an Unexpected Recombination Pattern

QUASI analysis of host immune responses to Gag polyproteins of human immunodeficiency virus type 1 by a systematic bioinformatics approachThis paper is one of a selection of papers published in this special issue entitled “Second International Symposium on Recent Advances in Basic, Clinical, and Social Medicine” and has undergone the Journal's usual peer review process.

There is a consensus that Gag-specific cytotoxic T lymphocyte (CTL) response plays a key role in the immune control of human immunodeficiency virus type 1 (HIV-1) infection. In this study, we analyzed all currently available gag sequences in the Los Alamos HIV sequence database and identified positive selection (PS) sites likely restricted by the host immune responses. We found that between 23.4% and 47.4% of PS sites were shared by clades A, B, and C of Gag, indicating similar positive selection pressure on Gag in different subtypes of HIV-1. Furthermore, a significant correlation was observed between the combined CTL and antibody responses and PS sites. The Gag regions of free from PS contained 9 CTL epitopes restricted by 11 HLA class I alleles associated with disease progression to acquired immune deficiency syndrome (AIDS). These analyses provide information important for the identification of cross-clade epitopes and development of a global HIV-1 vaccine.

HIV-2 CRF01_AB: First Circulating Recombinant Form of HIV-2

Five HIV-2-seropositive cases were recently identified in Japan, outside the HIV-2 endemic area of West Africa. To clarify the molecular epidemiology of HIV-2 in Japan, we analyzed sequences of these cases in detail. HIV-2 genetic groups were determined by gag and env sequences. For suspected recombinant isolates, the genetic structure was determined by full-length genomic analyses. To understand the history and evolution of HIV-2 recombinant isolates, we estimated the time of most recent common ancestor by Bayesian Markov chain Monte Carlo method. Three isolates were determined as recombinants of groups A and B, and their mosaic genome structures were identical with that of 7312A, a recombinant isolate reported in 1990 from Côte d'Ivoire. Our 3 isolates and 7312A fulfilled the criteria for determining a circulating recombinant form (CRF). These isolates were verified by the Los Alamos HIV sequence database as the first CRF of HIV-2, HIV-2 CRF01_AB. The mean time of most recent common ancestor of CRF01_AB was estimated as between 1964 and 1973, several decades after the estimated emergence of HIV-2. We recently identified HIV-2 CRF01_AB cases in Japan. This ectopic observation of the virus outside its original endemic area suggests an ongoing global spread of HIV-2 CRF01_AB.

Predicted co-receptor tropism and sequence characteristics of China HIV-1 V3 loops: implications for the future usage of CCR5 antagonists and AIDS vaccine development

The co-receptor tropism of any given HIV-1 isolate is closely associated with the progression of AIDS. Understanding the co-receptor tropism and genetic diversity of circulating HIV-1 strains is critical for AIDS treatment and vaccine development. All available China HIV-1 V3 sequences with known subtypes/circulating recombinant forms (CRFs) and transmission routes were retrieved from the Los Alamos HIV Sequence Database. HIV-1 co-receptor tropism was predicted using online tool HIV-1 PhenoPred. All C/CRF07_BC/CRF08_BC strains appeared to use CCR5 for cell entry (R5 strains), while 61.1% of subtype B and 38.7% of CRF01_AE were also R5, indicating a higher prevalence of R5 (76.9%) than X4. The prevalence of R5 remained relatively stable over the different sample years regardless of C/CRF07_BC/CRF08_BC, B, or CRF01_AE subtypes. The co-receptor usage of HIV-1 appeared to be associated with the different subtypes, rather than transmission route. Furthermore, the V3 sequences of C/CRF07_BC/CRF08_BC were more genetically homogeneous relative to both subtypes B and CRF01_AE. The higher prevalence of R5 and higher level of homogeneity of V3 sequences in C/CRF07_BC/CRF08_BC suggest that CCR5 antagonists will be promising drugs for future AIDS treatment in China, and that circulating R5 strains are valuable candidates for AIDS vaccine development.

Subtype and sequence analysis of HIV-1 strains in Heilongjiang Province

Human immunodeficiency virus (HIV-1) is divided into two types, HIV-1 (groups M, N and O) and HIV-2. Heilongjiang Province located in the northeast of China, and the feature of the subtype distribution and sequence characteristics of HIV-1 strains prevalent in Heilongjiang Province is still uncertain. The aim of this study was to investigate the subtype distribution and genetic characteristics of HIV-1 strains in one hospital in Heilongjiang Province. HIV-1 env gene was amplified by nested-PCR from peripheral blood mononuclear cells (PBMCs) obtained from 19 HIV-1 seropositive individuals in Heilongjiang Province. The C2-V3 region was sequenced. Aligned the nucleotide sequence of 19 samples with CLUSTAL W (BioEdit) software, results were acquired and used for phylogenetic tree analysis after artificial adjustment. Reference sequence, downloaded from Los Alamos HIV Sequence Database, was used to identify the subtype of obtained sequence. Genetic distance between sequences was assessed using the software MEGA 3.1 Kimura 2-parameter, and the Phylogenetic tree was reestablished with Neighbor-Joining method. Phylogenetic tree analysis showed that 19 Heilongjiang strains clustered closely to subtype B strain from Thailand and were far from other international subtype reference strains. Statistical test showed no significant discrepancy between the genetic distance of interclass and intra-class (P > 0.05). The analysis of V3 loop amino sequence of 19 Heilongjiang B strains revealed that V3 tip motif of 10 samples (52.63%) was GPGQ, and of 4 samples (21.53%) was GPGR. The subtype of 19 HIV-1 seropositive individuals in Heilongjiang Province is B', and it is introduced from He'nan Province. V3 tip motifs of the HIV-1 isolates are mainly GPGQ and GPGR.

Amino Acid Conservation in the gp41 Transmembrane Protein and Natural Polymorphisms Associated with Enfuvirtide Resistance across HIV-1 Variants

Information about gp41 variability across distinct HIV-1 subtypes is scarce, and yet such knowledge would be desirable for designing new drugs targeting this viral protein. Conserved gp41 residues in viruses derived from 79 individuals infected with distinct HIV-1 subtypes (29 A, 25 B, 8 C, 3 D, 4 F, 4 G, 2 H, 1 J, 1 U, and 2 CRF06_cpx) and naive for entry inhibitors were examined. Conservation of gp41 was also examined in 908, 56, and 3 HIV-1 group M, O, and N sequences, respectively, available at the Los Alamos HIV Sequence Database. Among the 345 residues in the full gp41 protein, 36% showed up to 90% conservation in all 987 group M sequences, as did 40% of 56 group O sequences and 49% of 3 group N sequences. The HR1 region (residues 29-82) showed a higher proportion of highly conserved residues than did the HR2 region (residues 116-161) in all groups (65 vs. 34% in group M, 57 vs. 46% in group O, and 80 vs. 52% in group N). Some secondary resistance mutations to enfuvirtide were found as natural polymorphisms (A30V and Q56K/R in group M, Q56R and S138A in group O, and S138A in group N). In fact, A30V was a signature change in clade G and CRF06_cpx, whereas Q56K/R was a signature change for clades A and J, as well as for CRF04_cpx, CRF09_cpx, CRF11_cpx, and CRF13_cpx. The relative conservation of amino acids in gp41 across HIV-1 variants indirectly highlights the critical role of this protein for HIV infectivity and makes it feasible to design new entry inhibitors with activity against diverse HIV-1 variants.

Unequal Evolutionary Rates in the Human Immunodeficiency Virus Type 1 (HIV-1) Pandemic: the Evolutionary Rate of HIV-1 Slows Down When the Epidemic Rate Increases

HIV-1 sequences in intravenous drug user (IDU) networks are highly homogenous even after several years, while this is not observed in most sexual epidemics. To address this disparity, we examined the human immunodeficiency virus type 1 (HIV-1) evolutionary rate on the population level for IDU and heterosexual transmissions. All available HIV-1 env V3 sequences from IDU outbreaks and heterosexual epidemics with known sampling dates were collected from the Los Alamos HIV sequence database. Evolutionary rates were calculated using phylogenetic trees with a t test root optimization of dated samples. The evolutionary rate of HIV-1 subtype A1 was found to be 8.4 times lower in fast spread among IDUs in the former Soviet Union (FSU) than in slow spread among heterosexual individuals in Africa. Mixed epidemics (IDU and heterosexual) showed intermediate evolutionary rates, indicating a combination of fast- and slow-spread patterns. Hence, if transmissions occur repeatedly during the initial stage of host infection, before selective pressures of the immune system have much impact, the rate of HIV-1 evolution on the population level will decrease. Conversely, in slow spread, where HIV-1 evolves under the pressure of the immune system before a donor infects a recipient, the virus evolution at the population level will increase. Epidemiological modeling confirmed that the evolutionary rate of HIV-1 depends on the rate of spread and predicted that the HIV-1 evolutionary rate in a fast-spreading epidemic, e.g., for IDUs in the FSU, will increase as the population becomes saturated with infections and the virus starts to spread to other risk groups.

Introduction of HIV Type 1 into an Isolated Population: Molecular Epidemiologic Study from Greenland

Introduction of HIV-1 into a population may not always give rise to a subsequent epidemic. Greenland is an isolated and sparsely populated island in The Danish Kingdom. We aimed to estimate the number of introductions of HIV-1 into Greenland, the number of subsequent epidemics, and the countries from which the virus was introduced. Phylogenetic analyses were performed on three regions of HIV-1 (gag, pol, and env) in samples from 70 Greenlandic patients. Furthermore, we included gene sequences from contemporary Danish HIV-1-infected patients and sequences from the Los Alamos HIV Sequence Database. All Greenlandic sequences were subtype B except one sequence found to be a recombinant (probably CRF13). Sequence clusters in the phylogenetic trees indicated that there had been at least nine introductions of HIV-1 into Greenland. One cluster, supported by bootstrap values of 81, 76, and 96% for gag, pol, and env, corresponding to one introduction, contained 53 (76%) of the Greenland patients. The patients in the cluster differed from other Greenlandic patients in epidemiological parameters. Two distinct subgroups within the main cluster were concentrated around the two largest Greenlandic towns. Although HIV-1 has been introduced into Greenland at least nine times, only one introduction gave rise to an epidemic. The phylogeny did not indicate from where the main Greenland cluster had been introduced as no database sequence from outside Greenland was genetically close to this cluster. The large diversity between the main Greenland cluster and the rest of the sequences is most likely due to a founder effect.

Codon volatility does not reflect selective pressure on the HIV-1 genome

Codon volatility is defined as the proportion of a codon's point-mutation neighbors that encode different amino acids. The cumulative volatility of a gene in relation to its associated genome was recently reported to be an indicator of selection pressure. We used this approach to measure selection on all available full-length HIV-1 subtype B genomes in the Los Alamos HIV Sequence Database, and compared these estimates against those obtained via established likelihood- and distance-based comparative methods. Volatility failed to correlate with the results of any of the comparative methods demonstrating that it is not a reliable indicator of selection pressure.

Semen-Specific Genetic Characteristics of Human Immunodeficiency Virus Type 1 env

Human immunodeficiency virus type 1 (HIV-1) in the male genital tract may comprise virus produced locally in addition to virus transported from the circulation. Virus produced in the male genital tract may be genetically distinct, due to tissue-specific cellular characteristics and immunological pressures. HIV-1 env sequences derived from paired blood and semen samples from the Los Alamos HIV Sequence Database were analyzed to ascertain a male genital tract-specific viral signature. Machine learning algorithms could predict seminal tropism based on env sequences with accuracies exceeding 90%, suggesting that a strong genetic signature does exist for virus replicating in the male genital tract. Additionally, semen-derived viral populations exhibited constrained diversity (P < 0.05), decreased levels of positive selection (P < 0.025), decreased CXCR4 coreceptor utilization, and altered glycosylation patterns. Our analysis suggests that the male genital tract represents a distinct selective environment that contributes to the apparent genetic bottlenecks associated with the sexual transmission of HIV-1.

Simian-human immunodeficiency virus escape from cytotoxic T-lymphocyte recognition at a structurally constrained epitope.

Virus-specific cytotoxic T lymphocytes (CTL) exert intense selection pressure on replicating simian immunodeficiency virus (SIV) and human immunodeficiency virus type 1 (HIV-1) in infected individuals. The immunodominant Mamu-A(*)01-restricted Gag p11C, C-M epitope is highly conserved among all sequenced isolates of SIV and therefore likely is structurally constrained. The strategies used by virus isolates to mutate away from an immunodominant epitope-specific CTL response are not well defined. Here we demonstrate that the emergence of a position 2 p11C, C-M epitope substitution (T47I) in a simian-human immunodeficiency virus (SHIV) strain 89.6P-infected Mamu-A(*)01(+) monkey is temporally correlated with the emergence of a flanking isoleucine-to-valine substitution at position 71 (I71V) of the capsid protein. An analysis of the SIV and HIV-2 sequences from the Los Alamos HIV Sequence Database revealed a significant association between any position 2 p11C, C-M epitope mutation and the I71V mutation. The T47I mutation alone is associated with significant decreases in viral protein expression, infectivity, and replication, and these deficiencies are restored to wild-type levels with the introduction of the flanking I71V mutation. Together, these data suggest that a compensatory mutation is selected for in SHIV strain 89.6P to facilitate the escape of that virus from CTL recognition of the dominant p11C, C-M epitope.

An HIV type 1 subtype B founder effect in Korea: gp160 signature patterns infer circulation of CTL-escape strains at the population level.

HIV-1 subtype B predominates in the Republic of Korea. Phylogenetic analyses of sequences for complete nef genes and env gene fragments encoding the V3 loop have identified a major monophyletic Korean subclade that is distinct from Western subtype B sequences in the Los Alamos HIV Sequence Database. This was investigated further by sequence analysis of complete env genes recovered from the DNA of peripheral blood mononuclear cells for matched groups of Koreans, four patients per group, previously assigned as being infected with either Korean or Western strains. The phylogenetic classifications were confirmed and analysis of the translation products identified 32 amino acid signature pattern differences, dispersed throughout gp160, which differentiate the two subclades. Twenty-three of these positions map to epitopes recognized by HLA-I-restricted cytotoxic T-lymphocytes (CTL) as catalogued in the Los Alamos HIV Immunology Database. The remaining nine map at or close to sites predicted to be targets for immunoproteasomes that are involved in producing peptides that bind to MHC Class I. These results suggest that a founder effect in the Korean population is based on the spread of CTL-escape/host-adapted HIV-1 strains.

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.