HIV-1 Intersubtype Recombinants Research Articles

Prevalence and clinical impacts of HIV-1 intersubtype recombinants in Uganda revealed by near-full-genome population and deep sequencing approaches.

HIV-1 subtypes A1 and D cocirculate in a rural community in Mbarara, Uganda. This study examines HIV-1 intersubtype recombination in this community under a full-genome sequencing context. We aim to estimate prevalence, examine time trends, and test for clinical correlates and outcomes associated with intersubtype recombinants. Near-full-genome HIV-1 Sanger sequence data were collected from plasma samples of 504 treatment-naïve individuals, who then received protease inhibitor or nonnucleoside reverse transcriptase inhibitor-containing regimens and were monitored for up to 7.5 years. Subtypes were inferred by Los Alamos Recombinant Identification Program (RIP) 3.0 and compared with Sanger/REGA and MiSeq/RIP. 'Nonrecombinants' and 'recombinants' infections were compared in terms of pretherapy viral load, CD4 cell count, posttherapy time to virologic suppression, virologic rebound, first CD4 rise above baseline and sustained CD4 recovery. Prevalence of intersubtype recombinants varied depending on the genomic region examined: gag (15%), prrt (11%), int (8%), vif (10%), vpr (2%), vpu (9%), GP120 (8%), GP41 (18%), and nef (4%). Of the 200 patients with near-full-genome data, prevalence of intersubtype recombination was 46%; the most frequently observed recombinant was A1-D (25%). Sanger/REGA and MiSeq/RIP yielded generally consistent results. Phylogenetic tree revealed most recombinants did not share common ancestors. No temporal trend was observed (all P > 0.1). Subsequent subtype switches were detected in 27 of 143 (19%) study participants with follow-up sequences. Nonrecombinant versus recombinants infections were not significantly different in any pre nor posttherapy clinical correlates examined (all P > 0.2). Intersubtype recombination was highly prevalent (46%) in Uganda if the entire HIV genome was considered, but was neither associated with clinical correlates nor therapy outcomes.

An in vitro Model to Mimic Selection of Replication-Competent HIV-1 Intersubtype Recombination in Dual or Superinfected Patients

The low frequency of HIV-1 recombinants within entire viral populations in both individual patients and culture-based infection models impedes investigation of the underlying factors contributing to either the occurrence of recombinants or the survival of recombinants once they are formed. So far, most of the related studies have no consideration of recombinants' functionality. Here, we established a functional recombinant production (FRP) system to produce pure and functional HIV-1 intersubtype Env recombinants and utilized 454 pyrosequencing to investigate the distribution of over 4000 functional and non-functional recombination breakpoints from either the FRP system or dual infection cultures. The results revealed that most of the breakpoints converged in gp41 (62%) and C1 (25.3%) domains of gp120, which has strong correlation with the similarity between the two recombining sequences. Yet, the breakpoints also appeared in C2 (5.2%) and C5 (4.6%) domains not correlated with the recombining sequence similarity. Interestingly, none of the intersubtype gp120 recombinants recombined between C1 and gp41 regions either from the FRP system or from the dual infection culture, and very few from the HIV epidemic were functional. The present study suggests that the selection of functional Env recombinants is one of the reasons for the predominance of C1 and gp41 Env recombinants in the HIV epidemic, and it provides an in vitro model to mimic the selection of replication-competent HIV-1 intersubtype recombination in dual or superinfected patients.

Complex Subtype Diversity of HIV-1 Among Drug Users in Major Kenyan Cities.

Drug users are increasingly recognized as a key population driving human immunodeficiency virus (HIV) spread in sub-Saharan Africa. To determine HIV-1 subtypes circulating in this population group and explore possible geographic differences, we analyzed HIV-1 sequences among drug users from Nairobi, Mombasa, and Kisumu in Kenya. We sequenced gag and env from 55 drug users. Subtype analysis from 220 gag clonal sequences from 54 of 55 participants (median = 4/participant) showed that 44.4% were A, 16.7% were C, 3.7% were D, and 35.2% were intersubtype recombinants. Of 156 env clonal sequences from 48 of 55 subjects (median = 3/participant), 45.8% were subtype A, 14.6% were C, 6.3% were D, and 33.3% were recombinants. Comparative analysis of both genes showed that 30 (63.8%) participants had concordant subtypes, while 17 (36.2%) were discordant. We identified one genetically linked transmission pair and two cases of dual infection. These data are indicative of extensive HIV-1 intersubtype recombination in Kenya and suggest decline in subtype D prevalence.

Identification of Two New HIV-1 Circulating Recombinant Forms (CRF87_cpx and CRF88_BC) from Reported Unique Recombinant Forms in Asia

The on-going generation of HIV-1 intersubtype recombination has led to new circulating recombinant forms (CRFs) and unique recombinant forms (URFs) in Asia. In this study, we evaluated whether previously reported URFs were actually CRFs. All available complete or near full-length HIV-1 URF sequences from Asia were retrieved from the HIV Los Alamos National Laboratory Sequence database, and phylogenetic, transmission cluster, and bootscan analyses were performed using MEGA 6.0, Cluster Picker 1.2.1, and SimPlot3.5.1. According to the criterion of new CRFs, two new HIV-1 CRFs (CRF87_cpx and CRF88_BC) were identified from these available URFs. CRF87_cpx comprised HIV-1 subtypes B, C, and CRF01_AE, and CRF88_BC comprised subtypes B and C. HIV Blast and bootscan analysis revealed that besides the three representative strains, there were two additional CRF87_cpx strains. Furthermore, we defined seven dominant URFs (dURF01-dURF07), each of which contained two strains sharing same recombination map and can be used as sequence references to facilitate the finding of new potential CRFs in future. These results will benefit the molecular epidemiological investigation of HIV-1 in Asia.

Analysis of HIV-1 intersubtype recombination breakpoints suggests region with high pairing probability may be a more fundamental factor than sequence similarity affecting HIV-1 recombination.

BackgroundWith increasing data on HIV-1, a more relevant molecular model describing mechanism details of HIV-1 genetic recombination usually requires upgrades. Currently an incomplete structural understanding of the copy choice mechanism along with several other issues in the field that lack elucidation led us to perform an analysis of the correlation between breakpoint distributions and (1) the probability of base pairing, and (2) intersubtype genetic similarity to further explore structural mechanisms.MethodsNear full length sequences of URFs from Asia, Europe, and Africa (one sequence/patient), and representative sequences of worldwide CRFs were retrieved from the Los Alamos HIV database. Their recombination patterns were analyzed by jpHMM in detail. Then the relationships between breakpoint distributions and (1) the probability of base pairing, and (2) intersubtype genetic similarities were investigated.ResultsPearson correlation test showed that all URF groups and the CRF group exhibit the same breakpoint distribution pattern. Additionally, the Wilcoxon two-sample test indicated a significant and inexplicable limitation of recombination in regions with high pairing probability. These regions have been found to be strongly conserved across distinct biological states (i.e., strong intersubtype similarity), and genetic similarity has been determined to be a very important factor promoting recombination. Thus, the results revealed an unexpected disagreement between intersubtype similarity and breakpoint distribution, which were further confirmed by genetic similarity analysis. Our analysis reveals a critical conflict between results from natural HIV-1 isolates and those from HIV-1-based assay vectors in which genetic similarity has been shown to be a very critical factor promoting recombination.ConclusionsThese results indicate the region with high-pairing probabilities may be a more fundamental factor affecting HIV-1 recombination than sequence similarity in natural HIV-1 infections. Our findings will be relevant in furthering the understanding of HIV-1 recombination mechanisms.Electronic supplementary materialThe online version of this article (doi:10.1186/s12985-016-0616-1) contains supplementary material, which is available to authorized users.

Characterization of Novel HIV-1 Intersubtype CRF01_AE/C and A1/C Recombinants from India.

We report here three novel HIV-1 intersubtype recombinants from India. One among those is a recombinant between subtype C and CRF01_AE and another two between A1 and C. A recombinant virus with CRF01_AE is reported for the first time from India.

Diverse forms of HIV-1 among Burmese long-distance truck drivers imply their contribution to HIV-1 cross-border transmission.

BackgroundThe China-Myanmar border is a particularly interesting region that has very high prevalence of and considerable diversity of HIV-1 recombinants. Due to the transient nature of their work, long-distance truck drivers (LDTDs) have a comparatively high potential to become infected with HIV-1 and further spread virus to other individuals in the area they travel within. In this study, we hypothesized that Burmese LDTDs crossing the China-Myanmar border frequently may potentially be involved in the cross-border transmission of HIV, and contribute to the extremely high prevalence of HIV-1 inter-subtype recombinants in this border region.MethodsA molecular epidemiology study was conducted among 105 Burmese LDTDs between 2008 and 2010. HIV-1 genetic fragments including p17, pol, vif-vpr, vpr-env, and C2V3 were amplified and sequenced. The subtype characterization and HIV-1 transmission were determined by both phylogenetic and phylogeographic analyses.ResultsDiverse forms of HIV-1, including subtypes CRF01_AE (41.9%), C (8.6%), B (4.8%), CRF02_AG (1.0%), and inter-subtype recombinants (33.3%), as well as dual infection (10.5%), were detected among the tested LDTDs. Phylogeographic analyses based on pure subtype revealed that 77.8% Burmese LDTDs acquired HIV-1 infection in Yunnan, and the others in Myanmar. Both the C-related and CRF01_AE-related recombinants from these LDTDs appeared to have close genetic relationship with those from IDUs in Myanmar and Dehong.ConclusionsBurmese LDTDs may contribute to HIV-1 transmission along the China-Myanmar border. The results may provide some new perspective for understanding the on-going generation and prevalence of HIV-1 recombinants in the border region.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2334-14-463) contains supplementary material, which is available to authorized users.

High Prevalence of HIV-1 Intersubtype B′/C Recombinants among Injecting Drug Users in Dehong, China

ObjectiveTo examine the distribution of HIV-1 genotypes among injecting drug users (IDUs) from Dehong, Yunnan province.Materials and MethodsBlood samples from a total of 95 HIV-positive IDUs were retrospectively analyzed. Samples were collected between 2005 and 2009 from four cities in Dehong prefecture, western Yunnan province, the geographical origin of the HIV epidemic in China. HIV-1 gag, partial pol, vpr-env fragment, half-genome, or near-full-length sequences were analyzed to determine the HIV-1 genotypes of each subject. Results were compared with findings from past studies of IDUs in Dehong and in neighboring Myanmar.ResultsWe observed a high prevalence of B′/C recombinants (82.4%) among IDUs in Dehong, the structural profiles of which do not match those previously reported in Dehong or in Myanmar. Furthermore, statistically significant differences in geographical and temporal distributions of HIV-1 genotypes were characterized by a predominance of HIV-1 B′/C recombinant forms among older subjects(p = 0.034), subjects from Longchuan district (p = 0.022), and subjects diagnosed between 2000 and 2004 (p = 0.004).ConclusionsThe increasing prevalence of multiple, new B′/C recombinant forms suggest that HIV-1 intersubtype recombination is substantial and ongoing in western Yunnan. This reflects the high-risk behavior of IDUs in this region and argues the need for stronger monitoring and prevention measures in Dehong and other high-prevalence areas around China.

Molecular Epidemiology of HIV Type 1 Subtypes in Rwanda

HIV-1 infection is characterized by genetic diversity, with multiple subtypes and recombinant variants circulating, particularly in sub-Saharan Africa. During the Rwandan genocide, many women experienced multiple rapes and some became HIV-1 infected. We studied plasma and peripheral blood mononuclear cells (PBMCs) from 30 infected women comprising two exposure groups: those with numerous contacts, raped multiple times, and women with one lifetime sexual partner and no history of rape. Population-based sequences from gag, pol, and env genes were analyzed to determine HIV-1 subtypes and intersubtype recombination. Individual plasma-derived variants from 12 women were also analyzed. Subtype A was found in 24/30 (80%), intersubtype recombination (AC and AD) in 4/30 (13%), and subtypes C and D in 1/30 each. In two subjects, the pattern of HIV-1 recombination differed between plasma and PBMC-derived sequences. Intersubtype recombination was common, although there were no significant differences in subtype or recombination rates between exposure groups.

HIV-1 Subtypes and Recombinants in Northern Tanzania: Distribution of Viral Quasispecies

This study analyzed the distribution and prevalence of HIV-1 subtypes, multiplicity of HIV-1 infection, and frequency of inter-subtype recombination among HIV-1-infected female bar and hotel workers in Moshi, Kilimanjaro Region, Tanzania, from 2004 to 2007. The HIV-1 viral sequences spanning the V1-C5 region of HIV-1 env gp120 were analyzed from 50 subjects by single genome amplification and sequencing (SGA/S) technique. A total of 1740 sequences were amplified and sequenced from the HIV-1 proviral DNA template. The median env sequences analyzed per subject per two time points was 38 (IQR 28–50) over one year of HIV infection. In a subset of 14 subjects, a total of 239 sequences were obtained from HIV-1 RNA template at the baseline visit. The most prevalent HIV-1 subtypes were A1 (56%) and C (30%), while HIV-1 subtype D and inter-subtype recombinant viruses were found in 6% and 8% of subjects respectively. Transmission of multiple HIV-1 variants was evident in 27% of the subjects infected with pure HIV-1 subtypes A1, C, or D. The HIV-1 inter-subtype recombinants were found in 8% including HIV-1 C/A, D/A, and complex mosaic recombinants. Multiple viral variants were found in two subjects infected with inter-subtype recombinants. One subject harbored quasispecies of both pure HIV-1 A1 and C/A recombinant. The other subject was infected with two complex mosaic inter-subtype recombinant variants belonging to subtype D. HIV-1 multiple infections and ongoing recombination contribute significantly to the genetic diversity of circulating HIV-1 in Tanzania and have important implications for vaccine design and the development of therapeutic strategies.

Extensive and complex HIV-1 recombination between B’, C and CRF01_AE among IDUs in south-east Asia

To investigate the subtype characterization of HIV-1 among IDUs in northern Myanmar. A molecular epidemiological investigation was conducted among IDUs in Laza and Maizayang cities of northern Myanmar. A total of 83 HIV-1-positive serums were collected from consenting IDUs during June to August 2009. HIV-1 p17, pol, vif-env, C2V3 fragments were amplified and sequenced. Phylogenetic and bootscanning analyses were performed. A very high proportion (86.1%) of HIV-1 intersubtype recombinants and very low proportion of subtypes B' (3.8%), C (7.6%) and CRF01_AE (1.3%) were found in this HIV-infected IDUs cohort. These recombinants cover all four kinds of recombination forms formed among CRF01_AE, B and C. The B/C and CRF01_AE/B/C recombinants are the two most dominant recombinants, accounting for 54.4 and 42.6% of all cases, respectively, and indicating the ongoing generation of extensive and complex HIV-1 recombination among CRF01_AE, B' and C in northern Myanmar. Intriguingly, most recombinants have different chimeric patterns from each other, forming 64 unique recombination forms (URFs) that are quite distinct from any previously identified circulating recombinant forms (CRFs) and URFs in Asia. The extremely high proportion of intersubtype recombinants, especially CRF01_AE/B'/C recombinants (42.6%), strongly suggests that northern Myanmar is a big forge for HIV-1 recombination among CRF01_AE, B' and C.

Viral replication is enhanced by an HIV-1 intersubtype recombination-derived Vpu protein

BackgroundMultiple HIV-1 intersubtype recombinants have been identified in human populations. Previous studies from our lab group have shown that the epidemic in Argentina is characterized by the high prevalence of a circulating recombinant form, CRF12_BF, and many related BF recombinant forms. In these genomic structures a recombination breakpoint frequently involved the vpu coding region. Due to the scarce knowledge of Vpu participation in the virion release process and its impact on pathogenesis and of the functional capacities of intersubtype recombinant Vpu proteins, the aim of this work was to perform a comparative analysis on virion release capacity and relative replication capacity among viral variants harboring either a BF recombinant Vpu or a subtype B Vpu.ResultsOur results showed that BF recombinant Vpu was associated to an increased viral particles production when compared to WT B variant in tetherin-expressing cell lines. This observation was tested in the context of a competition assay between the above mentioned variants. The results showed that the replication of the BF Vpu-harboring variant was more efficient in cell cultures than subtype B, reaching a higher frequency in the viral population in a short period of time.ConclusionThis study showed that as a result of intersubtype recombination, a structurally re-organized HIV-1 Vpu has an improved in vitro capacity of enhancing viral replication, and provides evidence of the changes occurring in this protein function that could play an important role in the successful spread of intersubtype recombinant variants.

Performance of OraQuick Advance ® Rapid HIV-1/2 Antibody Test for detection of antibodies in oral fluid and serum/plasma in HIV-1+ subjects carrying different HIV-1 subtypes and recombinant variants

Background Rapid, simple, low-cost, sensitive, and specific tests are needed to detect antibodies to all HIV-1 subtypes, especially in developing countries. Objective To evaluate the performance of a rapid diagnostic test for detection of HIV-1/2 antibodies in oral fluids and sera/plasma from subjects from geographic areas infected with different HIV-1 variants. Study design OraQuick Rapid HIV-1/2 Diagnostic Test was evaluated in sera and oral fluids from 100 subjects from Spain and South-America. It was also assessed in 56 plasma and 39 oral fluid specimens from 56 Africans carrying HIV-1 non-B subtypes or inter-subtype recombinants defined by phylogenetic analysis at pol and gp41 coding regions. All patients were previously diagnosed as HIV-1 positive by serological tests (Abbott AxSYM HIV-1/2; Western Blot HIV-1/HIV-2 and Pepti-LAV, BIO-RAD). Results OraQuick provided positive results in all 156 serum/plasma specimens regardless of the infecting HIV-1 subtype, and in 136/139 (97.8%) oral fluids. The three oral specimens (2.2%) that yielded false-negative results by OraQuick were taken from one subtype B-infected Spaniard and from two subtype D-infected Africans. The last two were also negative by Pepti-LAV using plasma samples. Ten additional sera and 32 oral fluids from HIV-negative individuals yielded negative results by OraQuick. This rapid test showed good sensitivity for detecting anti-HIV-1 antibodies in oral fluids and in serum/plasma specimens from subjects carrying different HIV-1 subtypes and recombinant variants. Conclusion OraQuick demonstrated its utility for detecting infections due to HIV-1 subtypes and recombinants common in developing countries.

In vitro dynamics of HIV-1 BF intersubtype recombinants genomic regions involved in the regulation of gene expression

HIV-1 intersubtype recombination is a very common phenomenon that has been shown to frequently affect different viral genomic regions. Vpr and Tat are viral proteins known to interact with viral promoter (LTR) during the replication cycle. This interaction is mainly involved in the regulation of viral gene expression, so, any structural changes in the LTR and/or these regulatory proteins may have an important impact on viral replication and spread. It has been reported that these genetic structures underwent recombination in BF variants widely spread in South America. To gain more insight of the consequences of the BF intersubtype recombination phenomenon on these different but functionally related genomic regions we designed and performed and in vitro study that allowed the detection and recovery of intersubtype recombinants sequences and its subsequent analysis. Our results indicate that recombination affects differentially these regions, showing evidence of a time-space relationship between the changes observed in the viral promoter and the ones observed in the Vpr/Tat coding region. This supports the idea of intersubtype recombination as a mechanism that promotes biological adaptation and compensates fitness variations.

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.

Long-range Recombination Gradient between HIV-1 Subtypes B and C Variants Caused by Sequence Differences in the Dimerization Initiation Signal Region

HIV-1 intersubtype recombinants have an increasingly important role in shaping the AIDS pandemic. We sought to understand the molecular mechanisms that generate intersubtype HIV-1 recombinants. We analyzed recombinants of HIV-1 subtypes B and C, and identified their crossover junctions in the viral genome from the 5′ long terminal repeat (LTR) to the end of pol. We identified 56 recombination events in 56 proviruses; the distribution of these events indicated an apparent recombination gradient: there were significantly more crossover junctions in the 3′ half than in the 5′ half of the region analyzed. HIV-1 subtypes B and C have different dimerization initiation signal (DIS). We hypothesized that the inability of subtype B and C RNAs to form perfect base-pairing of the DIS affects the dimeric RNA structure and causes a decrease in recombination events at the 5′ end of the viral genome. To test this hypothesis, we examined recombinants generated from a subtype C virus and a modified subtype B virus containing a subtype C DIS. In the 56 proviruses analyzed, we identified 96 recombination events, which are significantly more frequent than in the B/C recombinants. Furthermore, these crossover junctions were distributed evenly throughout the region analyzed, indicating that the recombination gradient was corrected by matching the DIS. Therefore, base-pairing at the DIS has an important function during HIV-1 reverse transcription, most likely in maintaining nucleic-acid structure in the complex. These findings reveal elements important to retroviral recombination and provide insights into the generation of HIV-1 intersubtype recombinants that are important to the AIDS epidemic.

The distribution of HIV-1 recombination breakpoints

We find that recombination breakpoints are non-randomly distributed across the genomes of HIV-1 intersubtype recombinants. In particular we find two recombination prone regions, “hot spots”, located approximately either side of the envelope gene. To investigate this, we test whether there is a correlation between the distribution of the recombinant breakpoints with (1) genetic similarity, (2) predicted locations of secondary RNA structure, (3) regions identified as recombinant hot spots from experimental studies and (4) the predicted locations of positively selected sites. No detectable relationship with RNA secondary structure was found. A weak relationship with genetic similarity exists but it does not account for the recombination hot spots. The comparison with the published experimental studies indicated that the identified recombination hot spots differ in their locations, indicating that selection is having an impact on HIV-1 recombinant structures in infected individuals. We observe an association between recombination prone regions and strong positive selection across the envelope gene in support of this hypothesis.

Analysis of HIV Type 1 Diversity in Pregnant Women from Four Latin American and Caribbean Countries

Worldwide, the distribution of HIV-1 subtypes and intersubtype recombinants is not homogeneous. In Latin America and the Caribbean, HIV-1 subtype B predominates. However, in the south of Brazil and in countries of the Southern cone (Argentina, Chile, Paraguay, and Uruguay) there is a different distribution of viral subtypes and intersubtype recombinants. The aim of this work was to analyze HIV-1 diversity in a cohort of pregnant women (with primarily heterosexual acquisition of the infection) who were diagnosed with HIV-1 infection during their current pregnancy and who received ARVs during pregnancy for perinatal transmission prophylaxis. Analysis of 121 partial pol sequences from subjects enrolled in Argentina, Brazil, the Bahamas, and Mexico was performed by phylogenetic and recombinant characterization. Different prevalences of subtype B were observed (100% for specimens from Mexico and the Bahamas, 61% for Brazil, and 30% for Argentina). Subtypes C and F were found, along with BC, BF, FC, and CBF recombinants in specimens from Brazilians. A high prevalence of BF recombinants was found (70%) in specimens from Argentina. The different patterns of HIV- 1 subtypes and intersubtype recombinants in South America (Argentina and Brazil) compared to those in Central and North America should be considered in the design of future HIV-1 vaccine trials.

Sequence determinants of breakpoint location during HIV-1 intersubtype recombination

Retroviral recombination results from strand switching, during reverse transcription, between the two copies of genomic RNA present in the virus. We analysed recombination in part of the envelope gene, between HIV-1 subtype A and D strains. After a single infection cycle, breakpoints clustered in regions corresponding to the constant portions of Env. With some exceptions, a similar distribution was observed after multiple infection cycles, and among recombinant sequences in the HIV Sequence Database. We compared the experimental data with computer simulations made using a program that only allows recombination to occur whenever an identical base is present in the aligned parental RNAs. Experimental recombination was more frequent than expected on the basis of simulated recombination when, in a region spanning 40 nt from the 5′ border of a breakpoint, no more than two discordant bases between the parental RNAs were present. When these requirements were not fulfilled, breakpoints were distributed randomly along the RNA, closer to the distribution predicted by computer simulation. A significant preference for recombination was also observed for regions containing homopolymeric stretches. These results define, for the first time, local sequence determinants for recombination between divergent HIV-1 isolates.

Analysis of HIV-1 sequences vertically transmitted to infants in Kisumu, Kenya

Background HIV-1 prevalence in Kenya among women aged between 15–19 years is approximately 23%. These women are prospective mothers and therefore can play an important role in mother-to-child transmission of HIV. The risk of a seropositve mother transmitting the virus to her infant is 25–35% in developing countries, such as Kenya, where antiretroviral drugs are not readily available. Objectives This study was undertaken to evaluate the molecular nature of HIV-1 strains, assess recombination and it's relevance in mother-to-child transmission in Kenya. Study design HIV-1 gag and gp120 sequences were derived from peripheral blood mononuclear cells (PBMC) of 16 infected mothers and infants, from Kisumu, Kenya. PCR, cloning, and phylogenetic analyses were conducted to examine any sequence differences between HIV-1 strains derived from mother–infant pairs. Results The cohort consisted of seven pairs harboring possible subtype A/D recombinants, eight pairs with apparent pure A or D strains and one possible dual infection. This dual infection comprised of a pure subtype A region and an A/D recombinant, and was detected in one of the mother's sample. Interestingly, only the recombinant virus was detected in the paired baby sample. Conclusions This study shows that HIV-1 inter-subtype recombinants can be effectively transmitted vertically to infants, and could possibly be favored in this setting where multiple subtypes infect women. Together, dual infections and the co-existence of multiple HIV-1 subtypes is encouraging the emergence of recombinant HIV strains and their rapid dispersal.