HIV-1 co-infection, superinfection and recombination

Sequencing of One Unique Recombinant CRF85_BC/CRF01_AE Genome and Two Partial Genomes from Ningxia, China

The recent emergence of new HIV-1 recombinant strains presents a new challenge to the control of HIV-1/AIDS and the development of an effective vaccine. We employed a near full-length genomic sequence analysis of a newly identified CRF85_BC recombinant strain in Ningxia, China, to determine its recombination pattern. Blood samples were collected from HIV-infected or AIDS patients in Ningxia in 2023. CRF85_BC subtype strains were detected from three samples using an in-house method, and one sample's near full-length genome sequence was also obtained. MEGA11, jpHMM, and Simplot software were used to identify subtypes and analyze recombination patterns. Neighbor-joining phylogenetic tree analysis showed that HIV-1 pol region sequences of three samples were CRF85_BC subtypes. One near full-length genome sequence of the recombinant strain was obtained, and jpHMM preliminarily judged that the recombinant strain was inserted with two subtype B fragments and two CRF01_AE fragments based on subtype C as the backbone. Further analysis using Simplot software revealed that the recombinant strain was the second-generation recombinant strain of CRF85_BC and CRF01_AE, and the recombination mode was based on the full-length genome of CRF85_BC, and CRF01_AE gene fragments that were inserted at positions 7365-8279 and 8431-9492, respectively. The results of the fragment phylogenetic tree verified its accuracy. One CRF01_AE and CRF85_BC second-generation recombinant strain was found in HIV-1 infected people in Ningxia, indicating that new HIV-1 recombinant strains continuously emerge and circulate in this region. Genomic surveillance of these recombinants should inform targeted interventions, such as prioritized contact tracing, to mitigate the formation of transmission clusters.

Identification of a Novel HIV-1 Circulating Recombinant Form (CRF150_Cpx) Among Men Who Have Sex with Men in China

Recent studies have reported increasing complexity in human immunodeficiency virus 1 (HIV-1) genotypes among men who have sex with men (MSM) in China. In an HIV-1 molecular epidemiological study conducted among MSM in Yunnan Province, China, we discovered that four samples could potentially represent a circulating recombinant form (CRF). In this study, we conducted further analysis on their nearly full-length genome (NFLG) sequences. The NFLG sequences formed a distinct monophyletic clade in the phylogenetic tree. Recombination analysis indicated that the four sequences were constructed upon the backbone of CRF149_01B, with the insertion of three CRF07_BC fragments. Consequently, they were designated as CRF150_cpx. Evolutionary analyses suggested that CRF150_cpx emerged between approximately 2014 and 2015. The identification of new CRFs not only deepens our understanding of HIV recombination but also aids in comprehending the prevalence and transmission history of HIV among specific populations.

Identification of a novel HIV-1 third-generation circulating recombinant form (CRF126_0755) in Guangdong, China

The genetic recombination patterns and genetic distribution of HIV-1 are valuable for elucidating the epidemic and genetic diversity of HIV. Numerous HIV-1 circulating recombinant forms (CRFs) have recently emerged and disseminated rapidly. In China, at least 32 CRFs have been reported to account for more than 80% of all HIV infections. However, CRFs derived from the CRF07_BC and CRF55_01B lineages have never been recorded. Here, a novel third-generation CRF involving HIV-1 was identified in four HIV-1-infected patients in Guangdong, China, who had no epidemiological association with each other. Phylogenetic and recombinant analyses confirmed that these strains shared highly similar recombination patterns, with the CRF07_BC backbone substituted by a CRF55_01B segment; therefore, these strains were classified as CRF126_0755. This is the first study of a CRF derived from CRF07_BC and CRF55_01B. Bayesian phylogenetic inference suggested that CRF126_0755 originated in approximately 2005-2007. The present findings reveal that the genotype composition of HIV-1 has become more complex than that of other viruses and highlight the urgent need for continuous molecular screening and epidemic surveillance within HIV-1-infected populations to advance our understanding of viral transmission mechanisms.

High HIV diversity, recombination, and superinfection revealed in a large outbreak among persons who inject drugs in Kentucky and Ohio, USA

We investigated transmission dynamics of a large human immunodeficiency virus (HIV) outbreak among persons who inject drugs (PWID) in KY and OH during 2017-20 by using detailed phylogenetic, network, recombination, and cluster dating analyses. Using polymerase (pol) sequences from 193 people associated with the investigation, we document high HIV-1 diversity, including Subtype B (44.6 per cent); numerous circulating recombinant forms (CRFs) including CRF02_AG (2.5 per cent) and CRF02_AG-like (21.8 per cent); and many unique recombinant forms composed of CRFs with major subtypes and sub-subtypes [CRF02_AG/B (24.3 per cent), B/CRF02_AG/B (0.5 per cent), and A6/D/B (6.4 per cent)]. Cluster analysis of sequences using a 1.5 per cent genetic distance identified thirteen clusters, including a seventy-five-member cluster composed of CRF02_AG-like and CRF02_AG/B, an eighteen-member CRF02_AG/B cluster, Subtype B clusters of sizes ranging from two to twenty-three, and a nine-member A6/D and A6/D/B cluster. Recombination and phylogenetic analyses identified CRF02_AG/B variants with ten unique breakpoints likely originating from Subtype B and CRF02_AG-like viruses in the largest clusters. The addition of contact tracing results from OH to the genetic networks identified linkage between persons with Subtype B, CRF02_AG, and CRF02_AG/B sequences in the clusters supporting de novo recombinant generation. Superinfection prevalence was 13.3 per cent (8/60) in persons with multiple specimens and included infection with B and CRF02_AG; B and CRF02_AG/B; or B and A6/D/B. In addition to the presence of multiple, distinct molecular clusters associated with this outbreak, cluster dating inferred transmission associated with the largest molecular cluster occurred as early as 2006, with high transmission rates during 2017-8 in certain other molecular clusters. This outbreak among PWID in KY and OH was likely driven by rapid transmission of multiple HIV-1 variants including de novo viral recombinants from circulating viruses within the community. Our findings documenting the high HIV-1 transmission rate and clustering through partner services and molecular clusters emphasize the importance of leveraging multiple different data sources and analyses, including those from disease intervention specialist investigations, to better understand outbreak dynamics and interrupt HIV spread.

Genetic characteristics of a novel HIV-1 recombinant lineage (CRF103_01B) and its prevalence in northern China

During the routine surveillance of HIV-1 pretreatment drug resistance in Beijing, five men who have sex with men (MSM) and a woman were observed to get infected by newly identified CRF103_01B strain. To elucidate the genetic characteristics, the near full-length genome (NFLG) was obtained. Phylogenetic inference indicated that CRF103_01B NFLG was composed of six mosaic segments. Segments IV and V of CRF103_01B were located among the clusters subtype B and CRF01_AE (group 5), respectively. The CRF103_01B strain was deduced to originate from Beijing MSM population around 2002.3-2006.4 and continued to spread among MSM population at a low level, then to the general population via heterosexual contact in northern China. Molecular epidemiology surveillance of CRF103_01B should be reinforced.

Predictive Factors of HIV-1 Drug Resistance and Its Distribution among Female Sex Workers in the Democratic Republic of the Congo (DRC)

The predictive factors of HIV-1 drug resistance and its distribution are poorly documented in female sex workers (FSWs) in the Democratic Republic of the Congo (DRC). However, the identification of predictive factors can lead to the development of improved and effective antiretroviral therapy (ART). The objective of the current study was to determine the predictive factors of HIV-1 drug resistance and its distribution based on FSWs in the studied regions in the Democratic Republic of the Congo (DRC). HIV-positive FSWs who were diagnosed as part of the DRC Integrated Biological and Behavioral Surveillance Survey (IBBS) were included in this study. A total of 325 FSWs participated. The HIV-1 viral load (VL) was measured according to the Abbott m2000sp and m2000rt protocols. The homogeneity chi-square test was conducted to determine the homogeneity of HIV-1 drug resistance distribution. Using a significance level of 0.05, multivariate analyses were performed to identify factors associated with HIV-1 drug resistance to ART. HIV drug resistance mutation (HIVDRM) distribution was homogeneous in the three study regions (p = 0.554) but differed based on the HIV-1 VLs of the FSWs. FSWs with high HIV-1 VLs harbored more HIVDRMs (p = 0.028) of predominantly pure HIV-1 strains compared with those that had low HIV-1 VLs. Sexually transmitted infection (STI) history (aOR [95%CI] = 8.51 [1.62, 44.74]), high HIV-1 VLs (aOR [95%CI] = 5.39 [1.09, 26.74]), and HIV-1-syphilis coinfection (aOR [95%CI] = 9.71 [1.84, 51.27]) were associated with HIV drug resistance among FSWs in the DRC. A history of STIs (e.g., abnormal fluid) in the 12 months prior to the survey, a high HIV-1 VL, and HIV-1-syphilis coinfection were associated with HIV-1 drug resistance among FSWs in the DRC. Efforts should be made to systematically test for other infections which increase the HIV-1 VL, in the case of HIV-1 coinfection, in order to maintain ART effectiveness across the DRC.

First complete-genome documentation of HIV-1 intersubtype superinfection with transmissions of diverse recombinants over time to five recipients

Human immunodeficiency virus type 1 (HIV-1) recombinants in the world are believed to be generated through recombination between distinct HIV-1 strains among coinfection or superinfection cases. However, direct evidence to support transmission of HIV-1 recombinants from a coinfected/superinfected donor to putative recipient is lacking. Here, we report on the origin and evolutionary relationship between a set of recombinants from a CRF01_AE/CRF07_BC superinfected putative donor and diverse CRF01_AE/CRF07_BC recombinants from five putative recipients. Interviews on sociodemographic characteristics and sexual behaviors for these six HIV-1-infected men who have sex with men showed that they had similar ways of partner seeking: online dating sites and social circles. Phylogenetic and recombination analyses demonstrated that the near-full-length genome sequences from six patients formed a monophyletic cluster different from known HIV-1 genotypes in maximum likelihood phylogenetic trees, were all composed of CRF01_AE and CRF07_BC fragments with two common breakpoints on env, and shared 4-7 breakpoints with each other. Moreover, 3' half-genomes of recombinant strains from five recipients had identical/similar recombinant structures with strains at longitudinal samples from the superinfected donor. Recombinants from the donor were paraphyletic, whereas five recipients were monophyletic or polyphyletic in the maximum clade credibility tree. Bayesian analyses confirmed that the estimated time to the most recent common ancestor (tMRCA) of CRF01_AE and CRF07_BC strains of the donor was 2009.2 and 2010.7, respectively, and all were earlier than the emergence of recombinants from five recipients. Our results demonstrated that the closely related unique recombinant forms of HIV-1 might be the descendent of a series of recombinants generated gradually in a superinfected patient. This finding highlights the importance of early initiation of antiretroviral therapy as well as tracing and testing of partners in patients with multiple HIV-1 infection.

HIV-1 subtypes and drug resistance mutations among female sex workers varied in different cities and regions of the Democratic Republic of Congo

Background

Complex mosaic structures of HIV-1 were found in the Democratic Republic of Congo (DRC). Currently, there is limited information on the circulating HIV-1 strains, the distribution of these strains and antiretroviral (ART) resistant viruses in different regions of the country, and the HIV-1 strains harbored by the high-risk groups like female sex workers (FSW) reported to be the source of recombinant and ART resistant viruses.

Methods

Dried Blood Spots (DBS), collected from 325 infected FSWs in ten cities from 2012 DRC HIV/STI Integrated Biological and Behavioral Surveillance Survey, were tested for HIV-1 genotypes and antiretroviral resistance mutations. Regional segregation of HIV-1 clades was detected using phylogenetics. The significance for differences in HIV-1 subtype and drug resistance mutations were evaluated using Chi-square tests.

Results

There were 145 (env) and 93 (pol) sequences analyzed. Based on env sequences, the predominant subtype was A1 (44%), and recombinants as defined pol sequences comprised 35% of the total sample. Paired sequences of pol and env from DRC FSW revealed mosaic recombinant in 54% of the sequences. Distinct geographic distributions of different HIV-1 subtypes and recombinants were observed. Subtype A1 was prevalent (40%) in Goma located in the East and significantly higher than in Mbuji-Mayi (p<0.05) in the South-central region, or in Lubumbashi in the South. Antiretroviral resistance was detected in 21.5% of 93 pol sequences analyzed, with the M184I/V and K103N mutations that confer high-level resistance to NRTI and NNRTI, respectively, being the most frequent mutations. However, the K103N mutant viruses were found only in the East.

Conclusion

HIV-1 variants found in DRC FSW reflect those reported to circulate in the general population from the corresponding geographical locations. HIV-1 mosaic genetics were readily detected in FSW. Importantly, ART resistance mutations to NNRTI and NRTI were common in the DRC sex workers.

Prediction of Multi peptides Vaccination from VP10,VP21, VP51 against Reverse Transcriptase Human immunodeficiency Viruses Using Immuno-informatics Approach.. [DOI: 10.1101/2019.12.16.877555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0]

The human immunodeficiency virus-(HIV) is group of the genus Lentivirus within the family of Retroviridae, subfamily Ortho retrovirinae. Based on genetic characteristics and differences in the viral antigens, HIV is classified into the types 1 and 2 (HIV-1, HIV-2). HIV is identical single – stranded RNA molecule that are enclosed within the core of the virus particle proteins, the genome of the HIV Provirus, also known as DNA, is generated by the Protease against reverse transcriptase RNA genome into DNA, degradation of the RNA and integration of the double – stranded HIV DNA into the human genome. The aim of this study is to determine antigenic peptides from p10, p21, and p51 proteins that can be used for multiple peptide vaccine design using In-Silico study. A total of 73 sequences of three proteins were obtained from NCBI and subjected to multiple sequence alignments using CLUSTALW tool to determine conserved regions.

Immune Epitope Data Base tools were used to determine B cell epitopes, these tools are Bepipred Linear B cell epitopes prediction, surface accessibility and antigenicity prediction. Epitope binding to MHC class I and class II and their population coverage were also determined using IEDB software. The analysis results are as follow, for B cell binding from p10 (708QGYSP712), from p21 (704QGYSP708,73CVPTDPNPQ81) and (346“FKNL349) from p51. All these peptides have high score in Linear B cell epitopes prediction, surface accessibility and antigenicity prediction. On another hand peptides that reacted to MHC class I were (47EANTTLFCA55,53FCASDAKAY61,55,ASDAKAYET63) form p10,(38YYGVPVWKE46,10PQEVFLVNV18and29AAGSTMGAA37) from p21 and (63“EWEFVNTPP71,70PPLVKLWYQ78and79EKEPIVGA87) from p51 protein respectively. It worth noting that the peptides (119IISLWDQSL127,108CVKLTPLCV116) from p10, (38YYGVPVWKE46,20LLQYWSQEL34,16FNMWKNNMV30) from p21 and (7WKGSPAIFQ21,11WEFVNTPPL25and58FLWMGYELH72) protein is also binds to MHC class II with high affinity. All T cell peptides had highest population coverage, and the combined coverage for all peptides in this study was found to be 100%. Using In-Silico studies will ensure less risk of virulence and side effects. Evaluation of antibodies response in animal models is needed to confirm efficacy of these epitopes in inducing protective immune response.

MosaicSolver: a tool for determining recombinants of viral genomes from pileup data

Viral recombination is a key evolutionary mechanism, aiding escape from host immunity, contributing to changes in tropism and possibly assisting transmission across species barriers. The ability to determine whether recombination has occurred and to locate associated specific recombination junctions is thus of major importance in understanding emerging diseases and pathogenesis. This paper describes a method for determining recombinant mosaics (and their proportions) originating from two parent genomes, using high-throughput sequence data. The method involves setting the problem geometrically and the use of appropriately constrained quadratic programming. Recombinants of the honeybee deformed wing virus and the Varroa destructor virus-1 are inferred to illustrate the method from both siRNAs and reads sampling the viral genome population (cDNA library); our results are confirmed experimentally. Matlab software (MosaicSolver) is available.

Stampidine as a promising antiretroviral drug candidate for pre-exposure prophylaxis against sexually transmitted HIV/AIDS

INTRODUCTION

Pre-exposure prophylaxis (PrEP) is an evolving new approach to prevention of sexually transmitted HIV-1 that employs antiretroviral (ARV) agents prior to potential HIV-1 exposure in an attempt to reduce the likelihood of HIV-1 infection postexposure. The identification of new ARV agents with potent activity against multidrug-resistant HIV remains an unmet and urgent challenge in the field of PrEP.

AREAS COVERED

This article reviews the preclinical and early clinical activity and safety profile of stampidine, a novel antiretroviral (ARV) drug candidate that exhibits remarkable subnanomolar to low nanomolar in vitro antiretroviral potency against genotypically and phenotypically nucleoside reverse transcriptase inhibitor (NRTI)-resistant primary clinical HIV isolates, non-nucleoside RT-resistant HIV-1 isolates. Stampidine has a favorable pharmacokinetic profile in mice, rats, dogs and cats with 25 or 50 mg/kg tolerable dose levels yielding micromolar plasma concentrations that are 1000-fold higher than its in vitro IC(50) value against HIV. Stampidine has a favorable, safety profile in mice, rats, dogs and cats and it showed significant in vivo ARV activity in HIV-infected Hu-PBL-SCID mice as well as FIV-infected domestic cats. Furthermore, it did not cause any maternal toxicity, developmental toxicity or teratogenicity in rabbits treated at 10 - 40 mg/kg/day dose levels. In a recently completed first-in-human Phase I clinical trial, stampidine did not cause dose-limiting toxicity at single dose levels ranging from 5 to 25 mg/kg.

EXPERT OPINION

The favorable safety and activity profile of stampidine warrants its further development as a promising next-generation PrEP candidate to prevent the sexual transmission of HIV-1. The discovery of stampidine as a potent antiretroviral agent represents a significant step forward in the development of effective therapeutic as well as preventive strategies against HIV/AIDS.

Transmission of two distinct HIV type 1 strains to an individual that were harbored for many years by another

The concept of transmission bottlenecks in HIV-1 infection is well established. Coinfections and superinfections have been increasingly documented and provide a founding cause for the expansion of viral diversity through recombination. It is still relatively unclear how HIV-1 will propagate and evolve in individuals infected with more than one viral strain. Here we report on the parallel transmission of genetically distant viral strains cocirculating in one individual over many years to a single recipient.

Multiple HIV-1 infections with evidence of recombination in heterosexual partnerships in a low risk Rural Clinical Cohort in Uganda

We report on the frequency of multiple infections, generation of recombinants and consequences on disease progression in 35 HIV-1 infected individuals from 7 monogamous and 6 polygamous partnerships within a Rural Clinical Cohort in Uganda. The env-C2V3, gag-p24 and pol-IN genes were sequenced. Single genome amplified half genome sequences were used to map recombination breakpoints. Three participants were dually infected with subtypes A and D, one case with subtype A and A/D recombinant and the fifth with 2 phylogenetically distinct A/D recombinants. Occurrence of A/D recombination was observed in two multiple infected individuals. Rate of late stage WHO events using Cox regression was 3 times greater amongst multiple infected compared to singly infected individuals (hazard ratio 3.35; 95% CI 1.09, 10.3; p = 0.049). We have shown that polygamous relationships involving subtype discordant partnerships was a major contributor of multiple infections with generation of inter subtype recombinants in our cohort.

T-cell responses in primary HIV-1 infection

PURPOSE OF REVIEW

Important immunological events, especially involving T cells, occur during primary HIV-1 infection. The qualitative nature of the primary immune response to the virus may determine long-term outcome. Whereas CD4 T cells are being rapidly depleted, CD8 T cells play an important role in the initial control of viral replication. There is significant individual variability in the extent of viral control. Understanding the mechanisms underlying these differences and the causes of the development of dysfunctional T-cell responses will allow the identification of opportunities for therapeutic intervention that might change the long-term outcome.

RECENT FINDINGS

Recent studies have revealed early dysfunction of T cells demonstrating increased expression of PD-1, CTLA-4 and reduced expression of CD127. Those studies suggest disruption of the interaction between CD4 and CD8 T cells. In addition, a few regions, mainly within the Gag protein, have been highlighted as potentially important targets for effective immune responses inducing viral control.

SUMMARY

Despite recent studies emphasizing the critical nature of acute HIV-1 infection, current intervention strategies have failed to influence disease progression. Recent findings have indicated potential new strategies to re-enable functional properties of T cells and direct these responses towards critical regions of the virus.

Multiple-infection and recombination in HIV-1 within a longitudinal cohort of women

BACKGROUND

Recombination between strains of HIV-1 only occurs in individuals with multiple infections, and the incidence of recombinant forms implies that multiple infection is common. Most direct studies indicate that multiple infection is rare. We determined the rate of multiple infection in a longitudinal study of 58 HIV-1 positive participants from The Women's Interagency HIV Study with a richer sampling design than previous direct studies, and we investigated the role of recombination and sampling design on estimating the multiple infection rate.

RESULTS

40% of our sample had multiple HIV-1 infections. This rate of multiple infection is statistically consistent with previous studies once differences in sampling design are taken into account. Injection drug use significantly increased the incidence of multiple infections. In general there was rapid elimination of secondary strains to undetectable levels, but in 3 cases a superinfecting strain displaced the initial infecting strain and in two cases the strains coexisted throughout the study. All but one secondary strain was detected as an inter- and/or intra-genic recombinant. Injection drug use significantly increased the rate of observed recombinants.

CONCLUSION

Our multiple infection rate is consistent with rates estimated from the frequency of recombinant forms of HIV-1. The fact that our results are also consistent with previous direct studies that had reported a much lower rate illustrates the critical role of sampling design in estimating this rate. Multiple infection and recombination significantly add to the genetic diversity of HIV-1 and its evolutionary potential, and injection drug use significantly increases both.

PL-100, a novel HIV-1 protease inhibitor displaying a high genetic barrier to resistance: an in vitro selection study

The development of new HIV inhibitors with distinct resistance profiles is essential in order to combat the development of multi-resistant viral strains. A drug discovery program based on the identification of compounds that are active against drug-resistant viruses has produced PL-100, a novel potent protease inhibitor (PI) that incorporates a lysine-based scaffold. A selection for resistance against PL-100 in cord blood mononuclear cells was performed, using the laboratory-adapted IIIb strain of HIV-1, and it was shown that resistance appears to develop slower against this compound than against amprenavir, which was studied as a control. Four mutations in protease (PR) were selected after 25 weeks: two flap mutations (K45R and M46I) and two novel active site mutations (T80I and P81S). Site-directed mutagenesis revealed that all four mutations were required to develop low-level resistance to PL-100, which is indicative of the high genetic barrier of the compound. Importantly, these mutations did not cause cross-resistance to currently marketed PIs. In contrast, the P81S mutation alone caused hypersensitivity to two other PIs, saquinavir (SQV) and nelfinavir (NFV). Analysis of p55Gag processing showed that a marked defect in protease activity caused by mutation P81S could only be compensated when K45R and M46I were present. These data correlated well with the replication capacity (RC) of the mutant viruses as measured by a standard viral growth assay, since only viruses containing all four mutations approached the RC of wild type virus. X-ray crystallography provided insight on the structural basis of the resistance conferred by the identified mutations.

A daily process investigation of alcohol-involved sexual risk behavior among economically disadvantaged problem drinkers living with HIV/AIDS

Alcohol use is believed to increase sexual risk behavior among people living with HIV/AIDS (PLWHA). As drinking and sexual risk acts often occur in the same social contexts, this association is difficult to confirm. In this study, electronic daily diaries were completed by 116 PLWHA over 5 weeks. This yielded a total of 1,464 records consisting of data pertaining to discrete occasions of anal and vaginal sex. Simultaneous within- and between-person multilevel analyses were conducted, including situational variables (partner type, partner serostatus, partner drinking) and individual difference variables (gender, level of alcohol dependence). The resulting model explains 27.5% of the variance and reveals that interactions among these situational and individual difference variables predict changes in the estimated rate of unprotected sex (US). Also, in defined contexts, the amount of alcohol consumed prior to sex significantly affects the rate of US among members of the sample. Implications are discussed.

Enhanced adaptation of vesicular stomatitis virus in cells infected with vaccinia virus

Infections involving different viruses (multiple infections) are common in nature and can take place between different strains of the same virus or between different virus species, including DNA and RNA viruses. The influence of multiple infections on viral evolution has been previously studied using different populations of the same virus. Here, we took a step forward by studying the evolution of an RNA virus (vesicular stomatitis virus, VSV) in the presence of a resident DNA virus (vaccinia virus, VV). Cell cultures were infected with a constant amount of VV, and VSV was added at four different post-VV-inoculation times and four different population sizes. The results showed that the presence of VV accelerates the adaptation of VSV to a cellular environment, especially at high population sizes. The effect of VV on VSV evolution was stronger when cells were incubated for longer times with VV prior to the addition of VSV. Our results suggest that cooperation between the two viruses rather than competition might be responsible for the enhanced rate of adaptation of VSV. Further studies are needed to discern whether infections involving different viruses could have an increased ability to escape antiviral strategies.

The possible contribution of HIV-1-induced syncytia to the generation of intersubtype recombinants in vitro

OBJECTIVE

To develop a method for single syncytia isolation and delineate the possible contribution of syncytia to intersubtype recombination.

DESIGN

We dually infected whole peripheral mononuclear blood cells with subtype A and D viruses and studied syncytia in vitro and developed a method to isolate individual syncytia to further study HIV variants/dual infections, viral isolation, proviral copies in single syncytia and possible intersubtype recombination in dual cultures containing syncytia using real time PCR.

METHODS

Cell culture-based single syncytia isolation, PCR and cloning to determine the nature of HIV variants and real-time PCR to determine proviral copies per individual syncytium and intersubtype recombination in dual cultures. Viral coculture from single syncytia and p24 antigen determination for assessing viral replication in vitro.

RESULTS

Our results show the feasibility that not only can single syncytia be successfully isolated, but the viruses from individual syncytia can also be grown in vitro. They also demonstrate the ability of single syncytia to bring diverse HIV-1 subtypes together along with the possible contribution to intersubtype recombination in vitro. Up to 40% of single syncytia harbored both input HIV-1 subtypes and single syncytium could harbor as many as 2000 proviral DNA copies, which exceeds the limit seen in a single cell.

CONCLUSION

These analyses are unique in experimentally confirming the previously held belief that single syncytia can harbor multiple HIV strains and that they can serve as a breeding ground for heterozygous virions and this may contribute toward viral diversity and intersubtype recombination.

Incidence of putative HIV superinfection and sexual practices among HIV-infected men who have sex with men

OBJECTIVES

To determine the upper limit for the incidence of clinically important HIV superinfection among HIV-infected men who have sex with men (MSM) and its relationship with engagement in unsafe sexual practices.

METHODS

This was a retrospective cohort and nested case-control study. Electronic files of all HIV-infected MSM not on antiretroviral therapy were reviewed. Those clients with sudden, unexplained and sustained declines in CD4 T-cell counts and increases in plasma HIV RNA were considered as being putatively superinfected with HIV and were recruited as cases, whereas those without these features were recruited as controls (four per case) to answer a self-administered questionnaire.

RESULTS

Ten cases were identified from 145 eligible MSM (7%, 95% confidence interval 3-11%), comprising a rate of 3.6 per 100 person-years at risk. Cases had an annual decline in CD4 T-cell counts of 201 cells microL(-1) compared with 9 cells microL(-1) for controls. There were no statistically significant differences between cases and controls with regard to sexual practices that may have exposed them to acquisition of HIV superinfection (P-value >or= 0.4), nor in their perceptions or beliefs of HIV superinfection (P-value >or= 0.3). Only a minority reported no previous knowledge of HIV superinfection (17%, 5/30). Overall, both cases and controls were engaging frequently in unsafe sexual practices with casual partners who were HIV infected (80 and 52%, respectively; P-value=0.4) or whose HIV serostatus was unknown (40 and 50%, respectively; P-value=1.0).

CONCLUSIONS

Despite considerable unsafe sexual practices occurring among this cohort of sexually active MSM the incidence of clinically significant HIV superinfection was likely to be less than 4% per year.

Characterization of HIV-1 subtypes and viral antiretroviral drug resistance in men who have sex with men in Beijing, China

OBJECTIVES

To characterize the HIV subtypes prevalent among men who have sex with men (MSM) in Beijing and to perform baseline genotypic analysis of anti-HIV drug resistance in this population.

DESIGN

In 2005, half of new HIV-1 infections occurred through unprotected sex in China. MSM have become the second most vulnerable group to HIV infection. HIV-1-prevalent subtypes among this population as well as their genetic and biological characteristics have not been well defined.

METHODS

A cohort consisting of 54 HIV-seropositive MSM were recruited with written informed consent. Samples of plasma and whole blood were collected to characterize prevalent HIV-1 subtypes with overlapped polymerase chain reaction followed by sequencing and phylogenic analysis. The genotypes of anti-HIV drug resistance were analysed.

RESULTS

Among the amplified gag sequences, HIV-1 subtype B accounted for 71.1% (32/45), followed by CRF01_AE for 24.4% (11/45) and CRF07_BC for 4.4% (2/45). A similar trend was observed among the amplified env sequences. Six antiretroviral therapy (ART)-naive participants (15%) carried drug-resistant mutations, with intermediate to high-level resistance both to drugs used in China including zidovudine, didanosine, nevirapine, stavudine, and lamivudine, and drugs not used in China such as delavirdine, efavirenz, tenofovir, emtricitabine and abacavir. We also have concerns over nelfinavir and atazanavir regarding their future use in China because low-level resistance was also seen against those drugs.

CONCLUSION

The HIV-1 strains prevalent among Beijing MSM include complex subtypes derived from recombination. High rates of HIV drug-resistant mutations in ART-naive patients represent a serious challenge for HIV prevention and treatment programmes in China.

Complex patterns of the HIV-1 epidemic in Kuala Lumpur, Malaysia: Evidence for expansion of circulating recombinant form CRF33_01B and detection of multiple other recombinants

The HIV protease-reverse transcriptase (PR-RT) (1047 bp), gp120-env (891 bp) and gp41-env (547 bp) regions from the plasma of 115 HIV-1-infected patients in Kuala Lumpur (KL), Malaysia were sequenced. Detailed phylogenetic and bootscanning analyses were performed to determine the mosaic structure of the HIV-1 strains and their recombination breakpoint(s). Among the 50 patient samples in which all three regions could be amplified, the HIV-1 CRF01_AE subtype (46%) was predominant followed by subtypes B (10%) and B' (6%). A total of 9/50 (18%) patients were infected with a CRF01_AE/B inter-subtype recombinant, displaying a recombinant form (RF)(PR-RT), CRF01_AE(gp120-env) and CRF01_AE(gp41-env). This RF was derived from the Thai variants of CRF01_AE and B' subtype, with two distinct B' subtype segments in the backbone of CRF01_AE, similar to the newly identified CRF33_01B. In addition, one sample demonstrated a close structural relationship with the new CRF33_01B in the PR-RT region but displayed B' segment in part of the env region (RF(PR-RT), CRF01_AE/B'(gp120-env) and B'(gp41-env)) indicating continuing evolution of CRF33_01B. The remaining 18% of samples were identified as unique recombinant forms (URFs).

Near full-length sequence analysis of a Unique CRF01_AE/B recombinant from Kuala Lumpur, Malaysia

A new HIV-1 circulating recombinant form (CRF), CRF33_01B, has been identified in Malaysia. Concurrently we found a unique recombinant form (URF), that is, the HIV-1 isolate 06MYKLD46, in Kuala Lumpur, Malaysia. It is composed of B or a Thai variant of the B subtype (B') and CRF01_AE. Here, we determined the near full-length genome of the isolate 06MYKLD46 and performed detailed phylogenetic and bootscanning analyses to characterize its mosaic composition and to further confirm the subtype assignments. Although the majority of the 06MYKLD46 genome is CRF01_AE, we found three short fragments of B or B' subtype inserted along the genome. These B or B' subtype regions were 716 and 335 bp, respectively, in the protease-reverse transcriptase (PR-RT) region, similar to those found in CRF33_01B, as well as an extra 590 bp in the env gene region. Thus we suggest that 06MYKLD46 is a possible second-generation HIV-1 recombinant derived from CRF33_01B.

Global epidemiology of HIV-AIDS

Although intravenous drug use is the major route of transmission in several countries, sexual transmission is the dominant mode of HIV spread globally, with a concomitant epidemic in infants borne to HIV-infected mothers. The HIV epidemic varies substantially from one geographic area to another, and three broad epidemic categories describe the diversity of features observed globally: low epidemic settings, centrzated epidemics, and generalized epidemics. The introduction of highly active antiretroviral therapy in industrialized countries has transformed AIDS from an inevitably fatal condition to a chronic, treatable condition, but this goal has yet to be realized in most resource-constrained settings that bear a disproportionate burden of infection. This article describes the modes of HIV transmission, geographic distribution of the evolving AIDS pandemic, and case studies of each of the three types of HIV epidemics, and presents global trends in AIDS and mortality.

High genetic variability of HIV-1 in female sex workers from Argentina

Background

A cross-sectional study on 625 Female Sex Workers (FSWs) was conducted between 2000 and 2002 in 6 cities in Argentina. This study describes the genetic diversity and the resistance profile of the HIV-infected subjects.

Results

Seventeen samples from HIV positive FSWs were genotyped by env HMA, showing the presence of 9 subtype F, 6 subtype B and 2 subtype C. Sequence analysis of the protease/RT region on 16 of these showed that 10 were BF recombinants, three were subtype B, two were subtype C, and one sample presented a dual infection with subtype B and a BF recombinant. Full-length genomes of five of the protease/RT BF recombinants were also sequenced, showing that three of them were CRF12_BF. One FSW had a dual HIV-1 infection with subtype B and a BF recombinant. The B sections of the BF recombinant clustered closely with the pure B sequence isolated from the same patient. Major resistance mutations to antiretroviral drugs were found in 3 of 16 (18.8%) strains.

Conclusion

The genetic diversity of HIV strains among FSWs in Argentina was extensive; about three-quarters of the samples were infected with diverse BF recombinants, near twenty percent had primary ART resistance and one sample presented a dual infection. Heterosexual transmission of genetically diverse, drug resistant strains among FSWs and their clients represents an important and underestimated threat, in Argentina.

Characterization of peripheral blood human immunodeficiency virus isolates from Hispanic women with cognitive impairment

Human immunodeficiency virus type 1 (HIV-1) tropism plays an important role in HIV-associated dementia. In this study, aimed at determining if the tropism and coreceptor usage of circulating viruses correlates with cognitive function, the authors isolated and characterized HIV from the peripheral blood of 21 Hispanic women using antiretroviral therapy. Macrophage tropism was determined by inoculation of HIV isolates onto monocyte-derived macrophages and lymphocyte cultures. To define coreceptor usage, the HIV isolates were inoculated onto the U87.CD4 glioma cell lines with specific CCR5 and CXCR4 coreceptors. HIV isolates from cognitively impaired patients showed higher levels of replication in mitogen-stimulated peripheral blood mononuclear cells than did isolates from patients with normal cognition (P < .05). The viral growth of HIV primary isolates in macrophages and lymphocytes did not differ between patients with and those without cognitive impairment. However, isolates from the cognitively impaired women preferentially used the X4 coreceptor (P < .05). These phenotypic studies suggest that cognitively impaired HIV-infected women receiving treatment may have a more highly replicating and more pathogenic X4 virus in the circulation that could contribute to their neuropathogenesis.

In vitro antiviral activity and cross-resistance profile of PL-100, a novel protease inhibitor of human immunodeficiency virus type 1

Despite the success of highly active antiretroviral therapy, the current emergence and spread of drug-resistant variants of human immunodeficiency virus (HIV) stress the need for new inhibitors with distinct properties. We designed, produced, and screened a library of compounds based on an original l-lysine scaffold for their potentials as HIV type 1 (HIV-1) protease inhibitors (PI). One candidate compound, PL-100, emerged as a specific and noncytotoxic PI that exhibited potent inhibition of HIV-1 protease and viral replication in vitro (K(i), approximately 36 pM, and 50% effective concentration [EC(50)], approximately 16 nM, respectively). To confirm that PL-100 possessed a favorable resistance profile, we performed a cross-resistance study using a panel of 63 viral strains from PI-experienced patients selected for the presence of primary PI mutations known to confer resistance to multiple PIs now in clinical use. The results showed that PL-100 retained excellent antiviral activity against almost all of these PI-resistant viruses and that its performance in this regard was superior to those of atazanavir, amprenavir, indinavir, lopinavir, nelfinavir, and saquinavir. In almost every case, the increase in the EC(50) for PL-100 observed with viruses containing multiple mutations in protease was far less than that obtained with the other drugs tested. These data underscore the potential for PL-100 to be used in the treatment of drug-resistant HIV disease and argue for its further development.

Proviral progeny of heterodimeric virions reveal a high crossover rate for human immunodeficiency virus type 2

Human immunodeficiency virus type 1 (HIV-1), the causative agent of AIDS in humans, exhibits a very high rate of recombination. Bearing in mind the significant epidemiological and clinical contrast between HIV-2 and HIV-1 as well as the critical role that recombination plays in viral evolution, we examined the nature of HIV-2 recombination. Towards this end, a strategy was devised to measure the rate of crossover of HIV-2 by evaluating recombinant progeny produced exclusively by heterodimeric virions. The results showed that HIV-2 exhibits a crossover rate similar to that of HIV-1 and murine leukemia virus, indicating that the extremely high rate of crossover is a common retroviral feature.

HIV/AIDS epidemiology, pathogenesis, prevention, and treatment

The HIV-1 pandemic is a complex mix of diverse epidemics within and between countries and regions of the world, and is undoubtedly the defining public-health crisis of our time. Research has deepened our understanding of how the virus replicates, manipulates, and hides in an infected person. Although our understanding of pathogenesis and transmission dynamics has become more nuanced and prevention options have expanded, a cure or protective vaccine remains elusive. Antiretroviral treatment has transformed AIDS from an inevitably fatal condition to a chronic, manageable disease in some settings. This transformation has yet to be realised in those parts of the world that continue to bear a disproportionate burden of new HIV-1 infections and are most affected by increasing morbidity and mortality. This Seminar provides an update on epidemiology, pathogenesis, treatment, and prevention interventions pertinent to HIV-1.

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.