High level of multidrug resistance mutations in HIV type 1 pol gene and resistance-associated mutations to enfuvirtide (T-20) among antiretroviral-experienced patients from central Brazil

Frequency of Fusion Inhibitor Resistance Mutations Among Therapy-Naïve HIV Patients

Glycoprotein 41 (gp41) of the human immunodeficiency virus type 1 (HIV-1) protein plays a critical role in membrane fusion. Gp41 binds to proteins in the plasma membrane of CD4+ T cells, particularly the T-cell antigen receptor (TCR). These findings indicate that gp41 is involved in the assembly of HIV-1 at the plasma membrane of T cells and affects the stimulation of the TCR. To control HIV-1, new inhibitors were introduced to target the gp41 protein. However, mutations in this region might reduce their efficacy. The Gp41 region was amplified from the sera of 30 patients using nested polymerase chain reaction. The sequences were analyzed by bioinformatics tools to identify mutations and gp41 structural features. Subtyping and the interaction between fusion inhibitors and gp41 proteins were also examined. As the first report from Iran, docking analysis between fusion inhibitors and Iranian gp41 proteins showed that mutations in gp41 could not reduce the efficacy of the fusion inhibitors. Most of the patients were infected with CRF35-AD. Several post-modification positions, including glycosylation and phosphorylation sites, were identified in the gp41 protein. Our findings revealed no known multinational drug resistance to gp41 inhibitors; thus, fusion inhibitors can effectively inhibit HIV in Iranian patients. In addition, the present study introduced a new gp41 region (36-44 aa), which considerably influences the interactions between gp41 inhibitors and the gp41 protein. This region may play a pivotal role in suppressing gp41 inhibitors in CFR35-AD. Furthermore, gp41 can be considered a good target for subtyping analysis via the phylogenetic method.

Broad-spectrum anti-HIV activity and high drug resistance barrier of lipopeptide HIV fusion inhibitor LP-19

Lipopeptide-19, a HIV fusion inhibitor (LP-19), has showed potent anti-HIV activity. However, there is still limited information of the antiviral activity against different subtype clinical isolates and the drug resistance barrier of LP-19. Therefore, 47 HIV clinical isolates were selected for this study. The viral features were identified, in which 43 strains are CCR5 tropisms, and 4 strains are CCR5/CXCR4 tropisms, and there are 6 subtype B', 15 CRF01_AE, 14 CRF07_BC, 2 CRF08_BC and 10 URF strains. These 47 viruses were used to detected and analyze the inhibitory activities of LP-19. The results showed that the average 50% inhibitory concentration (IC₅₀) and 90% inhibitory concentration (IC₉₀) of LP-19 were 0.50 nM and 1.88 nM, respectively. The average IC₅₀ of LP-19 to B', CRF01_AE, CRF07_BC, CRF08_BC, and URF strains was 0.76 nM, 0.29 nM, 0.38 nM, 0.85 nM, and 0.44 nM, respectively. C34 and Enfuvirtide (T-20), two fusion inhibitors, were compared on the corresponding strains simultaneously. The antiviral activity of LP-19 was 16.7-fold and 86-fold higher than that of C34 and T-20. The antiviral activity of LP-19, C34, and T-20 were further detected and showed IC₅₀ was 0.15 nM, 1.02 nM, and 66.19 nM, respectively. IC₅₀ of LP-19 was about 7-fold and 441-fold higher compared to C34 and T-20 against HIV-1 NL4-3 strains. NL4-3 strains were exposed to increasing concentrations of LP-19 and C34 in MT-2 cell culture. The culture virus was sequenced and analyzed. The results showed that A243V mutation site identified at weeks 28, 32, 38, and 39 of the cell culture in the gp41 CP (cytoplasmic domain) region. NL4-3/A243V viruses containing A243V mutation were constructed. Comparing the antiviral activities of LP-19 against HIV NL4-3 to HIV strains (only 1.3-fold), HIV did not show drug resistance when LP-19 reached 512-fold of the initial concentration under the drug pressure for 39 weeks. This study suggests that LP-19 has broad-spectrum anti-HIV activity, and high drug resistance barrier.

HIV-1 gp41 genetic diversity and enfuvirtide resistance-associated mutations among enfuvirtide-naïve patients in southern China

BACKGROUND

Human immunodeficiency virus (HIV) increasing molecular diversity and emergence of drug resistant mutants remain a major concern in China. Enfuvirtide (ENF/T-20) is the first entry inhibitor used in patients failing highly active antiretroviral therapy (HAART). However, data on HIV-1 gp41genetic diversity and primary ENF resistance-associated mutations among treatment-naïve patients in China is limited. The objective was to identify molecular diversity and ENF resistance patterns of HIV-1 in southern China, using envelope (env) gp41 sequences and bioinformatics tools, which may help optimize antiretroviral therapy.

METHODS

From November 2018 to January 2019, 439 blood plasma samples from ENF-naïve patients were collected from Shenzhen, Wuhan and Chongqing, of which 396 HIV env regions were sequenced and subtyped, and were performed the analysis of drug resistance-associated mutations (DRMs).

RESULTS

The main subtypes were circulating recombinant form (CRF) 01_AE (30.6 %) and CRF07_BC (48.7 %). CRF55_01B had been the fourth subtype in the study, and many rare CRFs were observed. Notably, CRF02_AG and CRF_BF strains typically found in Africa and US respectively were identified amongst Chinese patients. Known DRMs were detected in 27.5 % (109/396) of ENF treatment-naïve patients. One major DRM (L44 M), many secondary DRMs (including N126 K, E137 K, S138A), and lots of polymorphisms were found in the study, which have been proved to elevate resistance to ENF.

CONCLUSIONS

HIV-1 molecular diversity was observed in the study, which indicating that HIV-1 variability is becoming increasingly complex in southern China. A diverse set of primary DRMs discovered in this study described the serious threat to ART, which reminds us the urgent need of timely surveillance of HIV-1 viral diversity and drug resistance in China.

Identification of New HIV-1 Circulating Recombinant Forms CRF81_cpx and CRF99_BF1 in Central Western Brazil and of Unique BF1 Recombinant Forms

Intersubtype recombinants classified as circulating recombinant forms (CRFs) or unique recombinant forms (URFs) have been shown to play an important role in the complex and dynamic Brazilian HIV/AIDS epidemic. Previous pol region studies (2003–2013) in 828 patients from six states from Central Western, Northern and Northeastern Brazil reported variable rates of BF1, F1CB, BC, and CF1 mosaics. In this study HIV-1 subtype diversity BF1, F1CB, BC, and CF1 recombinants in pol were analyzed. Full/near-full/partial genome sequences were generated from F1CB and BF1 recombinants. Genomic DNA extracted from whole blood was used in nested-PCR to amplify four overlapping fragments encompassing the full HIV-1 genome. Phylogenetic trees were generated using the neighbor-joining/NJ method (MEGA 6.0). The time of the most recent common ancestor (TMRCA) of F1CB and BF1 clades was estimated using a Bayesian Markov Chain Monte Carlo approach (BEAST v1.8; BEAGLE). Bootscanning was used for recombination analyses (Simplot v3.5.1); separate NJ phylogenetic analysis of fragments confirmed subtypes. The phylogenetic analyses of protease/reverse-transcriptase sequences in 828 patients revealed 76% subtype B (n = 629), 6.4% subtype C (n = 53), 4.2% subtype F1 (n = 35), 13.4% intersubtype recombinants: 10.5% BF1 (n = 87), 2.3% BC (n = 19), 0.4% F1CB (n = 3), and 0.2% CF1 (n = 2). Two full and one partial BF1C genomes allowed the characterization of the CRF81_cpx that has 9 breakpoints dividing the genome into 10 subregions. Basic Local Alignment Search Tool searches (Los Alamos HIV Sequence Database) identified six other sequences with the same recombination profile in pol, five from Brazil, and one from Italy. The estimated median TMRCA of CRF81_cpx was 1999 (1992–2003). CRF60_BC-like sequences, originally described in Italy, were also found. Two full and one near full-length BF1 genomes led to the characterization of the new CRF99_BF1 that has six recombination breakpoints dividing the genome into seven subregions. Two new URFs BF1, with six recombination breakpoints and seven subregions were also characterized. The description of the first Brazilian BF1C CRF81_cpx and of the new CRF99_BF1 corroborate the important role of CRFs in the HIV/AIDS epidemic throughout Brazil. Our data also highlight the value of HIV-1 full-genome sequence studies in order to fully reveal the complexity of the epidemic in a huge country as Brazil.

Epidemiological and clinical profile of HIV-infected patients from Southwestern Goias State, Brazil

Knowledge about epidemiological distribution patterns of HIV infection in different geographic regions is relevant to understand the dynamics of the disease in Brazil. This study aims to characterize the epidemiological and clinical profile of HIV-infected patients from Southwestern Goias State, from 2005 to 2015. A standardized questionnaire was used to collect clinical-epidemiological, virological, and immunological data from the medical records of all HIV-infected patients (n=539) who were followed at the regional reference center of Jatai, Goias State, Brazil, from 2005 to 2015. We detected the prevalence of male patients and the heterosexual route of transmission, as well as an expressive number of young women infected with HIV. The HIV infection was more prevalent in reproductive ages (55.3%). Most patients presented clinical manifestations related to HIV infection at the time of diagnosis. Twenty-four patients presented coinfection with hepatitis C virus, syphilis, hepatitis B virus, leprosy or Chagas disease. Pneumonia caused by Pneumocystis jirovecii was the most common opportunistic infection, followed by neurotoxoplasmosis, tuberculosis, and neurocryptococcosis. Combined antiretroviral therapy improved CD4⁺ T-cell counts: the mean CD4⁺ T-cell counts after treatment was twice as high as those found at the first medical appointment; and highly active antiretroviral therapy promoted viral suppression in a significant number of patients. Considering the increasing distribution of HIV infection to the interior of Brazil, this descriptive study outlines the clinical-epidemiological characteristics of HIV infection in Southwestern Goias and contributes to develop local prevention strategies and public service plans.

Characterization of HIV-1 CRF90_BF1 and putative novel CRFs_BF1 in Central West, North and Northeast Brazilian regions

The Brazilian AIDS epidemic has been characterized by an increasing rate of BF1 recombinants and so far eight circulating recombinant forms/CRFs_BF1 have been described countrywide. In this study, pol sequences (protease/PR, reverse transcriptase/RT) of 87 BF1 mosaic isolates identified among 828 patients living in six Brazilian States from three geographic regions (Central West, North, Northeast) were analyzed. Phylogenetic and bootscan analyses were performed to investigate the evolutionary relationship and mosaic structure of BF1 isolates. Those analyses showed that 20.7% of mosaics (18 out of 87) were CRFs-like isolates, mostly represented by CRF28/CRF29_BF-like viruses (14 out of 18). We also identified five highly supported clusters that together comprise 42 out of 87 (48.3%) BF1 sequences, each cluster containing at least five sequences sharing a similar mosaic structure, suggesting possible new unidentified CRFs_BF1. The divergence time of these five potential new CRFs_BF1 clusters was estimated using a Bayesian approach and indicate that they probably originated between the middle 1980s and the middle 1990s. DNA was extracted from whole blood and four overlapping fragments were amplified by PCR providing full/near full length genomes (FLG/NFLG) and partial genomes. Eleven HIV-1 isolates from Cluster # 5 identified in epidemiologically unlinked individuals living in Central West and North regions provided FLG/NFLG/partial genome sequences with identical mosaic structure. These viruses differ from any known CRF_BF1 reported to date and were named CRF90_BF1 by the Los Alamos National Laboratory. This is the 9^th CRF_BF1 described in Brazil and the first one identified in Central West and North regions. Our results highlight the importance of continued molecular screening and surveillance studies, especially of full genome sequences to understand the evolutionary dynamics of the HIV-1 epidemic in a country of continental dimensions as Brazil.

HIV-1 genetic diversity and antiretroviral drug resistance among individuals from Roraima state, northern Brazil

The HIV-1 epidemic in Brazil has spread towards the Northern country region, but little is known about HIV-1 subtypes and prevalence of HIV strains with resistance mutations to antiretrovirals in some of the Northern states. HIV-1 protease (PR) and reverse transcriptase (RT) sequences were obtained from 73 treatment-naive and -experienced subjects followed between 2013 and 2014 at a public health reference unit from Roraima, the northernmost Brazilian state. The most prevalent HIV-1 clade observed in the study population was the subtype B (91%), followed by subtype C (9%). Among 12 HIV-1 strains from treatment-naïve patients, only one had a transmitted drug resistance mutation for NNRTI. Among 59 treatment-experienced patients, 12 (20%) harbored HIV-1 strains with acquired drug resistance mutations (ADRM) that reduce the susceptibility to two classes of antiretroviral drugs (NRTI and NNRTI or NRTI and PI), and five (8%) harbored HIV-1 strains with ADRM that reduced susceptibility to only one class of antiretroviral drugs (NNRTI or PI). No patients harboring HIV strains with reduced susceptibility to all three classes of antiretroviral drugs were detected. A substantial fraction of treatment-experienced patients with (63%) and without (70%) ADRM had undetectable plasma viral loads (<40 copies/ml) at the time of sampling. Among treatment-experienced with plasma viral loads above 2,000 copies/ml, 44% displayed no ADRM. This data showed that the HIV-1 epidemic in Roraima displayed a much lower level of genetic diversity and a lower prevalence of ADRM than that described in other Brazilian states.

Polymorphisms in the HIV-1 gp41 env gene, natural resistance to enfuvirtide (T-20) and pol resistance among pregnant Brazilian women

The selective pressure of antiretroviral drugs (ARVs) targeting HIV-1 pol can promote drug resistance mutations in other genomic regions, such as env. Drug resistance among women should be monitored to avoid horizontal and mother-to-child transmission. To describe natural resistance to T-20 (enfuvirtide), gp41 env polymorphisms, mutations in pol and HIV-1 subtypes, 124 pregnant women were recruited. For 98 patients, the gp41 env, protease (PR) and reverse transcriptase (RT) fragments were sequenced. The patients were ARV naïve (n = 30), taking mother-to-child transmission prophylaxis (n = 50), or being treated with highly active ARV therapy/HAART (n = 18). The Stanford and IAS/USA databases and other sources were used to analyze PR/RT, gp41 env resistance mutations. The HIV-1 genetic diversity was analyzed by REGA/phylogenetic analyses. The patients' median age was 25 years (range, 16-42), 18.4% had AIDS. The frequency of natural resistance to T-20 (N42D, L44M, and R46M-low-impact mutations) was 6.1% (6/98); 20.4% (20/98) had compensatory mutations in HR2. The prevalence of transmitted drug resistance in the pol was 13.3% (4/30), and the prevalence of secondary drug resistance was 33.3% (6/18). Two patients were infected with multidrug resistant/MDR viruses. The analysis of HIV-1 subtypes (PR/RT/gp41) revealed that 61.2% (60/98) were subtype B, 12.2% (12/98) were subtype C, 4.1% (4/98) were subtype F1, and 22.4% (22/98) were possible recombinants (BF1 = 20.4%; BC = 2%). Natural resistance to T-20 was not associated with pol resistance or previous ARV use. The high rate of secondary resistance, including MDR, indicates that the number of women that may need T-20 salvage therapy may be higher than anticipated.

Does genetic diversity of HIV-1 non-B subtypes differentially impact disease progression in treatment-naive HIV-1-infected individuals? A systematic review of evidence: 1996-2010

With 88% of HIV-1-infected individuals living in areas of high prevalence of non-B subtypes and with expanded global access to antiretroviral treatment (ART), studying disease progression amongst non-B subtypes gains relevance. Optimized clinical management is a possibility with knowledge of non-B subtype profiles at baseline, which is currently not possible due to lack of subtype-specific point-of-care assays. In a systematic review, we synthesized global evidence on differential disease progression amongst non-B subtypes in ART-naive individuals. Due to lack of consistent effect measures, we avoided pooling data and inferred patterns with respect to disease progression outcomes (ie, AIDS, Death, CD4, viral load changes). Subtypes C and D were more aggressive, followed by G, AE, and AG, and A being the least aggressive of all HIV-1 subtypes. Evidence of greater rates of disease progression in globally prevalent C and D subtypes highlight the importance of expanding early HIV detection, and determining subtype profile at baseline with CD4 staging to optimize the quality of ART delivery and care in global settings.

HIV type 1 molecular epidemiology in pol and gp41 genes among naive patients from Mato Grosso do Sul State, central western Brazil

Antiretroviral naive patients (n=49) were recruited in central western Brazil (Campo Grande City/Mato Grosso do Sul State, located across the Bolivia and Paraguay borders). HIV-1 protease (PR), reverse transcriptase (RT), and env gp41 HR1 fragments were sequenced. Genetic diversity was analyzed by REGA/phylogenetic analyses. Intersubtype recombinants were identified by SimPlot/phylogenetic trees. PR/RT resistance was analyzed by Calibrated Population Resistance/Stanford databases. T-20 resistance in gp41 was assessed by Stanford, Los Alamos, and other sources. Of HIV-1 subtypes 65.3% were B(PR)B(RT), 10.2% were C(PR)C(RT), and 8.2% were F1(PR)F1(RT). Intersubtype recombinants were 16.3%: four B/F1 and four B/C (two were "CRF31_BC-like"). The Pol-RT V75M mutation was detected in two homosexual partners; one patient had the T215S revertant mutation. T-20/gp41 resistance mutations were L44M (n=2) and V38A (n=1). The high percentage of non-B isolates (∼35%) highlights the importance of molecular surveillance studies in settings distant from the origin of the epidemic. Our data help elaborate the molecular epidemiological map of HIV-1 in Brazil.

Genetic and structural analysis of HIV-1 Rev responsive element related to V38A and T18A enfuvirtide resistance mutations

BACKGROUND

For the expression of late viral genes, HIV-1 efficiently exploits the nuclear export by using Rev viral protein, which specifically binds the RNA Rev Responsive Element (RRE). This region is contained within the gp120-gp41 encoding sequence. Enfuvirtide is the first approved HIV-1 fusion-inhibitor, and gp41 codons associated with primary enfuvirtide-resistance (amino-acids 36-45) are localized within the RRE structure. We previously found the co-presence of V38A+T18A resistance mutations in patients failing enfuvirtide.

METHODS

Collecting 476 and 135 HIV-1 B-subtype gp41 sequences from enfuvirtide-naïve and enfuvirtide-treated patients, respectively, two mutations previously found associated with enfuvirtide treatment, T18A and V38A, were analyzed. Moreover, the RNA secondary structure was displayed by CONTRAfold-software and the gp41 evolutionary pathways by a mutagenetic tree.

RESULTS

By modeling the RRE structure, we show that the T18 and V38 codons are base pairing within the RRE-stem-IIA, an important domain involved in Rev binding. While a structural RRE impairment in the presence of V38A alone was found, a restoration of the original RRE structure occurred in co-presence of V38A+T18A. By mutagenetic tree analysis, a compensatory evolution confirming our hypothesis on the structural modification mechanism was observed.

CONCLUSION

We show that enfuvirtide pressure may also affect specific RRE domains involved in Rev binding, thus requiring a compensatory evolution able to preserve the secondary structure of the RRE.

Molecular characteristics of HIV type 1 infection among prisoners from Central Western Brazil

Abstract This study among antiretroviral-experienced prisoners from central western Brazil investigated mutations associated with secondary resistance to nucleoside/nonnucleoside reverse transcriptase inhibitors (NRTI/NNRTI), protease inhibitors (Stanford HIV-1 Resistance/International Aids Society Databases), and HIV-1 subtypes (REGA/phylogenetic analyses/SimPlot). Twenty-seven prisoners from three prisons (16 males and four females from Mato Grosso do Sul State and seven males from Goiás State) had HIV-1 protease and reverse transcriptase fragments sequenced after nested PCR. Median age was 35 years. Seven males and two females were intravenous drug users, three males referred homosexual practice. Resistance mutations were present in 37% (10/27): NRTI+NNRTI mutations (n=5), NRTI mutations (n=3), multidrug-resistant mutations (n=2). Subtype B (48%), subtype C (11%), B/F1, B/C, and F1/B/C recombinants (40.7%) were detected. Possible intraprison transmissions were identified: two intravenous drug user females (subtype C); two clusters among homosexual males (subtype B and B/F1). High resistance rate and possible intraprison transmission highlight the need for improved prevention, counseling, and treatment strategies for prisoners.

Genotypic analysis of the gp41 HR1 region from HIV-1 isolates from enfuvirtide-treated and untreated patients

OBJECTIVE

To evaluate the polymorphisms and resistance mutations in gp41 HR1 region of HIV-1.

METHODS

The study included 28 HIV-positive patients undergoing enfuvirtide (ENF) treatment or not from Porto Alegre, Rio Grande do Sul state, and Rio de Janeiro, Rio de Janeiro state, between 2006 and 2009. Resistance mutations and polymorphisms of the gp41 HR1 region were detected using the genomic DNA of 12 ENF-untreated patients and 16 patients in ENF treatment, encompassing subtypes B, C, and F1. Sample subtypes were determined by neighbor-joining phylogenetic analysis with a Kimura's two-parameter correction.

RESULTS

A high prevalence of polymorphisms unrelated to resistance was observed. Among ENF-untreated patients, 16% showed mutations related with resistance. Among patients in ENF treatment, 50% had resistance-related mutations. Overall, 17% of all isolates showed the N42S polymorphism related to ENF hypersusceptibility. The presence of ENF resistance mutations in the group of treated patients reduced viral load. The V38A substitution was the most frequent among treatment-experienced patients followed by the G36D/E, N42D, and V38M substitutions.

CONCLUSIONS

The V38A substitution in the gp41 HR region was the most common resistance mutation among ENF-treated patients and was associated with increased viral load.

Analysis of HIV-1 BF pr/rt recombinant strains from Rio de Janeiro/Brazil reveals multiple unrelated mosaic structures

Due to the co-circulation of HIV-1 subtypes B and F1 in Brazil, a large variety of unique BF1 recombinant forms (URFs_BF1) and four circulating BF1 recombinant forms (CRF28, CRF29, CRF39 and CRF40) have been described. The aim of this study was to investigate mosaic structure and phylogenetic relationship among several BF1 (protease-reverse transcriptase, pr/rt) recombinant sequences obtained from a group of patients from Rio de Janeiro, Brazil, from 1994 to 2005. Phylogenetic relationships were estimated by Bayesian and SplitsTree methods. Recombination breakpoints were analyzed by Bootscan. Those samples presenting the same recombinant pattern in the pr/rt region were investigated in the integrase (int) and envelope (env) regions as a screening method for the detection of potential new CRFs candidates. Third out of 61 pr/rt HIV-1 BF1 recombinant sequences analyzed depicted unique recombinant structures and were classified URFs_BF1. The other 31 samples segregated in eight well-supported phylogenetic clusters composed of at least three samples sharing the same recombination pattern. Analyses of the int and env regions from these 31 samples revealed that 11 samples were URFs_BF1. Three and four sequences corresponded, respectively, to the previously described CRF39 and CRF40. Three samples displayed a CRF28-like mosaic structure, and one sample a CRF29-like mosaic pattern. The other nine BF1 samples segregate in three distinct clusters with the same recombination profile and could represent good candidates for new CRFs_BF profiles. The HIV-1 BF1 epidemic in Rio de Janeiro is characterized by a high prevalence (67%) of URFs_BF1 and a low prevalence (4.9-6.6%) of each CRFs_BF previously identified in Brazil.

Caveolin-1 modulates HIV-1 envelope-induced bystander apoptosis through gp41

Human immunodeficiency virus (HIV) envelope (Env)-mediated bystander apoptosis is known to cause the progressive, severe, and irreversible loss of CD4(+) T cells in HIV-1-infected patients. Env-induced bystander apoptosis has been shown to be gp41 dependent and related to the membrane hemifusion between envelope-expressing cells and target cells. Caveolin-1 (Cav-1), the scaffold protein of specific membrane lipid rafts called caveolae, has been reported to interact with gp41. However, the underlying pathological or physiological meaning of this robust interaction remains unclear. In this report, we examine the interaction of cellular Cav-1 and HIV gp41 within the lipid rafts and show that Cav-1 modulates Env-induced bystander apoptosis through interactions with gp41 in SupT1 cells and CD4(+) T lymphocytes isolated from human peripheral blood. Cav-1 significantly suppressed Env-induced membrane hemifusion and caspase-3 activation and augmented Hsp70 upregulation. Moreover, a peptide containing the Cav-1 scaffold domain sequence markedly inhibited bystander apoptosis and apoptotic signal pathways. Our studies shed new light on the potential role of Cav-1 in limiting HIV pathogenesis and the development of a novel therapeutic strategy in treating HIV-1-infected patients.