Dennis Maletich Junqueira

Reviewing the History of HIV-1: Spread of Subtype B in the Americas

The dispersal of HIV-1 subtype B (HIV-1B) is a reflection of the movement of human populations in response to social, political, and geographical issues. The initial dissemination of HIV-1B outside Africa seems to have included the passive involvement of human populations from the Caribbean in spreading the virus to the United States. However, the exact pathways taken during the establishment of the pandemic in the Americas remain unclear. Here, we propose a geographical scenario for the dissemination of HIV-1B in the Americas, based on phylogenetic and genetic statistical analyses of 313 available sequences of the pol gene from 27 countries. Maximum likelihood and Bayesian inference methods were used to explore the phylogenetic relationships between HIV-1B sequences, and molecular variance estimates were analyzed to infer the genetic structure of the viral population. We found that the initial dissemination and subsequent spread of subtype B in the Americas occurred via a single introduction event in the Caribbean around 1964 (1950–1967). Phylogenetic trees present evidence of several primary outbreaks in countries in South America, directly seeded by the Caribbean epidemic. Cuba is an exception insofar as its epidemic seems to have been introduced from South America. One clade comprising isolates from different countries emerged in the most-derived branches, reflecting the intense circulation of the virus throughout the American continents. Statistical analysis supports the genetic compartmentalization of the virus among the Americas, with a close relationship between the South American and Caribbean epidemics. These findings reflect the complex establishment of the HIV-1B pandemic and contribute to our understanding between the migration process of human populations and virus diffusion.

Co-circulation HIV-1 subtypes B, C, and CRF31_BC in a drug-naïve population from Southernmost Brazil: analysis of primary resistance mutations.

In Southernmost Brazil HIV‐1 subtypes B, C, and CRF31_BC co‐circulates and, since 1996 with the implementation of free access to highly active antiretroviral treatment (HAART), this epidemic is under a quite characteristic selective pressure. The profile of mutations and polymorphisms in the protease (PR) and reverse transcriptase (RT) genes of HIV‐1 from untreated patients living in Porto Alegre, Southernmost Brazil were evaluated in order to identify the subtypes and circulating drug resistant genotypes. Blood samples from 99 HIV‐1 positive drugs‐naïve patients were collected from 2006 to 2007 in Porto Alegre, Brazil. HIV PR and RT genes were amplified, sequenced, and subtyped. The HIV‐1 genotyping was performed by partial sequence analysis of the pol in the HIV Drug Resistance Database of Stanford University. Phylogenetic analyses allowed to classify the HIV samples according to their subtypes: B (26.2%), C (39.4%), F (1.1%), CRF31_CB (19.2%), and URF (14.1%). Eight (8.1%) samples showed primary resistance mutations according to the Calibrated Population Resistance tool based in the 2009 Surveillance Drug Resistance Mutation list. Two samples presented resistance mutations to PI, three NRTI and three NNRTI. There was no significant association between presence of resistant genotypes and subtypes, but resistance mutations seem to be less frequent in the subtype C. In addition, this study describes for the first time the mutational profile of CRF31_BC to PI, NRTI, and NNRTI. Genetic analyses of HIV‐1 from naïve patients are a promising and important method for surveillance of HIV infection. J. Med. Virol. 83:1682–1688, 2011.

Naturally occurring resistance mutations to HIV-1 entry inhibitors in subtypes B, C, and CRF31_BC

BACKGROUND Entry inhibitors are a class of antiretroviral (ARV) drugs that prevent HIV replication by blocking viral entry into the host cell. The investigation of naturally occurring mutations associated with entry inhibitors across subtypes is required because genetic differences between HIV-1 variants may influence the emergence of drug resistance. Despite the importance of subtype C, which predominates globally, the majority of studies include only subtype B strains. OBJECTIVES To investigate the presence of natural resistance mutations to entry inhibitors in HIV-1 subtypes B, C, and CRF31_BC strains. STUDY DESIGN Eighty samples were collected from antiretroviral-naïve patients. The gp41 gene from 67 patients and the gp120 gene from 65 patients were partially sequenced. Resistance mutations to entry inhibitors Enfuvirtide, Maraviroc, and Vicriviroc were screened. RESULTS ENF resistance-associated mutations of HR1 and HR2 on gp41 were not associated with any subtype. However, the major polymorphisms detected in HR1: N42S, L54M, and A67T were most prevalent in subtype C (p<0.001). Mutations A316T and R315Q in gp120, which are related to MVC and VCV reduced susceptibility respectively, were predominant in subtype C (p<0.05). CONCLUSIONS This study shows that many more resistance-associated mutations to entry inhibitors in ARV-naïve patients occur in subtype C compared with subtype B strains. However, further studies will be necessary to elucidate if the differential genetic background of HIV subtypes can affect the efficacy of treatment with entry inhibitors.

New insights into the in silico prediction of HIV protease resistance to nelfinavir.

The Human Immunodeficiency Virus type 1 protease enzyme (HIV-1 PR) is one of the most important targets of antiretroviral therapy used in the treatment of AIDS patients. The success of protease-inhibitors (PIs), however, is often limited by the emergence of protease mutations that can confer resistance to a specific drug, or even to multiple PIs. In the present study, we used bioinformatics tools to evaluate the impact of the unusual mutations D30V and V32E over the dynamics of the PR-Nelfinavir complex, considering that codons involved in these mutations were previously related to major drug resistance to Nelfinavir. Both studied mutations presented structural features that indicate resistance to Nelfinavir, each one with a different impact over the interaction with the drug. The D30V mutation triggered a subtle change in the PR structure, which was also observed for the well-known Nelfinavir resistance mutation D30N, while the V32E exchange presented a much more dramatic impact over the PR flap dynamics. Moreover, our in silico approach was also able to describe different binding modes of the drug when bound to different proteases, identifying specific features of HIV-1 subtype B and subtype C proteases.

Temporal dynamics of HIV-1 circulating subtypes in distinct exposure categories in southern Brazil

BackgroundThe HIV-1 epidemic in Brazil is predominantly driven by subtype B. However, in Brazilian Southern region subtype C prevails and a relatively high AIDS incidence rate is observed. The aim of the present study was to assess the temporal dynamics of HIV-1 subtypes circulating in patients from distinct exposure categories in Southern Brazil. For this purpose 166 HIV-1 samples collected at the years of 1998 (group I) and 2005–2008 (group II) were analyzed.ResultsAnalysis of group I revealed statistically significant (p < 0.05) associations between MSM and subtype B as well as between IDU and subtype C; while no statistical significant association between HIV-1 subtypes and exposure category was verified for group II. An overall temporal increase in the prevalence of subtype C and BC recombinants was observed in both HET and MSM populations, accompanied by a proportional decrease in the prevalence of the pure subtype B.ConclusionsThe present study shows an association between HIV subtypes and exposure categories at the middle 1990s in Southern Brazil. Our findings suggest that MSM and IDU populations might have played a major role in the introduction and initial dissemination of subtypes B and C, respectively, in Southern Brazil. This study also suggests a trend towards homogenization of HIV-1 strains across distinct exposure categories as a consequence of an overall increase in the prevalence of subtype C and BC recombinants in both HET and MSM populations.

Dissemination of nonpandemic Caribbean HIV-1 subtype B clades in Latin America.

Objective:To estimate the prevalence of the HIV-1 subtype B pandemic (BPANDEMIC) and Caribbean (BCAR) clades in Latin America and to reconstruct the spatiotemporal dynamics of dissemination of the BCAR clades in the region. Design:A total of 7654 HIV-1 subtype B pol sequences collected from 18 different Latin American countries between 1989 and 2011 were analyzed together with subtype B reference sequences representative of the BPANDEMIC (US/France = 300) and the BCAR (Caribbean = 279, Panama = 37) clades. Methods:Phylogeographic and evolutionary parameters were estimated from sequence data using maximum likelihood and Bayesian coalescent-based methods. Results:Nonpandemic BCAR strains were probably disseminated from the Caribbean islands of Hispaniola and Trinidad and Tobago into Latin America since the early 1970s. The BCAR strains reached nearly all countries from Latin America here analyzed and in some of them were spread locally, although their overall prevalence in the region is low. The BPANDEMIC clade comprises more than 90% of subtype B infections in most countries analyzed, with exception of Suriname, French Guyana and probably Guyana, where both BPANDEMIC and BCAR clades seem to circulate at a similar prevalence. Conclusion:This study demonstrates that nonpandemic subtype B lineages of Caribbean origin have been disseminated into Latin America shortly after the estimated introduction of subtype B in the continent. Despite their early dissemination, the BCAR strains account for a minor fraction of current HIV-1 subtype B infections in the region that are mainly driven by spreading of the globally disseminated BPANDEMIC clade.

Short-Term Dynamic and Local Epidemiological Trends in the South American HIV-1B Epidemic.

The human displacement and sexual behavior are the main factors driving the HIV-1 pandemic to the current profile. The intrinsic structure of the HIV transmission among different individuals has valuable importance for the understanding of the epidemic and for the public health response. The aim of this study was to characterize the HIV-1 subtype B (HIV-1B) epidemic in South America through the identification of transmission links and infer trends about geographical patterns and median time of transmission between individuals. Sequences of the protease and reverse transcriptase coding regions from 4,810 individuals were selected from GenBank. Maximum likelihood phylogenies were inferred and submitted to ClusterPicker to identify transmission links. Bayesian analyses were applied only for clusters including ≥5 dated samples in order to estimate the median maximum inter-transmission interval. This study analyzed sequences sampled from 12 South American countries, from individuals of different exposure categories, under different antiretroviral profiles, and from a wide period of time (1989–2013). Continentally, Brazil, Argentina and Venezuela were revealed important sites for the spread of HIV-1B among countries inside South America. Of note, from all the clusters identified about 70% of the HIV-1B infections are primarily occurring among individuals living in the same geographic region. In addition, these transmissions seem to occur early after the infection of an individual, taking in average 2.39 years (95% CI 1.48–3.30) to succeed. Homosexual/Bisexual individuals transmit the virus as quickly as almost half time of that estimated for the general population sampled here. Public health services can be broadly benefitted from this kind of information whether to focus on specific programs of response to the epidemic whether as guiding of prevention campaigns to specific risk groups.

Comprehensive Characterization of HIV-1 Molecular Epidemiology and Demographic History in the Brazilian Region Most Heavily Affected by AIDS

ABSTRACT The high incidence of AIDS cases and the dominance of HIV-1 subtype C infections are two features that distinguish the HIV-1 epidemic in the two southernmost Brazilian states (Rio Grande do Sul [RS] and Santa Catarina [SC]) from the epidemic in other parts of the country. Nevertheless, previous studies on HIV molecular epidemiology were conducted mainly in capital cities, and a more comprehensive understanding of factors driving this unique epidemic in Brazil is necessary. Blood samples were collected from individuals in 13 municipalities in the Brazilian southern region. HIV-1 env and pol genes were submitted to phylogenetic analyses for assignment of subtype, and viral population phylodynamics were reconstructed by applying Skygrid and logistic coalescent models in a Bayesian analysis. A high prevalence of subtype C was observed in all sampled locations; however, an increased frequency of recombinant strains was found in RS, with evidence for new circulating forms (CRFs). In the SC state, subtype B and C epidemics were associated with distinct exposure groups. Although logistic models estimated similar growth rates for HIV-1 subtype C (HIV-1C) and HIV-1B, a Skygrid plot reveals that the former epidemic has been expanding for a longer time. Our results highlight a consistent expansion of HIV-1C in south Brazil, and we also discuss how heterosexual and men who have sex with men (MSM) transmission chains might have impacted the current prevalence of HIV-1 subtypes in this region. IMPORTANCE The AIDS epidemic in south Brazil is expanding rapidly, but the circumstances driving this condition are not well known. A high prevalence of HIV-1 subtype C was reported in the capital cities of this region, in contrast to the subtype B dominance in the rest of the country. This study sought to comparatively investigate the HIV-1 subtype B and C epidemics by sampling individuals from several cities in the two states with the highest AIDS incidences in Brazil. Our analyses showed distinct epidemic growth curves for the two epidemics, and we also found evidence suggesting that separate transmission chains may be impacting the viral phylodynamics and the emergence of new recombinant forms.

Absence of A3Z3-Related Hypermutations in the env and vif Proviral Genes in FIV Naturally Infected Cats

Apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3 (APOBEC3; A3) proteins comprise an important family of restriction factors that produce hypermutations on proviral DNA and are able to limit virus replication. Vif, an accessory protein present in almost all lentiviruses, counteracts the antiviral A3 activity. Seven haplotypes of APOBEC3Z3 (A3Z3) were described in domestic cats (hap I–VII), and in-vitro studies have demonstrated that these proteins reduce infectivity of vif-defective feline immunodeficiency virus (FIV). Moreover, hap V is resistant to vif-mediated degradation. However, studies on the effect of A3Z3 in FIV-infected cats have not been developed. Here, the correlation between APOBEC A3Z3 haplotypes in domestic cats and the frequency of hypermutations in the FIV vif and env genes were assessed in a retrospective cohort study with 30 blood samples collected between 2012 and 2016 from naturally FIV-infected cats in Brazil. The vif and env sequences were analyzed and displayed low or undetectable levels of hypermutations, and could not be associated with any specific A3Z3 haplotype.

Mapping HIV-1 Subtype C gp120Epitopes Using a Bioinformatic Approach

Human Immunodeficiency Type-1 subtype C (HIV-1C) is rapidly diverging among populations causing more than 48% of infections worldwide. HIV-1C gp120s 128 sequences available at Genbank were aligned and submitted to phylogenetic analysis. Three major clusters were identified: 72 sequences aligned with a Brazilian 0072eference sequence; 44 sequences aligned with an Ethiopian sequence and 12 could be group along with Indian isolates. A search was made for conserved HIV-1C cytotoxic T lymphocyte (CTL) epitopes to A*0201, A*0301, A*1101 e B*07 human leukocyte antigen (HLA) alleles (using Epijen software). Five most conserved epitopes were recognized: QMHEDIISL, CTHGIKPVV, NLTNNVKTI, AITQACPKV, CTRPNNNTR. Our results showed a recognized evolutionary force of HIV-1 to escape from CTL responses mutating sites that can be negatively select by hosts immune system. The present study brings up a new approach to in silico epitope analysis taking into account geographical informations on virus diversity and host genetic background.