Ongoing HIV-1 evolution and reservoir reseeding in two elite controllers with genetically diverse peripheral proviral quasispecies

BACKGROUND Elite controllers (EC) are human immunodeficiency virus (HIV)-positive individuals who can maintain low viral loads for extended periods without antiretroviral therapy due to multifactorial and individual characteristics. Most have a small HIV-1 reservoir composed of identical proviral sequences maintained by clonal expansion of infected CD4+ T cells. However, some have a more diverse peripheral blood mononuclear cell (PBMC)-associated HIV-1 reservoir with unique sequences. OBJECTIVES To understand the turnover dynamics of the PBMC-associated viral quasispecies in ECs with relatively diverse circulating proviral reservoirs. METHODS We performed single genome amplification of the env gene at three time points during six years in two EC with high intra-host HIV DNA diversity. FINDINGS Both EC displayed quite diverse PBMCs-associated viral quasispecies (mean env diversity = 1.9-4.1%) across all time-points comprising both identical proviruses that are probably clonally expanded and unique proviruses with evidence of ongoing evolution. HIV-1 env glycosylation pattern suggests that ancestral and evolving proviruses may display different phenotypes of resistance to broadly neutralising antibodies consistent with persistent immune pressure. Evolving viruses may progressively replace the ancestral ones or may remain as minor variants in the circulating proviral population. MAIN CONCLUSIONS These findings support that the high intra-host HIV-1 diversity of some EC resulted from long-term persistence of archival proviruses combined with the continuous reservoir's reseeding and low, but measurable, viral evolution despite undetectable viremia.

Genome-wide analyses of HTLV-1aD strains from Cape Verde, Africa

We characterised and reported the first full-length genomes of Human T-cell Lymphotropic Virus Type 1 subgroup HTLV-1aD (CV21 and CV79). This subgroup is one of the major determinants of HTLV-1 infections in North and West Africa, and recombinant strains involving this subgroup have been recently demonstrated. The CV21 and CV79 strains from Cape Verde/Africa were characterised as pure HTLV-1aD genomes, comparative analyses including HTLV-1 subtypes and subgroups revealed HTLV-1aD signatures in the envelope, pol, and pX regions. These genomes provide original information that will contribute to further studies on HTLV-1a epidemiology and evolution.

Prevalence of HIV type 1 drug resistance mutations in treatment-naïve and experienced patients from resource-limited settings with universal access to antiretroviral therapy: a survey in two small Brazilian cities

Concerns have been raised that universal availability of antiretroviral agents in resource-limited settings might lead to the emergence and spread of resistant strains. We present the largest survey on human immunodeficiency virus type 1 (HIV-1) resistance among treatment-naïve and experienced patients followed in small, relatively underprivileged cities in Brazil with universal availability to standard of care antiretroviral combinations. Samples were collected between 2004 and 2006 from 95 patients followed in the cities of Saquarema and Santo Antonio de Pádua, state of Rio de Janeiro. A proviral fragment encompassing protease and reverse transcriptase (RT) regions was generated and drug susceptibility level was inferred. Among 50 strains from drug-naïve subjects, one (2 percent) had intermediate-level resistance to RT inhibitors. Among 38 patients on therapy as of sampling, 28 (73.7 percent) had plasma viral load (PVL) below detection limit (26 of whom without evidence of resistance mutations) and 11 (28.9 percent) harbored strains with reduced susceptibility. Only two strains harbored both protease and RT inhibitor mutations. Among seven patients who were off-treatment as of sampling, two (28.5 percent) harbored strains with reduced susceptibility to RT inhibitors. The relatively high frequency of undetectable PVL among patients on treatment and the overall low prevalence of resistance-associated mutations are reassuring. Continued surveillance, however, is necessary.

Autochthonous horizontal transmission of a CRF02_AG strain revealed by a human immunodeficiency virus type 1 diversity survey in a small city in inner state of Rio de Janeiro, Southeast Brazil

As part of an ongoing study on the features of AIDS spread towards small cities and rural areas, we present a molecular survey of human immunodeficiency virus type 1 (HIV-1) polymerase sequences recovered between 2004 and 2006 from 71 patients receiving care in the city of Saquarema, inner state of Rio de Janeiro. Phylogenetic reconstructions found the two prevalent lineages in the state (subtypes B [59 strains, 83.1 percent], F1 [6 strains; 8.4 percent], and BF1 recombinants [four strains; 5.6 percent]), as well as two (2.8 percent) CRF02_AG strains, which seems to be an emerging lineage in the capital. These CRF02_AG sequences were recovered from a married heterosexual couple who never traveled abroad, thus providing the first molecular evidence of autochthonous horizontal transmission of this lineage of major global importance. Also, three phylogenetic clusters of strains recovered from a total of 18.3 percent of the cohort were uncovered. Their close genetic relatedness suggests they were recovered from patients who probably took part in the same chain of viral spread. In conjunction with our previous surveys from inner Rio de Janeiro, these results suggest that although small cities harbor unique molecular features of HIV-1 infection, they also clearly reflect and may rapidly absorb the diversity recorded in large urban centers.

Anti-human immunodeficiency virus type 1 humoral immune response and highly active antiretroviral treatment

Highly active antiretroviral treatment (HAART) of human immunodeficiency type 1 (HIV-1) infection is very effective in controlling infection, but elimination of viral infection has not been achieved as yet, and upon treatment interruption an immediate rebound of viremia is observed. A combination of HAART with an immune stimulation might allow treatment interruption without this rebounding viremia, as the very low viremias observed with successful HAART may be insufficient to permit maintenance of a specific anti-HIV-1 immune response. The objective of this study was to compare the humoral immune response of individuals undergoing successful HAART (NF=no failure) with that of individuals with evidence of failure of therapy (FT) and to verify if the viremia peaks observed in individuals with therapy failure would act as a specific stimulus for the humoral anti-HIV-1 immune response. Antibodies binding to gp120 V3 genotype consensus peptides were more frequently observed for FT, mainly against peptides corresponding to sequences of genotypes prevalent in the Rio de Janeiro city area, B and F. HIV-1 neutralization of HIV-1 IIIB and of four primary isolates from Rio de Janeiro was less frequently observed for plasma from the NF than the FT group, but this difference was more expressive when plasma from individuals with detectable viremia were compared to that of individuals with undetectable viral loads in the year before sample collection. Although statistically significant differences were observed only in some specific comparisons, the study indicates that presence of detectable viremia may contribute to the maintenance of a specific anti-HIV-1 humoral immune response.

Epidemiologic features of HIV infection in three municipalities of inner Rio de Janeiro State, Brazil

In Brazil relatively little attention is being paid to the study of the features of the spread of the AIDS epidemic towards small cities and rural areas. We report a descriptive study on the epidemiological features of HIV infection among 208 adult patients seen between July 1999 and May 2006 in the municipal HIV/AIDS Programs of three cities of inner Rio de Janeiro State: Saquarema, Santo Antonio de Pádua and Miracema. A portrait of a heterosexual epidemic emerged, with an overall male to female ratio of 1.1. More than 90 percent were residents of the studied cities, demonstrating a local demand for HIV-related assistance and the importance of municipal HIV/AIDS Programs. Past or current use of snorted cocaine was reported by a quarter of the patients. Older age and male gender were independent predictors of having a diagnosis of AIDS at presentation. The latter is in accordance with a more recent wave of epidemic spread towards female gender. A low frequency of male circumcision, an important determinant of heterosexual HIV transmission, was recorded. Almost 60 percent of the patients first presented in advanced stages of HIV infection, suggesting the existence of a large pool of undiagnosed cases in the community.

No Brasil, relativamente pouca atenção vem sendo dispensada ao estudo das características do avanço da epidemia de Aids em direção aos pequenos municípios e áreas rurais. Apresentamos um estudo descritivo sobre as características epidemiológicas da infecção pelo HIV entre 208 pacientes adultos atendidos entre julho de 1999 e maio de 2006 pelos Programas Municipais de HIV/Aids de três municípios do interior do Estado do Rio de Janeiro: Saquarema, Santo Antonio de Pádua, e Miracema. Os resultados delineiam uma epidemia de perfil heterossexual, com uma razão de sexos homem-mulher de 1,1. Mais de 90 por cento eram residentes das cidades estudadas, demonstrando uma demanda local por assistência relacionada ao HIV e a importância dos Programas Municipais de HIV/Aids. Um quarto dos pacientes referiu antecedentes de uso de cocaína inalada. Variáveis idade e gênero masculino mostraram-se independentemente associadas a um diagnóstico de Aids quando da apresentação. Esta última mostra-se de acordo com um mais recente avanço da epidemia em direção às mulheres. Registramos uma baixa freqüência de circuncisão masculina, um importante determinante da transmissão heterossexual do HIV. Quase 60 por cento dos pacientes se apresentaram em estágios avançados de infecção HIV, o que sugere a existência de um grande reservatório de casos não diagnosticados na comunidade.

Molecular evidence that human immunodeficiency virus type 1 dissemination in a small Brazilian city was already taking place in the early 1990s

We recently performed a molecular epidemiology survey of human immunodeficiency virus type 1 (HIV-1) infection in Miracema, a small city in Southeast Brazil, and found multiple monophyletic clusters, consistent with independent introductions and spread of different viral lineages in the city. Here we apply Bayesian coalescent-based methods to the two largest subtype B clusters and estimate that the most recent common ancestors that gave rise to these two transmission chains were in circulation around 1991-1992. The finding that HIV-1 spread in this Brazilian small city was already taking place at a time Aids was considered a problem restricted to large urban centers may have important public health implications.

Human immunodeficiency virus type- 1 subtypes of infected patients in Espírito Santo, Brazil

Genetic variability of human immunodeficiency virus type - 1(HIV-1) is a potential threat for both diagnosis and treatment of HIV/AIDS, as well as the development of effective vaccines. Up to now, HIV subtypes circulating among HIV-positive patients in the state of Espírito Santo were not known. In the present study, blood samples from 100 therapy-naïve HIV-1 infected patients were collected and the HIV subtype was determined through the Heteroduplex Mobility Assay (HMA). Ninety-seven out of 100 studied samples were subtyped by HMA, 73 samples (75.2 percent) were from subtype B, 9 (9.3 percent) from subtype F, 3 (3.1 percent) from subtype C, 6 (6.2 percent) Benv/Fgag, and another 6 (6.2 percent) Fenv/Bgag, what suggests that recombinant viruses were present in the studied samples. Twenty-eight percent of the subtype B samples were represented by the Brazilian B" subtype, which were identified by RFLP with Fok I. Data presented here demonstrate that the epidemiological characteristics of the HIV epidemic in the state of Espírito Santo are similar to those from the other Southeastern states and helped to better understand the genetic polymorphism of HIV in Brazil.

HIV infection and AIDS in a small municipality in Southeast Brazil

OBJETIVO: Estudos sobre as características da infecção pelo HIV em pequenos municípios brasileiros são de grande importância para o desenho de estratégias de intervenção, para a alocação apropriada de recursos e melhoria da assistência. O objetivo foi investigar as características clínicas e epidemiológicas da infecção pelo HIV em um pequeno município. MÉTODOS: Foi realizado estudo descritivo em Miracema, município do noroeste do Estado do Rio de Janeiro, entre julho de 1999 e dezembro de 2003. Foram analisados todos os pacientes adultos com diagnóstico de infecção pelo HIV atendidos no Programa Municipal de HIV/Aids. Dados clínicos e epidemiológicos foram coletados prospectivamente por meio de questionário padronizado. RESULTADOS: Foram analisados no total 65 pacientes adultos que receberam atendimento no Programa Municipal de HIV/Aids. A maioria (34) eram mulheres (razão de sexos homem-mulher de 0,9). Encontrou-se preponderância absoluta de pacientes que nasceram em Miracema ou municípios vizinhos (94 por cento), moravam em Miracema (90,7 por cento), eram solteiros (70,8 por cento), atribuíam a aquisição da infecção ao contato heterossexual desprotegido (72,3 por cento) e tinham antecedentes de uso de cocaína inalada (27,7 por cento). Desordens do sistema nervoso central (incluindo cinco casos de neurocriptococose) e insuficiência respiratória aguda semelhante à pneumocistose pulmonar foram as principais causas de morbidade. A maioria dos pacientes (56,9 por cento) iniciou acompanhamento em estágios avançados de infecção pelo HIV. CONCLUSÕES: A preponderância de pacientes em estágios avançados de infecção pelo HIV sugere a existência de um grande reservatório de casos não diagnosticados na comunidade. Uma característica marcante da casuística foi a inversão da razão de sexos homem-mulher. Investigações adicionais cobrindo áreas geográficas maiores são urgentemente necessárias para o melhor entendimento do espectro clínico e epidemiológico da infecção pelo HIV em pequenos municípios brasileiros e áreas rurais.

A genotyping study of human immunodeficiency virus type-1 drug resistance in a small Brazilian municipality

In Brazil, surveillance studies on antiretroviral drug resistance among drug-naïve and treatment-experienced patients have focused primarily on patients living in large urban centers. As the epidemic spreads towards small municipalities and the innermost parts of the country, it will be essential to monitor the prevalence of antiretroviral drug resistance in these areas. We report the first survey on the prevalence of antiretroviral drug resistance in a small Brazilian municipality. Between July 1999 and March 2005, 72 adult human immunodeficiency virus type-1(HIV-1)-infected patients received care at the Municipal HIV/AIDS Program of the small, southeastern municipality of Miracema, state of Rio de Janeiro. A genotyping study of antiretroviral drug resistance was performed in 54 patients. Among 27 samples from treatment-experienced patients, 9 (33.3 percent) harbored strains with reduced drug susceptibility. Among these, 6 had reduced susceptibility to reverse transcriptase (RT) inhibitors and 3 to both RT and protease inhibitors. No primary antiretroviral drug resistance was recorded among 27 drug-naïve subjects. The relatively low prevalence of resistance mutations in the Miracema cohort argues against the concern that resource-poor settings should not implement widespread accessibility to standard of care antiretroviral combinations due to the possibility of sub-optimal adherence leading to the emergence and spread of drug-resistant strains.

Is human immunodeficiency virus/acquired immunodeficiency syndrome decreasing among Brazilian injection drug users? Recent findings and how to interpret them

We briefly review findings from Brazilian settings where the human immunodeficiency virus/acquired immunodeficiency syndrome (HIV/AIDS) epidemic among injection drug users (IDUs) seems to be decreasing, highlighting recent findings from Rio de Janeiro and discussing methodological alternatives. Former analyses using serologic testing algorithm for recent HIV seroconversion have shown that HIV incidence has been low in IDUs recruited by two different surveys carried out in Rio, where low injection frequencies and infection rates have been found among new injectors. The proportion of AIDS cases among IDUs in Rio has been fairly modest, compared to São Paulo and especially to the southernmost states. Notwithstanding, the interpretation of findings from serial surveys constitutes a challenge, magnified in the assessment of HIV spread among IDUs due to the dynamic nature of the drug scenes and limitations of sampling strategies targeting hard-to-reach populations. Assessment of epidemic trends may profit from the triangulation of data, but cannot avert biases associated with sampling errors. Efforts should be made to triangulate data from different sources, besides exploring specific studies from different perspectives. In an attempt to further assess the observed trends, we carried out original analyses using data from Brazilian AIDS databank.

Anti-human immunodeficiency virus-1 antibody titers in injection drug users compared to sexually infected individuals

Sera from infected injection drug users (IDU) have shown to have antibodies against synthetic human immunodeficiency virus-1 (HIV-1) envelope peptides more frequently. In this study, reactivity of 48 IDU plasma were compared to 60 plasmas obtained from sexually infected individuals (S). The overall reactivity of plasma from IDU compared to S was higher, and the reactivity titers were much higher for IDU plasma than S. IDU plasma also showed a broader antibody response. The higher reactivity titers were observed mainly for the gp41 immunodominant epitope and V3 peptides corresponding to the consensus sequences of HIV-1 subtypes/variants prevalent in Brazil (B, F, C) indicating the specificity in the higher immune response of IDU

Infecção pelo HIV e HTLV e Hepatites virais entre UDIs no Rio de Janeiro / HIV Infection and HTLV and viral hepatitis among UDIs in Rio de Janeiro

Procura caracterizar os usuários de drogas injetáveis em suas comunidades e definir fatores de risco para infecções pelo HIV, HTLV I/II e hepatites virais entre usuários de drogas injetáveis no Rio de Janeiro (DV)

Human immunodeficiency virus/acquired immunodeficiency syndrome and tropical diseases: a brazilian perspective

The paper summarizes recent findings on the epidemiology and pathogenesis of human immunodeficiency virus/acquired immunodeficiency syndrome (HIV/Aids), highlighting the role of co-infections with major tropical diseases. Such co-infections have been studied in the Brazilian context since the beginning of the Aids epidemic and are expected to be more frequent and relevant as the Aids epidemic in Brazil proceeds towards smaller municipalities and the countryside, where tropical diseases are endemic. Unlike opportunistic diseases that affect basically the immunocompromised host, most tropical diseases, as well as tuberculosis, are pathogenic on their own, and can affect subjects with mild or no immunosuppression. In the era of highly active anti-retroviral therapies (HAART), opportunistic diseases seem to be on decrease in Brazil, where such medicines are fully available. Benefiting from HAART in terms of restoration of the immune function, putative milder clinical courses are expected in the future for most co-infections, including tropical diseases. On the other hand, from an ecological perspective, the progressive geographic diffusion of Aids makes tropical diseases and tuberculosis a renewed challenge for Brazilian researchers and practitioners dealing with HIV/Aids in the coming years