Molecular Epidemiology of the virus of the imunodeficiência human being type 1 (HIV-1) in cities of the interior of the State of Rio de Janeiro, with emphasis in the cities of Miracema, Santo Antonio de Pádua and Saquarema, 2001 the 2006.
The AIDS epidemic in Brazil is spreading from the large urban centers to small cities and the innermost partsof the country, yet data on the features of HIV-1 infection in these places are scarce. Such spread is expected topose formidable medical, social and logistic challenges. By using mainly HIV-1 envelope and polymerasegenomic regions, the studies that compose this thesis try to translate HIV-1 nucleotide sequences intoknowledge on viral genetic diversity, molecular epidemiology and prevalence of antiretroviral drug resistancein inner Rio de Janeiro State. Not being feasible to study in detail all inner municipalities of the State, we focusour magnifying lens of investigation into three inner cities chosen as a convenience sample: Miracema andSanto Antonio de Pádua, in the northwestern sub-region, and Saquarema, in the Sun Coast sub-region. In theseplaces we might perhaps extract useful information that will lead to a better understanding of the features ofHIV-1 spread towards inner Rio de Janeiro State and Brazil. Between July 1999 and May 2006 a total of 208adult patients received care in the municipal HIV-1/AIDS program established in these cities. A portrait of aheterosexual epidemic emerged, with a male to female ratio of 1.1. Almost 60% of the patients first presentedin advanced stages of HIV-1 disease, which suggests the existence of a large pool of undiagnosed cases in thecommunity. Variables age and male gender were independent predictors of an AIDS-defining CDC stage atpresentation. More than 90% of the patients were residents of the studied cities, which demonstrate a huge localdemand for HIV-1-related counseling, testing and treatment. Therefore, the establishment of as manymunicipal HIV-1/AIDS programs should stand as a priority in our efforts to halt epidemic spread towards innerBrazil. We report a low frequency of male circumcision, an important determinant of HIV-1 heterosexualtransmission. Around one fourth of the cohort reported past use of inhaled cocaine. A total of 14.5% of CDCstage C patients from the 2 northwestern cities developed meningoencephalitis due to Cryptococcusneoformans. To the molecular epidemiology analyses we had the opportunity to study isolated cases from 26additional, non-metropolitan cities of the State. HIV-1 sequences were generated from samples from a total of221 patients. Sequences were assigned subtypes B (190; 86%), F1 (14; 6.3%), CEF02_AG (2; 0.9%), and D (2;0.9%), as well as BF1 intersubtype recombinant forms (13; 5.9%). Subtypes B and F1 are the most prevalentlineages in southeast Brazil, whereas subtypes D and CRF02_AG had previously been reported only fromisolated cases in the capital of Rio de Janeiro State. Moreover, we present the first molecular evidence ofautochthonous transmission of CRF02_AG in Brazil, an HIV-1 lineage of major global importance.Phylogenetic analysis of subtype D strains, in conjunction with other subtype D representatives generated inour laboratory, demonstrated that Brazilian autochthonous subtype D sequences share close genetic relatednesswith subtype D strains reported in the 1980s from South Africa, a country were this lineage occurs only inisolated cases. Our data suggest that this subtype has been successfully introduced in southeast Brazil as thefounder effect of an ancestral sequence of possible South African origin. One of the BF1 recombinant strainswas sequenced to full genome and found to share the same recombinant breakpoints with other 3 strainsrecovered from different studies from our laboratory, thus potentially standing as novel Brazilian CRF_BF.Data on the efficacy of antiretroviral therapy, performed by targeting the proviral compartment, demonstratethat 70% of the patients under treatment as of sampling had a plasma viral load below detection limit. One caseof primary resistance among 84 treatment-naïve subjects was recorded. Among samples from patients underantiretroviral therapy as of sampling, 31.1% had evidence of reduced susceptibility to at least one antiretroviraldrug. Only 5 cases of reduced susceptibility to protease inhibitors were recorded among the whole cohort. Therelatively low prevalence of antiretroviral drug resistance in these underprivileged settings contributes to the debate on the convenience of offering universal access to antiretroviral combinations in the underdevelopedworld. Our data suggest that underprivileged communities should not have denied their right to state-of-the-artantiretroviral combinations due to the possibility of suboptimal adherence leading to the emergence and spreadof resistant variants. Phylogenetic analyses of viral sequences provided evidence of a polyphyletic patternsuggestive of multiple viral introductions in the studied cities. Also, we recorded the occurrence of multiplemonophyletic clusters of sequences that share close genetic relatedness. These sequences were generated fromsamples obtained from patients who probably took part in the same chain of viral spread, suggesting theexistence of sexual networks and a high incidence molecular profile. Logistic regression analyses have foundthat always having lived in the studied city and having a known epidemiologic link within the cohort wereindependent predictors of being a patient whose sample yielded clustered sequences. The high frequency ofsamples that generated clustered sequences is an indication that multiple new infections have occurred in arelatively short period of time and further highlights the urgent need to perform incidence studies in innerBrazil. Coalescent analyses suggest that the most recent common ancestors that triggered the 2 largesttransmission chains recorded in the city of Miracema were in circulation in the early 1990s. The demonstrationthat the dissemination of these viral lineages was already taking place at a time AIDS was considered aproblem mainly restricted to the large urban areas of the country may have important public healthimplications. Phylogenetic analyses also demonstrated that monophyletic clusters from Miracema werephylogenetically unrelated to those from the neighboring Santo Antonio de Pádua, suggesting that in spite ofbeing very close to each other, each city experienced the independent introduction and subsequentdissemination of different subtype B lineages, in a pattern that resembles multiple scattered micro-epidemics.Phylogenetic reconstructions of envelope and polymerase data sets yielded the same overall results, thusdemonstrating that in spite of being a relatively conserved region of HIV-1 genome, polymerase sequences,which are being increasingly generated to allow genotypic analyses of drug resistance, can also be useful tostudies of epidemiologic relationships between populations, groups and people.
Advisor:Mariza Goncalves Morgado
School:Faculdades Oswaldo Cruz
Source Type:Master's Thesis
Keywords:HIV-1 Acquired Immunodeficiency Syndrome Anti-Retroviral Agents Epidemiology, Molecular
Date of Publication:06/25/2007