Analysis of the Origin and Evolutionary History of HIV-1 CRF28_BF and CRF29_BF Reveals a Decreasing Prevalence in the AIDS Epidemic of Brazil

HIV-1 subtype B and subtype F are prevalent in the AIDS epidemic of Brazil. Recombinations between these subtypes have generated at least four BF circulating recombinant forms (CRFs). CRF28_BF and CRF29_BF are among the first two BF recombinants being identified in Brazil and they contributed significantly to the epidemic. However, the evolution and demographic histories of the CRFs are unclear.A collection of gag and pol sequences sampled within Brazil was screened for CRF28_BF-like and CRF29_BF-like recombination patterns. A Bayesian coalescent framework was employed to delineate the phylogenetic, divergence time and population dynamics of the virus having CRF28_BF-like and CRF29_BF-like genotype. These recombinants were phylogenetically related to each other and formed a well-supported monophyletic clade dated to 1988-1989. The effective number of infections by these recombinants grew exponentially over a five-year period after their emergence, but then decreased toward the present following a logistic model of population growth. The demographic pattern of both recombinants closely resembles those previously reported for CRF31_BC.We revealed that HIV-1 recombinants of the CRF28_BF/CRF29_BF clade are still circulating in the Brazilian population. These recombinants did not exhibit a strong founder effect and showed a decreasing prevalence in the AIDS epidemic of Brazil. Our data suggested that multiple URFs may also play a role in shaping the epidemic of recombinant BF HIV-1 in the region

Avaliação da diversidade genética e cinética de produção das formas circulares do HIV-1 em cultivo celular: impacto na manutenção da infecção viral

Treatment resistant latent reservoirs remain a barrier to the HIV cure furthermore the maintenance and properties of these reservoirs are not completely understood. After HIV-1 infection, HIV-1 cDNA synthesis is initiated in the cytoplasm and proceeds at the same time as viral cDNA translocation to the host cell nucleus. Within the nucleus, linear full-length cDNA genomes can circularize to form circular forms containing either one long-terminal repeat (1-LTR circle) or two long-terminal repeats (2-LTR circle). 2-LTR circles have been used to assess ongoing HIV replication. The maintenance, genetic variability and properties of these circular forms of HIV-1 are not completely understood. In the present study we evaluated the kinetics of replication and genetic diversity of 2- LTR circular forms in a long culture in PBMC cells and we compared it with the viral RNA and proviral diversities. Our results demonstrated that 2-LTR circles remained stable up to 33 days of cell culture. Furthermore, we observe genetic variability in 2-LTR circles which is different from diversity found in proviral DNA and viral RNA. The diversification profiles obtained show that the divergence of sequences in the viral RNA is the greatest between all compartments. The observed variability was almost 2 times higher in 2-LTR circles than proviral DNA. The stability and genetic variability of the 2- LTR circles suggest an important role of this compartment in the process of maintenance and viral replication and highlights its relevance as a backup storage for HIV-1 genetic diversity.O tratamento de reservatórios virais lantentes permanece como uma barreira a cura do HIV. Após a infecção da célula pelo HIV-1, a síntese do cDNA viral paraé iniciada no citoplasma e procede ao mesmo tempo que a translocação do cDNA viral para o núcleo da célula hospedeira. No núcleo, alguns cDNAs lineares se circularizam formando formas circulares contendo uma ou duas LTRs (1-LTR ou 2-LTRs). As formas circulares de 2-LTRs têm sido utilizadas como marcadores da replicação persistente pelo HIV-1. A manutenção, a variabilidade genética e as propriedades das formas circulares do HIV-1 ainda não estão completamente esclarecidas. No presente estudo, avaliamos a cinética replicativa e diversidade genética das formas circulares de 2-LTRs em um cultivo de longa duração em PBMCs e comparamos com os compatimentos proviral e RNA viral. Os resultados demonstraram uma importante estabilidade das formas circulares de 2- LTRs por até 33 dias de cultivo. Ademais, observamos que existe variabilidade genética nas formas circulares de 2-LTRs e esta é diferente da encontrada nos compartimentos proviral e RNA viral. Os perfis de diversificação obtidos demonstram que a divergência das sequências no RNA viral é a maior entre todos os compartimentos. A divergência nas formas circulares foi cerca de 2 vezes maior do que a encontrada no DNA proviral. A estabilidade e variabilidade genética encontrada nas formas circulares sugerem uma importante participação deste compartimento no processo de replicação e manutenção viral e joga luz à relevância do reservatório viral informacional intracelular como back up da diversidade genética do HIV-1.Dados abertos - Sucupira - Teses e dissertações (2013 a 2016

Heavy metals investigation in bovine tissues in Brazil

The aim of this study was to investigate the presence of arsenic, lead, and cadmium residues in samples of liver, kidney, and muscle of cattle during the years of 2002 to 2008. A total of 1017 samples from 20 Brazilian States were used. The samples were analyzed at the National Agricultural Laboratory using the atomic absorption spectrometry technique. Arsenic residues were detected in 15.7% of liver samples and 28.7% of kidney samples although no results have exceeded the MRL. With regard to lead, 16 samples of liver and 74 samples of kidney were contaminated (5.2 and 10.9%, respectively). Among these samples, only one liver and two of kidney samples had lead levels above the MRL. Cadmium was found with levels below the MRL in 12.5% of the liver samples, and only 3 samples (1%) were quantified above the MRL. Among the kidney samples, 420 (60.8% of the total tested) had cadmium residues, and five of them exceeded the limits established by legislation. It is concluded that the Brazilian meat meets the legislation requirements without putting consumer's healthy at risk since as it satisfies the national and international food-safety conditions

High Rates of Human Immunodeficiency Virus Type 1 Mutational Profiles by Single-Genome Amplification after 48-Hour Propagation in Peripheral Blood Mononuclear Cells at Different Levels of Cell Activation

Human immunodeficiency virus type 1 (HIV-1) genetic diversity is one of the most important features of HIV-1 infections and the result of error accumulation during reverse transcription and of high viral turnover. HIV-1 reverse transcription is influenced by factors such as the level of nucleotides and/or the cellular activation state. HIV-1 diversity was investigated after 48 h of viral propagation in peripheral blood mononuclear cells (PBMCs) obtained from healthy donors in three different cell culture conditions: (1) resting PBMCs, (2) simultaneous infection and PBMC activation, and (3) PBMC activation 72 h before infection. Cellular DNA was extracted and proviruses of each culture condition were amplified. Single-genonne PCR clones were obtained and the protease and reverse transcriptase of the pol gene were sequenced. An elevated number of nucleotide substitutions in all three culture conditions were observed. in condition 1, the mutational rate observed ranged from 1.0 x 10(-3) to 2.1 x 10(-2), the genetic diversity was 0.6%, and hypermutation was observed in 7.1% of sequenced clones. in condition 2, the mutational rate ranged from 1.0 x 10(-3) to 1.0 x 10(-2), the genetic diversity was 0.8%, and hypermutation affected 6.7% of clones. in condition 3, the mutational rate ranged from 2.8 x 10(-3) to 1.1 x 10(-2), the genetic diversity was 1%, and 5.9% of clones were hypermutated. Substitutions occurred more frequently in some specific nucleotide stretches, and a common pattern for substitutions in all the different conditions was identified. There was a significant accumulation of mutations during the initial periods of in vitro HIV-1 propagation irrespective of culture conditions. the rapid accumulation of virus diversity might represent a viral strategy when colonizing new hosts. Complementary studies are necessary to allow for a better understanding of the initial periods of infection, which represent a crucial event related to disease progression. (C) 2014 S. Karger AG, BaselPontif Catholic Univ Parana, Med Course, Discipline Immunol, Londrina, Parana, BrazilUniversidade Federal de São Paulo, UNIFESP, Infect Dis Div Med, São Paulo, BrazilUniversidade Federal de São Paulo, UNIFESP, Dept Micro Immuno & Parasitol, Discipline Microbiol, São Paulo, BrazilUniversidade Federal de São Paulo, UNIFESP, Infect Dis Div Med, São Paulo, BrazilUniversidade Federal de São Paulo, UNIFESP, Dept Micro Immuno & Parasitol, Discipline Microbiol, São Paulo, BrazilWeb of Scienc

In Vivo HIV-1 Hypermutation and Viral Loads Among Antiretroviral-Naive Brazilian Patients

Hypermutation alludes to an excessive number of specific guanine-to-adenine (G- > A) substitutions in proviral DNA and this phenomenon is attributed to the catalytic activity of cellular APOBECs. Population studies relating hypermutation and the progression of infection by human immunodeficiency virus type 1 (HIV-1) have been performed to elucidate the effect of hypermutation on the natural course of HIV-1 infection. However, the many different approaches employed to assess hypermutation in nucleotide sequences render the comparison of results difficult. This study selected 157 treatment-naive patients and sought to correlate the hypermutation level of the proviral sequences in clinical samples with demographic variables, HIV-1 RNA viral load, and the level of CD4(+) T cells. Nested touchdown polymerase chain reaction (PCR) was performed with specific primers to detect hypermutation in the region of HIV-1 integrase, and the amplified sequences were run in agarose gels with HA-Yellow. the analysis of gel migration patterns using the k-means clustering method was validated by its agreement with the results obtained with the software Hypermut. Hypermutation was found in 31.2% of the investigated samples, and a correlation was observed between higher hypermutation levels and higher viral load levels. These findings suggest a high frequency of hypermutation detection in a Brazilian cohort, which can reflect a particular characteristic of this population, but also can result from the method approach by aiming at hypermutation-sensitive sites. Furthermore, we found that hypermutation events are pervasive during HIV-1 infection as a consequence of high viral replication, reflecting its role during disease progression.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Infectious Diseases Department of the Federal University of São Paulo (UNIFESP)Universidade Federal de São Paulo, BR-04039032 São Paulo, BrazilUniv São Paulo, Sch Med, São Paulo, BrazilUniversidade Federal de São Paulo, BR-04039032 São Paulo, BrazilFAPESP: 2007/50650-0Web of Scienc