DBCollHIV: a database system for collaborative HIV analysis in Brazil

We developed a database system for collaborative HIV analysis (DBCollHIV) in Brazil. The main purpose of our DBCollHIV project was to develop an HIV-integrated database system with analytical bioinformatics tools that would support the needs of Brazilian research groups for data storage and sequence analysis. Whenever authorized by the principal investigator, this system also allows the integration of data from different studies and/or the release of the data to the general public. The development of a database that combines sequences associated with clinical/epidemiological data is difficult without the active support of interdisciplinary investigators. A functional database that securely stores data and helps the investigator to manipulate their sequences before publication would be an attractive tool for investigators depositing their data and collaborating with other groups. DBCollHIV allows investigators to manipulate their own datasets, as well as integrating molecular and clinical HIV data, in an innovative fashion.

HIV-1 subtypes among intravenous drug users from two neighboring cities in São Paulo State, Brazil

In order to assess the molecular epidemiology of HIV-1 in two neighboring cities located near the epicenter of the HIV-1 epidemics in Brazil (Santos and São Paulo), we investigated 83 HIV-1 strains obtained from samples collected in 1995 from intravenous drug users. The V3 through V5 region of the envelope of gp 120 was analyzed by heteroduplex mobility analysis. Of the 95 samples, 12 (12.6 percent) were PCR negative (6 samples from each group); low DNA concentration was the reason for non-amplification in half of these cases. Of the 42 typed cases from São Paulo, 34 (81 percent, 95 percent confidence limits 74.9 to 87.0 percent) were B and 8 (19 percent, 95 percent confidence limits 12.9 to 25.0 percent) were F, whereas of the 41 typed cases from Santos, 39 (95 percent, 95 percent confidence limits 91.6 to 98.4 percent) were B and 2 (5 percent, 95 percent confidence limits 1.6 to 8.4 percent) were C. We therefore confirm the relationship between clade F and intravenous drug use in São Paulo, and the presence of clade C in Santos. The fact that different genetic subtypes of HIV-1 are co-circulating indicates a need for continuous surveillance for these subtypes as well as for recombinant viruses in Brazil

Accuracy of replication in the polymerase chain reaction. Comparison between Thermotoga maritima DNA polymerase and Thermus aquaticus DNA polymerase

For certain applications of the polymerase chain reaction (PCR), it may be necessary to consider the accuracy of replication. The breakthrough that made PCR user friendly was the commercialization of Thermus aquaticus (Taq) DNA polymerase, an enzyme that would survive the high temperatures needed for DNA denaturation. The development of enzymes with an inherent 3' to 5' exonuclease proofreading activity, lacking in Taq polymerase, would be an improvement when higher fidelity is needed. We used the forward mutation assay to compare the fidelity of Taq polymerase and Thermotoga maritima (ULTMATM) DNA polymerase, an enzyme that does have proofreading activity. We did not find significant differences in the fidelity of either enzyme, even when using optimal buffer conditions, thermal cycling parameters, and number of cycles (0.2 per cent and 0.13 per cent error rates for ULTMATM and Taq, respectively, after reading about 3,000 bases each). We conclude that for sequencing purposes there is no difference in using a DNA polymerase that contains an inherent 3' to 5' exonuclease activity for DNA amplification. Perhaps the specificity and fidelity of PCR are complex issues influenced by the nature of the target sequence, as well as by each PCR component.

Prevalência de anticorpos anti-HTLVI/II em doadores de sangue da Fundaçäo Pró-Sangue Hemocentro de Säo Paulo / Prevalence of anti-HTLVI/II antibodies in blood donors of Fundaçäo Pró-Sangue Hemocentro de Säo Paulo

O teste ELISA ant-HTLVI/II foi introduzido na triagem sorlógica de doadores de sangue na Fundaçäo Pró-sangue Hemocentro de Säo Paulo (FPS/HSP) em julho de 1991. NO período compreendido entre julho de 1991 e julho de 1994 foram submetidos à triagem serológica 597.727 doadores. Destes, 7682 foram recusados por terem apresentado reatividade no teste ELISA anti-HTLVI/II. A positividade observada, para o referido teste, foi diminuindo com o correr do tempo: 2,12 por cento em 1991; 1,6 por cento em 1992; 0,8 por cento em 1993 e 1,0 por cento em 1994, sendo esse fato atribuido a melhora da especialidade e reprodutividade dos kits comerciais. Foi utilizado o teste suplementar de Western Blot para confirmar os resultados dos testes ELISA. Em 249 amostras de soros de doadores, com resultado repetidamente positivo (RRP) no teste ELISA (hemobio), o poder confirmatório do Western Blot (Cambridge Biotech) foi de 24.9 por cento (IC/90 por cento: 20,4 por cento-29,39 por cento). Baseados nesses dados, considera-se uma expectativa de prevalência de indivíduos infectados pelo HTLVI/II, na populaçäo de doadores de sangue da FPS/HSP de 0,142 por cento (IC/90 por cento; 0,116 por cento-0,167 por cento). Em 437 amostras de soro de doadores que retornaram ao Banco de Sangue, para confirmar o resultado inicial e apresentaram RRP no teste ELISA, o poder confirmatório do Western Blot foi de 34,55 por cento (IC/90 por cento: 30,82 por cento-38,28 por cento)...