RESUMEN
A common basis to address the dynamics of directly transmitted infectious diseases, such as COVID-19, are compartmental (or SIR) models. SIR models typically assume homogenous population mixing, a simplification that is convenient but unrealistic. Here we validate an existing model of a scale-free fractal infection process using high-resolution data on COVID-19 spread in São Caetano, Brazil. We find that transmission can be described by a network in which each infectious individual has a small number of susceptible contacts, of the order of 2-5. This model parameter correlated tightly with physical distancing measured by mobile phone data, such that in periods of greater distancing the model recovered a lower average number of contacts, and vice versa. We show that the SIR model is a special case of our scale-free fractal process model in which the parameter that reflects population structure is set at unity, indicating homogeneous mixing. Our more general framework better explained the dynamics of COVID-19 in São Caetano, used fewer parameters than a standard SIR model and accounted for geographically localized clusters of disease. Our model requires further validation in other locations and with other directly transmitted infectious agents.
RESUMEN
OBJECTIVE: To determine the presence and identity of extracellular bacteriophage (phage) families, genera and species in the vagina of pregnant women. DESIGN: Descriptive, observational cohort study. SETTING: São Paulo, Brazil. POPULATION: Pregnant women at 21-24 weeks' gestation. METHODS: Vaginal samples from 107 women whose vaginal microbiome and pregnancy outcomes were previously determined were analysed for phages by metagenomic sequencing. MAIN OUTCOME MEASURES: Identification of phage families, genera and species. RESULTS: Phages were detected in 96 (89.7%) of the samples. Six different phage families were identified: Siphoviridae in 69.2%, Myoviridae in 49.5%, Microviridae in 37.4%, Podoviridae in 20.6%, Herelleviridae in 10.3% and Inviridae in 1.9% of the women. Four different phage families were present in 14 women (13.1%), three families in 20 women (18.7%), two families in 31 women (29.1%) and one family in 31 women (29.1%). The most common phage species detected were Bacillus phages in 48 (43.6%), Escherichia phages in 45 (40.9%), Staphylococcus phages in 40 (36.4%), Gokushovirus in 33 (30.0%) and Lactobacillus phages in 29 (26.4%) women. In a preliminary exploratory analysis, there were no associations between a particular phage family, the number of phage families present in the vagina or any particular phage species and either gestational age at delivery or the bacterial community state type present in the vagina. CONCLUSIONS: Multiple phages are present in the vagina of most mid-trimester pregnant women. TWEETABLE ABSTRACT: Bacteriophages are present in the vagina of most pregnant women.
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Bacteriófagos , Microbiota/fisiología , Vagina/microbiología , Adulto , Bacteriófagos/clasificación , Bacteriófagos/genética , Bacteriófagos/aislamiento & purificación , Brasil , Femenino , Edad Gestacional , Humanos , Metagenoma , Metagenómica/métodos , Metagenómica/estadística & datos numéricos , Embarazo , Resultado del Embarazo/epidemiologíaRESUMEN
BACKGROUND: A low prevalence of HIV in sickle cell disease (SCD) patients has been reported in the literature though mechanisms for this are not understood. METHODS: HIV risk behaviors were compared between SCD cases and non-SCD controls using a self-administered audio computer-assisted self-interview. SCD cases were recruited from a multi-center SCD cohort established in Brazil; controls were recruited from SCD social contacts. Categorical variables were analyzed using Chi-Square or Fisher exact test. Continuous variables were compared using the Mann-Whitney U test. RESULTS: There were 152 SCD cases and 154 age/location matched controls enrolled at three participating Brazilian centers during 2016-17. No significant differences in number of sexual partners (lifetime or previous 12 months), male-to-male sex partners or intravenous drug use were observed. Cases received more transfusions, surgeries, and acupuncture treatment. CONCLUSIONS: Besides the risk of transfusion-transmitted HIV, which is now exceedingly rare, SCD and non-SCD participants demonstrated similar HIV risk behaviors. Causes other than risk behaviors such as factors inherent to SCD pathophysiology may explain the reported low prevalence of HIV in SCD.
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Anemia de Células Falciformes/epidemiología , Infecciones por VIH/epidemiología , Conductas de Riesgo para la Salud , Adolescente , Adulto , Anciano , Transfusión Sanguínea , Brasil/epidemiología , Estudios de Casos y Controles , Estudios de Cohortes , Femenino , Humanos , Masculino , Persona de Mediana Edad , Prevalencia , Parejas Sexuales , Abuso de Sustancias por Vía IntravenosaRESUMEN
BACKGROUND AND AIM: The aim of the study was to compare the gut microbiomes from obese and lean patients with or without NASH to outline phenotypic differences. METHODS AND RESULTS: We performed a cross-sectional pilot study comprising biopsy-proven NASH patients grouped according to BMI. Microbiome DNA was extracted from stool samples, and PCR amplification was performed using primers for the V4 region of the 16S rRNA gene. The amplicons were sequenced using the Ion PGM Torrent platform, and data were analyzed using QIIME software. Macronutrient consumption was analyzed by a 7-day food record. Liver fibrosis ≥ F2 was associated with increased abundance of Lactobacilli (p = 0.0007). NASH patients showed differences in Faecalibacterium, Ruminococcus, Lactobacillus and Bifidobacterium abundance compared with the control group. Lean NASH patients had a 3-fold lower abundance of Faecalibacterium and Ruminococcus (p = 0.004), obese NASH patients were enriched in Lactobacilli (p = 0.002), and overweight NASH patients had reduced Bifidobacterium (p = 0.018). Moreover, lean NASH patients showed a deficiency in Lactobacillus compared with overweight and obese NASH patients. This group also appeared similar to the control group with regard to gut microbiome alpha diversity. Although there were qualitative differences between lean NASH and overweight/obese NASH, they were not statistically significant (p = 0.618). The study limitations included a small sample size, a food questionnaire that collected only qualitative and semi-quantitative data, and variations in group gender composition that may influence differences in FXR signaling, bile acids metabolism and the composition of gut microbiota. CONCLUSION: Our preliminary finding of a different pathogenetic process in lean NASH patients needs to be confirmed by larger studies, including those with patient populations stratified by sex and dietary habits.
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Bacterias/crecimiento & desarrollo , Ingestión de Energía , Microbioma Gastrointestinal , Cirrosis Hepática/microbiología , Hígado/patología , Enfermedad del Hígado Graso no Alcohólico/microbiología , Obesidad/microbiología , Adulto , Bacterias/clasificación , Bacterias/genética , Biopsia , Índice de Masa Corporal , Estudios de Casos y Controles , Disbiosis , Femenino , Humanos , Cirrosis Hepática/patología , Masculino , Persona de Mediana Edad , Enfermedad del Hígado Graso no Alcohólico/patología , Obesidad/diagnóstico , Proyectos Piloto , Datos Preliminares , Estudios Prospectivos , Ribotipificación , Factores de Riesgo , Adulto JovenRESUMEN
Cytotoxic T-lymphocyte-associated antigen 4 (CTLA-4) molecule is expressed on T-lymphocyte membrane and negatively influences the antigen-presenting process. Reduced expression of CTLA-4 due to gene polymorphisms is associated with increased risk of autoimmune disorders, whose physiopathology is similar to that of post-transfusion red blood cell (RBC) alloimmunization. Our goal was to evaluate if polymorphisms of CTLA-4 gene that affect protein expression are associated with RBC alloimmunization. This was a case-control study in which 134 sickle cell disease (SCD) patients and 253 non-SCD patients were included. All patients were genotyped for the polymorphisms 49A/G and -318C/T of CTLA-4 gene. The genotype frequency of -318C/T differed significantly between alloimmunized and nonalloimmunized SCD patients, irrespective of clinical confounders (p = .016). SCD patients heterozygous for -318T allele presented higher risk of alloantibody development (OR: 5.4, CI: 1.15-25.6). In conclusion, the polymorphism -318C/T of CTLA-4 gene is associated with RBC alloimmunization among SCD patients. This highlights the role played by CTLA-4 on post-transfusion alloantibody development.
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Anemia de Células Falciformes/genética , Enfermedades Autoinmunes/genética , Antígeno CTLA-4/genética , Eritrocitos/inmunología , Adulto , Anemia de Células Falciformes/sangre , Anemia de Células Falciformes/inmunología , Anemia de Células Falciformes/prevención & control , Células Presentadoras de Antígenos/inmunología , Células Presentadoras de Antígenos/patología , Enfermedades Autoinmunes/sangre , Enfermedades Autoinmunes/inmunología , Enfermedades Autoinmunes/patología , Antígeno CTLA-4/inmunología , Eritrocitos/patología , Femenino , Predisposición Genética a la Enfermedad , Genotipo , Humanos , Inmunización/efectos adversos , Isoanticuerpos/inmunología , Masculino , Persona de Mediana Edad , Polimorfismo de Nucleótido Simple/genética , Factores de Riesgo , Linfocitos T/inmunología , Linfocitos T/patologíaRESUMEN
OBJECTIVES: This study aimed to estimate the prevalence and characterise potential blood donors and non-donors in a well-populated and representative urban area of Southeastern Brazil. BACKGROUND: Studies on blood donation usually evaluate individuals who donate. Population-based studies may contribute to characterise those who never reach the blood centre, trying to increase the range of donors. STUDY DESIGN AND METHODS: This was a secondary analysis of a population-based survey and a blood donor motivation study [Recipient Epidemiology and Donor Evaluation study (REDS II) International]. In a cross-sectional study 4047 individuals representing a metropolitan area answered the question 'Have you ever donated blood at least once in your life?'. The profiles ('Yes/No') were compared. Non-donors from this reference population were compared with donors of a local blood center, in a case control analysis. RESULTS: A total of 69·0% of the population had never donated blood and was composed mostly of women, younger than 30 years old, people not contributing to social security and not subscribing to newspapers. In the case-control study, the likelihood of donating was higher for: men, younger than 50 years old, longer time of education, married, participating in political campaigns and with a good self-perception of health. The factors associated with no blood donation were: self-reported mixed or white race/ethnicity, income higher than two minimum wages and belonging to trade union, political, religious/spiritual, or other social group and worse self perception of health. CONCLUSIONS: This population-based study allowed us to characterise a high proportion of people that never reaches the blood centre. The results may be used to diversify the donor profile, creating strategies to target those least likely to donate blood, as women, white people and those with higher income and purchasing power.
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Donantes de Sangre , Encuestas y Cuestionarios , Población Urbana , Adulto , Factores de Edad , Anciano , Brasil , Femenino , Humanos , Masculino , Persona de Mediana Edad , Factores SocioeconómicosRESUMEN
The presence of Treponema pallidum DNA was assessed by real-time PCR in samples of blood donors with reactive serologic tests for syphilis. Treponema pallidum DNA was detected in two (1·02%) of 197 samples of VDRL>8, EIA+ and FTA-ABS+ donors, and in no sample from 80 VDRL−, EIA+ and FTA-ABS+ donors. Donors VDRL−, EIA+ and FTA-ABS+ lack demonstrable T. pallidum DNA in their blood and are unlike to transmit syphilis. Donors VDRL>8, EIA+ and FTA-ABS+ carry the risk of syphilis infectivity even in concomitance to antibodies detection. Serologic screening for syphilis may still play a role to prevent its transfusion transmission.
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Donantes de Sangre , ADN Bacteriano/sangre , Sífilis/epidemiología , Treponema pallidum/genética , Adolescente , Adulto , Brasil/epidemiología , ADN Bacteriano/genética , Femenino , Humanos , Masculino , Tamizaje Masivo , Persona de Mediana Edad , Prevalencia , Reacción en Cadena en Tiempo Real de la Polimerasa , Sífilis/sangre , Sífilis/prevención & control , Adulto JovenRESUMEN
BACKGROUND: Reducing risk of HIV window period transmission requires understanding of donor knowledge and attitudes related to HIV and risk factors. STUDY DESIGN AND METHODS: We conducted a survey of 7635 presenting blood donors at three Brazilian blood centres from 15 October through 20 November 2009. Participants completed a questionnaire on HIV knowledge and attitudes about blood donation. Six questions about blood testing and HIV were evaluated using maximum likelihood chi-square and logistic regression. Test seeking was classified in non-overlapping categories according to answers to one direct and two indirect questions. RESULTS: Overall, respondents were male (64%) repeat donors (67%) between 18 and 49 years old (91%). Nearly 60% believed blood centres use better HIV tests than other places; however, 42% were unaware of the HIV window period. Approximately 50% believed it was appropriate to donate to be tested for HIV, but 67% said it was not acceptable to donate with risk factors even if blood is tested. Logistic regression found that less education, Hemope-Recife blood centre, replacement, potential and self-disclosed test-seeking were associated with less HIV knowledge. CONCLUSION: HIV knowledge related to blood safety remains low among Brazilian blood donors. A subset finds it appropriate to be tested at blood centres and may be unaware of the HIV window period. These donations may impose a significant risk to the safety of the blood supply. Decreasing test-seeking and changing beliefs about the appropriateness of individuals with behavioural risk factors donating blood could reduce the risk of transfusing an infectious unit.
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Donantes de Sangre , Infecciones por VIH/diagnóstico , Adolescente , Adulto , Seguridad de la Sangre , Brasil , Estudios Transversales , Cultura , Femenino , Infecciones por VIH/sangre , Infecciones por VIH/prevención & control , Conocimientos, Actitudes y Práctica en Salud , Humanos , Masculino , Tamizaje Masivo/normas , Persona de Mediana Edad , Factores de Riesgo , Encuestas y Cuestionarios , Adulto JovenRESUMEN
OBJECTIVE: To identify the demographic characteristics, risk factors and motivations for donating among blood donors with reactive serologic tests for syphilis. BACKGROUND: Post-donation interviews with syphilis seropositive blood donors improve recruitment and screening strategies. METHODS: This case-control study compares 75 Venereal Disease Research Laboratory (VDRL) > 8, EIA+ (enzyme immunoassay) and FTA-ABS+ (fluorescent treponemal antibody); 80 VDRL-, EIA+ and FTA-ABS+; and 34 VDRL- and EIA- donors between 2004 and 2009. Donors were assessed by their demographic characteristics, sexual behaviour, history of alcohol and illicit drugs use, and motivations to donate. RESULTS: Donors with VDRL > 8 were more likely to be divorced [AOR = 12·53; 95% confidence interval (CI) 1·30-120·81], to have had more than six sexual partners (AOR=7·1; 95% CI 1·12-44·62) and to report male-male-sex in the past 12 months (AOR=8·18; 95% CI 1·78-37·60). Donors with VDRL-, EIA+ and FTA-ABS+ were less likely to be female (AOR=0·26; 95% CI 0·07-0·96), more likely to be older (AOR=10·2; 95% CI 2·45-42·58 ≥ 39 and <60 years old) and to have had more than six sexual partners in the past 12 months (AOR = 8·37; 95% CI 1·49-46·91). There was no significant difference among groups regarding illicit drugs use; 30·7% (VDRL > 8) and 12·5% (VDRL-, EIA+ and FTA-ABS+) of donors reported that they had been at risk for HIV infection (P = 0·004). One-third of donors came to the blood bank to help a friend or a relative who needed blood. CONCLUSION: Although donors exposed to syphilis reported and recognised some high risk behaviour, most were motivated by direct appeal to donate blood. Monitoring the risk profile of blood donors can benefit public health and improve blood safety.
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Donantes de Sangre , Selección de Donante/métodos , Motivación , Sífilis/sangre , Adulto , Factores de Edad , Anciano , Brasil/epidemiología , Femenino , Humanos , Masculino , Persona de Mediana Edad , Estudios Retrospectivos , Factores de Riesgo , Asunción de Riesgos , Sífilis/epidemiologíaRESUMEN
BACKGROUND: Chagas disease has a long clinically silent period following Trypanosoma cruzi infection and before development of overt clinical pathology; detectable biomarkers of infection and pathogenesis are urgently needed. We tested 22 biomarkers known to be associated with cardiomyopathy to evaluate if a biomarker signature could successfully classify T. cruzi seropositive subjects into clinical Chagas disease stage groups. METHODS: This cross-sectional retrospective case-control study enrolled T. cruzi seropositive blood donors (BD) who were further characterized as having chronic Chagas cardiomyopathy (CC-BD) or not (nonCC-BD) and seronegative (SN) control donors; we also included clinically diagnosed Chagas cardiomyopathy patients (CC-P). All subjects underwent a health history questionnaire, medical examination, electro- and echocardiograms (ECG and Echo) and phlebotomy. Biomarkers were measured on blinded samples by luminex bead array and Ortho VITROS. RESULTS: A clear biomarker pattern was observed only in more severe cardiac disease; this pattern included significantly elevated levels of inflammatory cytokines IFN-γ, IL-6, IL-10 and TNF-α and soluble cardiovascular disease biomarkers CK-MB, troponin, myoglobin, VCAM and NTproBNP while there were lower levels of MPO, PAI-1, and MCP-1. The markers determined to be the most predictive of disease by ROC curve analysis were NTproBNP and T. cruzi PCR status. CONCLUSIONS: Although many biomarkers demonstrated increased or decreased concentrations among the clinical forms of Chagas disease, NTproBNP and T. cruzi PCR were the only tests that would independently be of clinical value for disease staging, in concert with ECG, Echo and clinical assessments.
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Cardiomiopatía Chagásica/sangre , Citocinas/sangre , Adolescente , Adulto , Anciano , Anciano de 80 o más Años , Biomarcadores/sangre , Donantes de Sangre , Estudios de Casos y Controles , Cardiomiopatía Chagásica/patología , Cardiomiopatía Chagásica/terapia , Quimiocinas/sangre , Niño , Preescolar , Estudios Transversales , Femenino , Humanos , Lactante , Recién Nacido , Inflamación/sangre , Inflamación/patología , Masculino , Persona de Mediana Edad , Péptido Natriurético Encefálico/sangre , Fragmentos de Péptidos/sangre , Inhibidor 1 de Activador Plasminogénico/metabolismo , Estudios Retrospectivos , Trypanosoma cruzi/aislamiento & purificación , Adulto JovenRESUMEN
BACKGROUND: The significance of detection of Trypanosoma cruzi DNA in blood of antibody-positive patients for risk of development of Chagas heart disease is not well established. The objective of this study was to compare detection of T. cruzi DNA with known clinical and laboratory markers of Chagas cardiomyopathy (CC) severity. METHODS: This is a case-control study nested within a retrospective cohort developed in Brazil to understand the natural history of Chagas disease. The study enrolled 499 T. cruzi seropositive blood donors (SP-BD) and 488 frequency matched seronegative control donors (SN-BD) who had donated between 1996 and 2002, and 101 patients with clinically diagnosed CC. In 2008-2010 all enrolled subjects underwent a health questionnaire, medical examination, electrocardiograms and echocardiograms and polymerase chain reaction (PCR) analyses. A blinded panel of three cardiologists adjudicated the outcome of CC. Trypanosoma cruzi kinetoplast minicircle sequences were amplified by real-time PCR using an assay with a sensitivity of one parasite per 20 mL of blood. All testing was performed on coded samples. RESULTS: Rates of PCR detection of T. cruzi DNA were significantly (P = 0.003) higher in CC patients and SP-BD diagnosed with CC (79/105 [75.2 %]) compared with SP-BD without CC (143/279 [51.3%]). The presence of parasitaemia was significantly associated with known markers of disease progression such as QRS and QT interval duration, lower left ventricular ejection fraction, higher left ventricular index mass, and elevated troponin and NTpro-BNP levels. CONCLUSION: Trypanosoma cruzi PCR positivity is associated with presence and severity of cardiomyopathy, suggesting a direct role of parasite persistence in disease pathogenesis.
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Cardiomiopatía Chagásica/sangre , ADN Protozoario/sangre , Trypanosoma cruzi/genética , Adulto , Donantes de Sangre , Estudios de Casos y Controles , Cardiomiopatía Chagásica/parasitología , Femenino , Humanos , Masculino , Persona de Mediana Edad , Reacción en Cadena en Tiempo Real de la Polimerasa/métodos , Estudios Retrospectivos , Índice de Severidad de la Enfermedad , Trypanosoma cruzi/patogenicidadRESUMEN
OBJECTIVE: To determine whether the HIV-1 genomes that grow out in vitro from peripheral blood mononuclear cells (PBMC) better represent the in vivo quasi-species present in plasma or PBMC. RESULTS: For one patient (9606), PBMC culture represented more accurately the plasma rather than the in vivo PBMC quasi-species distribution, because a large number of tat-defective proviruses present in PBMC in vivo were not detected in plasma nor in the PBMC cultures. For a second patient (9605), PBMC culture was representative of both in vivo PBMC and plasma tat sequences, but selection of C2-V3 env sequences was observed in PBMC cultures compared with sequences present in both plasma and PBMC in vivo. This selection consisted of the absence in vitro of genomes with certain amino-acid substitutions at or near conserved glycosylation sites of the C2 region at positions 276 and 289. Site 276 has been reported to be important for viral infectivity, and these substitutions may therefore have affected infectivity. In the third patient (10095), selection of both tat and C2-V3 sequences was observed in culture as compared to plasma and PBMC in vivo. In contrast to the first two patients, this third patient contained V3 sequences in vivo that were predicted to impart syncytium induction and enhanced replication capacity. It was these sequences that grew out preferentially in vitro. CONCLUSION: This study suggests that short-term PBMC culture is representative of HIV-1 genomes present in PBMC and plasma in vivo to the degree that they are infectious.
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Genes env , Genes tat , Proteína gp120 de Envoltorio del VIH/genética , Infecciones por VIH/microbiología , VIH-1/aislamiento & purificación , Leucocitos Mononucleares/microbiología , Fragmentos de Péptidos/genética , Plasma/microbiología , Viremia/microbiología , Secuencia de Aminoácidos , Secuencia de Bases , Células Cultivadas , Efecto Citopatogénico Viral , ADN Viral/genética , Variación Genética , Genotipo , Glicosilación , Proteína gp120 de Envoltorio del VIH/metabolismo , VIH-1/genética , VIH-1/patogenicidad , Humanos , Datos de Secuencia Molecular , Fragmentos de Péptidos/metabolismo , Reacción en Cadena de la Polimerasa , Procesamiento Proteico-Postraduccional , Provirus/genética , Provirus/aislamiento & purificación , Selección Genética , Alineación de Secuencia , Especificidad de la Especie , Cultivo de VirusRESUMEN
OBJECTIVE: To determine the distribution of HIV-1 subtypes in Sao Paulo, Brazil. METHODS: Samples were obtained from 80 consecutive HIV-1-infected individuals attending the Immunodeficiency Clinic at the University of Sao Paulo in 1993. Peripheral blood mononuclear cells (PBMC) were separated by Ficoll-Hypaque gradient and a portion was used for routine CD4 counts; the remainder were frozen. PBMC were proteinase-K-digested and DNA-purified by organic extraction. Samples were amplified for the env region of HIV, and envelope sequence subtypes determined by heteroduplex mobility analysis using prototypic subtypes as references. A subset of these were also sequenced through the C2-V3 region of env. RESULTS: A total 69 of 80 samples yielded env polymerase chain reaction product enabling subtype determination; samples that did not amplify were those with low DNA yields. Among 12 injecting drug users (IDU) or sexual partners of IDU, four were typed as clade F and eight as clade B. Forty-three homosexual men or female sexual partners of bisexual men were typed as clade B. The 14 additional cases without known risk factors were typed as clade B. CONCLUSION: These data suggest that subtype F is related to injecting drug use in Brazil.
PIP: Serum samples from 80 consecutive HIV-1-infected individuals presenting to the Immunodeficiency Clinic at the University of Sao Paulo in 1993 were analyzed to determine the distribution of HIV-1 subtypes in the city. Peripheral blood mononuclear cells (PBMC) were separated using Ficoll-Hypaque gradient, a portion was used for routine CD4 counts, and the rest were frozen. PBMC were proteinase-K-digested and DNA-purified by organic extraction. The samples were amplified for the env region of HIV, and envelope sequence subtypes determined by heteroduplex mobility analysis using prototypic subtypes as references. A subset was also sequenced through the C2-V3 region of env. 69 samples yielded env polymerase chain reaction product enabling subtype determination. The samples which did not amplify had low DNA yields. Among 12 IV-drug users or their sex partners, four were typed as clade F and eight as clade B. 43 homosexual men or female sex partners of bisexual men were typed as clade B. The 14 additional cases with no known risk factor were typed as clade B.
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Síndrome de Inmunodeficiencia Adquirida/virología , Genes env , VIH-1/clasificación , VIH-1/genética , Secuencia de Aminoácidos , Secuencia de Bases , Brasil/epidemiología , ADN Viral/análisis , Femenino , VIH-1/aislamiento & purificación , Humanos , Masculino , Datos de Secuencia Molecular , Ácidos Nucleicos Heterodúplex , Estudios RetrospectivosRESUMEN
The significance of detection of human immunodeficiency virus (HIV) DNA by the polymerase chain reaction (PCR) in seronegative or seroconverting (SC) subjects remains controversial. In a previously reported study, we identified a case in which a specimen collected 12 months before seroconversion (pre-SC) was found repeatedly to be PCR positive in three experienced laboratories, while the 6-month pre-SC bleed was PCR-negative; PCR-based human leukocyte antigen (HLA)-DQA and -DRB typing of serial peripheral blood mononuclear cell (PBMC) samples from this case did not indicate a specimen mix-up or labeling error. To further investigate this case, we used HIV env sequence and DNA heteroduplex gel-shift analyses to characterize HIV quasispecies present in serial pre- and post-SC specimens. HIV env sequences and gel-shift pattern analyses from the 12-month pre-SC versus post-SC samples indicated that markedly distinct quasispecies were present, suggesting possible abortive infection followed by reinfection and subsequent seroconversion. However, the HIV burden of this pre-SC sample was very low (1 provirus/10(6) PBMCs), and the quasispecies was highly heterogeneous, findings suggesting long-term rather than recent HIV infection. To test the hypothesis that the index pre-SC sample was PCR positive owing to trace blood contamination during initial processing, we analyzed the three seropositive samples collected on the same date in 1985. One of these samples was highly related to the index pre-SC sample by env sequence and gel-shift methodologies.(ABSTRACT TRUNCATED AT 250 WORDS)
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ADN Viral/sangre , Anticuerpos Anti-VIH/sangre , Seronegatividad para VIH , Seropositividad para VIH/diagnóstico , VIH-1/genética , Secuencia de Bases , Western Blotting , Separación Celular , Secuencia de Consenso , Cartilla de ADN/química , ADN Viral/química , Errores Diagnósticos , Productos del Gen env/genética , Productos del Gen env/inmunología , Proteína gp120 de Envoltorio del VIH/genética , Proteínas gp160 de Envoltorio del VIH , VIH-1/inmunología , VIH-1/aislamiento & purificación , Antígeno HLA-DR2/genética , Humanos , Leucocitos Mononucleares/microbiología , Datos de Secuencia Molecular , Fragmentos de Péptidos/genética , Reacción en Cadena de la Polimerasa , Precursores de Proteínas/inmunología , Homología de Secuencia de Ácido NucleicoRESUMEN
The first exon of tat was sequenced from 23 provirus genomes randomly amplified directly from an HIV-1-infected individual's peripheral blood. Twelve of the 23 sequences constituted a distinct subset of the quasi-species detected. This subset had in common two inactivating mutations in the tat gene. In addition, two of these defective genomes each had a unique mutation. This is the second instance of a defective early gene being present in a high percentage of the proviruses present in the PBMCs of an HIV-1-infected individual, (the first reported by Martins LP et al.: J Virol 1991;65:4502-4507), and suggests that genomes defective in an early gene can participate in the infectious spread of HIV-1 in vivo.
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Virus Defectuosos/genética , Genes tat , Infecciones por VIH/microbiología , VIH-1/genética , Provirus/genética , Secuencia de Bases , Cartilla de ADN/genética , ADN Viral/sangre , ADN Viral/genética , Virus Defectuosos/aislamiento & purificación , Genoma Viral , VIH-1/aislamiento & purificación , Humanos , Datos de Secuencia Molecular , Mutación , Reacción en Cadena de la Polimerasa , Provirus/aislamiento & purificaciónRESUMEN
Viral DNA sequences were determined over the V3 region of env from 28 infected individuals living in the high HIV-1 prevalence Brazilian cities of Rio de Janeiro and São Paulo. Twenty-six belonged to envelope sequence subtype B, prevalent in North America and Europe, and one was classified as subtype F, found recently in Brazil and in Romania (one appeared to be a B/F recombinant). Octameric sequences at the tip of the subtype B V3 loops were variable and distinct from those prevalent in North America and Europe. The GPGR motif, prevalent in North American/European strains, was found in only 8 (28.5%) sequences, whereas GWGR was found in 12 (43%) and novel sequences in 8 (28.5%). Brazilian subtype B sequences also diverged from the consensus North American/European strains over the remainder of the V3 loop. These results suggest that Brazilian HIV-1 B strains may have important antigenic differences from prototype subtype B strains currently being evaluated for use in HIV vaccines. These results should be taken into account for future vaccine programs in Brazil.
Asunto(s)
Proteína gp120 de Envoltorio del VIH/genética , Infecciones por VIH/microbiología , VIH-1/genética , VIH-1/aislamiento & purificación , Fragmentos de Péptidos/genética , Polimorfismo Genético , Vacunas contra el SIDA/aislamiento & purificación , Secuencia de Aminoácidos , Secuencia de Bases , Brasil , Cartilla de ADN/genética , ADN Viral/genética , Femenino , Genes env , VIH-1/clasificación , Humanos , Masculino , Datos de Secuencia Molecular , Filogenia , Reacción en Cadena de la Polimerasa , ARN/genética , Homología de Secuencia de AminoácidoRESUMEN
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 (ULTMA) 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% and 0.13% error rates for ULTMA 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.
Asunto(s)
ADN Polimerasa Dirigida por ADN , Reacción en Cadena de la Polimerasa , Thermotoga maritima/enzimología , Thermotoga maritima/genética , Thermus/enzimología , Thermus/genética , Reproducibilidad de los ResultadosRESUMEN
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%) 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%, 95% confidence limits 74.9 to 87.0%) were B and 8 (19%, 95% confidence limits 12.9 to 25.0%) were F, whereas of the 41 typed cases from Santos, 39 (95%, 95% confidence limits 91.6 to 98.4%) were B and 2 (5%, 95% confidence limits 1.6 to 8.4%) 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.
Asunto(s)
Síndrome de Inmunodeficiencia Adquirida/epidemiología , VIH-1/genética , Abuso de Sustancias por Vía Intravenosa/virología , Adulto , Brasil/epidemiología , Femenino , VIH-1/clasificación , VIH-1/aislamiento & purificación , Análisis Heterodúplex , Humanos , Masculino , Prevalencia , Estudios ProspectivosRESUMEN
We investigated whether women positive for human immunodeficiency virus (HIV) infection were late in seeking an anonymous HIV counseling and testing service, and the factors associated with a low CD4 count, in São Paulo, Brazil. Seventy-one consecutive HIV-1-seropositive women were interviewed by means of a structured questionnaire. Blood samples were collected for CD4+ T-lymphocytes count and determination of HIV-1 subtypes. Hepatitis C, syphilis, human T-cell lymphotrophic virus type I (HTLV-I), and HTLV-II infections were assessed by serologic tests. More than 70% of the women had less than 500 CD4+ cells/mm3 (20% below 200). Low CD4 count was significantly associated with sex work history, condom use in the last 6 months, and seropositivity to HTLV-I and syphilis. There was no relation between low CD4 count and HIV-1 subtypes. These results indicate that in Sao Paulo many women are seeking an anonymous testing service late in the course of HIV infection. The main purposes of anonymous HIV testing services - early diagnosis of infection, and counseling to prevent infection - are not being achieved. Another strategy for reducing the interval between infection and diagnosis in women must be addressed.
Asunto(s)
Infecciones por VIH/epidemiología , Infecciones por VIH/prevención & control , VIH-1 , Aceptación de la Atención de Salud/estadística & datos numéricos , Adolescente , Adulto , Brasil/epidemiología , Recuento de Linfocito CD4 , Femenino , Infecciones por VIH/complicaciones , Infecciones por VIH/diagnóstico , Infecciones por HTLV-I/complicaciones , Infecciones por HTLV-I/epidemiología , Hepatitis C/complicaciones , Hepatitis C/epidemiología , Humanos , Encuestas y Cuestionarios , Sífilis/complicaciones , Sífilis/epidemiología , Salud de la MujerRESUMEN
The clinical significance of isolated anti-HBc is still a challenge. To elucidate the real importance of this finding in our blood donors, an investigation algorithm was tested. One hundred and twelve isolated anti-HBc seropositive blood donors underwent clinical evaluation and retesting of HBV markers. Those who presented repeatedly reactive isolated anti-HBc, received a single dose of hepatitis B recombinant vaccine to verify anti-HBs early response. A HBV-DNA determination by PCR was done for those who did not test positive to anti-HBs after vaccine. The level of anti-HBc was recorded as a ratio of the sample-to-cut-off values (S:C ratio) in 57 candidates at donation. Comparing true and false-positive anti-HBc results, the different S:C ratios of them were statistically significant and when less than 2, implying in a false-positive result probability over 80%. A high percent of false-positive results (16.07%) was verified after anti-HBc retesting. HBV immunity was characterized in 49.11%, either by anti-HBs detection in retesting (15.18%), or after a single dose HBV vaccination (33.93%). HBV-DNA was negative in all tested donors. In conclusion, this algorithm was useful to clarify the meaning of isolated anti-HBc in most of our blood donors.