Machine learning for predicting Chagas disease infection in rural areas of Brazil

INTRODUCTION

Chagas disease is a severe parasitic illness that is prevalent in Latin America and often goes unaddressed. Early detection and treatment are critical in preventing the progression of the illness and its associated life-threatening complications. In recent years, machine learning algorithms have emerged as powerful tools for disease prediction and diagnosis.

METHODS

In this study, we developed machine learning algorithms to predict the risk of Chagas disease based on five general factors: age, gender, history of living in a mud or wooden house, history of being bitten by a triatomine bug, and family history of Chagas disease. We analyzed data from the Retrovirus Epidemiology Donor Study (REDS) to train five popular machine learning algorithms. The sample comprised 2,006 patients, divided into 75% for training and 25% for testing algorithm performance. We evaluated the model performance using precision, recall, and AUC-ROC metrics.

RESULTS

The Adaboost algorithm yielded an AUC-ROC of 0.772, a precision of 0.199, and a recall of 0.612. We simulated the decision boundary using various thresholds and observed that in this dataset a threshold of 0.45 resulted in a 100% recall. This finding suggests that employing such a threshold could potentially save 22.5% of the cost associated with mass testing of Chagas disease.

CONCLUSION

Our findings highlight the potential of applying machine learning to improve the sensitivity and effectiveness of Chagas disease diagnosis and prevention. Furthermore, we emphasize the importance of integrating socio-demographic and environmental factors into neglected disease prediction models to enhance their performance.

Thinking out of the box: revisiting health surveillance based on medical records

Despite the considerable advances in the last years, the health information systems for health surveillance still need to overcome some critical issues so that epidemic detection can be performed in real time. For instance, despite the efforts of the Brazilian Ministry of Health (MoH) to make COVID-19 data available during the pandemic, delays due to data entry and data availability posed an additional threat to disease monitoring. Here, we propose a complementary approach by using electronic medical records (EMRs) data collected in real time to generate a system to enable insights from the local health surveillance system personnel. As a proof of concept, we assessed data from São Caetano do Sul City (SCS), São Paulo, Brazil. We used the "fever" term as a sentinel event. Regular expression techniques were applied to detect febrile diseases. Other specific terms such as "malaria," "dengue," "Zika," or any infectious disease were included in the dictionary and mapped to "fever." Additionally, after "tokenizing," we assessed the frequencies of most mentioned terms when fever was also mentioned in the patient complaint. The findings allowed us to detect the overlapping outbreaks of both COVID-19 Omicron BA.1 subvariant and Influenza A virus, which were confirmed by our team by analyzing data from private laboratories and another COVID-19 public monitoring system. Timely information generated from EMRs will be a very important tool to the decision-making process as well as research in epidemiology. Quality and security on the data produced is of paramount importance to allow the use by health surveillance systems.

Genome-wide association study of early ischaemic stroke risk in Brazilian individuals with sickle cell disease implicates ADAMTS2 and CDK18 and uncovers novel loci

Ischaemic stroke is a common complication of sickle cell disease (SCD) and without intervention can affect 11% of children with SCD before the age of 20. Within the Trans-Omics for Precision Medicine (TOPMed), a genome-wide association study (GWAS) of ischaemic stroke was performed on 1333 individuals with SCD from Brazil (178 cases, 1155 controls). Via a novel Cox proportional-hazards analysis, we searched for variants associated with ischaemic stroke occurring at younger ages. Variants at genome-wide significance (p < 5 × 10-8 ) include two near genes previously linked to non-SCD early-onset stroke (<65 years): ADAMTS2 (rs147625068, p = 3.70 × 10-9 ) and CDK18 (rs12144136, p = 2.38 × 10-9 ). Meta-analysis, which included the independent SCD cohorts Walk-PHaSST and PUSH, exhibited consistent association for variants rs1209987 near gene TBC1D32 (p = 3.36 × 10-10 ), rs188599171 near CUX1 (p = 5.89 × 10-11 ), rs77900855 near BTG1 (p = 4.66 × 10-8 ), and rs141674494 near VPS13C (1.68 × 10-9 ). Findings from this study support a multivariant model of early ischaemic stroke risk and possibly a shared genetic architecture between SCD individuals and non-SCD individuals younger than 65 years.

Molecular test for COVID-19 diagnosis based on a colorimetric genomagnetic assay

The world is in a long pandemic period caused by the SARS-CoV-2 virus and massive diagnostic tests to assist efforts to control the spread of the disease and also to avoid new coronavirus variants are still needed. Herein, we propose a simple and accurate saliva-based colorimetric test for the diagnosis of COVID-19. Magnetic beads (MBs) modified with a sequence of single-strand DNA (ssDNA) complementary to the N gene of the SARS-CoV-2 RNA were developed and used for magnetic capture and separation from a complex saliva sample. A second biotinylated ssDNA sequence was applied, and the colorimetric detection was carried out by adding streptavidin-horseradish peroxidase conjugate, H₂O_2, and tetramethylbenzidine (TMB) as chromogenic substrate. The test does not require viral RNA isolation, transcription, or amplification steps and can be performed at room temperature. The molecular assay test can be run using 96-well microplates, allowing the diagnosis of a large number of samples in 90 min. A simple support for magnets was designed and constructed using a 3D printer that allows the magnetic separations directly in the 96-well microplate. The colorimetric test showed an excellent ability to discriminate between healthy individuals and patients infected with SARS-CoV-2, with 92% and 100% of clinical sensitivity and specificity, respectively. This performance was similar to that achieved using the gold standard RT-PCR technique. The proposed genomagnetic assay offers an opportunity to greatly increase population testing, contribute to controlling the spread of the virus, and improve health equity in testing for COVID-19.

Post-acute sequelae of SARS-CoV-2 associates with physical inactivity in a cohort of COVID-19 survivors

The aim of this study was to determine whether Post-acute Sequelae of SARS-CoV-2 Infection (PASC) are associated with physical inactivity in COVID-19 survivors. This is a cohort study of COVID-19 survivors discharged from a tertiary hospital in Sao Paulo, Brazil. Patients admitted as inpatients due to laboratory-confirmed COVID-19 between March and August 2020 were consecutively invited for a follow-up in-person visit 6 to 11 months after hospitalization. Ten symptoms of PASC were assessed using standardized scales. Physical activity was assessed by questionnaire and participants were classified according to WHO Guidelines. 614 patients were analyzed (age: 56 ± 13 years; 53% male). Frequency of physical inactivity in patients exhibiting none, at least 1, 1-4, and 5 or more symptoms of PASC was 51%, 62%, 58%, and 71%, respectively. Adjusted models showed that patients with one or more persistent PASC symptoms have greater odds of being physically inactive than those without any persistent symptoms (OR: 1.57 [95% CI 1.04-2.39], P = 0.032). Dyspnea (OR: 2.22 [1.50-3.33], P < 0.001), fatigue (OR: 2.01 [1.40-2.90], P < 0.001), insomnia (OR: 1.69 [1.16-2.49], P = 0.007), post-traumatic stress (OR: 1.53 [1.05-2.23], P = 0.028), and severe muscle/joint pain (OR: 1.53 [95% CI 1.08-2.17], P = 0.011) were associated with greater odds of being physically inactive. This study suggests that PASC is associated with physical inactivity, which itself may be considered as a persistent symptom among COVID-19 survivors. This may help in the early identification of patients who could benefit from additional interventions tailored to combat inactivity (even after treatment of PASC), with potential beneficial impacts on overall morbidity/mortality and health systems worldwide.

Is Severity Score Associated With Indication for Hematopoietic Stem Cell Transplantation in Individuals With Sickle Cell Anemia?

Manifestations of sickle cell disease (SCD) begin early in childhood and cause morbidity and decreased life expectancy. Hematopoietic stem cell transplantation (HSCT) is curative but associated with risk of mortality attributable to the transplant. This risk should be counterbalanced with SCD morbidity and mortality. A severity score using a Bayesian network model was previously validated to predict the risk of death in adult individuals with SCD. The objective of this study is to calculate the severity scores of participants in a multicenter cohort of Brazilians with SCD, using a previously published Bayesian network-derived score, associated with risk of death and then compare the severity scores between participants with and without an indication for HSCT as defined by the Brazilian Ministry of Health (MoH) criteria. This is an observational, retrospective study. We analyzed 2063 individuals with sickle cell anemia from the Recipient Epidemiology and Donor Evaluation Study-III Brazil SCD cohort and applied a Bayesian network-derived score to compare candidates and non-candidates for HSCT according to the Brazilian MoH transplant criteria. Classical statistical methods were used to analyze data and make comparisons. We compared severity scores between cohort members with (n = 431) and without (n = 1632) HSCT indications according to Brazilian MoH. Scores were not different in adult participants with ≥1 HSCT indication when compared to those with no indication (mean 0.342 versus 0.292; median 0.194 versus 0.183, P = .354) and receiver operating characteristic curves did not demonstrate an obvious threshold to differentiate participants with or without HSCT indications. Severity score may predict risk of death but does not differentiate HSCT candidates. Current indications should be evaluated to ensure that patients with more severe disease who might benefit from HSCT are appropriately identified.

The Recipient Epidemiology and Donor Evaluation Study-IV-Pediatric (REDS-IV-P): A research program striving to improve blood donor safety and optimize transfusion outcomes across the lifespan

BACKGROUND

The Recipient Epidemiology and Donor Evaluation Study-IV-Pediatric (REDS-IV-P) is a new iteration of prior National Heart, Lung, and Blood Institute (NHLBI) REDS programs that focus on improving transfusion recipient outcomes across the lifespan as well as the safety and availability of the blood supply.

STUDY DESIGN AND METHODS

The US program includes blood centers and hospitals (22 including 6 free-standing Children's hospitals) in four geographic regions. The Brazilian program has 5 participating hemocenters. A Center for Transfusion Laboratory Studies (CTLS) and a Data Coordinating Center (DCC) support synergistic studies and activities over the 7-year REDS-IV-P program.

RESULTS

The US is building a centralized, vein-to-vein (V2V) database, linking information collected from blood donors, their donations, the resulting manufactured components, and data extracts from hospital electronic medical records of transfused and non-transfused patients. Simultaneously, the Brazilian program is building a donor, donation, and component database. The databases will serve as the backbone for retrospective and prospective observational studies in transfusion epidemiology, transfusion recipient outcomes, blood component quality, and emerging blood safety issues. Special focus will be on preterm infants, patients with sickle cell disease, thalassemia or cancer, and the effect of donor biologic variability and component manufacturing on recipient outcomes. A rapid response capability to emerging safety threats has resulted in timely studies related to Severe Acute Respiratory Syndrome Corona Virus-2 (SARS-CoV-2).

CONCLUSIONS

The REDS-IV-P program endeavors to improve donor-recipient-linked research with a focus on children and special populations while also maintaining the flexibility to address emerging blood safety issues.

A Genome-Wide Association Study Identifies Novel Susceptibility loci in Chronic Chagas Cardiomyopathy

BACKGROUND

Chagas disease is an infectious disease caused by the parasite Trypanosoma cruzi and is endemic from Latin American countries. The goal of our study was to identify novel genetic loci associated with chronic Chagas cardiomyopathy development in Chagas disease patients from different Latin American populations.

METHODS

We performed a cross-sectional, nested case-control study including 3 sample collections from Colombia, Argentina, and Bolivia. Samples were genotyped to conduct a genome-wide association study (GWAS). These results were meta-analyzed with summary statistic data from Brazil, gathering a total of 3413 Chagas disease patients. To identify the functional impact of the associated variant and its proxies, we performed an in silico analysis of this region.

RESULTS

The meta-analysis revealed a novel genome-wide statistically significant association with chronic Chagas cardiomyopathy development in rs2458298 (OR = 0.90, 95%CI = 0.87-0.94, P-value = 3.27 × 10-08), nearby the SAC3D1 gene. In addition, further in silico analyses displayed functional relationships between the associated variant and the SNX15, BAFT2, and FERMT3 genes, related to cardiovascular traits.

CONCLUSIONS

Our findings support the role of the host genetic factors in the susceptibility to the development of the chronic cardiac form of this neglected disease.

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Seroprevalence and Risk Factors Among Oligo/Asymptomatic Healthcare Workers: Estimating the Impact of Community Transmission

We evaluated the seroprevalence of SARS-CoV-2 and risk factors among 4987 oligo/asymptomatic healthcare workers; seroprevalence was 14% and factors associated with SARS-CoV-2 infection were lower educational level (aOR, 1.93; 95% CI, 1.03-3.60), using public transport to work (aOR, 1.65; 95% CI, 1.07-2.62), and working in cleaning or security (aOR, 2.05; 95% CI, 1.04-4.03).

An exploratory study of associations with spontaneous preterm birth in primigravid pregnant women with a normal cervical length

BACKGROUND

Predictors of spontaneous preterm birth in primigravid women remain undetermined.

AIM

We evaluated whether biomarkers in vaginal secretions and/or differences in the dominant bacterium in the vaginal microbiome predicted the risk for spontaneous preterm birth in primigravid women with a cervical length >25mm.

STUDY DESIGN

In a prospective study, 146 second trimester pregnant women with their first conception and a cervix >25mm were enrolled. The vaginal microbiome composition was characterized by analysis of 16S ribosomal RNA gene sequences. The concentrations of d- and l-lactic acid, matrix metalloproteinase (MMP) 2, 8 and 9 and tissue inhibitor of metalloproteinase (TIMP) 1 and 2 in vaginal secretions were measured by ELISA. Cervical length was determined by vaginal ultrasonography. Pregnancy outcome data were subsequently collected. There was a spontaneous preterm birth (SPTB) in 13 women (8.9%) while in an additional 8 women (5.5%) preterm delivery was medically indicated. Lactobacillus iners was the dominant vaginal bacterium in 61.5% of women with a SPTB but only in 31.2% of those who delivered at term (p = .0354). The vaginal concentration of TIMP-1 (p = .0419) and L-lactic acid (p = .0495) was higher in women with a SPTB as compared to those who delivered at term. Lactobacillus iners dominance was associated with elevated levels of TIMP-1 (p = .0434) and TIMP-2 (p = .0161) and lower levels of D-lactic acid (p < .0001) compared to when L. crispatus was dominant.

CONCLUSION

In this exploratory study of primigravid women, elevations in vaginal TIMP-1 and L- lactic acid and L. iners dominance in the vaginal microbiome are associated with an increased occurrence of SPTB.

Characterization of HIV risks in a Brazilian sickle cell disease population

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.

Identification of bacteriophages in the vagina of pregnant women: a descriptive study

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.

Level of literacy and clinical outcomes in patients with Chagas disease: SaMi-Trop project

Background

Chagas disease (CD) is a neglected tropical disease that affects mainly vulnerable population, whose majority has low ability to understand health information. This study aimed to assess the prevalence of health literacy (HL) and its association with sociodemographic, quality of life, health care aspects and worse clinical outcomes.

Methods

This is a cross-sectional study developed inside a cohort study (SaMi-Trop) including 1959 patients. It has been conducted in an endemic region to CD in Brazil. The eligible criteria for HL evaluation was the ability to read. The HL was assessed with SALPHA-18 scale and literacy was categorized in inadequate HL; adequate HL and; illiterate. Multiple models were adjusted using binary logistic regression, multinomial and beta regression models using the gamlss framework.

Results

Of the patients included, 1136 (74.1%) are illiterate. For HL assessment, only 397 managed to complete the HL evaluation. The prevalence of inadequate HL was 85.1% (338), only 59 patients (14.9%) had adequate HL. Our results are as following: 1) being illiterate increases the chance of using more drugs when compared to individuals with adequate HL - 1 or 2 drugs (OR: 1.96; CI: 1.06-3.62) and 3 to 4 medications (OR: 3.06; CI:1.44-6.52), to have hypertension (OR: 2.24; CI: 1.29-3.90), report an average self-perceived health (OR: 2.97; IC: 1.63-5.42) and report poor self-perceived health (OR: 3.67; CI: 1.71-7.89); 2) inadequate literacy increases the chance of using 3 to 4 medications (OR: 2.26; CI: 1.04-4.93) and report an average self-perceived health (OR: 2.48; CI: 1.34-4.62); 3) Illiterate patients present worst quality of life scores in Physical (OR: 0,730; CI: 0,583-0,914), Psychological (OR: 0,671; CI: 0,544-0,828) and Environmental (OR: 0,727; CI: 0,601-0,880) domains.

Conclusions

We found a high prevalence of inadequate HL; it was associated with worse clinical outcomes and poor self-perceived health.

Key messages

Our findings reinforce the importance of improving health communication in CD patients seeking to avoid unfavorable outcomes. A high prevalence of inadequate health literacy was observed in our study, which can impact the self-care ability of patients with CD.

Performance of a qualitative rapid chromatographic immunoassay to diagnose COVID-19 in patients in a middle-income country

•

COVID-19 diagnosis; high sensitivity and specificity qualitative rapid chromatographic immunoassays; can be used for the diagnosis of RT-PCR-negative patients.

Objectives

We evaluated a rapid chromatographic immunoassay (IgG/IgM antibodies) and an ELISA assay to diagnose COVID-19 in patient sat two Brazilian hospitals.

Methods

A total of 122 subjects with COVID-19 were included: 106 SARS-COV-2 RT-PCR-positive patients and 16 RT-PCR-negative patients with symptoms and chest computed tomography (CT) consistent with COVID-19. Ninety-six historical blood donation samples were used as controls. Demographic and clinical characteristics were retrieved from electronic records. Sensitivity and specificity were calculated, as were their 95% binomial confidence intervals using the Clopper-Pearson method. All analyses were performed in R version 3.6.3.

Results

The sensitivity of the chromatographic immunoassay in all RT-PCR-positive patients, irrespective of the timing of symptom onset, was 85.8% (95% binomial CI 77.7% to 91.9%). This increased with time after symptom onset, and at >14 days was 94.9% (85.9% to 98.9%). The specificity was 100% (96.4% to 100%). 15/16 (94%) RT- PCR-negative cases tested positive. The most frequent comorbidities were hypertension and diabetes mellitus and the most frequent symptoms were fever, cough, and dyspnea. All RT-PCR-negative patients had pneumonia. The most frequent thoracic CT findings were ground glass changes (n = 11, 68%), which were bilateral in 9 (56%) patients, and diffuse reticulonodular infiltrates (n = 5, 31%).

Conclusions

The COVID-19 rapid chromatographic immunoassay evaluated in this study had a high sensitivity and specificity using plasma, particularly after 14 days from symptom onset. ELISA and qualitative rapid chromatographic immunoassays can be used for the diagnosis of RT-PCR-negative patients.

Blood utilization and characteristics of patients treated with chronic transfusion therapy in a large cohort of Brazilian patients with sickle cell disease

BACKGROUND

Red blood cell (RBC) transfusions are used in sickle cell disease (SCD) to treat acute complications or as chronic transfusion therapy (CTT) to prevent severe manifestations. The objectives of this study were to describe blood utilization and adverse events (AEs) associated with RBCs in the Brazilian SCD population and compare characteristics of patients treated or not with CTT.

STUDY DESIGN AND METHODS

A SCD cohort was established at six Brazilian centers. Medical and blood bank records were abstracted for clinical and transfusion history. Two controls not treated with CTT matched on center, SCD genotype, sex, and age were selected for each CTT case within the cohort to compare characteristics between the two groups.

RESULTS

Most of the 2794-member cohort had received a transfusion (75.0% of children and 89.2% of adults) with 29.2% of patients receiving transfusion in the prior year. There were 170 (10.6%) children and 115 (9.2%) adults treated with CTT. Children not treated with CTT were more likely to have pain and acute chest hospitalizations in the prior year (25.3% vs. 11.9%, p = 0.0003; and 22.0% vs. 10.7%, p = 0.002, respectively). Both iron overload and alloimmunization were more common in CTT cases compared to controls (65.6% vs. 17.0% and 36.2% vs. 15.9%, respectively). A higher proportion of adults treated with CTT demonstrated oxygen saturation of greater than 95% compared to controls not treated (51.1% vs. 39.2%), while there was no difference in oxygenation between children treated or not. Of 4501 transfusion episodes, 28 (0.62%) AEs were reported. There was no difference in AEs associated with transfusions for acute indications versus CTT.

CONCLUSION

Red blood cell transfusion was common in Brazilian SCD patients, with utilization driven by CTT. Transfusion reactions were not common; however, alloimmunization and iron overload were frequent among those on CTT, highlighting the need for novel clinical strategies to mitigate these risks.

Prevalence of serologic markers of transfusion and sexually transmitted infections and their correlation with clinical features in a large cohort of Brazilian patients with sickle cell disease

BACKGROUND

Patients with sickle cell disease (SCD) often require red blood cell (RBC) transfusion for clinical complications, so may be exposed to transfusion-transmitted infections (TTIs). The prevalence of markers for human immunodeficiency virus (HIV), hepatitis C virus (HCV) and B (HBV), human T-cell lymphotropic virus (HTLV-1/2), Chagas disease, and syphilis in an SCD cohort in Brazil were studied.

STUDY DESIGN AND METHODS

Clinical history, interview data, blood samples, and medical chart review data were collected during cohort enrollment from November 2013 to May 2015. Serologic markers of infection were assessed. Standard measures of statistical association were calculated, and multivariable models were developed for the most prevalent infections to identify associated factors.

RESULTS

Infection markers were evident in 5.2% (144/2779) of the enrolled cohort. Anti-HCV was detected in 69 (2.5%), syphilis antibodies in 34 (1.2%), anti-HTLV-1/2 in 17 (0.6%), HBV surface antigen in 13 (0.5%), Chagas disease antibodies in 13 (0.5%), and anti-HIV in 8 (0.3%) of participants. Factors associated with increased odds of being anti-HCV reactive were older age, illegal drug use, increasing number of RBCs, more than three pain crises in the previous year, and geographic location. Syphilis was associated with older age, females, and smoking history.

CONCLUSION

HCV infection was more common in older patients who may have received RBCs before testing was performed on donations, suggesting possible historic transfusion transmission. The cohort showed decreasing rates of infections and a reduction in transfusion transmission markers in younger patients compared to historical literature except for syphilis, indicating contemporary reduced risk of TTI.

Social and behavioral characteristics of male blood donors and their sexual partners: an analysis to define risk subsets

BACKGROUND

Men who have sex with men in Brazil are deferred from donation for 1 year since their last sexual contact. Legal proceedings in front of the Brazilian Supreme Court could compel blood collection agencies to discontinue use of sexual orientation questions.

METHODS

Data from male participants in a completed HIV risk factor case-control study were used to evaluate whether it is possible to differentiate donors at lower and higher risk for HIV using two analytical approaches: latent class and random forest analyses.

RESULTS

Male blood donors were divided into three distinct risk profile classes. Class 1 includes donors who are heterosexual (96.4%), are HIV negative (88.7%), have a main partner (99.4%), and practice unprotected sex (77.8%). Class 2 includes donors who are men who have sex with men /bisexuals' (100.0%), are HIV positive (97.4%), and were not aware of their sexual partners' HIV status (80.3%). Class 3 includes donors who are heterosexual (84.1%), practice unprotected vaginal/anal heterosexual sex (66.8% vs. 40.9%), and were both HIV positive and HIV negative (49.5% vs. 50.5%). We also found that asking donors about their partner(s)' HIV serostatus could replace asking about donors' sexual orientation and types of partners with relatively minor shifts in sensitivity (0.76 vs. 0.58), specificity (0.89 vs. 0.94), and positive predictive value (0.85 vs. 0.88).

CONCLUSION

Sexual orientation questions on the donor questionnaire could be replaced without great loss in the sensitivity, specificity, and positive predictive value. Social and sexual behaviors of donors and their partners are proxies for HIV risk and can help to develop modified questions that will need controlled trials to be validated.

A new insight into CFTR allele frequency in Brazil through next generation sequencing

BACKGROUND

As of 2013, fewer than 20% of patients in the Brazilian CF Registry had two CFTR mutations identified. The aim of this study was to sequence the coding region of the CFTR in Brazilian CF patients and determine the frequency of mutations in this cohort.

METHODS

Patients with CF and those with suspected atypical CF or CFTR-related disorders were invited to enroll. Total DNA was extracted from blood samples, quantified, and purified. Library preparation was performed using Ion Xpress™ Plus gDNA and Amplicon Library preparation kits (Life Technologies), as well as sequencing using the Ion Torrent platform (Life Technologies).

RESULTS

A total of 141 patients were enrolled, and 45 mutations were identified. Among 126 CF patients, we identified mutations in 97.2% of alleles. The three most common mutations were F508del, G542X, and 3120 + 1G->A. Five novel pathogenic mutations were also identified.

CONCLUSIONS

Next generation sequencing (NGS) allowed the identification of mutations in most CF alleles and confirmed allelic heterogeneity in our population.

Genetic Characterization of a Panel of Diverse HIV-1 Isolates at Seven International Sites

HIV-1 subtypes and drug resistance are routinely tested by many international surveillance groups. However, results from different sites often vary. A systematic comparison of results from multiple sites is needed to determine whether a standardized protocol is required for consistent and accurate data analysis. A panel of well-characterized HIV-1 isolates (N = 50) from the External Quality Assurance Program Oversight Laboratory (EQAPOL) was assembled for evaluation at seven international sites. This virus panel included seven subtypes, six circulating recombinant forms (CRFs), nine unique recombinant forms (URFs) and three group O viruses. Seven viruses contained 10 major drug resistance mutations (DRMs). HIV-1 isolates were prepared at a concentration of 107 copies/ml and compiled into blinded panels. Subtypes and DRMs were determined with partial or full pol gene sequences by conventional Sanger sequencing and/or Next Generation Sequencing (NGS). Subtype and DRM results were reported and decoded for comparison with full-length genome sequences generated by EQAPOL. The partial pol gene was amplified by RT-PCR and sequenced for 89.4%-100% of group M viruses at six sites. Subtyping results of majority of the viruses (83%-97.9%) were correctly determined for the partial pol sequences. All 10 major DRMs in seven isolates were detected at these six sites. The complete pol gene sequence was also obtained by NGS at one site. However, this method missed six group M viruses and sequences contained host chromosome fragments. Three group O viruses were only characterized with additional group O-specific RT-PCR primers employed by one site. These results indicate that PCR protocols and subtyping tools should be standardized to efficiently amplify diverse viruses and more consistently assign virus genotypes, which is critical for accurate global subtype and drug resistance surveillance. Targeted NGS analysis of partial pol sequences can serve as an alternative approach, especially for detection of low-abundance DRMs.

Development of a Novel Multiplex Immunoassay Multi-cruzi for the Serological Confirmation of Chagas Disease

Background

Chagas disease is due to the parasite Trypanosoma cruzi, a protist disseminated by a Triatome vector. This disease is endemic to Latin America and considered by WHO as one of the 17 world’s neglected diseases. In Europe and in North America, imported cases are also detected, due to migration of population outside of the endemic region. Diagnosis of T. cruzi infection is usually made indirectly by the detection of specific antibodies to T. cruzi antigens. Following initial diagnostic evaluation or screening test (qualifying or discarding blood donation), a confirmation test is performed for samples initially reactive. The test presented in this study aims at the confirmation/refutation of the infectious status of human blood samples and will permit taking appropriate clinical measures.

Methodology/Principal Findings

We designed a novel array of twelve antigens and printed these antigens onto 96-well plates. We tested 248 positive samples T. cruzi, 94 unscreened blood donors’ samples from non-endemic area, 49 seronegative blood donors, 7 false-positive and 3 doubtful samples. The observed reactivities were analyzed to propose a decision-tree algorithm that correctly classifies all the samples, with the potential to discriminate false-positive results and sticky samples. We observed that antibodies levels (Sum of all antigens) was significantly higher for PCR positive than for PCR negative samples in all studied groups with Multi-cruzi.

Conclusion/Significance

The results described in this study indicate that the Multi-cruzi improves the serological confirmation of Chagas disease. Moreover the “sum of all antigens” detected by Multi-cruzi could reflect parasitemia level in patients–like PCR signals does—and could serve as an indicator of parasite clearance in longitudinal follow-ups. Validation of this assay is still required on an independent large collection of well characterized samples including typical false-reactive samples such as Leishmaniasis.

Eight million people are affected by Chagas disease worldwide, almost exclusively in South America. This chronic disease is initially asymptomatic but turns out to be life threatening in 30% of the cases, years after the infection. Two therapies are available, but their efficacy is maximal if the treatment is initiated shortly after contamination. In the absence of reliable symptoms, the in vitro diagnostic of Chagas Disease is thus a crucial tool to implement accurate clinical management. In order to permit universal access and a reliable confirmation of Chagas’s parasite presence, we have developed a new multiplex platform using a large number of selected antigens on easy handling 96 well ELISA microplates. In this manuscript, we present the first optimization data of the Multi-cruzi test that shows promising results for Chagas disease confirmation.

Hepatitis C: Prevalence of serologic markers and risk factors in blood donors at a large blood centre in South-eastern Brazil (2007-2010)

This study aimed to evaluate the trends of HCV seropositivity rates in first time blood donors from a reference blood centre in Southeast Brazil. Data from the period of 2007-2010 were analysed according to anti-HCV antibodies, donor demographic characteristics and type of donation. There was a marked and continuous decline in prevalence in the analysed period, and in 93,534 first time donors, the prevalence of anti-HCV was 0.09%. Anti-HCV were associated with less education and older age (≥ 35 years). The rates of anti-HCV observed in the present study were lower than in Brazil, but considerably higher than developed countries.

A comprehensive protocol to evaluate the use of blood and its components in Latin America and the Caribbean

Blood transfusion safety is a critical part of appropriate health care. Considering the limited information available on the use of blood and its components in Latin America and the Caribbean, the Grupo Cooperativo iberoamericano de Medicina Transfusional (Ibero-American Cooperative Group for Transfusion Medicine; GCIAMT), through its Research and International Affairs committees, carried out a project to develop a protocol that would facilitate the evaluation of blood usage at the country, jurisdiction, and institutional levels in varied country contexts. Experts in blood safety from the Pan American Health Organization (Washington, DC, United States), the University of São Paulo (São Paulo, Brazil), the Hemocentro of São Paulo (São Paulo, Brazil), and GCIAMT designed a 2-step comprehensive blood-use evaluation protocol: step 1 collects data from blood requests, and step 2, from medical charts. At a minimum, 1 000 analyzed requests are necessary; as such, study periods vary depending on the number of transfusion requests issued. An Internet-based application, the Modular Research System-Study Management System (MRS-SMS), houses the data and produces reports on how hospitals request blood, how blood is issued, who requires blood and blood components, and as an added benefit, how many blood units are wasted and what the real demand for blood is.

Motivation and social capital among prospective blood donors in three large blood centers in Brazil

BACKGROUND

Studies analyzing motivation factors that lead to blood donation have found altruism to be the primary motivation factor; however, social capital has not been analyzed in this context. Our study examines the association between motivation factors (altruism, self-interest, and response to direct appeal) and social capital (cognitive and structural) across three large blood centers in Brazil.

STUDY DESIGN AND METHODS

We conducted a cross-sectional survey of 7635 donor candidates from October 15 through November 20, 2009. Participants completed self-administered questionnaires on demographics, previous blood donation, human immunodeficiency virus testing and knowledge, social capital, and donor motivations. Enrollment was determined before the donor screening process.

RESULTS

Among participants, 43.5 and 41.7% expressed high levels of altruism and response to direct appeal, respectively, while only 26.9% expressed high levels of self-interest. More high self-interest was observed at Hemope-Recife (41.7%). Of participants, 37.4% expressed high levels of cognitive social capital while 19.2% expressed high levels of structural social capital. More high cognitive and structural social capital was observed at Hemope-Recife (47.3 and 21.3%, respectively). High cognitive social capital was associated with high levels of altruism, self-interest, and response to direct appeal. Philanthropic and high social altruism were associated with high levels of altruism and response to direct appeal.

CONCLUSION

Cognitive and structural social capital and social altruism are associated with altruism and response to direct appeal, while only cognitive social capital is associated with self-interest. Designing marketing campaigns with these aspects in mind may help blood banks attract potential blood donors more efficiently.

Pilot studies for development of an HIV subtype panel for surveillance of global diversity

The continued global spread and evolution of HIV diversity pose significant challenges to diagnostics and vaccine strategies. NIAID partnered with the FDA, WRAIR, academia, and industry to form a Viral Panel Working Group to design and prepare a panel of well-characterized current and diverse HIV isolates. Plasma samples that had screened positive for HIV infection and had evidence of recently acquired infection were donated by blood centers in North and South America, Europe, and Africa. A total of 80 plasma samples were tested by quantitative nucleic acid tests, p24 antigen, EIA, and Western blot to assign a Fiebig stage indicative of approximate time from initial infection. Evaluation of viral load using FDA-cleared assays showed excellent concordance when subtype B virus was tested, but lower correlations for subtype C. Plasma samples were cocultivated with phytohemagglutinin (PHA)-stimulated peripheral blood mononuclear cells (PBMCs) from normal donors to generate 30 viral isolates (50-80% success rate for samples with viral load >10,000 copies/ml), which were then expanded to 10(7)-10(9) virus copies per ml. Analysis of env sequences showed that sequences derived from cultured PBMCs were not distinguishable from those obtained from the original plasma. The pilot collection includes 30 isolates representing subtypes B, C, B/F, CRF04_cpx, and CRF02_AG. These studies will serve as a basis for the development of a comprehensive panel of highly characterized viral isolates that reflects the current dynamic and complex HIV epidemic, and will be made available through the External Quality Assurance Program Oversight Laboratory (EQAPOL).

Human immunodeficiency virus test-seeking blood donors in a large blood bank in São Paulo, Brazil

BACKGROUND

Persons with human immunodeficiency virus (HIV) risk behaviors are excluded from donation to reduce the risk of transfusion-transmitted infection. Persons donating to be tested for HIV may therefore deny risk behaviors.

STUDY DESIGN AND METHODS

A random sample of donors completed a survey on motivations, knowledge, and attitudes on the screening process. Donors were considered test seekers if they agreed with two statements "I think that blood donation is a good, fast, and anonymous way to get my blood tested" and "I donate to get my test results." This study was conducted from June to November 2006 at the largest blood bank in São Paulo, Brazil.

RESULTS

Of 3061 participants, 208 (7%) were test seekers. They tended to be male and had a lower educational level. They were more likely to have incorrect knowledge about blood safety (e.g., not knowing that a unit can test antibody negative and still transmit infection, 50% vs. 42%, p = 0.02), express dissatisfaction with screening questions (e.g., feeling that important questions were not asked, 14% vs. 5%, p < 0.01), and concur that donors do not answer questions truthfully (e.g., donors have more sexual partners than they admit, 29% vs. 18%, p < 0.01). Test seekers were more likely to believe that it is acceptable to donate blood to get tested for HIV (41% vs. 10%, p < 0.01).

CONCLUSIONS

Test-seeking motivation, coupled with low knowledge of window period risk, is counter to improving blood safety and to donor prevention needs. Donor education needs to be improved along with availability of appropriate HIV counseling and testing.

Seroprevalence of Kaposi sarcoma-associated herpesvirus and other serologic markers in the Brazilian Amazon

To determine the presence of Kaposi sarcoma–associated herpesvirus (KSHV) and other serologic markers, we tested serum specimens of 339 Amerindians, 181 rural non-Amerindians, and 1,133 urban blood donors (13 Amerindians) in the Brazilian Amazon. High KSHV seroprevalence in children and inverse association with herpes simplex virus type 2 indicates predominant nonsexual transmission among Amerindians.

Performance of the HerpeSelect (Focus) and Kalon enzyme-linked immunosorbent assays for detection of antibodies against herpes simplex virus type 2 by use of monoclonal antibody-blocking enzyme immunoassay and clinicovirological reference standards in Brazil

A total of 586 serum samples were used to evaluate the performance of type-specific herpes simplex virus type 2 (HSV-2) commercial enzyme-linked immunosorbent assays (ELISAs) by using the monoclonal antibody-blocking enzyme immunoassay (MAb-EIA) and a clinicovirological panel as reference standards. The Kalon and HerpeSelect ELISAs had similar sensitivities (93.5% and 93.8% compared with the results obtained by MAb-EIA, respectively, and 100% for both ELISAs compared with the results obtained with a clinicovirological panel). The Kalon ELISA had a higher specificity (96.5% and 96.8% compared with the results obtained by MAb-EIA and with a clinicovirological panel, respectively) than the HerpeSelect ELISA (86.9% and 94% compared with the results obtained by MAb-EIA and with a clinicovirological panel, respectively). A higher cutoff significantly improved the specificity of the HerpeSelect ELISA.

Estimated prevalence of immunity to poliomyelitis in the city of São Paulo, Brazil: a population-based survey

Objectives. Estimate the prevalence of immunity to poliomyelitis (anti-polio antibodies) in the city of São Paulo/Brazil through a population-based survey. Methods. A quantitative and inductive method was used to draw a representative sample of the population. Randomization and stratification (based on sex, age and residence region) was done, and 1,059 individuals were studied on a home-visit basis (structured questionnaires and blood samples). A microneutralization test was performed to detect anti-polio antibodies against serotypes 1, 2 and 3. Results. The estimated prevalence of immunity to poliomyelitis was high, with 94.6% prevalence of anti-polio 1 antibodies, 98.8% anti-polio 2 and 91.9% anti-polio 3. Despite this high prevalence, there were significantly lower prevalence levels in some groups, specially among age and residence region groups. Discussion. Routine child immunization and NIDs with OPV have provided excellent levels of serological immunity to poliomyelitis in the population of the city of São Paulo, Brazil. However, there may be specific groups with a lower prevalence of immunity. Estimations of the prevalence of immunity to poliomyelitis were made in a population-based survey, which could be used as an auxiliary tool for supporting the polio eradication program.

Late diagnosis of HIV infection in women seeking counseling and testing services in São Paulo, Brazil

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.

Hepatitis G virus: prevalence and sequence analysis in blood donors of São Paulo, Brazil

BACKGROUND AND OBJECTIVES

Hepatitis G virus (HGV) is a recently discovered viral agent transmitted by blood, which was firstly identified in patients with acute or chronic liver disease. HGV prevalence in US blood donors was recently found to average 1-2%. We report a much higher HGV frequency among blood donors of São Paulo, Brazil.

MATERIALS AND METHODS

200 serum samples were submitted to RT-PCR using primers directed to the 5' untranslated region and nonstructural 5A (NS5A) region. PCR products were analyzed by gel electrophoresis and Southern blot hybridization.

RESULTS

Of the 200 specimens, 18 (9%; 95% CI 5.4-13.8%) were positive by both sets of primers. Sequence analysis of the NS5A PCR products revealed a homology of 96.3%. Of the 18 HGV-positive samples, only one was positive for anti-HBc and all were anti-HCV- and HCV-RNA-negative.

CONCLUSION

Such a high prevalence of HGV in a nonsymptomatic population suggests that this is a benign agent.

HIV-1 diversity in Brazil: genetic, biologic, and immunologic characterization of HIV-1 strains in three potential HIV vaccine evaluation sites. Brazilian Network for HIV Isolation and Characterization

The Brazilian Network for HIV Isolation and Characterization was established for the surveillance of HIV variability in Brazil. Here, we report characterization of HIV strains and virus-specific immune responses from 35 clinical samples collected from three potential HIV vaccine sites. Three genetic subtypes of HIV-1 were identified by heteroduplex mobility assay (HMA) B (in 82.9% of the samples), F (14.3%), and C (2.9%). Phylogenetic analysis based on the C2V3/env DNA sequence from all 25 specimens examined was 100% concordant with HMA results. Four variants of subtype B with different tetrapeptides at the tip of the V3 loop were found: the GPGR motif (North American), GWGR motif (Brazilian B"), and two minor variants, GFGR and GPGS, as previously detected. No significant association was found between HIV-1 subtypes and the mode of transmission or biologic properties of HIV-1 isolates (derived from 88.6% of the specimens). Only 5 of 16 isolates studied were neutralized by the autologous sera. Consistent with previous results, no relation between viral subtype and peptide enzyme-linked immunosorbent assay (ELISA) seroreactivity or neutralization was evident. This study also demonstrated the effectiveness of the collaborative approach followed by Brazilian scientists when addressing a complex subject such as HIV variability.

T cell receptor V-segment frequencies in peripheral CD8+ T cells in aging

Infections are a major cause of illness and death amongst elderly people. Peripheral blood CD8+ T lymphocytes --which play a crucial role in host defence against viral infections--, are divided in subsets based upon the expression of several cell and activation markers. In senescence changes and variations in peripheral CD8+ T lymphocyte compartment have been described, and such a decrease in the CD8+CD45RA+ lymphocytes. In this report the T V alpha and Vbeta cell specificities repertoire usage in aging subjects were studied by the use of seven different monoclonal antibodies specific for defined regions of the TCR. Except for the Vbeta6subfamily, no differences between old and control subjects in frequency of T cells bearing selected V alphabeta epitopes, were observed.

Neutrophil function in elderly persons assessed by flow cytometry

It is well known that the immune response declines with senescence and it is suggested that these changes render an individual susceptible to infection, autoimmune phenomena and cancer. Bacterial and viral infections are a major cause of illness and death amongst aged subjects, and once infection is established, the elderly also have a diminished capacity to prevent its spread (1). The cellular and molecular basis for this age-related decline in immunocompetence are still unknown and, possibly, are related to an alteration in cell transduction mechanisms (2).

T cell receptor V-segment frequencies in aged individuals

The T V alpha and V beta cell specificities repertoire usage in aging subjects was studied by the use of seven different monoclonal antibodies specific for defined regions of the T cell receptor (TCR). Except for the V beta 8 subfamily, no differences were observed in the frequency of T cells bearing selected V alpha beta epitopes, between old and control subjects.

CD8+ T cell subsets in aging

Infections are major cause of illness and death amongst elderly people. Peripheral blood CD8+ T lymphocytes -which play a crucial role in host defence against viral infections-. are divided in subsets based upon the expression of several cell and activation markers. Since in senescence changes in peripheral blood CD8+ T lymphocyte compartment have been described, studies were performed to determine whether in aging there are variations in the peripheral blood CD8+CD38+, CD8+CD57+, CD8+HLA-DR+, CD8+CD45RA+ and CD8+CD45RO+ cell subset. A decrease in the CD8+CD45RA+ lymphocytes was observed, indicating that variations in the CD8+ compartment can take place with ageing.

Comparison of in vivo plasma and peripheral blood mononuclear cell HIV-1 quasi-species to short-term tissue culture isolates: an analysis of tat and C2-V3 env regions

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.

An individual with a high prevalence of a tat-defective provirus in peripheral blood

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.