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OBJECTIVE: We developed an in-house bioinformatics pipeline to improve the detection of respiratory pathogens in metagenomic sequencing data. This pipeline addresses the need for short-time analysis, high accuracy, scalability, and reproducibility in a high-performance computing environment. RESULTS: We evaluated our pipeline using ninety synthetic metagenomes designed to simulate nasopharyngeal swab samples. The pipeline successfully identified 177 out of 204 respiratory pathogens present in the compositions, with an average processing time of approximately 4 min per sample (processing 1 million paired-end reads of 150 base pairs). For the estimation of all the 470 taxa included in the compositions, the pipeline demonstrated high accuracy, identifying 420 and achieving a correlation of 0.9 between their actual and predicted relative abundances. Among the identified taxa, 27 were significantly underestimated or overestimated, including only three clinically relevant pathogens. We also validated the pipeline by applying it to a clinical dataset from a study on metagenomic pathogen characterization in patients with acute respiratory infections and successfully identified all pathogens responsible for the diagnosed infections. These findings underscore the pipeline's effectiveness in pathogen detection and highlight its potential utility in respiratory pathogen surveillance.

Asunto(s)

Metagenómica , Infecciones del Sistema Respiratorio , Metagenómica/métodos , Humanos , Infecciones del Sistema Respiratorio/microbiología , Infecciones del Sistema Respiratorio/diagnóstico , Metagenoma/genética , Biología Computacional/métodos , Reproducibilidad de los Resultados , Nasofaringe/microbiología , Nasofaringe/virología

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Background: The prevalence of chronic kidney disease (CKD) is increasing worldwide, especially in developing countries, due to factors such as lifestyle changes and the rise of non-communicable diseases. Populations living in socioeconomically disadvantaged areas are subject to a higher burden of CKD. However, the burden of CKD on Brazilian Indigenous people, especially those undergoing an advanced urbanisation process, has not yet been described. Methods: This cross-sectional study included 1715 Truká Indigenous adults from Cabrobó, Brazil. CKD was defined according to the Kidney Disease Improving Global Outcomes guidelines classification as a urinary albumin/creatinine ratio ≥30 mg/g and/or an estimated glomerular filtration rate <60 mL/min/1.73 m2. Univariate and multiple logistic regression models were used to evaluate factors associated with CKD. Odds ratio (OR) with a 95% confidence interval (CI) was used to measure association. Findings: Out of the 1654 participants analysed (61 excluded due to missing data), the prevalence of CKD was 10% (95% CI, 8.6%-11.5%), with a higher prevalence in women compared to men (12.4% versus 6.9%, p < 0.001). The mean age was 40.5 years, with 55.6% being women. In univariate analysis, female sex (OR, 1.9; 95% CI, 1.3-2.7), age ≥60 years (OR, 4.6; 95% CI, 3.2-6.6), cardiovascular disease (OR, 2.1; 95% CI, 1.1-4.1), and dyslipidemia (OR, 1.6; 95% CI, 1.1-2.4) were identified as associated factors with CKD. Multiple logistic regression analysis identified age ≥60 years, female sex, and dyslipidemia as independently associated factors with CKD. Interpretation: The prevalence of CKD among Truká Indigenous adults analysed is high and affects a higher proportion of women. Our study found no association between hypertension, diabetes, obesity, and CKD risk, despite their high prevalence. These findings assist in developing early CKD detection strategies in Brazilian Indigenous communities, supporting disease treatment and prevention. Funding: National Council for Scientific and Technological Development (CNPq)-Ministry of Science, Technology, and Innovation of Brazil, and the Maria Emília Foundation.

RESUMEN

BACKGROUND: The expansion of sequencing technologies as a result of the response to the COVID-19 pandemic enabled pathogen (meta)genomics to be deployed as a routine component of surveillance in many countries. Scaling genomic surveillance, however, comes with associated costs in both equipment and sequencing reagents, which should be optimized. Here, we evaluate the cost efficiency and performance of different read lengths in identifying pathogens in metagenomic samples. We carefully evaluated performance metrics, costs, and time requirements relative to choices of 75, 150 and 300 base pairs (bp) read lengths in pathogen identification. RESULTS: Our findings revealed that moving from 75 bp to 150 bp read length approximately doubles both the cost and sequencing time. Opting for 300 bp reads leads to approximately two- and three-fold increases, respectively, in cost and sequencing time compared to 75 bp reads. For viral pathogen detection, the sensitivity median ranged from 99% with 75 bp reads to 100% with 150-300 bp reads. However, bacterial pathogens detection was less effective with shorter reads: 87% with 75 bp, 95% with 150 bp, and 97% with 300 bp reads. These findings were consistent across different levels of taxa abundance. The precision of pathogen detection using shorter reads was comparable to that of longer reads across most viral and bacterial taxa. CONCLUSIONS: During disease outbreak situations, when swift responses are required for pathogen identification, we suggest prioritizing 75 bp read lengths, especially if detection of viral pathogens is aimed. This practical approach allows better use of resources, enabling the sequencing of more samples using streamlined workflows, while maintaining a reliable response capability.

Asunto(s)

COVID-19 , Secuenciación de Nucleótidos de Alto Rendimiento , Metagenómica , SARS-CoV-2 , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , COVID-19/virología , Humanos , SARS-CoV-2/genética , Metagenómica/métodos , Bacterias/genética

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Long COVID is characterized by persistent that extends symptoms beyond established timeframes. Its varied presentation across different populations and healthcare systems poses significant challenges in understanding its clinical manifestations and implications. In this study, we present a novel application of text mining technique to automatically extract unstructured data from a long COVID survey conducted at a prominent university hospital in São Paulo, Brazil. Our phonetic text clustering (PTC) method enables the exploration of unstructured Electronic Healthcare Records (EHR) data to unify different written forms of similar terms into a single phonemic representation. We used n-gram text analysis to detect compound words and negated terms in Portuguese-BR, focusing on medical conditions and symptoms related to long COVID. By leveraging text mining, we aim to contribute to a deeper understanding of this chronic condition and its implications for healthcare systems globally. The model developed in this study has the potential for scalability and applicability in other healthcare settings, thereby supporting broader research efforts and informing clinical decision-making for long COVID patients.

Asunto(s)

COVID-19 , Minería de Datos , Humanos , Minería de Datos/métodos , COVID-19/epidemiología , COVID-19/virología , Registros Electrónicos de Salud , Hospitalización , SARS-CoV-2/aislamiento & purificación , Brasil/epidemiología , Síndrome Post Agudo de COVID-19

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OBJECTIVES: Mass COVID-19 immunization campaigns altered the pandemic's progress by protecting the vaccine recipient and reducing transmission. However, evidence for indirect vaccine effectiveness (IVE) is limited due to the difficulties of ascertaining this type of protection. METHODS: Using linked national Brazilian databases, we adapted the test-negative design to evaluate the IVE against symptomatic infection. We analyzed data from January 1 to December 1, 2021 (pre-omicron) and January 1 to April 30, 2022 (omicron BA.1 and BA.2). We compared the probability of testing positive across various levels of second ancestral-strain monovalent COVID-19 vaccine dose coverage, including only unvaccinated individuals in the main analysis and both vaccinated and unvaccinated individuals in additional analyses. Sensitivity analysis focused on children younger than 12 years who did not have access to COVID-19 vaccines during the pre-omicron period. RESULTS: We included 11,039,315 unvaccinated individuals tested during the pre-omicron study period. IVE was minimal until 30% vaccination coverage (<10%), then it followed a dose-dependent pattern, peaking at 37.7 (95% confidence interval 32-42.8) at 70% coverage. For children younger than 12 years, IVE peaked at 59.8% (95% confidence interval 52.7-65.9) at 70% coverage. During the omicron period, IVE remained constant at about 5% across all comparisons. CONCLUSIONS: Our findings confirm that high vaccination coverage using vaccines that prevent infection indirectly protects the community. However, IVE was substantially higher during the pre-omicron period.

Asunto(s)

Vacunas contra la COVID-19 , COVID-19 , SARS-CoV-2 , Eficacia de las Vacunas , Humanos , COVID-19/prevención & control , COVID-19/epidemiología , Brasil/epidemiología , Vacunas contra la COVID-19/inmunología , Vacunas contra la COVID-19/administración & dosificación , Femenino , Adulto , SARS-CoV-2/inmunología , Masculino , Niño , Persona de Mediana Edad , Estudios de Casos y Controles , Adolescente , Adulto Joven , Preescolar , Lactante , Cobertura de Vacunación/estadística & datos numéricos , Anciano , Vacunación Masiva/métodos , Vacunación

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BACKGROUND: Detecting and foreseeing pathogen dispersion is crucial in preventing widespread disease transmission. Human mobility is a fundamental issue in human transmission of infectious agents. Through a mobility data-driven approach, we aimed to identify municipalities in Brazil that could comprise an advanced sentinel network, allowing for early detection of circulating pathogens and their associated transmission routes. METHODS: In this modelling and validation study, we compiled a comprehensive dataset on intercity mobility spanning air, road, and waterway transport from the Brazilian Institute of Geography and Statistics (2016 data), National Transport Confederation (2022), and National Civil Aviation Agency (2017-23). We constructed a graph-based representation of Brazil's mobility network. The Ford-Fulkerson algorithm was used to rank the 5570 Brazilian cities according to their suitability as sentinel locations, allowing us to predict the most suitable locations for early detection and to track the most likely trajectory of a newly emerged pathogen. We also obtained SARS-CoV-2 genetic data from Brazilian municipalities during the early stage (Feb 25-April 30, 2020) of the virus's introduction and the gamma (P.1) variant emergence in Manaus (Jan 6-March 1, 2021), for the purposes of model validation. FINDINGS: We found that flights alone transported 79·9 million (95% CI 58·3-101·4 million) passengers annually within Brazil during 2017-22, with seasonal peaks occurring in late spring and summer, and road and river networks had a maximum capacity of 78·3 million passengers weekly in 2016. By analysing the 7 746 479 most probable paths originating from source nodes, we found that 3857 cities fully cover the mobility pattern of all 5570 cities in Brazil, 557 (10·0%) of which cover 6 313 380 (81·5%) of the mobility patterns in our study. By strategically incorporating mobility patterns into Brazil's existing influenza-like illness surveillance network (ie, by switching the location of 111 of 199 sentinel sites to different municipalities), our model predicted that mobility coverage would have a 33·6% improvement from 4 059 155 (52·4%) mobility patterns to 5 422 535 (70·0%) without expanding the number of sentinel sites. Our findings are validated with genomic data collected during the SARS-CoV-2 pandemic period. Our model accurately mapped 22 (51%) of 43 clade 1-affected cities and 28 (60%) of 47 clade 2-affected cities spread from São Paulo city, and 20 (49%) of 41 clade 1-affected cities and 28 (58%) of 48 clade 2-affected cities spread from Rio de Janeiro city, Feb 25-April 30, 2020. Additionally, 224 (73%) of the 307 suggested early-detection locations for pathogens emerging in Manaus corresponded with the first cities affected by the transmission of the gamma variant, Jan 6-16, 2021. INTERPRETATION: By providing essential clues for effective pathogen surveillance, our results have the potential to inform public health policy and improve future pandemic response efforts. Our results unlock the potential of designing country-wide clinical sample collection networks with mobility data-informed approaches, an innovative practice that can improve current surveillance systems. FUNDING: Rockefeller Foundation.

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COVID-19 , SARS-CoV-2 , Humanos , Brasil/epidemiología , COVID-19/transmisión , COVID-19/epidemiología , Ciudades , Transportes

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BACKGROUND: Chikungunya virus outbreaks have been associated with excess deaths at the ecological level. Previous studies have assessed the risk factors for severe versus mild chikungunya virus disease. However, the risk of death following chikungunya virus disease compared with the risk of death in individuals without the disease remains unexplored. We aimed to investigate the risk of death in the 2 years following chikungunya virus disease. METHODS: We used a population-based cohort study and a self-controlled case series to estimate mortality risks associated with chikungunya virus disease between Jan 1, 2015, and Dec 31, 2018, in Brazil. The dataset was created by linking national databases for social programmes, notifiable diseases, and mortality. For the matched cohort design, individuals with chikungunya virus disease recorded between Jan 1, 2015, and Dec 31, 2018, were considered as exposed and those who were arbovirus disease-free and alive during the study period were considered as unexposed. For the self-controlled case series, we included all deaths from individuals with a chikungunya virus disease record, and each individual acted as their own control according to different study periods relative to the date of disease. The primary outcome was all-cause natural mortality up to 728 days after onset of chikungunya virus disease symptoms, and secondary outcomes were cause-specific deaths, including ischaemic heart diseases, diabetes, and cerebrovascular diseases. FINDINGS: In the matched cohort study, we included 143 787 individuals with chikungunya virus disease who were matched, at the day of symptom onset, to unexposed individuals using sociodemographic factors. The incidence rate ratio (IRR) of death within 7 days of chikungunya symptom onset was 8·40 (95% CI 4·83-20·09) as compared with the unexposed group and decreased to 2·26 (1·50-3·77) at 57-84 days and 1·05 (0·82-1·35) at 85-168 days, with IRR close to 1 and wide CI in the subsequent periods. For the secondary outcomes, the IRR of deaths within 28 days after disease onset were: 1·80 (0·58-7·00) for cerebrovascular diseases, 3·75 (1·33-17·00) for diabetes, and 3·67 (1·25-14·00) for ischaemic heart disease, and there was no evidence of increased risk in the subsequent periods. For the self-controlled case series study, 1933 individuals died after having had chikungunya virus disease and were included in the analysis. The IRR of all-cause natural death within 7 days of symptom onset of chikungunya virus disease was 8·75 (7·18-10·66) and decreased to 1·59 (1·26-2·00) at 57-84 days and 1·09 (0·92-1·29) at 85-168 days. For the secondary outcomes, the IRRs of deaths within 28 days after disease onset were: 2·73 (1·50-4·96) for cerebrovascular diseases, 8·43 (5·00-14·21) for diabetes, and 2·38 (1·33-4·26) for ischaemic heart disease, and there was no evidence of increased risk at 85-168 days. INTERPRETATION: Chikungunya virus disease is associated with an increased risk of death for up to 84 days after symptom onset, including deaths from cerebrovascular diseases, ischaemic heart diseases, and diabetes. This study highlights the need for equitable access to approved vaccines and effective anti-chikungunya virus therapeutics and reinforces the importance of robust vector-control efforts to reduce viral transmission. FUNDING: Brazilian National Research Council (CNPq), Fundação de Amparo à Pesquisa do Estado da Bahia, Wellcome Trust, and UK Medical Research Council. TRANSLATION: For the Portuguese translation of the abstract see Supplementary Materials section.

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Fiebre Chikungunya , Humanos , Fiebre Chikungunya/mortalidad , Fiebre Chikungunya/epidemiología , Brasil/epidemiología , Masculino , Femenino , Adulto , Persona de Mediana Edad , Estudios de Cohortes , Factores de Riesgo , Anciano , Adulto Joven , Adolescente , Niño , Preescolar , Virus Chikungunya , Brotes de Enfermedades

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Globally, millions of lives are impacted every year by infectious diseases outbreaks. Comprehensive and innovative surveillance strategies aiming at early alert and timely containment of emerging and reemerging pathogens are a pressing priority. Shortcomings and delays in current pathogen surveillance practices further disturbed informing responses, interventions, and mitigation of recent pandemics, including H1N1 influenza and SARS-CoV-2. We present the design principles of the architecture for an early-alert surveillance system that leverages the vast available data landscape, including syndromic data from primary health care, drug sales, and rumors from the lay media and social media to identify areas with an increased number of cases of respiratory disease. In these potentially affected areas, an intensive and fast sample collection and advanced high-throughput genome sequencing analyses would inform on circulating known or novel pathogens by metagenomics-enabled pathogen characterization. Concurrently, the integration of bioclimatic and socioeconomic data, as well as transportation and mobility network data, into a data analytics platform, coupled with advanced mathematical modeling using artificial intelligence or machine learning, will enable more accurate estimation of outbreak spread risk. Such an approach aims to readily identify and characterize regions in the early stages of an outbreak development, as well as model risk and patterns of spread, informing targeted mitigation and control measures. A fully operational system must integrate diverse and robust data streams to translate data into actionable intelligence and actions, ultimately paving the way toward constructing next-generation surveillance systems.

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Inteligencia Artificial , Subtipo H1N1 del Virus de la Influenza A , Humanos , Subtipo H1N1 del Virus de la Influenza A/genética , Mapeo Cromosómico , Ciencia de los Datos , Brotes de Enfermedades/prevención & control

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Background: The emergence of coronavirus disease 2019 (COVID-19) in 2020 highlighted the relevance of surveillance systems in detecting early signs of potential outbreaks, thus enabling public health authorities to act before the pathogen becomes widespread. Syndromic digital surveillance through web applications has played a crucial role in monitoring the spread of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus. However, this approach requires expensive infrastructure, which is not available in developing countries. Pre-existing sources of information, such as encounters in primary health care (PHC), can provide valuable data for a syndromic surveillance system. Here we evaluated the utility of PHC data to identify early warning signals of the first COVID-19 outbreak in Bahia-Brazil in 2020. Methods: We compared the weekly counts of PHC encounters due to respiratory complaints and the number of COVID-19 cases in 2020 in Bahia State - Brazil. We used the data from December 2016 to December 2019 to predict the expected number of encounters in 2020. We analysed data aggregated by geographic regions (n = 34) and included those where historical PHC data was available for at least 70% of the population. Results: Twenty-one out of 34 regions met the inclusion criteria. We observed that notification of COVID-19 cases was preceded by at least two weeks with an excess of encounters of respiratory complaints in 18/21 (86%) of the regions analysed and four weeks or more in 10/21 (48%) regions. Conclusions: Digital syndromic surveillance systems based on already established PHC databases may add time to preparedness and response to emerging epidemics.

Asunto(s)

COVID-19 , Epidemias , Trastornos Respiratorios , Enfermedades Respiratorias , Humanos , COVID-19/epidemiología , Brotes de Enfermedades , SARS-CoV-2 , Atención Primaria de Salud

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COVID-19 vaccination during pregnancy is safe and effective in reducing the risk of complications. However, the uptake is still below targets worldwide. This study aimed to explore the factors associated with COVID-19 vaccination uptake among pregnant women since data on this topic is scarce in low-to-middle-income countries. A retrospective cohort study included linked data on COVID-19 vaccination and pregnant women who delivered a singleton live birth from August 1, 2021, to July 31, 2022, in Rio de Janeiro City, Brazil. Multiple logistic regression was performed to identify factors associated with vaccination during pregnancy, applying a hierarchical model and describing odds ratio with 95% confidence intervals. Of 65,304 pregnant women included in the study, 53.0% (95% CI, 52-53%) received at least one dose of COVID-19 vaccine during pregnancy. Higher uptake was observed among women aged older than 34 (aOR 1.21, 95%CI 1.15-1.28), black (aOR 1.10, 1.04-1.16), or parda/brown skin colour (aOR 1.05, 1.01-1.09), with less than eight years of education (aOR 1.09, 1.02-1.17), living without a partner (aOR 2.24, 2.16-2.34), more than six antenatal care appointments (aOR 1.92, 1.75-2.09), and having a previous child loss (OR 1.06, 1.02-1.11). These results highlight the need for targeted educational campaigns, trustful communication, and accessibility strategies for specific populations to improve vaccination uptake during pregnancy.

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COVID-19 , Mujeres Embarazadas , Femenino , Humanos , Embarazo , Brasil/epidemiología , COVID-19/epidemiología , COVID-19/prevención & control , Vacunas contra la COVID-19 , Estudios Retrospectivos , Vacunación

RESUMEN

BACKGROUND: COVID-19 vaccines have been shown to protect pregnant individuals against mild and severe COVID-19 outcomes. However, limited safety data are available for inactivated (CoronaVac) and mRNA (BNT162b2) vaccines during pregnancy regarding their effect on birth outcomes and neonatal mortality, especially in low- and middle-income countries. METHODS: We conducted a retrospective population-based cohort study in Rio de Janeiro, Brazil, with 17 513 singleton live births conceived between 15 May 2021 and 23 October 2021. The primary exposure was maternal vaccination with CoronaVac or mRNA BNT162b2 vaccines and sub-analyses were performed by the gestational trimester of the first dose and the number of doses given during pregnancy. The outcomes were pre-term birth (PTB), small for gestational age (SGA), low birthweight (LBW), low Apgar 5 and neonatal death. We used the Cox model to estimate the hazard ratio (HR) with a 95% CI and applied the inverse probability of treatment weights to generate adjusted HRs. RESULTS: We found no significant increase in the risk of PTB (HR: 0.98; 95% CI 0.88, 1.10), SGA (HR: 1.09; 95% CI 0.96, 1.27), LBW (HR: 1.00; 95% CI 0.88, 1.14), low Apgar 5 (HR: 0.81; 95% CI 0.55, 1.22) or neonatal death (HR: 0.88; 95% CI 0.56, 1.48) in women vaccinated with CoronaVac or BNT162b2 vaccines. These findings were consistent across sub-analyses stratified by the gestational trimester of the first dose and the number of doses given during pregnancy. We found mild yet consistent protection against PTB in women who received different vaccine platforms during the third trimester of pregnancy (any vaccines, HR: 0.78; 95% CI 0.63, 0.98; BNT162b2, HR: 0.75; 95% CI 0.59, 0.99). CONCLUSIONS: This study provides evidence that COVID-19 vaccination in all trimesters of pregnancy, irrespective of the vaccine type, is safe and does not increase the risk of adverse birth outcomes or neonatal deaths.

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Vacuna BNT162 , COVID-19 , Mortalidad Infantil , Muerte Perinatal , Complicaciones Infecciosas del Embarazo , Nacimiento Prematuro , Femenino , Humanos , Recién Nacido , Embarazo , Vacuna BNT162/efectos adversos , Brasil/epidemiología , Estudios de Cohortes , COVID-19/prevención & control , Vacunas contra la COVID-19/efectos adversos , Complicaciones Infecciosas del Embarazo/epidemiología , Complicaciones Infecciosas del Embarazo/prevención & control , Nacimiento Prematuro/epidemiología , Estudios Retrospectivos

RESUMEN

Visceral leishmaniasis is an opportunistic disease in HIV-1 infected individuals, unrecognized as a determining factor for AIDS diagnosis. The growing geographical overlap of HIV-1 and Leishmania infections is an emerging challenge worldwide, as co-infection increases morbidity and mortality for both infections. Here, we determined the prevalence of people living with HIV (PWH) with a previous or ongoing infection by Leishmania infantum and investigated the virological and immunological factors associated with co-infection. We adopted a two-stage cross-sectional cohort (CSC) design (CSC-I, n = 5,346 and CSC-II, n = 317) of treatment-naïve HIV-1-infected individuals in Bahia, Brazil. In CSC-I, samples collected between 1998 and 2013 were used for serological screening for leishmaniasis by an in-house Enzyme-Linked Immunosorbent Assay (ELISA) with SLA (Soluble Leishmania infantum Antigen), resulting in a prevalence of previous or ongoing infection of 16.27%. Next, 317 PWH were prospectively recruited from July 2014 to December 2015 with the collection of sociodemographic and clinical data. Serological validation by two different immunoassays confirmed a prevalence of 15.46 and 8.20% by anti-SLA, and anti-HSP70 serology, respectively, whereas 4.73% were double-positive (DP). Stratification of these 317 individuals in DP and double-negative (DN) revealed a significant reduction of CD4+ counts and CD4+/CD8+ ratios and a tendency of increased viral load in the DP group, as compared to DN. No statistical differences in HIV-1 subtype distribution were observed between the two groups. However, we found a significant increase of CXCL10 (p = 0.0076) and a tendency of increased CXCL9 (p = 0.061) in individuals with DP serology, demonstrating intensified immune activation in this group. These findings were corroborated at the transcriptome level in independent Leishmania- and HIV-1-infected cohorts (Swiss HIV Cohort and Piaui Northeast Brazil Cohort), indicating that CXCL10 transcripts are shared by the IFN-dominated immune activation gene signatures of both pathogens and positively correlated to viral load in untreated PWH. This study demonstrated a high prevalence of PWH with L. infantum seropositivity in Bahia, Brazil, linked to IFN-mediated immune activation and a significant decrease in CD4+ levels. Our results highlight the urgent need to increase awareness and define public health strategies for the management and prevention of HIV-1 and L. infantum co-infection.

RESUMEN

BACKGROUND: Chronic kidney disease (CKD) is a prevalent disease worldwide, with increasing incidence particularly in low- and middle-income countries. Indigenous communities have poorer CKD outcomes due to limited access to healthcare. They are also experiencing a shift toward a sedentary lifestyle and urbanization-related dietary changes, increasing the risk of CKD-related risk factors. AIM: To determine the prevalence of CKD in older Brazilian indigenous and identify the main associated risk factors. METHODS: This cross-sectional study analyzed demographic and clinical data of 229 older indigenous individuals aged 60 years and above in 2022-2023. CKD was defined as an estimated glomerular filtration rate < 60 mL/min/1.73 m2 or a urinary albumin-creatinine ratio > 30 mg/g. Data were presented categorically and analyzed using the Chi-square test or Fisher's exact test. RESULTS: The prevalence of CKD in the population was 26.6%, with higher prevalence in women and increasing with age. The prevalence of hypertension and diabetes was 67.7% and 24.0%, respectively, and these comorbidities were associated with CKD: hypertension (OR = 5.12; 95% CI 2.2-11.9) and diabetes (OR = 5.5; 95% CI 3.7-8.2). No association was found between the prevalence of CKD and obesity, dyslipidemia, cardiovascular disease, or smoking. DISCUSSION: The study found a higher prevalence of CKD among older indigenous populations in Brazil compared to non-indigenous populations, which is exacerbated by risk factors, such as aging, hypertension, diabetes, and lifestyle changes, emphasizing the importance of early detection and intervention in these communities. CONCLUSION: Older persons' indigenous individuals have a high prevalence of CKD, which is correlated with factors, such as sex, age, diabetes mellitus, and hypertension.

Asunto(s)

Diabetes Mellitus , Hipertensión , Insuficiencia Renal Crónica , Humanos , Femenino , Anciano , Anciano de 80 o más Años , Estudios Transversales , Brasil/epidemiología , Insuficiencia Renal Crónica/epidemiología , Diabetes Mellitus/epidemiología , Factores de Riesgo , Hipertensión/epidemiología , Hipertensión/complicaciones , Tasa de Filtración Glomerular , Prevalencia , Pueblos Indígenas

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The Americas, particularly Brazil, were greatly impacted by the widespread Zika virus (ZIKV) outbreak in 2015 and 2016. Efforts were made to implement genomic surveillance of ZIKV as part of the public health responses. The accuracy of spatiotemporal reconstructions of the epidemic spread relies on the unbiased sampling of the transmission process. In the early stages of the outbreak, we recruited patients exhibiting clinical symptoms of arbovirus-like infection from Salvador and Campo Formoso, Bahia, in Northeast Brazil. Between May 2015 and June 2016, we identified 21 cases of acute ZIKV infection and subsequently recovered 14 near full-length sequences using the amplicon tiling multiplex approach with nanopore sequencing. We performed a time-calibrated discrete phylogeographic analysis to trace the spread and migration history of the ZIKV. Our phylogenetic analysis supports a consistent relationship between ZIKV migration from Northeast to Southeast Brazil and its subsequent dissemination beyond Brazil. Additionally, our analysis provides insights into the migration of ZIKV from Brazil to Haiti and the role Brazil played in the spread of ZIKV to other countries, such as Singapore, the USA, and the Dominican Republic. The data generated by this study enhances our understanding of ZIKV dynamics and supports the existing knowledge, which can aid in future surveillance efforts against the virus.

Asunto(s)

Infección por el Virus Zika , Virus Zika , Humanos , Virus Zika/genética , Brasil/epidemiología , Filogenia , Américas/epidemiología

RESUMEN

BACKGROUND: Indigenous people have historically suffered devastating impacts from epidemics and continue to have lower access to healthcare and be especially vulnerable to respiratory infections. We estimated the coverage and effectiveness of Covid-19 vaccines against laboratory-confirmed Covid-19 cases among indigenous people in Brazil. METHODS: We linked nationwide Covid-19 vaccination data with flu-like surveillance records and studied a cohort of vaccinated indigenous people aged ≥ 5 years between 18th January 2021 and 1st March 2022. We considered individuals unexposed from the date they received the first dose of vaccine until the 13th day of vaccination, partially vaccinated from the 14th day after the first dose until the 13th day after receiving the second dose, and fully vaccinated onwards. We estimated the Covid-19 vaccination coverage and used Poisson regression to calculate the relative risks (RR) and vaccine effectiveness (VE) of CoronaVac, ChAdOx1, and BNT162b2 against Covid-19 laboratory-confirmed cases incidence, mortality, hospitalisation, and hospital-progression to Intensive Care Unit (ICU) or death. VE was estimated as (1-RR)*100, comparing unexposed to partially or fully vaccinated. RESULTS: By 1st March 2022, 48.7% (35.0-62.3) of eligible indigenous people vs. 74.8% (57.9-91.8) overall Brazilians had been fully vaccinated for Covid-19. Among fully vaccinated indigenous people, we found a lower risk of symptomatic cases (RR: 0.47, 95%CI: 0.40-0.56) and mortality (RR: 0.47, 95%CI: 0.14-1.56) after the 14th day of the second dose. VE for the three Covid-19 vaccines combined was 53% (95%CI:44-60%) for symptomatic cases, 53% (95%CI:-56-86%) for mortality and 41% (95%CI:-35-75%) for hospitalisation. In our sample, we found that vaccination did not reduce Covid-19 related hospitalisation. However, among hospitalised patients, we found a lower risk of progression to ICU (RR: 0.14, 95%CI: 0.02-0.81; VE: 87%, 95%CI:27-98%) and Covid-19 death (RR: 0.04, 95%CI:0.01-0.10; VE: 96%, 95%CI: 90-99%) after the 14th day of the second dose. CONCLUSIONS: Lower coverage but similar Covid-19 VE among indigenous people than overall Brazilians suggest the need to expand access, timely vaccination, and urgently offer booster doses to achieve a great level of protection among this group.

Asunto(s)

COVID-19 , Vacunas , Humanos , Vacunas contra la COVID-19 , COVID-19/epidemiología , COVID-19/prevención & control , Brasil/epidemiología , Estudios de Cohortes , Vacuna BNT162 , Pueblos Indígenas

RESUMEN

Background: There is limited data on the prevalence and risk factors for long COVID and few prospective studies with appropriate control groups and adequate sample sizes. We performed a prospective study to determine the prevalence and risk factors for long COVID. Methods: We recruited individuals aged ≥15 years who were clinically suspected of having an acute SARS-CoV-2 infection from September 2020 to April 2021. We collected nasopharyngeal swabs three to five days following symptom onset for analysing using reverse transcriptase polymerase chain reaction (RT-PCR). We also collected clinical and sociodemographic characteristics from both SARS-CoV-2 positive and negative participants using structured questionnaires. We followed-up the participants via telephone interview to assess early outcomes and persistent symptoms. For COVID-19 cases, 5D-3L EuroQol questionnaire was used to assess the impact of symptoms on quality of life. Results: We followed 814 participants (412 COVID-19 positive and 402 COVID-19 negative persons). Most (n = 741/814) had mild symptoms. Both groups had similar sociodemographic and clinical characteristics, except for the hospitalization rate (15.8% in the COVID-19 positive vs 1.5% in the COVID-19 negative group). One month after disease onset, 122/412 (29.6%) individuals in the COVID-19 positive (long COVID) and 24 (6%) in the COVID-19 negative group reported residual symptoms. In the long COVID group, fatigue, olfactory disorder, and myalgia were the most frequent symptoms in the acute phase. Compared to recovered individuals, older age and having more than five symptoms during the acute phase were risk factors for long COVID. Quality of life was evaluated in 102 out of 122 cases of long COVID, with 57 (55.9%) reporting an impact in at least one dimension of the European Quality of Life 5 Dimensions 3 Level (EQ-5D-3L) questionnaire. Conclusions: In this prospective study consisting predominantly of individuals with mild disease, the persistence of symptoms after an acute respiratory illness was associated with a diagnosis of COVID-19. Polysymptomatic acute disease and older age were risk factors for long COVID.

Asunto(s)

COVID-19 , Humanos , COVID-19/epidemiología , SARS-CoV-2 , Síndrome Post Agudo de COVID-19 , Estudios Prospectivos , Estudios de Cohortes , Calidad de Vida , Prevalencia , Grupos Control , Factores de Riesgo

RESUMEN

BACKGROUND: BCG vaccination, originally used to prevent tuberculosis, is known to "train" the immune system to improve defence against viral respiratory infections. We investigated whether a previous BCG vaccination is associated with less severe clinical progression of COVID-19 METHODS: A case-control study comparing the proportion with a BCG vaccine scar (indicating previous vaccination) in cases and controls presenting with COVID-19 to health units in Brazil. Cases were subjects with severe COVID-19 (O2 saturation < 90%, severe respiratory effort, severe pneumonia, severe acute respiratory syndrome, sepsis, and septic shock). Controls had COVID-19 not meeting the definition of "severe" above. Unconditional regression was used to estimate vaccine protection against clinical progression to severe disease, with strict control for age, comorbidity, sex, educational level, race/colour, and municipality. Internal matching and conditional regression were used for sensitivity analysis. RESULTS: BCG was associated with high protection against COVID-19 clinical progression, over 87% (95% CI 74-93%) in subjects aged 60 or less and 35% (95% CI - 44-71%) in older subjects. CONCLUSIONS: This protection may be relevant for public health in settings where COVID-19 vaccine coverage is still low and may have implications for research to identify vaccine candidates for COVID-19 that are broadly protective against mortality from future variants. Further research into the immunomodulatory effects of BCG may inform COVID-19 therapeutic research.

Asunto(s)

COVID-19 , Humanos , Anciano , COVID-19/prevención & control , Vacuna BCG , SARS-CoV-2 , Vacunas contra la COVID-19 , Estudios de Casos y Controles , Vacunación , Progresión de la Enfermedad

RESUMEN

OBJECTIVE: The aim of this study was to investigate whether the degree of urbanization influences the prevalence of chronic kidney disease in Brazilian indigenous people. METHODS: This is a cross-sectional study conducted between 2016 and 2017 in northeastern Brazil and includes individuals aged between 30 and 70 years from two specific indigenous groups who volunteered to participate in the study: the Fulni-ô people (lowest degree of urbanization) and the Truká group (greater degree of urbanization). Cultural and geographical parameters were used to characterize and measure the magnitude of urbanization. We excluded individuals with known cardiovascular disease or renal failure who required hemodialysis. Chronic kidney disease was defined as a single measurement of an estimated glomerular filtration rate <60 mL/min/1.73 m2 using the Chronic Kidney Disease Epidemiology Collaboration creatinine equation. RESULTS: A total of 184 indigenous people from the Fulni-ô group and 96 from the Truká group with a median age of 46 years (interquartile range: 15.2) were included. We found a chronic kidney disease rate of 4.3% in the total indigenous population, generally affecting an older population: 41.7% over 60 years old (p<0.001). The Truká people had a chronic kidney disease prevalence of 6.2%, with no differences in kidney dysfunction across age groups. The Fulni-ô participants had a chronic kidney disease prevalence of 3.3%, with a higher proportion of kidney dysfunction in older participants (of the six Fulni-ô indigenous people with chronic kidney disease, five were older). CONCLUSION: Our results suggest that a higher degree of urbanization seems to negatively influence the prevalence of chronic kidney disease in Brazilian indigenous people.

Asunto(s)

Insuficiencia Renal Crónica , Urbanización , Humanos , Adolescente , Anciano , Adulto , Persona de Mediana Edad , Brasil/epidemiología , Estudios Transversales , Insuficiencia Renal Crónica/epidemiología , Tasa de Filtración Glomerular , Pueblos Indígenas , Riñón , Creatinina

RESUMEN

BACKGROUND: We described the prevalence of cardiovascular risk factors in groups of Brazilian Indigenous people at different degrees of urbanization. METHODS: The Project of Atherosclerosis among Indigenous populations (Projeto de Aterosclerose em Indígenas; PAI) is a cross-sectional study conducted in Northeast Brazil between August 2016-June 2017. It included three populations: Fulni-ô Indigenous people (lowest degree of urbanization), Truká Indigenous people (greater urbanization), and a highly urbanized non-Indigenous local cohort (control group). Participants were assessed to register sociodemographic, anthropometric, as well as clinical and laboratory-derived cardiovascular (CV) risk parameters. Age-adjusted prevalence of hypertension was also computed. Nonparametric tests were used for group comparisons. RESULTS: Here we included 999 participants, with a predominance of females in all three groups (68.3% Control group, 65.0% Fulni-ô indigenous group, and 60.1% Truká indigenous group). Obesity was present in 45.6% of the urban non-Indigenous population, 37.7% Truká and in 27.6% Fulni-ô participants. The prevalence of hypertension was 29.1% (n = 297) with lower prevalence in the less urbanized Fulni-ô people (Fulni-ô - 18.2%; Truká - 33.9%; and Control - 33.8%; p < 0.001). In the elderly male population, the prevalence of hypertension was 18.7% in the Fulni-ô, 45.8% in the Truká, and 54.5% in the control group. Of the 342 participants that self-reported hypertension, 37.5% (n = 68) showed uncontrolled blood pressure (BP). Uncontrolled BP was more prevalent among Truká people when compared to Fulni-ô people and non-Indigenous participants (45.4%, 22.9%, and 40.7%, respectively; p < 0.001). CONCLUSIONS: We found a higher cardiovascular risk in communities with a higher degree of urbanization, suggesting that living in towns and cities may have a negative impact on these aspects of cardiovascular health.

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The lifestyles and environments of traditional indigenous and city-living communities differ. We compared rates of obesity and hypertension in members of two under-studied Indigenous groups in Northeast Brazil and a nearby urbanized group. We found higher rates of obesity and hypertension amongst members of the more urbanized community, suggesting that living in towns and cities may have a negative impact on these aspects of cardiovascular health. These results suggest those living in the city should modify their lifestyle and monitor their cardiovascular health more carefully if possible.

RESUMEN

SUMMARY OBJECTIVE: The aim of this study was to investigate whether the degree of urbanization influences the prevalence of chronic kidney disease in Brazilian indigenous people. METHODS: This is a cross-sectional study conducted between 2016 and 2017 in northeastern Brazil and includes individuals aged between 30 and 70 years from two specific indigenous groups who volunteered to participate in the study: the Fulni-ô people (lowest degree of urbanization) and the Truká group (greater degree of urbanization). Cultural and geographical parameters were used to characterize and measure the magnitude of urbanization. We excluded individuals with known cardiovascular disease or renal failure who required hemodialysis. Chronic kidney disease was defined as a single measurement of an estimated glomerular filtration rate <60 mL/min/1.73 m2 using the Chronic Kidney Disease Epidemiology Collaboration creatinine equation. RESULTS: A total of 184 indigenous people from the Fulni-ô group and 96 from the Truká group with a median age of 46 years (interquartile range: 15.2) were included. We found a chronic kidney disease rate of 4.3% in the total indigenous population, generally affecting an older population: 41.7% over 60 years old (p<0.001). The Truká people had a chronic kidney disease prevalence of 6.2%, with no differences in kidney dysfunction across age groups. The Fulni-ô participants had a chronic kidney disease prevalence of 3.3%, with a higher proportion of kidney dysfunction in older participants (of the six Fulni-ô indigenous people with chronic kidney disease, five were older). CONCLUSION: Our results suggest that a higher degree of urbanization seems to negatively influence the prevalence of chronic kidney disease in Brazilian indigenous people.