Early detection of the SARS-CoV-2 P.1 variant in Rio Grande do Sul, Brazil: a case report.
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ABSTRACT:
SUBMITTER: Volpato FCZ
PROVIDER: S-EPMC8564027 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BackgroundBrazil is the third country most affected by Coronavirus disease-2019 (COVID-19), but viral evolution in municipality resolution is still poorly understood in Brazil and it is crucial to understand the epidemiology of viral spread. We aimed to track molecular evolution and spread of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Esteio (Southern Brazil) using phylogenetics and phylodynamics inferences from 21 new genomes in global and regional context. Importantly, the case fatality rate (CFR) in Esteio (3.26%) is slightly higher compared to the Rio Grande do Sul (RS) state (2.56%) and the entire Brazil (2.74%).ResultsWe provided a comprehensive view of mutations from a representative sampling from May to October 2020, highlighting two frequent mutations in spike glycoprotein (D614G and V1176F), an emergent mutation (E484K) in spike Receptor Binding Domain (RBD) characteristic of the B.1.351 and P.1 lineages, and the adjacent replacement of 2 amino acids in Nucleocapsid phosphoprotein (R203K and G204R). E484K was found in two genomes from mid-October, which is the earliest description of this mutation in Southern Brazil. Lineages containing this substitution must be subject of intense surveillance due to its association with immune evasion. We also found two epidemiologically-related clusters, including one from patients of the same neighborhood. Phylogenetics and phylodynamics analysis demonstrates multiple introductions of the Brazilian most prevalent lineages (B.1.1.33 and B.1.1.248) and the establishment of Brazilian lineages ignited from the Southeast to other Brazilian regions.ConclusionsOur data show the value of correlating clinical, epidemiological and genomic information for the understanding of viral evolution and its spatial distribution over time. This is of paramount importance to better inform policy making strategies to fight COVID-19.
| S-EPMC8136996 | biostudies-literature
Project description:Mutations in the SARS-CoV-2 genome can alter the virus' fitness, leading to the emergence of variants of concern (VOC). In Brazil, the Gamma variant dominated the pandemic in the first half of 2021, and from June onwards, the first cases of Delta infection were documented. Here, we investigate the introduction and dispersal of the Delta variant in the RS state by sequencing 1077 SARS-CoV-2-positive samples from June to October 2021. Of these samples, 34.7% were identified as Gamma and 65.3% as Delta. Notably, 99.2% of Delta sequences were clustered within the 21J lineage, forming a significant Brazilian clade. The estimated clock rate was 5.97 × 10-4 substitutions per site per year. The Delta variant was first reported on 17 June in the Vinhedos Basalto microregion and rapidly spread, accounting for over 70% of cases within nine weeks. Despite this, the number of cases and deaths remained stable, possibly due to vaccination, prior infections, and the continued mandatory mask use. In conclusion, our study provides insights into the Delta variant circulating in the RS state, highlighting the importance of genomic surveillance for monitoring viral evolution, even when the impact of new variants may be less severe in a given region.
| S-EPMC10745878 | biostudies-literature
Project description:Since starts the coronavirus disease 2019 (COVID-19) pandemic identified the presence of genomic fragments of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in various environmental matrices: domestic sewage, surface waters, and contaminated freshwater. Environmental monitoring of SARS-CoV-2 is a tool for evaluating trend curves over the months, compared to several clinical cases of the disease. The objective of this study was to monitor the SARS-CoV-2 in environmental samples collected in different sites in a metropolitan area of Porto Alegre, Southern Brazil. During 10 months from 2020 to 2021, 300 samples were collected weekly and biweekly from nine points located in 3 cities: one point from a wastewater treatment plant (WWTP) in São Leopoldo (fortnightly collection), two points in Dilúvio Stream in Porto Alegre (fortnightly collection), two points in Pampa and Luiz Rau Streams (weekly collection), and two points in public fountains (fortnightly collection) in Novo Hamburgo. After collection, samples were concentrated by ultracentrifugation, and viral nucleic acids were extracted using MagMax® Core Nucleic Acid Purifications kits and submitted to RT-qPCR, using E, N1, and N2 gene targets of SARS-CoV-2. Only 7% (3/41) samples from public fountains were positive, with a mean viral load (VL) of SARS-CoV-2 RNA of 5.02 × 101 gc/l (2.41~8.59 × 101 gc/l), while the streams had average VL of 7.43 × 105 gc/l (Pampa), 7.06 × 105 gc/l (Luiz Rau), 2.01 × 105 gc/l (Dilúvio), and 4.46 × 105 cg/l (WWTP). The results showed varying levels of viral presence in different sample types, with a demonstrated correlation between environmental viral load and clinical COVID-19 cases. These findings contribute to understanding virus persistence and transmission pathways in the environment. Continuous monitoring, especially in less developed regions, is crucial for early detection of vaccine resistance, new variants, and potential COVID-19 resurgence.
| S-EPMC10791933 | biostudies-literature
Project description:The emergence of SARS-CoV-2 P.1 lineage coincided with a surge in hospitalisations in the North region of Brazil. In the South region's Rio Grande do Sul state, severe COVID-19 case numbers rose 3.8 fold in February 2021. During that month, at a COVID-19 referral hospital in this state, whole-genome sequencing of a subset of cases' specimens (n = 27) revealed P.1 lineage SARS-CoV-2 in most (n = 24). Findings raise concerns regarding a possible association between lineage P.1 and rapid case and hospitalisation increases.
| S-EPMC7995561 | biostudies-literature
Project description:Background:Work-related mental disorders are an acknowledged global health problem. Objective:The aim of the present study was to investigate the prevalence of and factors associated with common mental disorders and suicidal ideation among public health workers. Methods:We conducted a cross-sectional study with municipal healthcare workers. We collected sociodemographic and occupational data including employment relationship, job area, professional category, length of work in current job and interpersonal conflict in the workplace (ICW). The analyzed mental health indicators were common mental disorders (CMD) and suicidal ideation by means of the Self Reporting Questionnaire (SRQ-20). Statistical analysis included the ?2 test and Poisson regression. Results:The prevalence of CMD and suicidal ideation was 20.3% and 11.6%, respectively, among the 597 participants. Permanent and younger employees exhibited higher CMD rates, while suicidal ideation predominated among the participants with higher educational level and the widowed/separated/divorced. Physicians, administrative employees, cleaning personnel and community health agents exhibited the highest rates of CMD. In turn, there was no association between professional category and suicidal ideation on multivariate analysis. ICW was associated with poorer mental health indicators, the association being stronger when conflict involved supervisors and coworkers. Conclusion:Both analyzed indicators (CMD and suicidal ideation) point to a worrisome situation as concerns the mental health of professionals charged of collective health care. The possible limitations of the questionnaire applied notwithstanding, ICW was the main factor associated with poorer mental health indicators. These findings point to the need to develop specific approaches to improve the psychosocial work environment.
| S-EPMC7104836 | biostudies-literature
Project description:BackgroundAccording to official records, dengue was introduced in Brazil in the 80's; since then several epidemics have occurred. Meanwhile, in Rio Grande do Sul (RS, Southern Brazil) the first autochthonous case occurred only in 2007.Methodology and principal findingsIn this study we report laboratory surveillance of dengue cases and seasonality of positive cases, describe serotypes and characterize the epidemiological pattern of dengue in RS from 2007 to 2013. A total of 9,779 serum samples from patients with suspected dengue fever were collected and submitted to molecular and/or serological analyses for dengue virus identification and serotyping, based on viral isolation, NS1 antigen detection and qRT-PCR, or Dengue IgM capture ELISA and MAC-ELISA. The first autochthonous dengue case in RS was confirmed in 2007 (DENV-3). While in 2008 and 2009 only imported cases were registered, autochthonous infection waves have been occurring since 2010. The highest number of dengue infections occurred in 2010, with DENV-1 and DENV-2 outbreaks in Northwestern RS. In 2011, another DENV-1 and DENV-2 outbreak occurred in the Northwestern region; moreover, DENV-4 was detected in travelers. In 2012, DENV-1 and DENV-4 co-circulated. DENV-2 circulation was only detected again in 2013, in high frequency (56.7%), co-circulating with DENV-4 (35%). Most infections occur in adults during summer. Differences in prevalence between genders were observed in 2007 (60% females), 2008 (60.8% males) and 2009 (77.5% males).ConclusionsAccording to results of dengue surveillance, there was an increase in the number of dengue cases in RS and of cities infested with Aedes aegypti, possibly as a consequence of introduction of new serotypes and the difficulty of health programs to control the vector.
| S-EPMC4130601 | biostudies-literature
Project description:Current information on the epidemiology of physical inactivity among older adults is lacking, making it difficult to target the inactive and to plan for interventions to ameliorate adverse effects.To present statewide representative findings on the prevalence of physical inactivity among older community residents, its correlates and associated health service use.A representative non-institutionalized random sample of 6963 individuals in Rio Grande do Sul, Brazil, aged ≥60 years, was interviewed face-to-face. Information was obtained on demographic characteristics, social resources, health conditions and behaviors, health service use, and physical inactivity. Controlled logistic regression was used to determine the association of physical inactivity with these characteristics.Overall, 62% reported no regular physical activity. Physical inactivity was significantly more prevalent among women, older persons, those with lower education and income, Afro-Brazilians (73%; White: 61%; "other": 64%), those no longer married, and was associated with multiple individual health conditions and impaired activities of daily living (ADL). In adjusted analyses, associations remained for sociodemographic characteristics, social participation, impaired self-rated health, ADL, vision, and depression (odds ratios (OR) 1.2-1.7). Physically inactive respondents were less likely to report outpatient visits (OR 0.81), but more likely to be hospitalized (OR 1.41).Physical inactivity is highly prevalent, particularly among Afro -Brazilians. It is associated with adverse sociodemographic characteristics; lack of social interaction; and poor self-rated health, ADL, vision, and depression; although not with other health conditions. Self-care may be neglected, resulting in hospitalization.
| S-EPMC4336142 | biostudies-other
Project description:BackgroundLeptospirosis is an epidemic-prone neglected disease that affects humans and animals, mostly in vulnerable populations. The One Health approach is a recommended strategy to identify drivers of the disease and plan for its prevention and control. In that context, the aim of this study was to analyze the distribution of human cases of leptospirosis in the State of Rio Grande do Sul, Brazil, and to explore possible drivers. Additionally, it sought to provide further evidence to support interventions and to identify hypotheses for new research at the human-animal-ecosystem interface.Methodology and findingsThe risk for human infection was described in relation to environmental, socioeconomic, and livestock variables. This ecological study used aggregated data by municipality (all 496). Data were extracted from secondary, publicly available sources. Thematic maps were constructed and univariate analysis performed for all variables. Negative binomial regression was used for multivariable statistical analysis of leptospirosis cases. An annual average of 428 human cases of leptospirosis was reported in the state from 2008 to 2012. The cumulative incidence in rural populations was eight times higher than in urban populations. Variables significantly associated with leptospirosis cases in the final model were: Parana/Paraiba ecoregion (RR: 2.25; CI95%: 2.03-2.49); Neossolo Litolítico soil (RR: 1.93; CI95%: 1.26-2.96); and, to a lesser extent, the production of tobacco (RR: 1.10; CI95%: 1.09-1.11) and rice (RR: 1.003; CI95%: 1.002-1.04).ConclusionUrban cases were concentrated in the capital and rural cases in a specific ecoregion. The major drivers identified in this study were related to environmental and production processes that are permanent features of the state. This study contributes to the basic knowledge on leptospirosis distribution and drivers in the state and encourages a comprehensive approach to address the disease in the animal-human-ecosystem interface.
| S-EPMC4643048 | biostudies-literature
Project description:Leptospirosis is an infectious disease caused by Leptospira spp. and affects animals and humans. Reports of leptospirosis in bats have increased and prompted epidemiological research in Brazil. This study aimed to perform a molecular and epidemiological investigation of pathogenic Leptospira spp. in bat kidneys. The total DNA was extracted from 102 kidney samples from chiropterous of different species and cities in Rio Grande do Sul State (RS), Brazil. The polymerase chain reaction was used to amplify a fragment corresponding to lipL32 gene, which is only present in pathogenic Leptospira spp. lipL32 gene was detected in 22.5% (23/102) of the bat kidney tissues. Phylogenetic analysis showed that L. interrogans is circulating in bats in RS. Most species of the bats collected were insectivores. Pathogenic Leptospira spp. detection in bats demonstrated that these animals participate in the infection chain of leptospirosis and, therefore, may play as reservoirs and disseminators of this microorganism. Thus, it is important to monitor infectious agents, especially with zoonotic potential in bats.
| S-EPMC9542444 | biostudies-literature
Project description:Background: Consumption of maté, an infusion of the herb Ilex paraguariensis (yerba maté), is associated with increased risk of esophageal squamous cell carcinoma (ESCC), but the carcinogenic mechanism is unclear. Commercial brands of yerba maté contain high levels of carcinogenic polycyclic aromatic hydrocarbons (PAHs), which are acquired during the traditional drying process. The purpose of this study was to characterize exposure to PAHs in maté drinkers over a wide range of maté consumption.Methods: We recruited 244 adults who answered a questionnaire and collected a fasting spot urine specimen. We quantified urinary concentrations of seven PAH metabolites and assessed associations between self-reported recent maté consumption and urinary PAH metabolites by multivariate regression.Results: Recent maté consumption showed a significant dose-response association with 6 of 7 PAH metabolites in unadjusted models (Ptrend < 0.05). After adjustment for creatinine and potential confounders, concentrations of 2-naphthol, 1-hydroxyphenanthrene, and the sum of 2- and 3-hydroxyphenanthrene remained significantly associated with recent maté intake. The sum of the urinary concentrations of the phenanthrene metabolites was similar or higher among maté drinkers who did not smoke than among smokers who did not drink matéConclusions: Urinary concentrations of PAH metabolites were significantly associated with self-reported amounts of recent maté intake, and drinking maté increased urinary concentrations of some PAH metabolites as much as smoking cigarettes.Impact: Drinking maté is a source of exposure to potentially carcinogenic PAHs, consistent with the hypothesis that the PAH content of maté may contribute to the increased risk of ESCC in maté drinkers. Cancer Epidemiol Biomarkers Prev; 27(3); 331-7. ©2017 AACR.
| S-EPMC5835188 | biostudies-literature