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The Zika virus (ZIKV) epidemic in the Americas established ZIKV as a major public health threat and uncovered its association with severe diseases, including microcephaly. However, genetic epidemiology in some at-risk regions, particularly Central America and Mexico, remains limited. We report 61 ZIKV genomes from this region, generated using metagenomic sequencing with ZIKV-specific enrichment, and combine phylogenetic, epidemiological, and environmental data to reconstruct ZIKV transmission. These analyses revealed multiple independent ZIKV introductions to Central America and Mexico. One introduction, likely from Brazil via Honduras, led to most infections and the undetected spread of ZIKV through the region from late 2014. Multiple lines of evidence indicate biannual peaks of ZIKV transmission in the region, likely driven by varying local environmental conditions for mosquito vectors and herd immunity. The spatial and temporal heterogeneity of ZIKV transmission in Central America and Mexico challenges arbovirus surveillance and disease control measures., (Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.)

The present study aimed to determine the genetic diversity of isolates of Mycobacterium tuberculosis (Mtb) from presumed drug-resistant tuberculosis patients from several states of Brazil. The isolates had been submitted to conventional drug susceptibility testing for first- and second-line drugs. Multidrug-resistant (MDR-TB) (54.8%) was the most frequent phenotypic resistance profile, in addition to an important high frequency of pre-extensive resistance (p-XDR-TB) (9.2%). Using whole-genome sequencing (WGS), we characterized 298 Mtb isolates from Brazil. Besides the analysis of genotype distribution and possible correlations between molecular and clinical data, we determined the performance of an in-house WGS pipeline with other online pipelines for Mtb lineages and drug resistance profile definitions. Sub-lineage 4.3 (52%) was the most frequent genotype, and the genomic approach revealed a p-XDR-TB level of 22.5%. We detected twenty novel mutations in three resistance genes, and six of these were observed in eight phenotypically resistant isolates. A cluster analysis of 170 isolates showed that 43.5% of the TB patients belonged to 24 genomic clusters, suggesting considerable ongoing transmission of DR-TB, including two interstate transmissions. The in-house WGS pipeline showed the best overall performance in drug resistance prediction, presenting the best accuracy values for five of the nine drugs tested. Significant associations were observed between suffering from fatal disease and genotypic p-XDR-TB (p = 0.03) and either phenotypic (p = 0.006) or genotypic (p = 0.0007) ethambutol resistance. The use of WGS analysis improved our understanding of the population structure of MTBC in Brazil and the genetic and clinical data correlations and demonstrated its utility for surveillance efforts regarding the spread of DR-TB, hopefully helping to avoid the emergence of even more resistant strains and to reduce TB incidence and mortality rates. [ABSTRACT FROM AUTHOR]

Policies for reducing the environmental impact of light-duty vehicles are restarting in Brazil. While electrification attracts more engagement than other forms of carbon footprint reduction, the use of ethanol could achieve faster gains with the existing infrastructure. The prominence of entry-level cars has reduced, which may be due to several factors, making these vehicles uneconomical for manufacturers to produce. This situation is different from those in other countries. It is our premise that other modes, such as walking, cycling, and public transportation, are the main methods of decarbonization. However, most need improvements in terms of security and attractiveness for consumers. Hence, the internal combustion engine will dominate the Brazilian fleet for quite some time. This article discusses the policies used to incentivize the implementation of entry-level vehicles in contrast with electric vehicles based on regression models of the Brazilian fleet. By providing a history of the 1.0 L engine in Brazil, this article debates replacing the indirect displacement taxation with direct CO2 taxation, which can make the Brazilian entry-level car practical again, with the possibility of adopting some incentives. This logic will cause a fleet renovation and more rational energy use. The distinguishing feature of this article is the proposition of possible public policies based on a regression model of the national fleet. The key findings show that the fleet is getting older and heavier, consuming more energy, and emitting greater amounts of CO2 per unit of displacement, for example, 1.0 L. Furthermore, the carbon footprint of the electricity mix is similar to that of the produced ethanol (from well to wheel, the carbon footprint is the same). This highlights the necessity for national policy adjustments and effective public policies to reduce carbon emissions from the energy sector for small vehicles. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Airborne geophysical data (AGD) have great potential to represent soil-forming factors. Because of that, the objective of this study was to evaluate the importance of AGD in predicting soil attributes such as aluminum saturation (ASat), base saturation (BS), cation exchange capacity (CEC), clay, and organic carbon (OC). The AGD predictor variables include total count (μR/h), K (potassium), eU (uranium equivalent), and eTh (thorium equivalent), ratios between these elements (eTh/K, eU/K, and eU/eTh), factor F or F-parameter, anomalous potassium (Kd), anomalous uranium (Ud), anomalous magnetic field (AMF), vertical derivative (GZ), horizontal derivatives (GX and GY), and mafic index (MI). The approach was based on applying predictive modeling techniques using (1) digital elevation model (DEM) covariates and Sentinel-2 images with AGD; and (2) DEM covariates and Sentinel-2 images without the AGD. The study was conducted in Bom Jardim, a county in Rio de Janeiro-Brazil with an area of 382,430 km², with a database of 208 soil samples to a predefined depth (0–30 cm). Non-explanatory covariates for the selected soil attributes were excluded. Through the selected covariables, the random forest (RF) and support vector machine (SVM) models were applied with separate samples for training (75%) and validation (25%). The model's performance was evaluated through the R-squared (R2), root mean square error (RMSE), and mean absolute error (MAE), as well as null model values and coefficient of variation (CV%). The RF algorithm showed better performance with AGD (R2 values ranging from 0.15 to 0.23), as well as the SVM model (R2 values ranging from 0.08 to 0.23) when compared to RF (R2 values ranging from 0.10 to 0.20) and SVM (R2 values ranging from 0.04 to 0.10) models without AGD. Overall, the results suggest that AGD can be helpful for soil mapping. Nevertheless, it is crucial to acknowledge that the accuracy of AGD in predicting soil properties could vary depending on various common factors in DSM, such as the quality and resolution of the covariates and available soil data. Further research is needed to determine the optimal approach for using AGD in soil mapping. [ABSTRACT FROM AUTHOR]

The rate of technological progress is an important metric used for predicting the energy consumption and greenhouse gas emissions of future light-duty fleets. A trade-off between efficiency and performance is essential due to its implications on fuel consumption and efficiency improvement. These values are not directly available in the Brazilian fleet. Hence, this is the main gap in knowledge that has to be overcome. Tendencies in all relevant parameters were also unknown, and we have traced them as well, established on several publications data and models. We estimate the three indicators mentioned above for the Brazilian fleet from 1990 to 2020. Although the rate of technological progress was lower in Brazil than that in developed countries, it has increased from 0.39% to 0.61% to 1.7% to 1.9% in subsequent decades. Performance improvements offset approximately 31% to 39% of these efficiency gains. Moreover, the vehicle market is shifting toward larger vehicles, thus offsetting some efficiency improvements. We predict the fleet fuel efficiency for the years 2030 and 2035 using the above-mentioned factors. The predicted values for efficiency can vary by a factor of two. Thus, trade-off policies play a vital role in steering toward the desired goals of reducing the transportation sector's impact on the environment. [ABSTRACT FROM AUTHOR]

Uruguay is one of the few countries in the Americas that successfully contained the coronavirus disease 19 (COVID-19) epidemic during the first half of 2020. Nevertheless, the intensive human mobility across the dry border with Brazil is a major challenge for public health authorities. We aimed to investigate the origin of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains detected in Uruguayan localities bordering Brazil as well as to measure the viral flux across this ∼1,100 km uninterrupted dry frontier. Using complete SARS-CoV-2 genomes from the Uruguayan–Brazilian bordering region and phylogeographic analyses, we inferred the virus dissemination frequency between Brazil and Uruguay and characterized local outbreak dynamics during the first months (May–July) of the pandemic. Phylogenetic analyses revealed multiple introductions of SARS-CoV-2 Brazilian lineages B.1.1.28 and B.1.1.33 into Uruguayan localities at the bordering region. The most probable sources of viral strains introduced to Uruguay were the Southeast Brazilian region and the state of Rio Grande do Sul. Some of the viral strains introduced in Uruguayan border localities between early May and mid-July were able to locally spread and originated the first outbreaks detected outside the metropolitan region. The viral lineages responsible for Uruguayan urban outbreaks were defined by a set of between four and 11 mutations (synonymous and non-synonymous) with respect to the ancestral B.1.1.28 and B.1.1.33 viruses that arose in Brazil, supporting the notion of a rapid genetic differentiation between SARS-CoV-2 subpopulations spreading in South America. Although Uruguayan borders have remained essentially closed to non-Uruguayan citizens, the inevitable flow of people across the dry border with Brazil allowed the repeated entry of the virus into Uruguay and the subsequent emergence of local outbreaks in Uruguayan border localities. Implementation of coordinated bi-national surveillance systems is crucial to achieve an efficient control of the SARS-CoV-2 spread across this kind of highly permeable borderland regions around the world. [ABSTRACT FROM AUTHOR]

Zika virus (ZIKV) became a worldwide public health emergency after its introduction in the Americas. Brazil was implicated as central in the ZIKV dispersion, however, a better understanding of the pathways the virus took to arrive in Brazil and the dispersion within the country is needed. An updated genome dataset was assembled with publicly available data. Bayesian phylogeography methods were applied to reconstruct the spatiotemporal history of ZIKV in the Americas and with more detail inside Brazil. Our analyses reconstructed the Brazilian state of Pernambuco as the likely point of introduction of ZIKV in Brazil, possibly during the 2013 Confederations Cup. Pernambuco played an important role in spreading the virus to other Brazilian states. Our results also underscore the long cryptic circulation of ZIKV in all analyzed locations in Brazil. Conclusions: This study brings new insights about the early moments of ZIKV in the Americas, especially regarding the Brazil-Haiti cluster at the base of the American clade and describing for the first time migration patterns within Brazil. [ABSTRACT FROM AUTHOR]