Biology subjects

de Souza, V. C.

Publications and source records attributed to de Souza, V. C..

6 recordsLinked to original sources

bioRxiv2025

Unraveling Dengue Serotype 3 Transmission in Brazil: Evidence for Multiple Introductions of the 3III_B.3.2 Lineage

Dengue, caused by DENV 1-4, remains a global public health concern, with Brazil experiencing some of the largest epidemics. The reemergence of DENV-3 in Brazil between 2023 and 2024 has raised concerns about new outbreaks due to the absence of sustained circulation of this serotype in recent years. This study investigates the dynamics of DENV-3 in Brazil, focusing on the spread of the 3III_B.3.2 lineage within genotype 3III and its introduction routes. We analyzed 1,536 DENV-3 genomes, all classified as genotype 3III, the dominant DENV-3 genotype in Brazil since 2001. Phylogenetic analysis identified the 3III_B.3.2 lineage in all recent Brazilian cases, with detections also reported in Central America, the United States, and Europe. At least six independent introduction events of this lineage into Brazil were identified, with the Caribbean region and Costa Rica as the primary sources. The earliest introduction likely occurred in late 2022 in Roraima, followed by introductions in Sao Paulo, Minas Gerais, and Para. While one instance of interstate transmission was detected -- from Sao Paulo to Minas Gerais -- our findings indicate that external introductions, rather than domestic spread, were the primary drivers of DENV-3 circulation during this period. These results underscore the importance of continued genomic surveillance and coordinated public health strategies to monitor and mitigate future outbreaks.

bioinformatics↗

bioRxiv2024

Comprehensive Molecular Epidemiology of Influenza Viruses in Brazil: Insights from a Nationwide Analysis

Influenza A and B viruses pose significant global health threats, with substantial impacts on morbidity and mortality. Understanding their molecular epidemiology in Brazil, a key hub for the circulation and dissemination of these viruses in South America, remains limited. This study, part of the Center for Viral Surveillance and Serological Assessment (CeVIVAS) project, addresses this by analyzing data and samples from all Brazilian macroregions, along with publicly available sequences from 2021-2023. Phylogenetic analysis of the Hemagglutinin (HA) segment of Influenza A/H1N1pdm09, A/H3N2, and Influenza B/Victoria-lineage revealed the predominance of A/H3N2 2a.3 strain in 2021 and early 2022. This was succeeded by A/H3N2 2b until October 2022, after which A/H1N1pdm09 5a.2a and 5a.2a.1 lineages became prevalent, maintaining this status throughout 2023. B/Victoria circulated at low levels between December 2021 and September 2022, becoming co-prevalent with A/H1N1pdm09 5a.2a and 5a.2a.1 lineages. Comparing the vaccine strain A/Darwin/9/2021 with circulating A/H3N2 viruses from 2021-2023 revealed shared mutations to aspartic acid at residues 186 and 225, altering the RBD domains charge. For A/H1N1pdm09, the 2022 consensus of 5a.2a.1 and the vaccine strain A/Victoria/2570/2019 had 14 amino acid substitutions. Key residues such as H180, D187, K219, R223, E224, and T133 are involved in hydrogen interactions with sialic acids, while N130, K142, and D222 may influence distance interactions based on docking analyses. Distinct Influenza A lineage frequency patterns across Brazils macroregions underscore regional variations in virus circulation. This study characterizes the dynamics of Influenza A and B viruses in Brazil, offering valuable insights into their circulation patterns. These findings have significant public health implications, informing strategies to mitigate transmission risks, optimize vaccination efforts, and enhance outbreak control measures. Author summaryThis study investigates the molecular epidemiology of Influenza A and B viruses in Brazil from 2021 to 2023. Utilizing data from the Center for Viral Surveillance and Serological Assessment (CeVIVAS) and public databases, we performed a comprehensive phylogenetic analysis of the Hemagglutinin segments of Influenza A/H1N1pdm09, A/H3N2, and B/Victoria-lineage viruses across all Brazilian macroregions. Key findings reveal that the A/H3N2 2a.3 strain was predominant in 2021 and early 2022, followed by A/H3N2 2b, and later by A/H1N1pdm09 5a.2a and 5a.2a.1 lineages in late 2022 and throughout 2023. The B/Victoria strain circulated at low levels initially and later co-prevailed with A/H1N1pdm09 lineages. Comparing the vaccine strain A/Darwin/9/2021 with circulating A/H3N2 viruses from 2021-2023 and A/Victoria/2570/2019 with 5a.2a.1 of A/H1N1pdm09 circulating in 2022 revealed significant mutations which could affect the interaction of the viruses with sialic acids and potentially impact vaccine efficacy. Notably, we identified a substitution pattern among the predominant Influenza subtypes and observed distinct regional variations in Influenza A lineage frequencies across Brazil. These findings are critical for optimizing vaccination strategies and provide valuable data to inform public health policy and improve health outcomes.

evolutionary biology↗

bioRxiv2024

Proposing a Systematic Lineage Classification Below the Genotype Level for Dengue Serotypes 1 and 2

Dengue virus (DENV), a mosquito-borne flavivirus, is causing a significant outbreak in Brazil. The recent surge in complete DENV genome sequences necessitates a standardized classification system for an improved understanding of viral dynamics and transmission patterns. Traditionally, DENV classification relies on serotypes and genotypes but lacks a consensus for sub-genotype classification. This hinders comprehensive analyses of viral diversity. We address this gap by proposing a novel lineage classification system for DENV using a semi-automatic workflow, leveraging the use of complete genome sequences to classify and re-evaluate DENV genetic diversity. This system offers a more granular classification scheme compared to current methods. The proposed hierarchical nomenclature, incorporating serotype, genotype, subgenotype, lineage, and sublineage, facilitates precise tracking of viral introductions and evolutionary events. This information might have crucial implications for public health interventions, enabling more targeted control strategies and improved monitoring of vaccine effectiveness during future outbreaks.

bioinformatics↗

bioRxiv2022

Dynamics of annatto pigment synthesis and accumulation revealed by integrated chemical, anatomical, and RNA-Seq analyses

Bixin is a commercially valuable apocarotenoid pigment found in the seed aril of Bixa orellana. The dynamics and regulation of its biosynthesis and accumulation during seed development remain largely unknown. Here, we combined chemical, anatomical, and transcriptomic data to provide stage-specific resolution of the cellular and molecular events occurring during B. orellana seed development. Seeds at five developmental stages (S1-S5) were used for analysis of bixin content and seed anatomy, and three of them (S1, S3 and S4) selected for Illumina HiSeq sequencing. Bixin accumulated sharply during seed development, particularly during the S2 stage, peaking at the S4 stage, and then decreasing slightly in the S5 stage. Anatomical analysis revealed that bixin accumulated in the large central vacuole of specialized cells, which were scattered throughout the developing mesotesta at the S2 stage, but enlarged progressively at later stages, until they occupied most of the parenchyma in the aril. A total of 13 million reads were generated and assembled into 73,381 protein-encoding contigs, from which 312 were identified as containing 1-deoxy-D-xylulose-5-phosphate/2-C-methyl-D-erythritol-4-phosphate (DOXP/MEP), carotenoid, and bixin pathways genes. Differential expression analysis of these genes revealed that 50 of them were differentially expressed between all the seed developmental stages, including seven carotenoid cleavage dioxygenases, eight aldehyde dehydrogenases and 22 methyltransferases. Taken together, these results provide a comprehensive description of the cellular and molecular events related to the dynamics of bixin synthesis and accumulation during seed development in B. orellana.

plant biology↗

bioRxiv2019

Oropouche virus detection in saliva and urine

Oropouche virus (OROV) is an arthropod-borne virus of the Peribunyaviridae family, transmitted to humans primarily by Culicoides paraensis. It is one of the main arboviruses that infect humans in Brazil, mainly in the Amazon region. We report the OROV detection in the saliva and urine five days after the symptoms onset. Results were further confirmed by nucleotide sequencing and phylogenetic analysis. To our knowledge, this is the first report that OROV may be detected in the saliva and urine of infected patients. In addition, our results may contribute to the current knowledge regarding the natural history of Oropouche fever.

microbiology↗

bioRxiv2018

Chikungunya virus outbreak in the Amazon region: replacement of the Asian genotype by an ECSA lineage

BackgroundSince its first detection in the Caribbean in late 2013, chikungunya virus (CHIKV) has affected 51 countries in the Americas. The CHIKV epidemic in the Americas was caused by the CHIKV-Asian genotype. In August 2014, local transmission of the CHIKV-Asian genotype was detected in the Brazilian Amazon region. However, a distinct lineage, the CHIKV-East-Central-South-America (ECSA)-genotype, was detected nearly simultaneously in Feira de Santana, Bahia state, northeast Brazil. The genomic diversity and the dynamics of CHIKV in the Brazilian Amazon region remains poorly understood despite its importance to better understand the epidemiological spread and public health impact of CHIKV in the country.\n\nMethodology/Principal FindingsWe report a large CHIKV outbreak (5,928 notified cases between August 2014 and August 2018) in Boa vista municipality, capital city of Roraimas state, located in the Brazilian Amazon region. In just 48 hours, we generated 20 novel CHIKV-ECSA genomes from the Brazilian Amazon region using MinION portable genome sequencing. Phylogenetic analyses revealed that despite an early introduction of the Asian genotype in 2015 in Roraima, the large CHIKV outbreak in 2017 in Boa Vista was caused by an ECSA-lineage most likely introduced from northeastern Brazil.\n\nEpidemiological analyses suggest a basic reproductive number of R0 of 1.66, which translates in an estimated 39 (95% CI: 36 to 45) % of Roraimas population infected with CHIKV-ECSA. Finally, we find a strong association between Google search activity and the local laboratory-confirmed CHIKV cases in Roraima.\n\nConclusions/SignificanceThis study highlights the potential of combining traditional surveillance with portable genome sequencing technologies and digital epidemiology to inform public health surveillance in the Amazon region. Our data reveal a large CHIKV-ECSA outbreak in Boa Vista, limited potential for future CHIKV outbreaks, and indicate a replacement of the Asian genotype by the ECSA genotype in the Amazon region.\n\nAuthor SummaryUntil the end of 2017, Brazil notified the highest number of infections caused by chikungunya virus (CHIKV) in the Americas. We investigated a large CHIKV outbreak in Boa vista municipality in the Brazilian Amazon region. Rapid portable genome sequencing of 20 novel isolates and subsequent genetic analysis revealed that ECSA lineage was introduced from northeastern Brazil to Roraima around July 2016. Epidemiological analyses suggest a basic reproductive number of R0 of 1.66, which suggests that approximately 39% of Roraimas population was infected with CHIKV-ECSA. Given the dominance of the CHIKV-Asian genotype in the Americas, our data highlights the rapid spread of a less understood and poorly characterized CHIKV-ECSA genotype in Brazil. Investigations on potential associations between public health impact of CHIKV and genetic diversity of circulating strains are warranted to better evaluate its impact in Brazil and beyond.

epidemiology↗