Dengue virus (DENV) is currently causing epidemics of unprecedented scope in endemic settings and expanding to new geographical areas. It is therefore critical to track this virus using genomic surveillance. However, the complex patterns of viral genomic diversity make it challenging to use the existing genotype classification system. Here, we propose adding 2 sub-genotypic levels of virus classification, named major and minor lineages. These lineages have high thresholds for phylogenetic distance and clade size, rendering them stable between phylogenetic studies. We present assignment tools to show that the proposed lineages are useful for regional, national, and subnational discussions of relevant DENV diversity. Moreover, the proposed lineages are robust to classification using partial genome sequences. We provide a standardized neutral descriptor of DENV diversity with which we can identify and track lineages of potential epidemiological and/or clinical importance. Information about our lineage system, including methods to assign lineages to sequence data and propose new lineages, can be found at: dengue-lineages.org.

Dengue, caused by dengue virus (DENV) 1–4, remains a global public health concern, with Brazil experiencing some of the largest epidemics. The re-emergence 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 analysed 1536 DENV-3 genomes, including 11 newly generated in this study, 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 USA, and Europe. At least six independent introduction events of this lineage into Brazil were identified, with the Caribbean region as the primary source. The earliest introduction likely occurred in late 2022 in Roraima, followed by introductions in São Paulo, Minas Gerais, and Pará. While one instance of interstate transmission was detected—from São 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.

Influenza A and B viruses represent significant global health threats, contributing substantially to morbidity and mortality rates. However, a comprehensive understanding of the molecular epidemiology of these viruses in Brazil, a continental-size country and a crucial hub for the entry, circulation, and dissemination of influenza viruses within South America, still needs to be improved. This study addresses this gap by consolidating data and samples across all Brazilian macroregions, as part of the Center for Viral Surveillance and Serological Assessment project, together with an extensive number of other Brazilian sequences provided by a public database during the epidemic seasons spanning 2021–23. Phylogenetic analysis of the hemagglutinin segment of influenza A/H1N1pdm09, A/H3N2, and influenza B/Victoria-lineage viruses revealed that in 2021 and in the first semester of 2022, the A/H3N2 2a.3 strain was the predominant circulating strain. Subsequently, the A/H3N2 2b became the prevalent strain until October, when it was substituted by A/H1N1pdm09 5a.2a and 5a.2a.1 lineages. This scenario was maintained during the year of 2023. B/Victoria emerged and circulated at low levels between December 2021 and September 2022 and then became coprevalent with A/H1N1pdm09 5a.2a and 5a.2a.1 lineages. The comparison between the vaccine strain A/Darwin/9/2021 and circulating viruses revealed shared mutations to aspartic acid at residues 186 and 225 across all A/H3N2 lineages from 2021 to 2023, altering the charge in the receptor-binding domain. For A/H1N1pdm09, the 2022 consensus of 5a.2a.1 and the vaccine strain A/Victoria/2570/2019 showed 14 amino acid substitutions. Key residues H180, D187, K219, R223, E224, and T133 are involved in hydrogen interactions with sialic acids, while N130, K142, and D222 may contribute to distance interactions based on docking analyses. Importantly, distinct influenza A lineage frequency patterns were observed across Brazil’s macroregions, underscoring the regional variations in virus circulation. This study characterizes influenza A and B viruses circulating in Brazil, providing insights into their circulation patterns and dynamics across Brazilian macroregions. These findings hold significant implications for public health interventions, informing strategies to mitigate transmission risks, optimize vaccination efforts, and enhance outbreak control measures.

Currently only four genome sequences for Limnothrix spp. are publicly available, and information on the genetic properties of cyanobacteria belonging to this genus is limited. In this study, we report the draft genome of Limnothrix sp. CACIAM 69d, isolated from the reservoir of a hydroelectric dam located in the Amazon ecosystem, from where cyanobacterial genomic data are still scarce. Comparative genomic analysis of Limnothrix revealed the presence of key enzymes in the cyanobacterial central carbon metabolism and how it is well equipped for environmental sulfur and nitrogen acquisition. Additionally, this work covered the analysis of Limnothrix CRISPR-Cas systems, pathways related to biosynthesis of secondary metabolites and assembly of extracellular polymeric substances and their exportation. A trans-AT PKS gene cluster was identified in two strains, possibly related to the novel toxin Limnothrixin biosynthesis. Overall, the draft genome of Limnothrix sp. CACIAM 69d adds new data to the small Limnothrix genome library and contributes to a growing representativeness of cyanobacterial genomes from the Amazon region. The comparative genomic analysis of Limnothrix made it possible to highlight unique genes for each strain and understand the overall features of their metabolism.

Enterovirus D68 (EV-D68) is a leading cause of acute respiratory disease outbreaks, especially among children. EV-D68 infections can rapidly progress to severe clinical complications and potentially fatal outcomes. In Brazil, no diagnostic or genomic surveillance of this virus is currently performed. Between July and September 2023, cases of acute EV-D68 infection were identified among pediatric patients in several municipalities within the State of Alagoas, Northeast Brazil. Infections were confirmed by RT-qPCR using nasopharyngeal samples, and the complete EV-D68 genomes were sequenced and analyzed through phylogenetic inference. EV-D68 RNA was identified in four children aged 1–9 years from four geographically distinct municipalities in Alagoas. All infections were associated with lower respiratory tract symptoms, including dyspnea and wheezing; however, no fatalities were reported. Complete genomic sequencing revealed that the samples belonged to genotype B, subgenotype B3. This is the first study to report complete genomic data on EV-D68 infections from Brazil and South America. Enhanced genomic surveillance and focused EV-D68 diagnosis are critical to better understanding and managing the regional and national dissemination of this virus.

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.