Circulation of Dengue Virus Serotype 1 Genotype V and Dengue Virus Serotype 2 Genotype III in Tocantins State, Northern Brazil, 2021-2022.

In Brazil, the state of Tocantins, located in north-central Brazil, has experienced a significant number of cases of arboviral disease, particularly Dengue virus (DENV). This study aimed to deepen the knowledge on DENV circulation within that state by conducting full genome sequencing of viral genomes recovered from 61 patients between June 2021 and July 2022. There were a total of 8807 and 20,692 cases in 2021 and 2022, respectively, as reported by the state's Secretary of Health. Nucleotide sequencing confirmed the circulation of DENV serotype 1, genotype V and DENV serotype 2, genotype III in the State. Younger age groups (4 to 43 years old) were mostly affected; however, no significant differences were detected regarding the gender distribution of cases in humans. Phylogenetic analysis revealed that the circulating viruses belong to DENV-1 genotype V American and DENV-2 genotype III Southeast Asian/American. The Bayesian analysis of DENV-1 genotype V genomes sequenced here are closely related to genomes previously sequenced in the state of São Paulo. Regarding the DENV-2 genotype III genomes, these clustered in a distinct, well-supported subclade, along with previously reported isolates from the states of Goiás and São Paulo. The findings reported here suggest that multiple introductions of these genotypes occurred in the Tocantins state. This observation highlights the importance of major population centers in Brazil on virus dispersion, such as those observed in other Latin American and North American countries. In the SNP analysis, DENV-1 displayed 122 distinct missense mutations, while DENV-2 had 44, with significant mutations predominantly occurring in the envelope and NS5 proteins. The analyses performed here highlight the concomitant circulation of distinct DENV-1 and -2 genotypes in some Brazilian states, underscoring the dynamic evolution of DENV and the relevance of surveillance efforts in supporting public health policies.

The Omicron Lineages BA.1 and BA.2 (Betacoronavirus SARS-CoV-2) Have Repeatedly Entered Brazil through a Single Dispersal Hub.

Brazil currently ranks second in absolute deaths by COVID-19, even though most of its population has completed the vaccination protocol. With the introduction of Omicron in late 2021, the number of COVID-19 cases soared once again in the country. We investigated in this work how lineages BA.1 and BA.2 entered and spread in the country by sequencing 2173 new SARS-CoV-2 genomes collected between October 2021 and April 2022 and analyzing them in addition to more than 18,000 publicly available sequences with phylodynamic methods. We registered that Omicron was present in Brazil as early as 16 November 2021 and by January 2022 was already more than 99% of samples. More importantly, we detected that Omicron has been mostly imported through the state of São Paulo, which in turn dispersed the lineages to other states and regions of Brazil. This knowledge can be used to implement more efficient non-pharmaceutical interventions against the introduction of new SARS-CoV variants focused on surveillance of airports and ground transportation.

Genomic Epidemiology Reveals the Circulation of the Chikungunya Virus East/Central/South African Lineage in Tocantins State, North Brazil.

The chikungunya virus (CHIKV) is a mosquito-borne virus of the family Togaviridae transmitted to humans by Aedes spp. mosquitoes. In Brazil, imported cases have been reported since June 2014 through two independent introductions, one caused by Asian Lineage in Oiapoque, Amapá state, North Region, and another caused by East/Central/South African (ECSA) in Feira de Santana, Bahia state, Northeast Region. Moreover, there is still limited information about the genomic epidemiology of the CHIKV from surveillance studies. The Tocantins state, located in Northern Brazil, reported an increase in the number of CHIKV cases at the end of 2021 and the beginning of 2022. Thus, to better understand the dispersion dynamics of this viral pathogen in the state, we generated 27 near-complete CHIKV genome sequences from four cities, obtained from clinical samples. Our results showed that the newly CHIKV genomes from Tocantins belonged to the ECSA lineage. Phylogenetic reconstruction revealed that Tocantins' strains formed a single well-supported clade, which appear to be closely related to isolates from the Rio Grande do Norte state (Northeast Brazil) and the Rio de Janeiro state (Southeast Brazil), that experienced an explosive ECSA epidemic between 2016-2019. Mutation analyses showed eleven frequent non-synonymous mutations in the structural and non-structural proteins, indicating the autochthonous transmission of the CHIKV in the state. None of the genomes recovered within the Tocantins samples carry the A226V mutation in the E1 protein associated with increased transmission in A. albopictus. The study presented here highlights the importance of continued genomic surveillance to provide information not only on recording mutations along the viral genome but as a molecular surveillance tool to trace virus spread within the country, to predict events of likely occurrence of new infections, and, as such, contribute to an improved public health service.

Complete chloroplast genome sequence of Caryocar brasiliense Camb. (Caryocaraceae) and comparative analysis brings new insights into the plastome evolution of Malpighiales.

Caryocar brasiliense (Caryocaraceae) is a Neotropical tree species widely distributed in Brazilian Savannas. This species is very popular in central Brazil mainly by the use of its fruits in the local cuisine, and indeed it is one of the candidates, among Brazilian native plants, for fast track incorporation into cropping systems. Here we sequenced the complete chloroplast genome of C. brasiliense and used the data to access its genomic resources using high-throughput sequencing. The chloroplast exhibits a genome length of 165,793 bp and the typical angiosperm quadripartite structure with two copies of an inverted repeat sequence (IRa and IRb) of 34,902 bp each, separating a small single copy (SSC) region of 11,852 bp and a large single copy (LSC) region of 84,137 bp. The annotation analysis identified 136 genes being 87 protein-coding, eight rRNA and 37 tRNA genes. We identified 49 repetitive DNA elements and 85 microsatellites. A bayesian phylogenetic analysis helped to understand previously unresolved relationships in Malpighiales, placing Caryocaraceae as a separated group in the order, with high supported nodes. This study synthetizes valuable information for further studies allowing a better understanding of evolutionary patterns in the group and providing resources for future breeding programs.

The complete chloroplast genome of Stryphnodendron adstringens (Leguminosae - Caesalpinioideae): comparative analysis with related Mimosoid species.

Stryphnodendron adstringens is a medicinal plant belonging to the Leguminosae family, and it is commonly found in the southeastern savannas, endemic to the Cerrado biome. The goal of this study was to assemble and annotate the chloroplast genome of S. adstringens and to compare it with previously known genomes of the mimosoid clade within Leguminosae. The chloroplast genome was reconstructed using de novo and referenced-based assembly of paired-end reads generated by shotgun sequencing of total genomic DNA. The size of the S. adstringens chloroplast genome was 162,169 bp. This genome included a large single-copy (LSC) region of 91,045 bp, a small single-copy (SSC) region of 19,014 bp and a pair of inverted repeats (IRa and IRb) of 26,055 bp each. The S. adstringens chloroplast genome contains a total of 111 functional genes, including 77 protein-coding genes, 30 transfer RNA genes, and 4 ribosomal RNA genes. A total of 137 SSRs and 42 repeat structures were identified in S. adstringens chloroplast genome, with the highest proportion in the LSC region. A comparison of the S. adstringens chloroplast genome with those from other mimosoid species indicated that gene content and synteny are highly conserved in the clade. The phylogenetic reconstruction using 73 conserved coding-protein genes from 19 Leguminosae species was supported to be paraphyletic. Furthermore, the noncoding and coding regions with high nucleotide diversity may supply valuable markers for molecular evolutionary and phylogenetic studies at different taxonomic levels in this group.