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.

Brevundimonas brasiliensis sp. nov.: a New Multidrug-Resistant Species Isolated from a Patient in Brazil.

To increase knowledge on Brevundimonas pathogens, we conducted in-depth genomic and phenotypic characterization of a Brevundimonas strain isolated from the cerebrospinal fluid of a patient admitted in a neonatal intensive care unit. The strain was identified as a member of the genus Brevundimonas based on Vitek 2 system results and 16S rRNA gene sequencing and presented a multidrug resistance profile (MDR). Several molecular and biochemical tests were used to characterize and identify the species for in-depth results. The draft genome assembly of the isolate has a total length of 3,261,074 bp and a G+C of 66.86%, similar to other species of the genus. Multilocus sequence analysis, Type (Strain) Genome Server, digital DNA-DNA hybridization, and average nucleotide identity confirmed that the Brevundimonas sp. studied represents a distinct species, for which we propose the name Brevundimonas brasiliensis sp. nov. In silico analysis detected antimicrobial resistance genes (AMRGs) mediating resistance to ß-lactams (penP, blaTEM-16, and blaBKC-1) and aminoglycosides [strA, strB, aac(6')-Ib, and aac(6')-Il]. We also found AMRGs encoding the AcrAB efflux pump that confers resistance to a broad spectrum of antibiotics. Colistin and quinolone resistance can be attributed to mutation in qseC and/or phoP and GyrA/GyrB, respectively. The Brevundimonas brasiliensis sp. nov. genome contained copies of type IV secretion system (T4SS)-type integrative and conjugative elements (ICEs); integrative mobilizable elements (IME); and Tn3-type and IS3, IS6, IS5, and IS1380 families, suggesting an important role in the development and dissemination of antibiotic resistance. The isolate presented a range of virulence-associated genes related to biofilm formation, adhesion, and invasion that can be relevant for its pathogenicity. Our findings provide a wealth of data to hinder the transmission of MDR Brevundimonas and highlight the need for monitoring and identifying new bacterial species in hospital environments. IMPORTANCE Brevundimonas species is considered an opportunistic human pathogen that can cause multiple types of invasive and severe infections in patients with underlying pathologies. Treatment of these pathogens has become a major challenge because many isolates are resistant to most antibiotics used in clinical practice. Furthermore, there are no consistent therapeutic results demonstrating the efficacy of antibacterial agents. Although considered a rare pathogen, recent studies have provided evidence of the emergence of Brevundimonas in clinical settings. Hence, we identified a novel pathogenic bacterium, Brevundimonas brasiliensis sp. nov., that presented a multidrug resistance (MDR) profile and carried diverse genes related to drug resistance, virulence, and mobile genetic elements. Such data can serve as a baseline for understanding the genomic diversity, adaptation, evolution, and pathogenicity of MDR Brevundimonas.

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.

Efetividade da marcação combinada de p16 e ki67 na referência de mulheres com citologia ASC-US ou LSIL para colposcopia / Effectiveness of combined p16 and ki67 labeling in the referral of women with ASC-US or LSIL cytology for colposcopy

Objetivo: Analisar o desempenho do teste de Dupla Marcação (DM) por p16 e Ki67 em amostras de células cervicais para detecção de lesões precursoras do câncer do colo do útero, comparando-o à repetição imediata da citologia em mulheres com resultado de citologia de rastreamento ASC-US ou LSIL. Metodologia: Trata-se de um estudo transversal que recrutou 121 mulheres nas unidades de Atenção Primária de Saúde dos municípios de Palmas e Porto Nacional, em Tocantins, e da cidade do Rio de Janeiro, com citologia de rastreamento com resultado ASC-US ou LSIL. As mulheres foram referidas aos Serviços de Referência do Colo participantes em Tocantins e no Rio de Janeiro. As participantes realizaram o exame de colposcopia e coleta de espécime para Citologia em Meio Líquido (CML) e para DM para p16 e Ki67. Os resultados dos testes foram comparados ao padrão-ouro misto definido pela colposcopia, histologia (quando obtido espécime histológico) na avaliação inicial, ou citologia, colposcopia e histologia (quando obtido espécime histológico) no seguimento de pelo menos 12 meses, definindo as que tinham lesão precursora (NIC II ou NIC III) ou não. Resultados: Das 121 mulheres recrutadas, 76 mulheres foram consideradas para esta análise por terem pelo menos um exame de triagem realizado (CML ou DM por p16-Ki67) e conclusão diagnóstica. Dessas, 42 apresentavam exame prévio de ASC-US e 34 de LSIL. A maioria (86,8%) estava na faixa etária recomendada para o rastreamento (25 a 64 anos). Objetivo: Analisar o desempenho do teste de Dupla Marcação (DM) por p16 e Ki67 em amostras de células cervicais para detecção de lesões precursoras do câncer do colo do útero, comparando-o à repetição imediata da citologia em mulheres com resultado de citologia de rastreamento ASC-US ou LSIL. Metodologia: Trata-se de um estudo transversal que recrutou 121 mulheres nas unidades de Atenção Primária de Saúde dos municípios de Palmas e Porto Nacional, em Tocantins, e da cidade do Rio de Janeiro, com citologia de rastreamento com resultado ASC-US ou LSIL. As mulheres foram referidas aos Serviços de Referência do Colo participantes em Tocantins e no Rio de Janeiro. As participantes realizaram o exame de colposcopia e coleta de espécime para Citologia em Meio Líquido (CML) e para DM para p16 e Ki67. Os resultados dos testes foram comparados ao padrão-ouro misto definido pela colposcopia, histologia (quando obtido espécime histológico) na avaliação inicial, ou citologia, colposcopia e histologia (quando obtido espécime histológico) no seguimento de pelo menos 12 meses, definindo as que tinham lesão precursora (NIC II ou NIC III) ou não. Resultados: Das 121 mulheres recrutadas, 76 mulheres foram consideradas para esta análise por terem pelo menos um exame de triagem realizado (CML ou DM por p16-Ki67) e conclusão diagnóstica. Dessas, 42 apresentavam exame prévio de ASC-US e 34 de LSIL. A maioria (86,8%) estava na faixa etária recomendada para o rastreamento (25 a 64 anos). Oito mulheres (10,5%) apresentaram NIC II ou III como conclusão diagnóstica. Verificou-se que o teste da DM de p16 e Ki67 identificou um número maior de mulheres com um desses diagnósticos, encaminhando 50% das mulheres com ASC-US ou LSIL na citologia de rastreamento para colposcopia, mas deixando de identificar 50% dessas mulheres. Esse teste mostrou-se 2,5 vezes mais sensível do que o exame citopatológico de repetição imediata. Conclusão: O teste de DM por p16 e Ki67 se mostrou mais capaz de identificar mulheres com lesões precursoras com resultado citopatológico prévio ASC-US ou LSIL e sem aumento relevante de encaminhamentos para colposcopia em comparação à citologia de repetição imediata.(AU)

Objective: To access p16/Ki-67 double staining (DS) in cervical cells performance for detecting precursor lesions of cervical cancer, in comparison to immediate repetition of the liquid-based cervical cytology (LBCC) in women with screening cytology results of atypical squamous cells of undetermined significance (ASC-US) or low-grade squamous intraepithelial lesion (LSIL). Methodology: This study recruited 121 women in primary health care units in Palmas and Porto Nacional, Tocantins, and in Rio de Janeiro, Brazil, with screening cytology showing ASC-US or LSIL. Women were addressed to the Cervical Referral Services (SRC) in each state and examined with colposcopy, LBCC and DS-p16/Ki-67. Histological results were available for women in which a cervical biopsy was obtained during initial evaluation or duringa follow-up up to 12 months, discerning cases with precursor lesions (CIN2 or CIN3) or not. Results: From the 121 recruited women, 76 screened positive in at least one exam (LBCC or DS-p16/Ki-67) and had a diagnostic conclusion. From these, 42 and 34 patients had previous ASC-US and LSIL exams, respectively. Most patients (86,8%) were within the recommended age group for screening in Brazil (25 to 64 years-old). CIN2-3 were found in 8 women (10,5%). DS-p16/Ki-67 identified a greater number of women with CIN2-3, addressing 50% of the women to colposcopy, but failing to detect these lesions in 50% of cases. DS-p16/Ki-67 was2,5x more sensitive than the immediate repetition of the LBCC. Conclusion: DS-p16/Ki-67 is more efficient to identify women with precursor lesions with screening cytopalotogical ASC-US or LSIL results, and without relevant increase in referring patients to colposcopy, in comparison to immediate repetition of the LBCC.(AU)

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.

Genomic Epidemiology of SARS-CoV-2 in Tocantins State and the Diffusion of P.1.7 and AY.99.2 Lineages in Brazil.

Tocantins is a state in the cross-section between the Central-West, North and Northeast regions of Brazilian territory; it is a gathering point for travelers and transportation from the whole country. In this study, 9493 genome sequences, including 241 local SARS-CoV-2 samples (collected from 21 December 2020, to 16 December 2021, and sequenced in the MinION platform) were analyzed with the following aims: (i) identify the relative prevalence of SARS-CoV-2 lineages in the state of Tocantins; (ii) analyze them phylogenetically against global SARS-CoV-2 sequences; and (iii) hypothesize the viral dispersal routes of the two most abundant lineages found in our study using phylogenetic and phylogeographic approaches. The performed analysis demonstrated that the majority of the strains sequenced during the period belong to the Gamma P.1.7 (32.4%) lineage, followed by Delta AY.99.2 (27.8%), with the first detection of VOC Omicron. As expected, there was mainly a dispersion of P.1.7 from the state of São Paulo to Tocantins, with evidence of secondary spreads from Tocantins to Goiás, Mato Grosso, Amapá, and Pará. Rio de Janeiro was found to be the source of AY.99.2 and from then, multiple cluster transmission was observed across Brazilian states, especially São Paulo, Paraiba, Federal District, and Tocantins. These data show the importance of trade routes as pathways for the transportation of the virus from Southeast to Northern Brazil.