Genomic epidemiology unveils the dynamics and spatial corridor behind the Yellow Fever virus outbreak in Southern Brazil.

Despite the considerable morbidity and mortality of yellow fever virus (YFV) infections in Brazil, our understanding of disease outbreaks is hampered by limited viral genomic data. Here, through a combination of phylogenetic and epidemiological models, we reconstructed the recent transmission history of YFV within different epidemic seasons in Brazil. A suitability index based on the highly domesticated Aedes aegypti was able to capture the seasonality of reported human infections. Spatial modeling revealed spatial hotspots with both past reporting and low vaccination coverage, which coincided with many of the largest urban centers in the Southeast. Phylodynamic analysis unraveled the circulation of three distinct lineages and provided proof of the directionality of a known spatial corridor that connects the endemic North with the extra-Amazonian basin. This study illustrates that genomics linked with eco-epidemiology can provide new insights into the landscape of YFV transmission, augmenting traditional approaches to infectious disease surveillance and control.

Increased interregional virus exchange and nucleotide diversity outline the expansion of chikungunya virus in Brazil.

The emergence and reemergence of mosquito-borne diseases in Brazil such as yellow fever, zika, chikungunya, and dengue have had serious impacts on public health. Concerns have been raised due to the rapid dissemination of the chikungunya virus across the country since its first detection in 2014 in Northeast Brazil. In this work, we carried out on-site training activities in genomic surveillance in partnership with the National Network of Public Health Laboratories that have led to the generation of 422 chikungunya virus genomes from 12 Brazilian states over the past two years (2021-2022), a period that has seen more than 312 thousand chikungunya fever cases reported in the country. These genomes increased the amount of available data and allowed a more comprehensive characterization of the dispersal dynamics of the chikungunya virus East-Central-South-African lineage in Brazil. Tree branching patterns revealed the emergence and expansion of two distinct subclades. Phylogeographic analysis indicated that the northeast region has been the leading hub of virus spread towards other regions. Increased frequency of C > T transitions among the new genomes suggested that host restriction factors from the immune system such as ADAR and AID/APOBEC deaminases might be driving the genetic diversity of the chikungunya virus in Brazil.

Increased interregional virus exchange and nucleotide diversity outline the expansion of the chikungunya virus ECSA lineage in Brazil.

The emergence and reemergence of mosquito-borne diseases in Brazil such as Yellow Fever, Zika, Chikungunya, and Dengue have had serious impacts on public health. Concerns have been raised due to the rapid dissemination of the chikungunya virus (CHIKV) across the country since its first detection in 2014 in Northeast Brazil. Faced with this scenario, on-site training activities in genomic surveillance carried out in partnership with the National Network of Public Health Laboratories have led to the generation of 422 CHIKV genomes from 12 Brazilian states over the past two years (2021-2022), a period that has seen more than 312 thousand chikungunya fever cases reported in the country. These new genomes increased the amount of available data and allowed a more comprehensive characterization of the dispersion dynamics of the CHIKV East-Central-South-African (ECSA) lineage in Brazil. Tree branching patterns revealed the emergence and expansion of two distinct subclades. Phylogeographic analysis indicated that the northeast region has been the leading hub of virus spread towards other regions. Increased frequency of C>T transitions among the new genomes suggested that host restriction factors from the immune system such as ADAR and AID/APOBEC deaminases might be driving CHIKV ECSA lineage genetic diversity in Brazil.

Perfil da hepatite C em Goiás: epidemiologia, distribuição genotípica e carga viral / Profile of hepatitis C in Goiás: epidemiology, genotypic distribution and viral load

O Virus da Hepatite C (HCV) possui vasta diversidade. Com base nas variações genômicas, existem oito genótipos, designados de G1 a G8, com prevalências distintas de acordo com a região geográfica observada. Objetivo: O objetivo do estudo foi avaliar o perfil epidemiológico, genotípico e carga viral (CV) do HCV. Métodos: Estudo observacional analítico do tipo transversal, com dados de janeiro de 2018 a dezembro de 2021. O estudo analisou dados referentes a genotipagem, CV e do Formulário de Solicitação de CV do HCV, obtidos no Laboratório Estadual de Saúde Pública do estado de Goiás. Resultados: A maioria dos casos de HCV, concentram-se nas macrorregiões de saúde Centro Sudeste (42,90%) e Centro Oeste (34,15%) do Estado, com maior frequência do G1, seguido do G3 e presença dos G2, G4 e G5. O G1 vem diminuindo a frequência no decorrer dos anos, enquanto o G3 aumenta. Em geral, 49,33% dos casos apresentam alta CV (> 1.000.000 UI/mL). Em relação ao sexo, 31,75% dos indivíduos do sexo masculino apresentaram CV nessa mesma faixa, e o sexo feminino com 17,58%. A CV foi consideravelmente alta entre os casos analisados, com o sexo feminino, apresentando CV significativamente menor que o sexo masculino. Foram identificados o subtipo 1d e o G5 incomuns na região Central do Brasil. Conclusão: Os dados apresentados demonstram que o HCV pode estar em expansão, com o aparecimento de novos genótipos, subtipos e demonstra uma mudança na distribuição genotípica, no estado de Goiás nos últimos anos

The Hepatitis C Virus (HCV) has vast diversity. Based on genomic variations, there are eight genotypes, designated from G1 to G8, with different prevalences according to the geographical region observed. Objective: The objective of the study was to evaluate the epidemiological, genotypic and viral load (CV) profile of HCV. Methods: Cross-sectional analytical observational study, with data from January 2018 to December 2021. The study analyzed data relating to genotyping, CV and the HCV CV Request Form, obtained from the State Public Health Laboratory of the state of Goiás. Results: The majority of HCV cases are concentrated in the Central Southeast (42.90%) and Central West (34.15%) health macro-regions of the State, with a higher frequency in G1, followed by G3 and the presence of G2Genotype, G4 and G5. G1 has been decreasing in frequency over the years, while G3 is increasing. In general, 49.33% of cases have high CV (> 1,000,000 IU/mL). In relation to sex, 31.75% of males had CV in the same range, and females had 17.58%. The CV was considerably high among the cases analyzed, with females presenting a significantly lower CV than males. Subtype 1d and G5, uncommon in the Central region of Brazil, were identified. Conclusion: The data presented demonstrate that HCV may be expanding, with the emergence of new genotypes, subtypes and demonstrates a change in genotypic distribution in the state of Goiás in recent years

Emergence of Dengue Virus Serotype 2 Cosmopolitan Genotype, Brazil.

We used nanopore sequencing and phylogenetic analyses to identify a cosmopolitan genotype of dengue virus serotype 2 that was isolated from a 56-year-old male patient from the state of Goiás in Brazil. The emergence of a cosmopolitan genotype in Brazil will require risk assessment and surveillance to reduce epidemic potential.

A Retrospective Overview of Zika Virus Evolution in the Midwest of Brazil.

Since the introduction of the Zika virus (ZIKV) into Brazil in 2015, its transmission dynamics have been intensively studied in many parts of the country, although much is still unknown about its circulation in the midwestern states. Here, using nanopore technology, we obtained 23 novel partial and near-complete ZIKV genomes from the state of Goiás, located in the Midwest of Brazil. Genomic, phylogenetic, and epidemiological approaches were used to retrospectively explore the spatiotemporal evolution of the ZIKV-Asian genotype in this region. As a likely consequence of a gradual accumulation of herd immunity, epidemiological data revealed a decline in the number of reported cases over 2018 to 2021. Phylogenetic reconstructions revealed that multiple independent introductions of the Asian lineage have occurred in Goiás over time and revealed a complex transmission dynamic between epidemic seasons. Together, our results highlight the utility of genomic, epidemiological, and evolutionary methods to understand mosquito-borne epidemics. IMPORTANCE Despite the considerable morbidity and mortality of arboviral infections in Brazil, such as Zika, chikungunya, dengue fever, and yellow fever, our understanding of these outbreaks is hampered by the limited availability of genomic data to track and control the epidemic. In this study, we provide a retrospective reconstruction of the Zika virus transmission dynamics in the state of Goiás by analyzing genomic data from areas in Midwest Brazil not covered by other previous studies. Our study provides an understanding of how ZIKV initiates transmission in this region and reveals a complex transmission dynamic between epidemic seasons. Together, our results highlight the utility of genomic, epidemiological, and evolutionary methods to understand mosquito-borne epidemics, revealing how this toolkit can be used to help policymakers prioritize areas to be targeted, especially in the context of finite public health resources.

Field and classroom initiatives for portable sequence-based monitoring of dengue virus in Brazil.

Brazil experienced a large dengue virus (DENV) epidemic in 2019, highlighting a continuous struggle with effective control and public health preparedness. Using Oxford Nanopore sequencing, we led field and classroom initiatives for the monitoring of DENV in Brazil, generating 227 novel genome sequences of DENV1-2 from 85 municipalities (2015-2019). This equated to an over 50% increase in the number of DENV genomes from Brazil available in public databases. Using both phylogenetic and epidemiological models we retrospectively reconstructed the recent transmission history of DENV1-2. Phylogenetic analysis revealed complex patterns of transmission, with both lineage co-circulation and replacement. We identified two lineages within the DENV2 BR-4 clade, for which we estimated the effective reproduction number and pattern of seasonality. Overall, the surveillance outputs and training initiative described here serve as a proof-of-concept for the utility of real-time portable sequencing for research and local capacity building in the genomic surveillance of emerging viruses.

Prevalence and lethality among patients with histoplasmosis and AIDS in the Midwest Region of Brazil.

Histoplasmosis is a systemic mycosis that is considered an important public health problem. In this work, we performed a descriptive, observational, cross-sectional and retrospective study with a secondary data analysis of medical records from 2000 to 2012 at a tertiary hospital. The study sample consisted of 275 patients with laboratory-confirmed Disseminated Histoplasmosis (DH)/AIDS. The results showed that the prevalence of DH associated with AIDS was 4.4%. The majority of patients were young adult men with fever in 84.2%, cough in 63.4%, weight loss in 63.1%, diarrhoea in 44.8% and skin manifestations in 27.6% of patients. In the overall cohort, the CD4 counts were low, but not significantly different in survivors and non-survivors. Higher levels of urea and lower levels of haemoglobin and platelets were observed in non-survivor patients (<.05). The global lethality was 71.3% (196/275). The results with high prevalence and lethality highlight the need to adopt measures to facilitate early diagnosis, proper treatment and improved prognosis.