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(1) Background: The HIV subtype D is generally associated with a faster decline in CD4+ T cell counts, a higher viral load, and a faster progression to AIDS. However, it is still poorly characterized in Brazil. In this study, we used genomics and epidemiological data to investigate the transmission dynamics of HIV subtype D in the state of Bahia, Northeast Brazil. (2) Methods: To achieve this goal, we obtained four novel HIV-1 subtype D partial pol genome sequences using the Sanger method. To understand the emergence of this novel subtype in the state of Bahia, we used phylodynamic analysis on a dataset comprising 3704 pol genome sequences downloaded from the Los Alamos database. (3) Results: Our analysis revealed three branching patterns, indicating multiple introductions of the HIV-1 subtype D in Brazil from the late 1980s to the late 2000s and a single introduction event in the state of Bahia. Our data further suggest that these introductions most likely originated from European, Eastern African, Western African, and Southern African countries. (4) Conclusion: Understanding the distribution of HIV-1 viral strains and their temporal dynamics is crucial for monitoring the real-time evolution of circulating subtypes and recombinant forms, as well as for designing novel diagnostic and vaccination strategies. We advocate for a shift to active surveillance, to ensure adequate preparedness for future epidemics mediated by emerging viral strains. [ABSTRACT FROM AUTHOR]

Tracking the spread of SARS-CoV-2 variants of concern is crucial to inform public health efforts and control the ongoing pandemic. Here, we report genetic evidence for circulation of the P.1 variant in Northeast Brazil. We advocate for increased active surveillance to ensure adequate control of this variant throughout the country. Author summary: In recent months' variants of SARS-CoV-2 that have more mutations on the Spike protein has brought concern all over the world. These have been called 'variants of concern' (VOC) as it has been suggested that their genome mutations might impact transmission, immune control, and virulence. The P.1 variant, also known as 20J/501Y.V3, was first identified in travelers from Brazil during routine airport screening in Tokyo, Japan, in early January 2021. This VOC has 17 amino acid changes, ten of which are in its spike protein, including three designated to be of particular concern: N501Y, E484K and K417T. Since its first detection, despite it has presented sustained transmission worldwide, much is still unknown about its circulation into Brazilian regions. Here, through an active monitoring conducted by public health authorities of the Bahia state (Northeast Brazil), we report genetic evidence for circulation of the P.1 variant into the state. Our findings reinforce that continued genomic surveillance strategies are needed to assist in the monitoring and understanding of the circulating and co-circulating SARS-CoV-2 variants, which might help to attenuate their public health impact worldwide. [ABSTRACT FROM AUTHOR]

Yellow fever virus (YFV) causes a clinical syndrome of acute hemorrhagic hepatitis. YFV transmission involves non-human primates (NHP), mosquitoes and humans. By late 2016, Brazil experienced the largest YFV outbreak of the last 100 years, with 2050 human confirmed cases, with 681 cases ending in death and 764 confirmed epizootic cases in NHP. Among affected areas, Bahia state in Northeastern was the only region with no autochthonous human cases. By using next generation sequence approach, we investigated the molecular epidemiology of YFV in NHP in Bahia and discuss what factors might have prevented human cases. We investigated 47 YFV positive tissue samples from NHP cases to generate 8 novel YFV genomes. ML phylogenetic tree reconstructions and automated subtyping tools placed the newly generated genomes within the South American genotype I (SA I). Our analysis revealed that the YFV genomes from Bahia formed two distinct well-supported phylogenetic clusters that emerged most likely of an introduction from Minas Gerais and Espírito Santo states. Vegetation coverage analysis performed shows predominantly low to medium vegetation coverage in Bahia state. Together, our findings support the hypothesis of two independent YFV SA-I introductions. We also highlighted the effectiveness of the actions taken by epidemiological surveillance team of the state to prevented human cases. Author summary: Between 2016 and 2018, Brazil witnessed the largest YFV outbreak since years, with 2.154 cases and 745 deaths. Here we report the introduction of the virus in the state of Bahia suggesting two independent introductions from Minas Gerais and Espirito Santo. We also highlight the actions taken by epidemiological surveillance division that may have prevent human infections. [ABSTRACT FROM AUTHOR]

In May 2015 the first autochthonous Zika virus infection was reported in Brazil. Rapid and urgent measures are needed to contain the ongoing outbreak. Here we report the full-length ZIKV coding sequence from Bahia. Genetic analysis of outbreak sequences will be essential for characterizing the diversity of circulating strains, identifying hotspots of virus transmission and guiding public health control. Rapid and urgent measures are needed to contain the ongoing outbreak. [ABSTRACT FROM AUTHOR]

• The etiology of most encephalitis cases remained unknown. • Chikungunya virus was the predominant virus associated with encephalitis cases. • Chikungunya virus is a significant cause of encephalitis in Brazil. Encephalitis is a severe neurological syndrome for which herpesvirus and enteroviruses are the most common etiological agents. Arboviruses, a wildly diverse group of pathogens, are also critical epidemiological agents associated with encephalitis. In Brazil, little is known about the causative agents of encephalitis. We conducted a hospital surveillance for encephalitis between 2020 and 2022. Molecular (RT-PCR and qPCR) and serological (virus-specific IgM and viral antigens) techniques were performed in cerebrospinal fluid and serum samples obtained from study participants. In the 43 participants evaluated, the etiologic agent or the presence of IgM was detected in 16 (37.2%). Nine (20.9%) cases were positive for chikungunya virus (CHIKV), three (7.0%) for dengue virus, two (4.7%) for human adenovirus, one (2.3%) for varicella-zoster virus, and one (2.3%) for enterovirus. Whole-genome sequencing revealed that the CHIKV identified belongs to the East/Central/South African lineage. Herein, CHIKV is a common pathogen identified in encephalitis cases. Our results reinforce previous evidence that chikungunya represents a significant cause of encephalitis during CHIKV outbreaks and epidemics and add to existing information on the epidemiology of encephalitis in Brazil. [ABSTRACT FROM AUTHOR]