Clinical profile of Oropouche Fever in Bahia, Brazil: unexpected fatal cases / Perfil clínico de la fiebre de Oropouche en Bahía, Brasil: casos fatales inesperados

Oropouche virus (OROV) is an arbovirus transmitted to humans by mosquitoes, with the Culicoides paraensis mosquito species as its primary vector, causing Oropouche fever. Records of an outbreak in Brazil have so far been restricted to Central-North region of the country. However, an increase in the occurrence of cases of this disease has been observed in the state of Bahia, where the rapid spread of the OROV virus is configured as an outbreak in the South and East macro-regions of great concern for public health. This is a case-based study of acute OROV infection that led to the death of two young women without comorbidities amid an outbreak of the disease. The patient's biological samples were subjected to routine real-time PCR assays for the diagnosis of Oropouche fever and other pathologies. In addition, serological tests and metagenomics were performed during the laboratory investigation. This study shows the need for an active and efficient surveillance system to control the spread of this virus, as well as the importance of carrying out prospective studies to better clarify the natural history of this disease.

El virus Oropouche (OROV) es un arbovirus transmitido al ser humano por mosquitos, siendo el mosquito de la especie Culicoides paraensis su vector principal, causante de la fiebre de Oropouche. Los registros de un brote en Brasil hasta ahora se han restringido a la región Centro-Norte del país. Sin embargo, se ha observado un aumento en la ocurrencia de casos de esta enfermedad en el estado de Bahía, donde la rápida propagación del virus OROV se configura como un brote en las macrorregiones Sur y Este de gran preocupación para la salud pública. Se trata de un estudio de caso de infección aguda por OROV que provocó la muerte de dos mujeres jóvenes sin comorbilidades en medio de un brote de la enfermedad. Las muestras biológicas de la paciente fueron sometidas a ensayos rutinarios de PCR en tiempo real para el diagnóstico de la fiebre de Oropouche y otras patologías. Además, se realizaron pruebas serológicas y metagenómicas durante la investigación de laboratorio. Este estudio muestra la necesidad de un sistema de vigilancia activo y eficiente para controlar la propagación de este virus, así como la importancia de realizar estudios prospectivos para esclarecer mejor la historia natural de esta enfermedad.

Detection of encephalitis-causing viruses reveals predominance of chikungunya virus in the state of Bahia, Brazil.

OBJECTIVES: 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. METHODS: 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. RESULTS: 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. CONCLUSION: 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.

Phylogenetic Reconstructions Reveal the Circulation of a Novel Dengue Virus-1V Clade and the Persistence of a Dengue Virus-2 III Genotype in Northeast Brazil.

Dengue fever is among the most significant public health concerns in Brazil. To date, the highest number of Dengue notifications in the Americas has been reported in Brazil, with cases accounting for a total number of 3,418,796 reported cases as of mid-December 2022. Furthermore, the northeastern region of Brazil registered the second-highest incidence of Dengue fever in 2022. Due to the alarming epidemiological scenario, in this study, we used a combination of portable whole-genome sequencing, phylodynamic, and epidemiological analyses to reveal a novel DENV-1 genotype V clade and the persistence of DENV-2 genotype III in the region. We further report the presence of non-synonymous mutations associated with non-structural domains, especially the NS2A (non-structural protein 2A), as well as describe synonymous mutations in envelope and membrane proteins, distributed differently between clades. However, the absence of clinical data at the time of collection and notification, as well as the impossibility of monitoring patients in order to observe worsening or death, restricts our possibility of correlating mutational findings with possible clinical prognoses. Together, these results reinforce the crucial role of genomic surveillance to follow the evolution of circulating DENV strains and understand their spread across the region through inter-regional importation events, likely mediated by human mobility, and also the possible impacts on public health and outbreak management.

Genomic epidemiology reveals how restriction measures shaped the SARS-CoV-2 epidemic in Brazil

Brazil has experienced some of the highest numbers of COVID-19 cases and deaths globally and from May 2021 made Latin America a pandemic epicenter. Although SARS-CoV-2 established sustained transmission in Brazil early in the pandemic, important gaps remain in our understanding of virus transmission dynamics at the national scale. Here, we describe the genomic epidemiology of SARS-CoV-2 using near-full genomes sampled from 27 Brazilian states and a bordering country - Paraguay. We show that the early stage of the pandemic in Brazil was characterised by the co-circulation of multiple viral lineages, linked to multiple importations predominantly from Europe, and subsequently characterized by large local transmission clusters. As the epidemic progressed under an absence of effective restriction measures, there was a local emergence and onward international spread of Variants of Concern (VOC) and Variants Under Monitoring (VUM), including Gamma (P.1) and Zeta (P.2). In addition, we provide a preliminary genomic overview of the epidemic in Paraguay, showing evidence of importation from Brazil. These data reinforce the usefulness and need for the implementation of widespread genomic surveillance in South America as a toolkit for pandemic monitoring that provides a means to follow the real-time spread of emerging SARS-CoV-2 variants with possible implications for public health and immunization strategies.

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.

Early genomic detection of SARS-CoV-2 P.1 variant in Northeast Brazil

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. Article Summary LineActive genomic surveillance of SARS- CoV-2 suspected cases from recent travelers reveals the circulation of the P1 variant of concern in Bahia state, Northeast Brazil.

Monitoramento da qualidade da amostra para análise de RT-PCR da Covid-19 no LACEN-BA / Sample quality monitoring for Covid-19 RT-PCR analysis at LACEN-BA / Monitoreo de la calidad de la muestra para el análisis Covid-19 RT-PCR en LACEN-BA

A pandemia da Covid-19 tem se apresentado como um dos maiores desafios sanitários desse século. Em dezembro de 2019, na China, o agente etiológico foi identificado como um novo coronavírus, nomeado SARS-CoV-2. No Brasil, o primeiro caso confirmado da Covid-19 ocorreu em fevereiro de 2020 e, no mês seguinte, a Secretaria da Saúde do Estado da Bahia (Sesab) confirmou o primeiro caso na Bahia.O Laboratório Central de Saúde Pública Prof. Gonçalo Moniz (Lacen-BA) centralizou o diagnóstico laboratorial para confirmação dos casos suspeitos de Covid-19 dos 417 municípios baianos, utilizando a técnica de RT-PCR. Este estudo tem como objetivo identificar e analisar as não conformidades das amostras suspeitas de Covid-19 encaminhadas ao Lacen-BA. Trata-se de um estudo descritivo, cujos dados foram obtidos por meio de consulta aos relatórios de amostras e exames em desacordo, disponíveis no sistema Gerenciador de Ambiente Laboratorial (GAL), gerados mensalmente, no período de abril a outubro de 2020. Para garantir a qualidade das amostras recebidas, foram definidos critérios de aceitação/rejeição de amostras e criado o formulário de notificação de não conformidades, assegurando a rastreabilidade das amostras de Covid-19. Através de relatórios diários do sistema GAL, selecionou-se os nove principais motivos de não conformidades, sendo o mais frequente "requisição cancelada pela gerência do GAL devido à expiração do prazo de triagem", com 72,8% dos registros. A inserção da padronização de processos na etapa pré-analítica permite trabalhar com segurança, garantindo a qualidade da amostra a ser processada e, consequentemente, um resultado fidedigno, dentro do prazo acordado.

The Covid-19 pandemic is one of the greatest health challenges of this century. In December 2019, in China, the etiologic agent was identified as a new coronavirus, named SARS-CoV-2. In Brazil, the first case of Covid-19 was confirmed in February 2020 and, in the following month, the Department of Health of the State of Bahia (Sesab) confirms the first case in the state. The Central Public Health Laboratory Prof. Gonçalo Moniz (Lacen/BA) centralized the laboratory diagnosis to confirm the suspected cases of Covid-19 of the 417 municipalities of the state, using the RT-PCR technique. This study aims at identifying and analyzing the non-conformities of the suspected samples of Covid-19 sent to Lacen-BA. This is a descriptive study whose data were obtained by consulting there reports of samples and exams in disagreement, available in the Laboratory Environment Manager (GAL) system, generated monthly, from April to October,2020. To guarantee the quality of the samples received, acceptance / rejection criteria for the samples were defined and a form for the notification of non-conformities was created, ensuring the traceability of the Covid-19 samples. Daily reports from the Laboratory Environment Manager system based the selection of nine main reasons for non-conformities, among which "requisition canceled by the management of the GAL due to the expiration of the screening period" was present in 72.8% of the records. Process standardization, in the pre-analytical stage, allows working with security, guaranteeing the quality of the sample to be processed and a reliable result within the established period.

La pandemia del Covid-19 se ha presentado como uno de los desafíos de salud más grandes de este siglo. En diciembre de 2019, China identificó el agente etiológico del nuevo coronavirus llamado SARS-CoV-2. En Brasil, se notificó el primer caso del Covid-19 en febrero de 2020 y, al mes siguiente, la Secretaría de Salud del Estado de Bahía (Sesab) confirmaba el primer caso en Bahía. El Laboratorio Central de Salud Pública Prof. Gonçalo Moniz (Lacen/BA) centralizó el diagnóstico de laboratorio para confirmar los casos sospechosos del coronavirus de los 417 municipios de Bahía, mediante la técnica de RT-PCR. Este estudio tiene como objetivo identificar y analizar las no conformidades de las muestras sospechosas del Covid-19 enviadas al Lacen/BA. Este es un estudio descriptivo cuyos datos se obtuvieron consultando los informes de muestras y pruebas en desacuerdo disponibles en el sistema Laboratory Environment Manager (GAL), generados mensualmente, de abril a octubre/2020. Con el fin de garantizar la calidad de las muestras recibidas, se definieron criterios de aceptación/rechazo de las muestras y se elaboró un formulario para la notificación de no conformidades, asegurando la trazabilidad de las muestras. Por medio de informes diarios del sistema Laboratory Environment Manager, se seleccionaron nueve principales causas de no conformidades, de las cuales la más frecuente fue "requisición cancelada por la gerencia del GAL por vencimiento del período de cribado" con el 72,8% de los registros. La inserción de la estandarización de procesos en la etapa preanalítica permite trabajar con seguridad, garantizando la calidad de la muestra que procesar y, en consecuencia, un resultado confiable dentro del plazo acordado.

Experiência do laboratório central de Saúde Pública da Bahia no enfrentamento da pandemia da Covid-19 / Experience of the central laboratory of Public Health of Bahia in coping with the Covid-19 pandemic / Experiencia del laboratorio central de Salud Pública de Bahía en el afrontamiento de la pandemia Covid-19

A Covid-19 é uma doença infecciosa causada pelo novo coronavírus, denominado SARS-CoV-2, que causou um surto de pneumonia viral incomum em pacientes em Wuhan, na China, no final do ano de 2019. O vírus se disseminou pelo mundo em grandes proporções, atingindo o status epidemiológico de pandemia. Diante desse cenário, que afetou toda a Federação brasileira, o Laboratório Central de Saúde Pública Professor Gonçalo Moniz (Lacen-BA) tem exercido papel fundamental no diagnóstico da Covid-19 e na vigilância genômica do SARS-CoV-2. Nesse sentido, este estudo tem como objetivo descrever as estratégias implementadas pelo Lacen-BA para ampliar a capacidade diagnóstica e atender a demanda da rede SUS-BA no contexto da pandemia da Covid-19. Trata-se de um estudo descritivo-observacional, orientado por um modelo lógico sustentado em quatro dimensões: parque tecnológico, metodologias analíticas, descentralização do exame e monitoramento de indicadores de resultados. As iniciativas de gestão possibilitaram ampliação da capacidade instalada e operacional, mediante modernização da estrutura física, renovação do parque tecnológico, reorganização dos fluxos e processos de trabalho, aporte de novas tecnologias analíticas e estruturação de dashboard para monitorar indicadores e subsidiar o processo decisório. O Lacen-BA, enquanto coordenador da Rede Estadual de Laboratórios de Saúde Pública e sistema de apoio da Rede de Atenção à Saúde (RAS), constitui-se então em estruturas policêntricas essenciais para o diagnóstico descentralizado e regionalizado da Covid-19, contribuindo para a integração sistêmica das ações e serviços no contexto da regionalização da saúde, de modo a garantir a universalidade do acesso e integralidade dos cuidados aos usuários do SUS.

Covid-19 is an infectious disease caused by the new coronavirus, called SARS-CoV-2, which caused an outbreak of unusual viral pneumonia in patients in Wuhan, China, at the end of 2019 and spread across the world, in large proportions, reaching the epidemiological status of a pandemic. Considering this epidemiological scenario that affected the entire Brazilian Federation, the Central Laboratory of Public Health Professor Gonçalo Moniz (Lacen-BA) has played a fundamental role in the diagnosis of Covid-19 and the genomic surveillance of SARS-CoV-2. In this sense, this study aims at describing the strategies implemented by Lacen-BA to expand the diagnostic capacity to meet the demand of the SUS-BA network, in the context of the Covid-19 pandemic. This is a descriptive-observational study, guided by a logical model based on four dimensions: technological park, analytical methodologies, decentralization of the exam and monitoring of result indicators. The management initiatives enabled the expansion of the installed and operational capacity by modernizing the physical structure, renewing the technological park, reorganizing workflows and processes, providing new analytical technologies, structuring the dashboard to monitor indicators and support the decision-making process. The Lacen-BA, as coordinator of the State Public Health Laboratory Network and support system of the Health Care Network (RAS), constitutes essential polycentric structures for the decentralized and regionalized diagnosis of Covid-19, which can contribute to the systemic integration of actions and services in the context of regionalization of health to guarantee the universality of access and comprehensive care to SUS users.

El covid-19 es una enfermedad infecciosa causada por el nuevo coronavirus, llamado SARS-CoV-2, que provocó un brote de neumonía viral inusual en pacientes en Wuhan, China, a fines de 2019, y que se extendió por el mundo, en grandes proporciones hasta alcanzar el estado epidemiológico de pandemia. Ante este escenario epidemiológico que afectó a Brasil, el Laboratorio Central de Salud Pública Profesor Gonçalo Moniz (Lacen-BA) ha jugado un papel fundamental en el diagnóstico del covid-19 y la vigilancia genómica del SARS-CoV-2. En este sentido, este estudio tiene como objetivo describir las estrategias implementadas por Lacen-BA para ampliar la capacidad de diagnóstico y atender la demanda de la red SUS-BA, en el contexto de la pandemia del Covid-19. Este estudio es descriptivo-observacional, guiado por un modelo lógico con base en cuatro dimensiones: parque tecnológico, metodologías analíticas, descentralización del examen y seguimiento de indicadores de resultado. Las iniciativas de gestión permitieron ampliar la capacidad instalada y operativa al modernizar la estructura física, renovar el parque tecnológico, reorganizar los flujos y procesos de trabajo, brindar nuevas tecnologías analíticas y estructuración del cuadro de mando para monitorear indicadores, y apoyar la toma de decisiones. Lacen-BA, como coordinador de la Red Estadual de Laboratorios de Salud Pública y sistema de apoyo de la Red de Atención a la Salud (RAS), constituye estructuras policéntricas imprescindibles para el diagnóstico descentralizado y regionalizado del Covid-19, que pueden contribuir a la integración sistémica de acciones y servicios en el contexto de la regionalización de la salud, a fin de garantizar la universalidad del acceso y la atención integral a los usuarios del SUS.

Yellow fever transmission in non-human primates, Bahia, Northeastern Brazil.

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.