ABSTRACT
O relato descreveu o primeiro curso presencial visando capacitar profissionais de saúde pública na realização de vigilância genômica em tempo real, durante períodos pandêmicos. Relato de experiência sobre um curso teórico-prático com foco em pesquisa e vigilância genômica, incluindo tecnologias de sequenciamento móvel, bioinformática, filogenética e modelagem epidemiológica. O evento contou com 162 participantes e foi o primeiro grande treinamento presencial realizado durante a epidemia de covid-19 no Brasil. Não foi detectada infecção pelo SARS-CoV-2 ao final do evento em nenhum participante, sugerindo a segurança e efetividade de todas as medidas de segurança adotadas. Os resultados do evento sugerem que é possível executar capacitação profissional com segurança durante pandemias, desde que seguidos todos os protocolos de segurança.
The objective of this report was to describe the first face-to-face course aimed at training public health professionals in performing real-time genomic surveillance during the pandemic period. Experience report on a theoretical-practical course focusing on genomic research and surveillance, including mobile sequencing technologies, bioinformatics, phylogenetics and epidemiological modeling. There were 162 participants in the event and it was the first major face-to-face training course conducted during the COVID-19 epidemic in Brazil. No cases of SARS-CoV-2 infection was detected among the participants at the end of the event, suggesting the safety and effectiveness of all safety measures adopted. The results of this experience suggest that it is possible to conduct professional training safely during pandemics, as long as all safety protocols are followed.
Este estudio tuvo como objetivo describir el primer curso presencial para capacitar a los profesionales de la salud pública para llevar a cabo la vigilancia genómica en tiempo real durante los períodos de pandemia. Este es un informe de experiencia en un curso teórico-práctico centrado en la investigación y vigilancia genómica, que incluye secuenciación móvil, bioinformática, filogenética y tecnologías de modelado epidemiológico. Este evento contó con la asistencia de 162 participantes y fue la primera gran capacitación presencial realizada durante la epidemia de COVID-19 en Brasil. No se detectó infección por SARS-CoV-2 al final del evento en ningún participante, lo que sugiere la seguridad y efectividad de todas las medidas de seguridad adoptadas. Por lo tanto, los resultados del evento sugieren que es posible realizar entrenamientos profesionales de manera segura durante pandemias, siempre y cuando se sigan todos los protocolos de seguridad.
Subject(s)
Humans , Male , Female , Technology Transfer , Computational Biology/education , Health Human Resource Training , Professional Training , COVID-19/epidemiology , Brazil/epidemiology , Public Health , Health Personnel/education , Genomics/education , Epidemics , SARS-CoV-2/isolation & purification , COVID-19/geneticsABSTRACT
BACKGROUND In Brazil, the yellow fever virus (YFV) is maintained in a sylvatic cycle involving wild mosquitoes and non-human primates (NHPs). The virus is endemic to the Amazon region; however, waves of epidemic expansion reaching other Brazilian states sporadically occur, eventually causing spillovers to humans. OBJECTIVES To report a surveillance effort that led to the first confirmation of YFV in NHPs in the state of Minas Gerais (MG), Southeast region, in 2021. METHODS A surveillance network was created, encompassing the technology of smartphone applications and coordinated actions of several research institutions and health services to monitor and investigate NHP epizootics. FINDINGS When alerts were spread through the network, samples from NHPs were collected and YFV infection confirmed by reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and genome sequencing at an interval of only 10 days. Near-complete genomes were generated using the Nanopore MinION sequencer. Phylogenetic analysis indicated that viral genomes were related to the South American genotype I, clustering with a genome detected in the Amazon region (state of Pará) in 2017, named YFVPA/MG sub-lineage. Fast YFV confirmation potentialised vaccination campaigns. MAIN CONCLUSIONS A new YFV introduction was detected in MG 6 years after the beginning of the major outbreak reported in the state (2015-2018). The YFV strain was not related to the sub-lineages previously reported in MG. No human cases have been reported, suggesting the importance of coordinated surveillance of NHPs using available technologies and supporting laboratories to ensure a quick response and implementation of contingency measures to avoid YFV spillover to humans.
ABSTRACT
INTRODUÇÃO: Os Arbovírus transmitidos por mosquitos, como Dengue (DENV),Chikungunya (CHIKV), Zika (ZIKV) e Febre Amarela (YFV), são considerados importantes desafios para a saúde pública. Além do cenário causado pelo DENV, responsável por epidemias há décadas e endêmico em quase todo o país, a introdução do CHIKV e do ZIKV no Brasil traz grande preocupação. Os Arbovírus são transmitidos por mosquitos do gênero Aedes,particularmente Ae. aegypti e suas doenças relacionadas resultam em aumento dos custos financeiros associados ao diagnóstico e ao tratamento. MATERIAIS E MÉTODOS: Para facilitar o diagnóstico e o desenvolvimento de estratégias de prevenção e tratamento de forma eficiente, foram desenvolvidas ferramentas de bioinformática capazes de genotipar esses vírus baseando-se em modelos evolutivos apropriados de forma automática, precisa e rápida. Nesta plataforma, sequências destes arbovírus são selecionadas no Genbank por meio de um Sistema Configurável Automático de Mineração (SCAM), para obter um conjunto eficiente de sequências referências que foram utilizadas no desenvolvimento das ferramentas.RESULTADOS: Este processo envolveu o alinhamento das sequências referências seguidas por reconstruções de árvores filogenéticas. Para atribuir os genótipos às sequências dos usuários, a ferramenta analisa as sequências uma a uma, através da identificação pelo programa BLAST, seguido pelo alinhamento com o programa ClustalW e posteriormente com a reconstrução filogenética utilizando o programa PAUP*. A classificação genotípica ocorre quando as sequencias do usuário se agrupam filogeneticamente com o bootstrap igual ou superior a 70%. CONCLUSÃO: Essas novas ferramentas de genotipagem automáticas fornecem uma classificação precisa para esses arbovírus mesmo quando as sequências do usuário são oriundas de tecnologias de última geração (NGS), lendo, portanto, fragmentos curtos.
INTRODUCION: Mosquito-borne Arboviruses such as Dengue (DENV), Chikungunya (CHIKV), Zika (ZIKV) and Yellow Fever (YFV) are considered major public health challenges. In addition to the scenario caused by DENV, which has been responsible for epidemics for decades and endemic throughout most of the country, the introduction of CHIKV and ZIKV in Brazil is a major concern. Arboviruses are transmitted by mosquitoes of the genus Aedes, particularly Ae. Aegypti and its related diseases result in increased financial costs associated with diagnosis and treatment. MATERIAL AND METHODS: To facilitate the diagnosis, prevention and treatment strategies efficiently, bioinformatics tools have been developed for the genotyping of these viruses based on appropriate evolutionary models in na automatically, accurately and rapidly manner. In this platform, sequences of these arboviruses are selected in Genbank by means of an Automatic Mining Configurable System (SCAM), to obtain an efficient set of reference sequences that were used in the development of the tools. RESULT: This process involved the alignment of the reference sequences followed by phylogenetic tree reconstructions. To assign the genotypes to the user sequences, the tool analyzes the sequences one by one, through identification by the BLAST program, followed by the alignment with the ClustalW program and later with the phylogenetic reconstruction using the PAUP* program. The genotypic classification occurs when the user sequences are grouped phylogenetically with the bootstrap equal to or greater than 70%. CONCLUSION: These new automatic genotyping tools provide an accurate classification for these arboviruses even when the user sequences are derived from next-generation technologies (NGS), thus reading short fragments.