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Introducción: La cuantificación de SARS-CoV-2 en aguas residuales es una herramienta que permite determinar la tendencia de la circulación viral en un área geográfica determinada. Objetivo: Cuantificar el virus SARS-CoV-2 en 15 plantas de tratamiento de aguas residuales en diferentes ciudades de Chile para establecer una comparación con las variables de: i) casos activos por cada 100.000 habs.; ii) positividad diaria (casos nuevos); y iii) fases del plan de confinamiento. Metodología: SARS-CoV-2 se concentró a partir de muestras de aguas residuales. Para obtener el número de genomas del virus por litro se realizó una cuantificación absoluta utilizando qRT-PCR. Resultados: Entre enero y junio de 2021 se procesaron 253 muestras, siendo todas positivas para la presencia del virus. Asimismo, se logró determinar que la tasa de casos activos por cada 100.000 habs. es la variable que mejor se ajusta a las tendencias obtenidas con la cuantificación de la carga viral en las aguas residuales. Conclusiones: La cuantificación de SARS-CoV-2 en las aguas residuales de manera permanente es una herramienta eficiente para determinar la tendencia del virus en un área geográfica determinada y, en conjunto con una vigilancia genómica, puede constituirse en una vigilancia centinela ideal generando alertas sobre futuros brotes.
Background: The quantification of SARS-CoV-2 in wastewater is a tool that allows determining the trend of viral circulation in a particular geographical area. Aim: To quantify the SARS-CoV-2 virus in 15 wastewater treatment plants in different Chilean cities to establish a comparison with the variables of: i) Active cases per 100,000 inhabitants; ii) daily positivity (novel cases); and iii) phases of the lockdown strategy. Methods: SARS-CoV-2 was concentrated from wastewater samples. To obtain the number of virus genomes per liter, absolute quantification was performed using qRT-PCR. Results: Between January and June 2021, 253 samples were processed, all of which were positive for the presence of the virus. Likewise, it will be determined that the rate of active cases per 100,000 inhabitants is the variable that best fits the trends obtained with the quantification of the viral load in wastewater. Conclusions: The quantification of SARS-CoV-2 in wastewater as a continuous strategy is an efficient tool to determine the trend of the viral circulation in a delimited geographical area and, combined with genomic surveillance, it can constitute an ideal sentinel surveillance alert on future outbreaks.
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BACKGROUND The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants has become a major concern contributing to increased morbidity and mortality worldwide. OBJECTIVES Here we describe the replacement of the Gamma variant of concern (VOC) with Delta in the western Brazilian Amazon. METHODS In this study, we analysed 540 SARS-CoV-2 positive samples determined by qualitative real-time RT-PCR selected in the state of Rondônia between June and December 2021. The positive cohort was sequenced through next-generation sequencing (NGS) and each sample was quantified using real-time RT-qPCR, the whole genome sequence was obtained, SARS-CoV-2 lineages were classified using the system Pango and the maximum likelihood (ML) method was used to conduct phylogenetic analyses. FINDINGS A total of 540 high-quality genomes were obtained, where the Delta VOC showed the highest prevalence making up 72%, with strain AY.43 being the most abundant, while the Gamma VOC was present in 28%, where the P.1 strain was the most frequent. In this study population, only 32.96% (178/540) had completed the vaccination schedule. MAIN CONCLUSIONS This study highlighted the presence of Gamma and Delta variants of SARS-CoV-2 in RO. Furthermore, we observed the replacement of the Gamma VOC with the Delta VOC and its lineages.
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ABSTRACT Monkeypox virus (MPXV), a zoonotic virus endemic to the African continent, has been reported in 33 non-endemic countries since May 2022. We report an almost complete genome of the first confirmed case of MPXV in Brazil. Shotgun metagenomic sequencing was completed in 18 hours, from DNA extraction to consensus sequence generation.
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RESUMEN Las vacunas son productos biológicos que contienen antígenos que buscan generar protección contra a la exposición real de un agente patógeno. En cuanto a su importancia, hacen parte de las intervenciones más costo-efectivas en salud pública, siendo superadas únicamente por el agua potable. A grandes rasgos, podemos dividir las vacunas en vivas atenuadas e inactivadas; no obstante, el nuevo coronavirus ha producido la emergencia de plataformas innovadoras que utilizan mecanismos intracelulares y moleculares con el mismo objetivo de generar inmunidad. Se realizó una búsqueda sistemática de la literatura utilizando las bases de datos electrónicas Pubmed, Scopus y Web of Science. Todos los tipos de diseño de estudio fueron considerados, sin embargo, se prefierieron aquellos redactados en idioma inglés o español. Se hace una revisión de la literatura presente sobre las plataformas existentes para generar inmunidad frente al coronavirus SARS-CoV-2 y se desarrolla cada una según su ruta y forma de acción en aquellas basadas en subunidades proteicas, vector viral recombinante, ácidos nucleicos, virus inactivados, partículas virales y virus vivos atenuados. Los mecanismos por los cuales dichas vacunas generan inmunogenicidad son diferentes, no obstante, la constante inserción de mutaciones por parte del virus sigue siendo un objeto de interés y preocupación por los investigadores.
ABSTRACT Vaccines are biological products containing antigens that aim to generate protection against real exposure to an infectious pathogen. They constitute the most cost-effective interventions in public health, being surpassed only by drinking water. Generally speaking, we can divide the vaccines into live attenuated and inactive; However, the new coronavirus has produced innovative platforms that use intracellular and molecular mechanisms with the same objective of generating immunity. A systematic literature search was carried out using the PUBMED, SCOPUS, and Web of Science electronic databases. All types of study design were selected, those written in English or Spanish were prioritized. We reviewed the existing platforms to generate immunity against the SARS-CoV-2 coronavirus. Each one is developed according to its route and form of action, and can be classified as protein subunits, recombinant viral vector, nucleic acids, inactivated viruses, viral particles, and live attenuated viruses. The mechanisms by which these vaccines generate immunogenicity are different; however, the constant insertion of mutations by the virus remains an object of interest and concern for researchers.
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BACKGROUND Despite efforts to mitigate the impact of dengue virus (DENV) epidemics, the virus remains a public health problem in tropical and subtropical regions around the world. Most DENV cases in the Americas between January and July 2019 were reported in Brazil. São Paulo State in the southeast of Brazil has reported nearly half of all DENV infections in the country. OBJECTIVES To understand the origin and dynamics of the 2019 DENV outbreak. METHODS Here using portable nanopore sequencing we generated20 new DENV genome sequences from viremic patients with suspected dengue infection residing in two of the most-affected municipalities of São Paulo State, Araraquara and São José do Rio Preto. We conducted a comprehensive phylogenetic analysis with 1,630 global DENV strains to better understand the evolutionary history of the DENV lineages that currently circulate in the region. FINDINGS The new outbreak strains were classified as DENV2 genotype III (American/Asian genotype). Our analysis shows that the 2019 outbreak is the result of a novel DENV lineage that was recently introduced to Brazil from the Caribbean region. Dating phylogeographic analysis suggests that DENV2-III BR-4 was introduced to Brazil in or around early 2014, possibly from the Caribbean region. MAIN CONCLUSIONS Our study describes the early detection of a newly introduced and rapidly-expanding DENV2 virus lineage in Brazil.