ABSTRACT
Different approaches are in use to improve our knowledge about the causative agent of coronavirus disease (COVID-19). Cell culture-based methods are the better way to perform viral isolation, evaluate viral infectivity, and amplify the virus. Furthermore, next-generation sequencing (NGS) have been essential to analyze a complete genome and to describe new viral species and lineages that have arisen over time. Four naso-oropharyngeal swab samples, collected from April to July of 2020, were isolated and sequenced aiming to produce viral stocks and analyze the mutational profile of the found lineage. B.1.1.33 was the lineage detected in all sequences. Although the samples belong to the same lineage, it was possible to evaluate different mutations found including some that were first described in these sequences, like the S:H655Y and T63N. The results described here can help to elicit how the pandemic started to spread and how it has been evolving in south Brazil.
Subject(s)
COVID-19 , SARS-CoV-2 , Brazil , Genome, Viral , Humans , Mutation , Phylogeny , SARS-CoV-2/geneticsABSTRACT
Due to the high rate of transmissibility, Brazil became the new COVID-19 outbreak epicenter and, since then, is being monitored to understand how SARS-CoV-2 mutates and spreads. We combined genomic and structural analysis to evaluate genomes isolated from different regions of Brazil and show that the most prevalent mutations were located in the S, N, ORF3a and ORF6 genes, which are involved in different stages of viral life cycle and its interaction with the host cells. Structural analysis brought to light the positions of these mutations on protein structures, contributing towards studies of selective structure-based drug discovery and vaccine development.
Subject(s)
COVID-19/genetics , Mutation/genetics , SARS-CoV-2/genetics , Viral Proteins/genetics , Brazil , Genome, Viral , Genomics , Humans , SARS-CoV-2/pathogenicity , Severity of Illness IndexABSTRACT
The first case of COVID-19 was reported in China in December 2019, and, as the virus has spread worldwide, the World Health Organization declared it a pandemic. Estimates on the number of COVID-19 cases do not reflect it real magnitude as testing is limited. Population based data on the proportion of the population with antibodies is relevant for planning public health policies. We aim to assess the prevalence of SARS-CoV-2 antibodies, presence of signs and symptoms of COVID-19, and adherence to isolation measures. A random sample comprising 133 sentinel cities from all states of the country will be selected. Three serological surveys, three weeks apart, will be conducted. The most populous municipality in each intermediate region of the country, defined by the Brazilian Institute of Geography and Statistics, was chosen as sentinel city. In each city, 25 census tracts will be selected, and 10 households will be systematically sampled in each tract, totaling 33,250 participants. In each household, one inhabitant will be randomly selected to be interviewed and tested for antibodies against SARS-CoV-2, using WONDFO SARS-CoV-2 Antibody Test. By evaluating a representative sample of Brazilian sentinel sites, this study will provide essential information for the design of health policies. Resumo O COVID-19 é causado pelo vírus SARS-CoV-2, sendo o primeiro caso relatado na China em dezembro de 2019. O vírus se espalhou pelo mundo, levando a Organização Mundial da Saúde a declarar uma pandemia. As estimativas do número de casos de COVID-19 não refletem sua magnitude real, pois os testes são limitados em muitos países. Dados populacionais sobre a proporção da população com anticorpos são relevantes para o planejamento de políticas públicas de saúde. Nosso objetivo é avaliar a prevalência de anticorpos SARS-CoV-2, a presença de sinais e de sintomas de COVID-19 e a adesão a medidas de isolamento. Uma amostra aleatória composta por 133 cidades sentinelas de todos os estados do país será selecionada. Serão realizados três levantamentos sorológicos, com três semanas de intervalo. Em cada cidade, serão selecionados 25 setores censitários e 10 famílias serão amostradas aleatoriamente em cada setor. Em cada domicílio, um habitante será selecionado aleatoriamente para ser entrevistado e testado para anticorpos contra SARS-CoV-2, usando o Teste de Anticorpo WONDFO SARS-CoV-2, que foi validado antes do trabalho de campo. Ao avaliar uma amostra representativa dos locais sentinela ao longo do tempo, este estudo fornecerá informações essenciais para o desenho de políticas de saúde.
ABSTRACT
The first case of COVID-19 was reported in China in December 2019, and, as the virus has spread worldwide, the World Health Organization declared it a pandemic. Estimates on the number of COVID-19 cases do not reflect it real magnitude as testing is limited. Population based data on the proportion of the population with antibodies is relevant for planning public health policies. We aim to assess the prevalence of SARS-CoV-2 antibodies, presence of signs and symptoms of COVID-19, and adherence to isolation measures. A random sample comprising 133 sentinel cities from all states of the country will be selected. Three serological surveys, three weeks apart, will be conducted. The most populous municipality in each intermediate region of the country, defined by the Brazilian Institute of Geography and Statistics, was chosen as sentinel city. In each city, 25 census tracts will be selected, and 10 households will be systematically sampled in each tract, totaling 33,250 participants. In each household, one inhabitant will be randomly selected to be interviewed and tested for antibodies against SARS-CoV-2, using WONDFO SARS-CoV-2 Antibody Test. By evaluating a representative sample of Brazilian sentinel sites, this study will provide essential information for the design of health policies. Resumo O COVID-19 é causado pelo vírus SARS-CoV-2, sendo o primeiro caso relatado na China em dezembro de 2019. O vírus se espalhou pelo mundo, levando a Organização Mundial da Saúde a declarar uma pandemia. As estimativas do número de casos de COVID-19 não refletem sua magnitude real, pois os testes são limitados em muitos países. Dados populacionais sobre a proporção da população com anticorpos são relevantes para o planejamento de políticas públicas de saúde. Nosso objetivo é avaliar a prevalência de anticorpos SARS-CoV-2, a presença de sinais e de sintomas de COVID-19 e a adesão a medidas de isolamento. Uma amostra aleatória composta por 133 cidades sentinelas de todos os estados do país será selecionada. Serão realizados três levantamentos sorológicos, com três semanas de intervalo. Em cada cidade, serão selecionados 25 setores censitários e 10 famílias serão amostradas aleatoriamente em cada setor. Em cada domicílio, um habitante será selecionado aleatoriamente para ser entrevistado e testado para anticorpos contra SARS-CoV-2, usando o Teste de Anticorpo WONDFO SARS-CoV-2, que foi validado antes do trabalho de campo. Ao avaliar uma amostra representativa dos locais sentinela ao longo do tempo, este estudo fornecerá informações essenciais para o desenho de políticas de saúde.
ABSTRACT
The first case of COVID-19 was reported in China in December 2019, and, as the virus has spread worldwide, the World Health Organization declared it a pandemic. Estimates on the number of COVID-19 cases do not reflect it real magnitude as testing is limited. Population based data on the proportion of the population with antibodies is relevant for planning public health policies. We aim to assess the prevalence of SARS-CoV-2 antibodies, presence of signs and symptoms of COVID-19, and adherence to isolation measures. A random sample comprising 133 sentinel cities from all states of the country will be selected. Three serological surveys, three weeks apart, will be conducted. The most populous municipality in each intermediate region of the country, defined by the Brazilian Institute of Geography and Statistics, was chosen as sentinel city. In each city, 25 census tracts will be selected, and 10 households will be systematically sampled in each tract, totaling 33,250 participants. In each household, one inhabitant will be randomly selected to be interviewed and tested for antibodies against SARS-CoV-2, using WONDFO SARS-CoV-2 Antibody Test. By evaluating a representative sample of Brazilian sentinel sites, this study will provide essential information for the design of health policies.