ABSTRACT
INTRODUCTION: This epidemiological household survey aimed to estimate the prevalence of the current and past SARS-CoV-2 infections in Ribeirão Preto, a municipality of southeast Brazil. METHODS: The survey was conducted in two phases using a clustered sampling scheme. The first phase spanned May 1-3 and involved 709 participants. The second phase spanned June 11-14, 2020, and involved 646 participants. RESULTS: During the first phase, RT-PCR performed on nasopharyngeal swabs was positive at 0.14%. The serological tests were positive in 1.27% of the patients during the first phase and 2.79% during the second phase. People living in households with more than five members had a prevalence of 10.83% (95%CI: 1.58-74.27) higher than those living alone or with someone other. Considering the proportion of the positive serological test results with sex and age adjustments, approximately 2.37% (95%CI: 1.32-3.42) of the population had been cumulatively infected by mid-June 2020, which is equivalent to 16,670 people (95%CI: 9,267-24,074). Considering that 68 deaths from the disease in the residents of the city had been confirmed as at the date of the second phase of the survey, the infection fatality rate was estimated to be 0.41% (95%CI: 0.28-0.73). Our results suggest that approximately 88% of the cases of SARS-CoV-2 infection at the time of the survey were not reported to the local epidemiological surveillance service. CONCLUSIONS: The findings of this study provide in-depth knowledge of the COVID-19 pandemic in Brazil and are helpful for the preventive and decision-making policies of public managers.
Subject(s)
COVID-19 , SARS-CoV-2 , Brazil/epidemiology , Humans , Pandemics , PrevalenceABSTRACT
The Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of an unprecedented worldwide pandemic. Brazil demonstrates one of the highest numbers of confirmed SARS-CoV-2 cases, and São Paulo State is the epicenter of the pandemics in the country. Nevertheless, little is known about the SARS-CoV-2 circulation in other cities in the State than São Paulo city. The objective of this study was to analyze phylogenetically SARS-CoV-2 strains circulating in city of Ribeirão Preto at the beginning of the pandemic and during the actual second wave. Twenty-nine nasopharyngeal SARS-CoV-2 RNA positive samples were sequenced by nanopore technology (18 obtained at the initial period of the pandemic and 11 during the second wave) and analyzed them phylogenetically. The performed analysis demonstrated that the majority of the strains obtained in the initial period of the pandemic in Ribeirão Preto belonged mainly to the B1.1.33 lineage (61.1%), but B.1.1 (27.8%) and B.1.1.28 (11.1%) lineages were also identified. In contrast, the second wave strains were composed exclusively by the Brazilian variant of concern (VOC) P.1 (91%) and P.2 (9%) lineages. The obtained phylogenetic results were suggestive of successive SARS-CoV-2 lineage substitution in this Brazilian region by the P.1 VOC. The performed study examines the SARS-CoV-2 genotypes in Ribeirão Preto city via genomic surveillance data. The obtained findings can contribute for continuous long-term genomic surveillance of SARS-CoV-2 due to the accelerated dynamics of viral lineage substitution, predict further waves and examine lineage behavior during SARS-CoV-2 vaccination.