Spatial, spatio-temporal, and origin-destination flow analyses of patients with severe acute respiratory syndrome hospitalized for COVID-19 in Southeastern Brazil, 2020-2021

ABSTRACT Brazil experienced one of the fastest increasing numbers of coronavirus disease (COVID-19) cases worldwide. The Sao Paulo State (SPS) reported a high incidence, particularly in Sao Paulo municipality. This study aimed to identify clusters of incidence and mortality of hospitalized patients with severe acute respiratory syndrome for COVID-19 in the SPS, in 2020-2021, and describe the origin flow pattern of the cases. Cases and mortality risk area clusters were identified through different analyses (spatial clusters, spatio-temporal clusters, and spatial variation in temporal trends) by weighting areas. Ripley's K12-function verified the spatial dependence between the cases and infrastructure. There were 517,935 reported cases, with 152,128 cases resulting in death. Of the 470,441 patients hospitalized and residing in the SPS, 357,526 remained in the original municipality, while 112,915 did not. Cases and death clusters were identified in the Sao Paulo metropolitan region (SPMR) and Baixada Santista region in the first study period, and in the SPMR and the Campinas, Sao Jose do Rio Preto, Barretos, and Sorocaba municipalities during the second period. We highlight the priority areas for control and surveillance actions for COVID-19, which could lead to better outcomes in future outbreaks.

SARS-CoV-2 reinfection in a healthcare professional in inner Sao Paulo during the first wave of COVID-19 in Brazil

Coronavirus Disease 2019 pandemic remains a threat to public health. We report 2 cases of Coronavirus Disease 2019 infection in the same healthcare professional in Brazil. Genomic analysis identified that primoinfection was caused by the endemic lineage B.1.1.33 while reinfection by the lineage B.1.1.44, a lineage with an additional V1176F mutation in S protein.

SARS-CoV-2 reinfection: report of two cases in Southeast Brazil

From February 26, 2020 to March 11, 2021, coronavirus disease 2019 (COVID-19) pandemic resulted in 11,439,558 cases and 277,102 deaths in Brazil. Among them, 2,195,130 cases and 63,965 deaths occurred in Sao Paulo State, Southeast Brazil. The recent emergence and rise of new variants of SARS-CoV-2 is of concern because of their higher transmissibility and possible association with more severe disease. Cases of SARS-CoV-2 reinfections have been described since December 2020 in Brazil. This report describes two cases of COVID-19 reinfection, that occurred five and six months after the first infection, during the second wave of the pandemic in Sao Paulo State. Both patients presented mild symptoms in the two COVID-19 episodes and different lineages of SARS-CoV-2 were identified: B.1.1.33 and B.1.1.28 lineages in case 1 and B1.1.128 and P. 2 lineages in case 2.

Epidemiological characteristics of influenza-like illness outbreaks in long-term care facilities of the state of São Paulo, Brazil / Características epidemiológicas dos surtos de síndrome gripal em instituições de longa permanência para idosos no estado de São Paulo, Brasil

Long-term care facilities for older adults present a high risk of outbreaks since they concentrate often more frail and vulnerable individuals. OBJECTIVE: To describe the epidemiological characteristics of influenza-like illness outbreaks and cases among older people in long-term care facilities in the state of São Paulo, Brazil. METODS: The analysis was performed through an exploratory and descriptive approach, with records from the outbreak module of the National System of Notifiable Diseases between January 2020 and June 2021. RESULTS: Outbreaks of influenza-like illness in this department represented 24.93% of all notifications. The highest concentration was seen in the state capital and metropolitan area. A total of 1 018 confirmed outbreaks were observed, involving 6 110 cases and 1 240 deaths among older people. Of these cases, 71.67% were confirmed for coronavirus disease 19 (COVID-19), 12.77% for the influenza virus, and 15.56% for other respiratory viruses. The percentages regarding death outcomes were similar, with a 20.29% lethality of influenza-like illness. Within the studied group, the older adults were the most affected. A statistical difference was observed between cases and deaths. CONCLUSIONS: Owing to the current scenario and the known vulnerabilities of these facilities, there is an urgent need for joint and articulated action by various administrative levels in order to minimize the devastating effects of influenza-like illness outbreaks (especially of COVID19) in older adults at long-term care homes. The strengthening of information systems and their interoperability are considered of utmost importance in order to improve the quality of information on outbreaks, which is essential during a pandemic.

Instituições de longa permanência para idosos são locais que apresentam um alto risco de surtos epidêmicos, visto que concentram indivíduos, frequentemente mais frágeis e vulneráveis. OBJETIVO: Descrever as características epidemiológicas de surtos de síndrome gripal entre idosos em instituições de longa permanência no estado de São Paulo. MÉTODOS: A análise foi realizada através de uma abordagem exploratória e descritiva, utilizando-se de registros do Sistema de Informações de Agravos de Notificação, módulo surto, entre janeiro de 2020 e junho de 2021. RESULTADOS: Surtos de síndrome gripal neste departamento representaram 24,93% do total de notificações. A maior concentração de surtos ocorreu na capital e região metropolitana. Foram observados 1018 surtos confirmados, envolvendo 6110 casos e 1240 óbitos em idosos. Entre estes casos, 71,67% foram confirmados para COVID-19, 12,77% para o vírus Influenza e 15,56%, para outros vírus respiratórios. Óbitos apresentaram porcentagens semelhantes, com a letalidade de síndrome gripal sendo de 20,29%. No grupo estudado, idosos mais longevos foram os mais acometidos. Houve diferença estatística entre casos e óbitos. CONCLUSÕES: Devido ao cenário atual e às conhecidas vulnerabilidades destas instituições, há a necessidade urgente de uma ação conjunta e articulada por parte de diversas esferas administrativas para minimizar os efeitos devastadores de surtos de síndrome gripal, especialmente os de COVID-19, em instituições de longa permanência. O fortalecimento de sistemas de informação e sua interoperabilidade são considerados de vital importância para melhorar a qualidade da informação sobre surtos institucionais, a qual é essencial durante uma pandemia.

COVID-19 no estado de São Paulo: a evolução de uma pandemia / COVID-19 in the state of São Paulo: the evolution of a pandemic

RESUMO: Objetivo: Descrever, de forma retrospectiva, os casos graves de pacientes hospitalizados e os óbitos relacionados à epidemia de COVID-19 no estado de São Paulo, desde a data do primeiro registro, com início de sintomas em 10 de fevereiro de 2020 até registros disponíveis em 20 de maio de 2021. Métodos: Trata-se de um estudo descritivo realizado por meio da base de dados do Sistema de Vigilância Epidemiológica da Gripe. Foram calculadas as taxas de incidência, mortalidade e incidência acumulada no período, estratificadas por faixa etária e agrupadas de acordo com cada Departamento Regional de Saúde. Os casos graves foram geocodificados para a análise de seu espalhamento pelo estado e foi calculado o R efetivo, que estima o potencial de propagação de um vírus em uma população. Resultados: Houve aumento significativo dos casos graves e óbitos registrados no período de um ano, e as taxas de incidência e mortalidade foram heterogêneas no estado. Os períodos mais críticos em relação à incidência de casos graves ocorreram entre maio e julho de 2020 e entre março e abril de 2021. Os Departamentos Regionais de Saúde de São José do Rio Preto, Grande São Paulo e Araçatuba concentraram as maiores taxas de incidência e mortalidade. Os casos graves e óbitos foram mais frequentes nos homens e na população acima de 60 anos, e as principais condições de risco relacionadas aos óbitos foram cardiopatia (59%) e diabetes (42,8%). Conclusões: Espera-se que esses resultados ofereçam embasamento e possam contribuir para uma ação de controle mais eficiente da COVID-19, além de permitir o entendimento histórico de sua evolução no estado.

ABSTRACT: Objectives: To retrospectively describe severe cases of hospitalized patients and deaths related to the COVID-19 epidemic in the state of São Paulo, starting from the date of the first record, with symptoms onset on 02/10/2020 up to 05/20/2021. Methods: This is a descriptive study carried out using the Influenza Epidemiological Surveillance System (Sistema de Vigilância Epidemiológica da Gripe - SIVEP-Gripe) database. The rates of incidence, mortality, and accumulated incidence in the period were calculated, stratified by age group and Regional Health Department (RHD). In addition, severe cases were geocoded to analyze their spread across the state; and the Effective R, which determines the spread potential of a virus within a population, was calculated. Results: There was a significant increase in severe cases and deaths recorded in the period of one year, with incidence and mortality rates being heterogeneous within the state. The most critical periods regarding the incidence of severe cases occurred between May and July 2020 and between March and April 2021. The RHD in São José do Rio Preto, Expanded São Paulo, and Araçatuba concentrated the highest incidence and mortality rates. Severe cases and deaths were more frequent in men and in the population over 60 years, while the main risk conditions related to deaths were heart disease (59%) and diabetes (42,8%). Conclusions: These results not only provide a detailed profile for more efficient control action plan, but will also allow the historical understanding of the COVID-19 evolution within the state of São Paulo.

Molecular analysis of rubella virus in travelers suspected of measles infection in São Paulo, Brazil / Análise molecular do vírus da rubéola em turistas suspeitos de infecção por sarampo em São Paulo, Brasil

OBJECTIVE: To identify measles virus genotypes in three cases of travelers suspected of measles infection. METHODS: Samples (blood and urine) were collected for serology, virus isolation, and genotyping. Sera were analyzed for IgM antibodies against measles virus and rubella virus by enzyme-linked immunosorbent assay (ELISA) (Siemens - Marburg, Germany). Clinical samples (lymphocytes and urine) were inoculated into Statens Serum Institute rabbit corneal epithelial cell line- ATCC CL 60 (SIRC) and Vero Slam cells. RNA was extracted from clinical samples and cell culture was inoculated and processed by polymerase chain reaction (PCR) with oligonucleotides specific for measles virus (MV) and rubella virus (RV). RESULTS: All patients showed IgM negative serology for MV and positive IgM for RV. RV belonging to genotypes 1B, 1C, and 1E were isolated from patients who came from Finland, Peru, and Germany, respectively. Genotype 1B has been found in Europe and on the East Coast of South America; 1C has been found in Peru and the West Coast of South America, and 1E, first identified in 1997, now appears to have worldwide distribution. CONCLUSION: Information about RV and MV genotypes circulating in São Paulo is essential for the control of measles, rubella, and congenital rubella syndrome (CRS) in Brazil.

OBJETIVO: Identificar o genótipo do vírus do sarampo em três viajantes suspeitos de infecção por sarampo. MÉTODOS: Amostras (sangue e urina) foram coletadas para sorologia, isolamento viral e genotipagem. As sorologias para pesquisa de IgM para o vírus do sarampo e da rubéola foi realizada utilizando-se o kit de ELISA (Siemens - Marburg, Alemanha). As amostras clínicas (linfócito e urina) foram inoculadas na SIRC (Statens Serum Institute rabbit corneal epithelial cell line-ATCC CL 60) e nas células Vero Slam. O RNA foi extraído das amostras clínicas e das células inoculadas e processadas por PCR, utilizando oligonucleotideos específicos para sarampo e rubéola. RESULTADOS: Todos os pacientes apresentaram sorologia IgM negativa para sarampo e positivo para rubéola. Os vírus da rubéola isolados dos pacientes que vieram da Finlândia, Peru e Alemanha pertencem aos genótipos 1B, 1C e 1E, respectivamente. O genótipo 1B foi encontrado na Europa e na costa oriental da América do Sul, o genótipo 1C foi encontrado no Peru e na costa oeste da América do Sul e o genótipo 1E, identificado pela primeira vez em 1997, agora aparenta ser um genótipo com distribuição mundial. CONCLUSÃO: O conhecimento dos genótipos de sarampo e rubéola que circulam em São Paulo é essencial para o controle do sarampo, rubéola e síndrome da rubéola congênita.

Three year seroepidemiological study of varicella-zoster virus in São Paulo, Brazil

A serosurvey of varicella has been carried out in children attending the public school network of São Paulo city, Brazil, from 1992 to 1994. This study was performed in order to establish the age related prevalence of antibodies against varicella-zoster virus (VZV) and its age specific transmission dynamics pattern in these children. Among 2500 schools in the city of São Paulo public network, 304 were randomly selected; 7 children of a given age (ranging from 1 to 15 years) were randomly selected in each school, and blood samples were obtained by fingerprick into filter paper. Blood eluates were analyzed for the presence of antibodies to VZV by ELISA. Proportion of seropositivity were calculated for each age group. Samples consisted of 1768 individuals in 1992, 1758 in 1993, and 1817 in 1994, resulting in 5343 eluates. A high proportion of seropositive children from 1 to 3 years of age was observed, ascending until 10 years of age and reaching a plateau around 90 percent afterwards. VZV transmission in this community was similar along the three years of the study. In children attending public schools in the city of São Paulo, contact with VZV occurs in early childhood. If immunization against VZV is considered it should be introduced as soon as possible.