Tracking excess deaths associated with the COVID-19 epidemic as an epidemiological surveillance strategy-preliminary results of the evaluation of six Brazilian capitals.

INTRODUCTION: In March 2020, the World Health Organization declared the coronavirus disease (COVID-19) outbreak a pandemic. In Brazil, 110 thousand cases and 5,901 deaths were confirmed by the end of April 2020. The scarcity of laboratory resources, the overload on the service network, and the broad clinical spectrum of the disease make it difficult to document all the deaths due to COVID-19. The aim of this study was to assess the mortality rate in Brazilian capitals with a high incidence of COVID-19. METHODS: We assessed the weekly mortality between epidemiological week 1 and 16 in 2020 and the corresponding period in 2019. We estimated the expected mortality at 95% confidence interval by projecting the mortality in 2019 to the population in 2020, using data from the National Association of Civil Registrars (ARPEN-Brasil). RESULTS: In the five capitals with the highest incidence of COVID-19, we identified excess deaths during the pandemic. The age group above 60 years was severely affected, while 31% of the excess deaths occurred in the age group of 20-59 years. There was a strong correlation (r = 0.94) between excess deaths and the number of deaths confirmed by epidemiological monitoring. The epidemiological surveillance captured only 52% of all mortality associated with the COVID-19 pandemic in the cities examined. CONCLUSIONS: Considering the simplicity of the method and its low cost, we believe that the assessment of excess mortality associated with the COVID-19 pandemic should be used as a complementary tool for regular epidemiological surveillance.

In vivo synthesis of bacterial amyloid curli contributes to joint inflammation during S. Typhimurium infection.

Reactive arthritis, an autoimmune disorder, occurs following gastrointestinal infection with invasive enteric pathogens, such as Salmonella enterica. Curli, an extracellular, bacterial amyloid with cross beta-sheet structure can trigger inflammatory responses by stimulating pattern recognition receptors. Here we show that S. Typhimurium produces curli amyloids in the cecum and colon of mice after natural oral infection, in both acute and chronic infection models. Production of curli was associated with an increase in anti-dsDNA autoantibodies and joint inflammation in infected mice. The negative impacts on the host appeared to be dependent on invasive systemic exposure of curli to immune cells. We hypothesize that in vivo synthesis of curli contributes to known complications of enteric infections and suggest that cross-seeding interactions can occur between pathogen-produced amyloids and amyloidogenic proteins of the host.

Disruption of ATRX-RNA interactions uncovers roles in ATRX localization and PRC2 function.

Heterochromatin in the eukaryotic genome is rigorously controlled by the concerted action of protein factors and RNAs. Here, we investigate the RNA binding function of ATRX, a chromatin remodeler with roles in silencing of repetitive regions of the genome and in recruitment of the polycomb repressive complex 2 (PRC2). We identify ATRX RNA binding regions (RBRs) and discover that the major ATRX RBR lies within the N-terminal region of the protein, distinct from its PHD and helicase domains. Deletion of this ATRX RBR (ATRXΔRBR) compromises ATRX interactions with RNAs in vitro and in vivo and alters its chromatin binding properties. Genome-wide studies reveal that loss of RNA interactions results in a redistribution of ATRX on chromatin. Finally, our studies identify a role for ATRX-RNA interactions in regulating PRC2 localization to a subset of polycomb target genes.

Use of excess mortality associated with the COVID-19 epidemic as an epidemiological surveillance strategy - preliminary results of the evaluation of six Brazilian capitals / Uso do excesso de mortalidade associado à epidemia de COVID-19 como estratégia de vigilância epidemiológica ­ resultados preliminares da avaliação de seis capitais brasileiras

In early 2020, the World Health Organization (WHO) recognized the pandemic situation of the new coronavirus (severe acute respiratory syndrome coronavirus 2, SARS-CoV-2), which causes Coronavirus Disease-2019 (COVID-19). In Brazil by the end of April 2020, another 110 thousand cases and 5,000 deaths had been confirmed. The scarcity of laboratory resources and overload of the care network, added to the broad clinical spectrum of the disease, can make it difficult to capture all mortality from this disease through epidemiological surveillance based on individual notification of cases. The aim of this study was to evaluate the excess of deaths in Brazilian capitals with the highest incidence of COVID-19, as a way of validating the method, we also evaluated a capital with low incidence. We assessed weekly mortality from all causes during the year 2020, up to the epidemiological week 17, compared with the previous year. The data were obtained through the National Civil Registry Information Center (CNIRC, acronym in Portuguese). We estimate the expected mortality and the 95% confidence interval by projecting the observed mortality in 2019 for the population of 2020. In the five capitals with the highest incidences it was possible to identify excess deaths in the pandemic period, the age group most affected were those over 60 years old, 31% of the excess deaths occurred in the population between 20 and 59 years old. There was a strong correlation (r = 0.94) between the excess of deaths in each city and the number of deaths confirmed by epidemiological surveillance. There was no excess of deaths in the capital with the lowest incidence, nor among the population under 20 years old. We estimate that epidemiological surveillance managed to capture only 52% of all mortality associated with the COVID-19 pandemic in the cities studied. Considering the simplicity of the method, its low cost and reliability for assessing the real burden of the disease, we believe that the assessment of excess mortality associated with the COVID-19 pandemic should be widely used as a complementary tool to regular epidemiological surveillance and its use should be encouraged by WHO.

No início de 2020 a Organização Mundial da Saúde (OMS) reconheceu a situação de pandemia do novo coronavírus (severe acute respiratory syndrome coronavirus 2, SARS-CoV-2), causador da Coronavirus Disease-2019 (COVID-19). No Brasil até o final de abril de 2020 já tinham sido confirmados mais 110 mil casos e de 5 mil óbitos. A escassez de recursos laboratoriais e sobrecarga da rede assistencial, somados ao amplo espectro clínico da doença, pode dificultar a captação de toda a mortalidade por esta doença pela vigilância epidemiológica baseada na notificação individual dos casos. O objetivo deste estudo foi avaliar o excesso de mortes nas capitais brasileiras com maiores incidências de COVID-19, como forma de validação do método avaliamos, também, uma capital com baixa incidência. Nós avaliamos a mortalidade semanal por todas as causas durante o ano de 2020, até a semana epidemiológica 17, comparando com o ano anterior. Os dados foram obtidos através da Central Nacional de Informações do Registro Civil (CNIRC). Nós estimamos a mortalidade esperada e o intervalo de confiança de 95% projetando a mortalidade observada em 2019 para a população de 2020. Nas cinco capitais com maiores incidências foi possível identificar excesso de mortes no período da pandemia, a faixa etária mais afetada foram aqueles com mais de 60 anos, 31% do excesso de mortes ocorreu na população entre 20 e 59 anos. Houve uma forte correlação (r=0.94) entre o excesso de mortes em cada cidade e o número de mortes confirmados pela vigilância epidemiológica. Não houve excesso de mortes na capital com mais baixa incidência, nem entre a população com menos de 20 anos. Estimamos que a vigilância epidemiológica conseguiu captar apenas 52% de toda a mortalidade associada à pandemia de COVID-19 nas cidades estudadas. Considerando a simplicidade do método, seu baixo custo e confiabilidade para avaliação da carga real da doença, acreditamos que a avaliação do excesso de mortalidade associado à pandemia de COVID-19 deveria ser amplamente utilizada como ferramenta complementar à vigilância epidemiológica regular e ter seu uso incentivado pela OMS.

Tracking excess deaths associated with the COVID-19 epidemic as an epidemiological surveillance strategy-preliminary results of the evaluation of six Brazilian capitals

Abstract INTRODUCTION: In March 2020, the World Health Organization declared the coronavirus disease (COVID-19) outbreak a pandemic. In Brazil, 110 thousand cases and 5,901 deaths were confirmed by the end of April 2020. The scarcity of laboratory resources, the overload on the service network, and the broad clinical spectrum of the disease make it difficult to document all the deaths due to COVID-19. The aim of this study was to assess the mortality rate in Brazilian capitals with a high incidence of COVID-19. METHODS: We assessed the weekly mortality between epidemiological week 1 and 16 in 2020 and the corresponding period in 2019. We estimated the expected mortality at 95% confidence interval by projecting the mortality in 2019 to the population in 2020, using data from the National Association of Civil Registrars (ARPEN-Brasil). RESULTS: In the five capitals with the highest incidence of COVID-19, we identified excess deaths during the pandemic. The age group above 60 years was severely affected, while 31% of the excess deaths occurred in the age group of 20-59 years. There was a strong correlation (r = 0.94) between excess deaths and the number of deaths confirmed by epidemiological monitoring. The epidemiological surveillance captured only 52% of all mortality associated with the COVID-19 pandemic in the cities examined. CONCLUSIONS: Considering the simplicity of the method and its low cost, we believe that the assessment of excess mortality associated with the COVID-19 pandemic should be used as a complementary tool for regular epidemiological surveillance.

STAT2 dependent Type I Interferon response promotes dysbiosis and luminal expansion of the enteric pathogen Salmonella Typhimurium.

The mechanisms by which the gut luminal environment is disturbed by the immune system to foster pathogenic bacterial growth and survival remain incompletely understood. Here, we show that STAT2 dependent type I IFN signaling contributes to the inflammatory environment by disrupting hypoxia enabling the pathogenic S. Typhimurium to outgrow the microbiota. Stat2-/- mice infected with S. Typhimurium exhibited impaired type I IFN induced transcriptional responses in cecal tissue and reduced bacterial burden in the intestinal lumen compared to infected wild-type mice. Although inflammatory pathology was similar between wild-type and Stat2-/- mice, we observed decreased hypoxia in the gut tissue of Stat2-/- mice. Neutrophil numbers were similar in wild-type and Stat2-/- mice, yet Stat2-/- mice showed reduced levels of myeloperoxidase activity. In vitro, the neutrophils from Stat2-/- mice produced lower levels of superoxide anion upon stimulation with the bacterial ligand N-formylmethionyl-leucyl-phenylalanine (fMLP) in the presence of IFNα compared to neutrophils from wild-type mice, indicating that the neutrophils were less functional in Stat2-/- mice. Cytochrome bd-II oxidase-mediated respiration enhances S. Typhimurium fitness in wild-type mice, while in Stat2-/- deficiency, this respiratory pathway did not provide a fitness advantage. Furthermore, luminal expansion of S. Typhimurium in wild-type mice was blunted in Stat2-/- mice. Compared to wild-type mice which exhibited a significant perturbation in Bacteroidetes abundance, Stat2-/- mice exhibited significantly less perturbation and higher levels of Bacteroidetes upon S. Typhimurium infection. Our results highlight STAT2 dependent type I IFN mediated inflammation in the gut as a novel mechanism promoting luminal expansion of S. Typhimurium.

Bacterial amyloid curli acts as a carrier for DNA to elicit an autoimmune response via TLR2 and TLR9.

Bacterial biofilms are associated with numerous human infections. The predominant protein expressed in enteric biofilms is the amyloid curli, which forms highly immunogenic complexes with DNA. Infection with curli-expressing bacteria or systemic exposure to purified curli-DNA complexes triggers autoimmunity via the generation of type I interferons (IFNs) and anti-double-stranded DNA antibodies. Here, we show that DNA complexed with amyloid curli powerfully stimulates Toll-like receptor 9 (TLR9) through a two-step mechanism. First, the cross beta-sheet structure of curli is bound by cell-surface Toll-like receptor 2 (TLR2), enabling internalization of the complex into endosomes. After internalization, the curli-DNA immune complex binds strongly to endosomal TLR9, inducing production of type I IFNs. Analysis of wild-type and TLR2-deficient macrophages showed that TLR2 is the major receptor that drives the internalization of curli-DNA complexes. Suppression of TLR2 internalization via endocytosis inhibitors led to a significant decrease in Ifnß expression. Confocal microscopy analysis confirmed that the TLR2-bound curli was required for shuttling of DNA to endosomal TLR9. Structural analysis using small-angle X-ray scattering revealed that incorporation of DNA into curli fibrils resulted in the formation of ordered curli-DNA immune complexes. Curli organizes parallel, double-stranded DNA rods at an inter-DNA spacing that matches up well with the steric size of TLR9. We also found that production of anti-double-stranded DNA autoantibodies in response to curli-DNA was attenuated in TLR2- and TLR9-deficient mice and in mice deficient in both TLR2 and TLR9 compared to wild-type mice, suggesting that both innate immune receptors are critical for shaping the autoimmune adaptive immune response. We also detected significantly lower levels of interferon-stimulated gene expression in response to purified curli-DNA in TLR2 and TLR9 deficient mice compared to wild-type mice, confirming that TLR2 and TLR9 are required for the induction of type I IFNs. Finally, we showed that curli-DNA complexes, but not cellulose, were responsible elicitation of the immune responses to bacterial biofilms. This study defines the series of events that lead to the severe pro-autoimmune effects of amyloid-expressing bacteria and suggest a mechanism by which amyloid curli acts as a carrier to break immune tolerance to DNA, leading to the activation of TLR9, production of type I IFNs, and subsequent production of autoantibodies.