Estimation of Excess Deaths in Turin from COVID-19 and other causes, October to November 2020

Introduction

Understanding the effect of COVID-19 on mortality during this emergency and evaluating unexplained increases in deaths due to nonspecific outcomes can provide a more complete picture of this period and give better instrument to deal with the pandemy in the future.

Objective

The aim is to evaluate in the city of Turin the excess in the number of deaths from October to November 2020.

Methods

The number of excess deaths was defined as the difference between the deaths observed in the pandemic period of 2020 and the deaths expected for the years 2014-2019.

Results

There were approximately 2047 total all causes deaths in Turin October 1 to November 30 2020, representing 630 more deaths than would typically be expected at that time of year. This excess was higher between men than in women. The number of excess all cause death was higher in 80 years old, less evident between 60-79 years old and very few between under 60 years old. Regarding the place of death, the number of excess all cause death was higher in hospital or in some health institutions for old people. Regarding the causes of deaths the explanation of these excess of deaths was COVID-19 infection only for a part of deaths and there are some excess of deaths not caused by COVID-19. The cause of excess of death not COVID-19 seems to be due to cardiovascular diseases, respiratory diseases, psychiatric disorders, neurological diseases, diabetes or nephrological diseases and to other undefinited causes.

Conclusions

The results showed during pandemic an increase of mortality respect to the expected mortality. Only a part of this excess deaths is due to COVID-19 but there is a relevant percentage of excess of deaths apparentely not due to COVID-19 but probably due to other causes. A better knowledge of these phenomena could help to improve any gaps in territorial assistance and provide indications for the future management of the pandemic in Europe.

Key messages

Increase of mortality in pandemic respect to the expected mortality. There is an excess of deaths apparentely not due to COVID-19.

An overview of the TROPICS NASA Earth Venture Mission

The Time-Resolved Observations of Precipitation structure and storm Intensity with a Constellation of Smallsats (TROPICS) mission was selected by NASA as part of the Earth Venture-Instrument (EVI-3) program. The overarching goal for TROPICS is to provide nearly all-weather observations of 3D temperature and humidity, as well as cloud ice and precipitation horizontal structure, at high temporal resolution to conduct high-value science investigations of tropical cyclones. TROPICS will provide rapid-refresh microwave measurements (median refresh rate better than 60 min for the baseline mission) which can be used to observe the thermodynamics of the troposphere and precipitation structure for storm systems at the mesoscale and synoptic scale over the entire storm life cycle. TROPICS comprises six CubeSats in three low-Earth orbital planes. Each CubeSat will host a high-performance radiometer to provide temperature profiles using seven channels near the 118.75 GHz oxygen absorption line, water vapour profiles using three channels near the 183 GHz water vapour absorption line, imagery in a single channel near 90 GHz for precipitation measurements (when combined with higher-resolution water vapour channels), and a single channel near 205 GHz which is more sensitive to precipitation-sized ice particles. This observing system offers an unprecedented combination of horizontal and temporal resolution to measure environmental and inner-core conditions for tropical cyclones on a nearly global scale and is a major leap forward in the temporal resolution of several key parameters needed for assimilation into advanced data assimilation systems capable of utilizing rapid-update radiance or retrieval data. Launch readiness is currently projected for late 2019.

Mitochondrial DNA damage induces apoptosis in senescent cells

Senescence is a cellular response to damage and stress. The senescence response prevents cancer by suppressing the proliferation of cells with a compromised genome and contributes to optimal wound healing in normal tissues. Persistent senescent cells are also thought to drive aging and age-associated pathologies through their secretion of inflammatory factors that modify the tissue microenvironment and alter the function of nearby normal or transformed cells. Understanding how senescent cells alter the microenvironment would be aided by the ability to induce or eliminate senescent cells at will in vivo. Here, we combine the use of the synthetic nucleoside analog ganciclovir (GCV) with herpes simplex virus thymidine kinase (HSVtk) activity to create or eliminate senescent human cells. We show that low concentrations of GCV induce senescence through the accumulation of nuclear DNA damage while higher concentrations of GCV, similar to those used in vivo, kill non-dividing senescent cells via mitochondrial DNA (mtDNA) damage and caspase-dependent apoptosis. Using this system, we effectively eliminated xenografted normal human senescent fibroblasts or induced senescence in human breast cancer cells in vivo. Thus, cellular senescence and mtDNA damage are outcomes of synthetic nucleoside analog treatment, indicating that the GCV-HSVtk combination can be used effectively to promote the targeted formation or eradication of senescent cells.

The impact of the summer 2003 heat waves on mortality in four Italian cities

This study evaluates the impact of the 2003 heat wave on cause-specific mortality and the role of demographic characteristics and socioeconomic conditions that may have increased the risk of mortality in four Italian cities: Bologna, Milan, Rome and Turin. Daily mortality counts, for the resident population by age, sex and cause of death were considered. Daily excess mortality was calculated as the difference between the number of deaths observed and the smoothed average. The impact of heat on health is measured in terms of maximum apparent temperature. The greatest excess in mortality was observed in the north west of Italy (Turin, +23% and Milan, +23%). The old (75-84 years) and the very old (85+ years) were the age groups most affected, and when stratifying by sex, the increase in mortality seemed to be greater among females. The greatest excess in mortality was registered in those with low socioeconomic status in Rome (+17.8%) and in those with lower education levels in Turin (+43%). The analysis of cause-specific mortality not only confirms results from previous studies of an increase in heat-related mortality by respiratory and cardiovascular diseases, but also shows a significant excess in mortality for diseases of the central nervous system and for metabolic/endocrine disorders. Results from 2003 highlight the necessity of targeting future prevention programmes at the susceptible sub-groups identified. The introduction of warning systems alongside efficient preventive plans and the monitoring of mortality during heat waves may represent a valid tool for the reduction of heat-related deaths.

The impact of the summer 2003 heat waves on mortality in four Italian cities

This study evaluates the impact of the 2003 heat wave on cause-specific mortality and the role of demographic characteristics and socioeconomic conditions that may have increased the risk of mortality in four Italian cities: Bologna, Milan, Rome and Turin. Daily mortality counts, for the resident population by age, sex and cause of death were considered. Daily excess mortality was calculated as the difference between the number of deaths observed and the smoothed average. The impact of heat on health is measured in terms of maximum apparent temperature. The greatest excess in mortality was observed in the north west of Italy (Turin, +23% and Milan, +23%). The old (75-84 years) and the very old (85+ years) were the age groups most affected, and when stratifying by sex, the increase in mortality seemed to be greater among females. The greatest excess in mortality was registered in those with low socioeconomic status in Rome (+17.8%) and in those with lower education levels in Turin (+43%). The analysis of cause-specific mortality not only confirms results from previous studies of an increase in heat-related mortality by respiratory and cardiovascular diseases, but also shows a significant excess in mortality for diseases of the central nervous system and for metabolic/endocrine disorders. Results from 2003 highlight the necessity of targeting future prevention programmes at the susceptible sub-groups identified. The introduction of warning systems alongside efficient preventive plans and the monitoring of mortality during heat waves may represent a valid tool for the reduction of heat-related deaths.

Induction of cytotoxic T lymphocyte and antibody responses to enhanced green fluorescent protein following transplantation of transduced CD34(+) hematopoietic cells

Genetic modification of hematopoietic stem cells often results in the expression of foreign proteins in pluripotent progenitor cells and their progeny. However, the potential for products of foreign genes introduced into hematopoietic stem cells to induce host immune responses is not well understood. Gene marking and induction of immune responses to enhanced green fluorescent protein (eGFP) were examined in rhesus macaques that underwent nonmyeloablative irradiation followed by infusions of CD34(+) bone marrow cells transduced with a retroviral vector expressing eGFP. CD34(+) cells were obtained from untreated animals or from animals treated with recombinant human granulocyte colony-stimulating factor (G-CSF) alone or G-CSF and recombinant human stem cell factor. Levels of eGFP-expressing cells detected by flow cytometry peaked at 0.1% to 0.5% of all leukocytes 1 to 4 weeks after transplantation. Proviral DNA was detected in 0% to 17% of bone marrow--derived colony-forming units at periods of 5 to 18 weeks after transplantation. However, 5 of 6 animals studied demonstrated a vigorous eGFP-specific cytotoxic T lymphocyte (CTL) response that was associated with a loss of genetically modified cells in peripheral blood, as demonstrated by both flow cytometry and polymerase chain reaction. The eGFP-specific CTL responses were MHC-restricted, mediated by CD8(+) lymphocytes, and directed against multiple epitopes. eGFP-specific CTLs were able to efficiently lyse autologous CD34(+) cells expressing eGFP. Antibody responses to eGFP were detected in 3 of 6 animals. These data document the potential for foreign proteins expressed in CD34(+) hematopoietic cells and their progeny to induce antibody and CTL responses in the setting of a clinically applicable transplantation protocol. (Blood. 2001;97:1951-1959)

Inhibition of natural killer cell-mediated cytotoxicity by Kaposi's sarcoma-associated herpesvirus K5 protein

Kaposi's sarcoma-associated herpesvirus (KSHV) K3 and K5 proteins dramatically downregulate MHC class I molecules. However, although MHC class I downregulation may protect KSHV-infected cells from cytotoxic T lymphocyte recognition, these cells become potential targets for natural killer (NK) cell-mediated lysis. We now show that K5 also downregulates ICAM-1 and B7-2, which are ligands for NK cell-mediated cytotoxicity receptors. As a consequence, K5 expression drastically inhibits NK cell-mediated cytotoxicity. Conversely, de novo expression of B7-2 and ICAM-1 resensitizes the K5-expressing cells to NK cell-mediated cytotoxicity. This is a novel viral immune evasion strategy where KSHV K5 achieves immune avoidance by downregulation of cellular ligands for NK cell-mediated cytotoxicity receptors.

Activation of lymphocyte signaling by the R1 protein of rhesus monkey rhadinovirus

Rhesus monkey rhadinovirus (RRV) is a gamma-2 herpesvirus that exhibits a considerable degree of similarity to the human Kaposi's sarcoma-associated herpesvirus (KSHV). The R1 protein of RRV is distantly related to the K1 protein of KSHV, and R1, like K1, can contribute to cell growth transformation. In this study we analyzed the ability of the cytoplasmic tail of R1 to function as a signal transducer. The cytoplasmic domain of the R1 protein contains several tyrosine residues whose phosphorylation is induced in cells expressing Syk kinase. Expression of a CD8 chimera protein containing the extracellular and transmembrane domains of CD8 fused to the cytoplasmic domain of R1 mobilized intracellular calcium and induced cellular tyrosine phosphorylation in B cells upon stimulation with anti-CD8 antibody. None of the CD8-R1 cytoplasmic deletion mutants tested were able to mobilize intracellular calcium or to induce tyrosine phosphorylation to a significant extent upon addition of anti-CD8 antibody. Expression of wild-type R1 protein activated nuclear factor of activated T lymphocytes (NFAT) eightfold in B cells in the absence of antibody stimulation; expression of the CD8-R1C chimera strongly induced NFAT activity (60-fold) but only upon the addition of anti-CD8 antibody. We conclude that the cytoplasmic domain of R1 is capable of transducing signals that elicit B-lymphocyte activation events. The signal-inducing properties of R1 appear to be similar to those of K1 but differ in that the required sequences are distributed over a much longer stretch of the cytoplasmic domain (>150 amino acids). In addition, the induction of calcium mobilization was considerably longer in duration and stronger with R1 than with K1.

Identifying the target cell in primary simian immunodeficiency virus (SIV) infection: highly activated memory CD4(+) T cells are rapidly eliminated in early SIV infection in vivo

It has recently been shown that rapid and profound CD4(+) T-cell depletion occurs almost exclusively within the intestinal tract of simian immunodeficiency virus (SIV)-infected macaques within days of infection. Here we demonstrate (by three- and four-color flow cytometry) that this depletion is specific to a definable subset of CD4(+) T cells, namely, those having both a highly and/or acutely activated (CD69(+) CD38(+) HLA-DR(+)) and memory (CD45RA(-) Leu8(-)) phenotype. Moreover, we demonstrate that this subset of helper T cells is found primarily within the intestinal lamina propria. Viral tropism for this particular cell type (which has been previously suggested by various studies in vitro) could explain why profound CD4(+) T-cell depletion occurs in the intestine and not in peripheral lymphoid tissues in early SIV infection. Furthermore, we demonstrate that an acute loss of this specific subset of activated memory CD4(+) T cells may also be detected in peripheral blood and lymph nodes in early SIV infection. However, since this particular cell type is present in such small numbers in circulation, its loss does not significantly affect total CD4(+) T cell counts. This finding suggests that SIV and, presumably, human immunodeficiency virus specifically infect, replicate in, and eliminate definable subsets of CD4(+) T cells in vivo.

Recombinant simian immunodeficiency virus expressing green fluorescent protein identifies infected cells in rhesus monkeys

We engineered recombinant derivatives of simian immunodeficiency virus (SIV) to express enhanced green fluorescent protein (EGFP). Replacement of vpr sequences with EGFP resulted in a genome that did not produce detectable levels of replication-competent virus. Replication-competent virus and bright fluorescence of infected cells were obtained with two other constructs, one in which SIV nef sequences were replaced by EGFP and another in which EGFP was inserted into the SIV nef locus and HIV-1 nef sequences were expressed by downstream placement of an internal ribosomal entry site. These strains were infectious in rhesus monkeys and green fluorescing cells were detected in the tissues of infected monkeys by FACS analysis and by direct microscopic visualization. EGFP sequences were absent from recovered virus by 8 weeks following infection. We conclude that recombinant SIV that is engineered to express EGFP can be used to directly detect productively infected cells and aid in the immunophenotypic characterization of these cells within the first 2 weeks of infection of rhesus monkeys.

Identification of an immunoreceptor tyrosine-based activation motif of K1 transforming protein of Kaposi's sarcoma-associated herpesvirus

Kaposi's sarcoma-associated herpesvirus (KSHV) is consistently identified in Kaposi's sarcoma and body cavity-based lymphoma. KSHV encodes a transforming protein called K1 which is structurally similar to lymphocyte receptors. We have found that a highly conserved region of the cytoplasmic domain of K1 resembles the sequence of immunoreceptor tyrosine-based activation motifs (ITAMs). To demonstrate the signal-transducing activity of K1, we constructed a chimeric protein in which the cytoplasmic tail of the human CD8alpha polypeptide was replaced with that of KSHV K1. Expression of the CD8-K1 chimera in B cells induced cellular tyrosine phosphorylation and intracellular calcium mobilization upon stimulation with an anti-CD8 antibody. Mutational analyses showed that the putative ITAM of K1 was required for its signal-transducing activity. Furthermore, tyrosine residues of the putative ITAM of K1 were phosphorylated upon stimulation, and this allowed subsequent binding of SH2-containing proteins. These results demonstrate that the KSHV transforming protein K1 contains a functional ITAM in its cytoplasmic domain and that it can transduce signals to induce cellular activation.

Gastrointestinal tract as a major site of CD4+ T cell depletion and viral replication in SIV infection

Human and simian immunodeficiency virus (HIV and SIV) replicate optimally in activated memory CD4(+) T cells, a cell type that is abundant in the intestine. SIV infection of rhesus monkeys resulted in profound and selective depletion of CD4+ T cells in the intestine within days of infection, before any such changes in peripheral lymphoid tissues. The loss of CD4+ T cells in the intestine occurred coincident with productive infection of large numbers of mononuclear cells at this site. The intestine appears to be a major target for SIV replication and the major site of CD4+ T cell loss in early SIV infection.

Dye efflux studies suggest that hematopoietic stem cells expressing low or undetectable levels of CD34 antigen exist in multiple species

We previously described a method for isolating murine hematopoietic stem cells capable of reconstituting lethally irradiated recipients, which depends solely on dual-wavelength flow cytometric analysis of murine bone marrow cells stained with the fluorescent DNA-binding dye Hoechst 33342. This method, which appears to rely on the differential ability of stem cells to efflux the Hoechst dye, defines an extremely small and homogeneous population of cells (termed SP cells). We show here that dual-wavelength analysis of Hoechst dye-stained human, rhesus and miniature swine bone marrow cells reveals a small, distinct population of cells that efflux the dye in a manner identical to murine SP cells. Like the murine SP cells, both human and rhesus SP cells are primarily CD34-negative and lineage marker-negative. In vitro culture studies demonstrated that rhesus SP cells are highly enriched for long-term culture-initiating cells (LTC-ICs), an indicator of primitive hematopoietic cells, and have the capacity for differentiation into T cells. Although rhesus SP cells do not initially possess any hematopoietic colony-forming capability, they acquire the ability to form colonies after long-term culture on bone marrow stroma, coincident with their conversion to a CD34-positive phenotype. These studies suggest the existence of a hitherto unrecognized population of hematopoietic stem cells that lack the CD34 surface marker classically associated with primitive hematopoietic cells.

Four color immunofluorescence detection using two 488-nm lasers on a Becton Dickinson FACS Vantage flow cytometer

Multiparameter flow cytometric analysis is sometimes limited by the availability of directly conjugated monoclonal antibodies or streptavidin-conjugated secondary reagents. While many manufacturers offer a wide variety of monoclonal antibodies or streptavidin reagents directly conjugated to 488-nm excitable fluorochromes, there are not many available that are directly conjugated to 360-nm (UV) or 630-nm (HeNe) excitable fluorochromes. For this reason we attempted to develop a four color immunofluorescence staining protocol on a FACS Vantage using four 488-nm excitable fluorochromes. The fixed configuration of the FACS Vantage limits the feasibility of using four 488-nm excitable fluorochrome simultaneously because of the five fluorescence detectors, two are always electronically delayed. This means that only three signals-FL1, FL2, and FL3-can be detected off the primary 488-nm laser beam. FL4 and FL5 are always delayed, only detecting signals off the second laser beam. Our instrument is configured with an ILT air cooled 488-nm laser in the second position that is used in order to conserve the Coherent Enterprise laser when using only 488-nm excitable fluorochromes. Because of this, we were able to develop a four-color immunofluorescence staining protocol using only 488-nm excitable fluorochromes.

Tap: a novel cellular protein that interacts with tip of herpesvirus saimiri and induces lymphocyte aggregation

Tip of herpesvirus saimiri associates with Lck and down-regulates Lck-mediated activation. We identified a novel cellular Tip-associated protein (Tap) by a yeast two-hybrid screen. Tap associated with Tip following transient expression in COS-1 cells and stable expression in human Jurkat-T cells. Expression of Tip and Tap in Jurkat-T cells induced dramatic cell aggregation. Aggregation was likely caused by the up-regulated surface expression of adhesion molecules including integrin alpha, L-selectin, ICAM-3, and H-CAM. Furthermore, NF-kappaB transcriptional factor of aggregated cells had approximately 40-fold higher activity than that of parental cells. Thus, Tap is likely to be an important cellular mediator of Tip function in T cell transformation by herpesvirus saimiri.

Characterization of gut-associated lymphoid tissue (GALT) of normal rhesus macaques

This study characterizes the gut-associated lymphoid tissue (GALT) of normal healthy rhesus macaques and compares the percentages of T and B cell subsets to those of systemic lymphoid tissue. Lymphocytes from the systemic lymphoid tissue (spleen, axillary, and inguinal lymph nodes), mesenteric lymph nodes (MLN), and intestinal epithelium (IEL) and lamina propria (LPL) of the jejunum, ileum, and colon were examined from both adult and juvenile, normal rhesus macaques. Lymphocytes were analyzed for expression of CD2, CD3, CD4, CD8, CD25, gamma delta TCR, and CD20 by two- or three-color flow cytometric analysis. Sections of jejunum, ileum, and colon were examined for CD3, CD20, and CD103 expression by immunohistochemistry. Peyer's patches were also examined for CD3, CD4, CD8, and CD20 expression by immunohistochemistry. Most IEL and LPL were CD103+, CD3+ T cells with significantly fewer CD20+ B cells. The IEL were predominantly CD3+CD8+ (63-80%), with very few CD4+ cells, whereas CD4:CD8 ratios in the LPL ranged from 0.74 to 1.3. Three to 38% of the IEL were gamma delta TCR positive, but gamma delta expression was rare in the LPL and MLN. gamma delta TCR expression was also higher in the IEL of younger animals. LPL had higher expression of CD25 compared to IEL and systemic tissues, particularly in aged animals. CD4+CD8+, double-positive and CD3+CD4-CD8- double-negative cells were also observed in GALT. These results demonstrate that GALT of rhesus macaques is remarkably similar to that of humans, further justifying the use of these animals as models for various intestinal disorders.

A simple fluorescence method for surface antigen phenotyping of lymphocytes undergoing DNA fragmentation

Apoptosis, a metabolically active process of programmed cell death characterized by DNA fragmentation, is believed to play an important role in development of lymphocyte repertoires and in embryogenesis. Studies of this phenomenon would be greatly facilitated by the development of a simple assay capable of identifying and isolating intact apoptotic cells. A rapid fluorescence assay which identifies relatively small, intact cells containing fragmented DNA is described in this report. Thymocytes in which DNA fragmentation is induced by culture with or without dexamethasone are readily identified by their bright blue fluorescence after a 15 min treatment with Hoechst 33342, a DNA binding fluorochrome which diffuses through cell membranes. Since Hoechst 33342 staining does not require destruction of the cell membrane, it is possible to directly phenotype cell surface antigen expression on Hoechst 33342bright lymphocytes by conventional immunofluorescence techniques and to evaluate membrane integrity of Hoechst 33342bright cells by dye exclusion criteria. The advantages of this system are that it: (1) is rapid and simple, (2) quantitates the percentage of cells fragmenting their DNA and presumably undergoing apoptosis, (3) permits standard immunofluorescence staining of cell surface markers to identify even minor cell subsets of presumably apoptotic cells within heterogeneous populations, (4) provides the tools (fluorescence activated cell sorting) for purifying intact cells containing fragmented DNA for further biochemical studies, and (5) provides a means for identifying cells which exclude vital dyes and in which DNA fragmentation will eventually result in cell death.

Creating a useful panel of anti-T cell monoclonal antibodies

Monoclonal antibodies to human T lymphocyte surface markers were produced by cell fusions between splenocytes from mice, immunized with T lineage cells, and mouse myeloma cells. Our approaches to immunization, clone selection and analysis of the resultant monoclonal antibodies with similar reactivities were produced. In one example, we found that several distinct monoclonal antibodies identified the same T inducer subset yet, apparently, recognized epitopes of the differentiation antigen(s) on these cells.