Targeted plasma proteomics reveals signatures discriminating COVID-19 from sepsis with pneumonia.

BACKGROUND: COVID-19 remains a major public health challenge, requiring the development of tools to improve diagnosis and inform therapeutic decisions. As dysregulated inflammation and coagulation responses have been implicated in the pathophysiology of COVID-19 and sepsis, we studied their plasma proteome profiles to delineate similarities from specific features. METHODS: We measured 276 plasma proteins involved in Inflammation, organ damage, immune response and coagulation in healthy controls, COVID-19 patients during acute and convalescence phase, and sepsis patients; the latter included (i) community-acquired pneumonia (CAP) caused by Influenza, (ii) bacterial CAP, (iii) non-pneumonia sepsis, and (iv) septic shock patients. RESULTS: We identified a core response to infection consisting of 42 proteins altered in both COVID-19 and sepsis, although higher levels of cytokine storm-associated proteins were evident in sepsis. Furthermore, microbiologic etiology and clinical endotypes were linked to unique signatures. Finally, through machine learning, we identified biomarkers, such as TRIM21, PTN and CASP8, that accurately differentiated COVID-19 from CAP-sepsis with higher accuracy than standard clinical markers. CONCLUSIONS: This study extends the understanding of host responses underlying sepsis and COVID-19, indicating varying disease mechanisms with unique signatures. These diagnostic and severity signatures are candidates for the development of personalized management of COVID-19 and sepsis.

Social isolation during the COVID-19 pandemic in Spain: a population study.

Since March of 2020, billions of people worldwide have been asked to limit their social contacts in an effort to contain the spread of the SARS-CoV-2 virus. However, little research has been carried out to date on the impact of such social distancing measures on the social isolation levels of the population. In this paper, we study the impact of the pandemic on the social isolation of the Spanish population, by means of 32,359 answers to a citizen survey collected over a period of 7 months. We uncover (1) a significant increase in the prevalence of social isolation in the population, reaching almost 26%; (2) gender and age differences, with the largest prevalence of isolation among middle-aged individuals; (3) a strong relationship between economic impact and social isolation; and (4) differences in social isolation, depending on the number of COVID-19 protection measures and on the perception of coronavirus infection risk by our participants. Our research sheds quantitative light on the sociological impact of the pandemic, and enables us to identify key factors in the interplay between the deployment of non-pharmaceutical interventions to contain the spread of an infectious disease and a population's levels of social isolation.

Observational retrospective analysis of vaccination against SARS-CoV-2 and seizures: VACCI-COVID registry.

BACKGROUND: We aimed to assess the risk of developing new-onset seizures or seizure decompensations in people with epilepsy (PWE) associated with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccines. METHODS: A retrospective observational study in a tertiary hospital was conducted. Clinical records of all patients attended because of seizures or epilepsy at outpatient clinics, emergency department, or admitted to our hospital from January to December 2021 were reviewed, including patients older than 16 years who received some dose of coronavirus disease 2019 (COVID-19) vaccines. RESULTS: A total of 418 vaccinated PWE were analyzed: 6.2% presented an increase in seizure frequency and 1% reported different seizure types during the next month after vaccination. However, 61.5% had another possible cause for this decompensation. Having monthly seizures (1-3/month) was the only associated risk factor (OR 4.9, p < 0.001) while being seizure free > 1 year had a protective role (OR 0.36, p = 0.019). Patients with epileptic encephalopathies or a history of COVID-19 infection were not at increased risk of seizure decompensation. Besides this, 15 patients presented new-onset seizures within the first month post-vaccination, mean time from vaccination 15 ±â€¯8 days, 67% after the second dose. Again, 53.3% had another possible trigger for seizures. Eight debuted with status epilepticus or cluster of seizures. CONCLUSIONS: A small proportion of PWE (6.2%) had an increase in seizure frequency after COVID-19 vaccination and 15 patients had new-onset seizures during the first month after vaccination, though another reason for seizure exacerbation was identified in 61.5% and 53.3%, respectively. Severe acute respiratory syndrome COVID-19 vaccines appear to have little impact on the generation or decompensation of seizures.

The Karolinska KI/K COVID-19 Immune Atlas: An open resource for immunological research and educational purposes.

The Karolinska KI/K COVID-19 Immune Atlas project was conceptualized in March 2020 as a part of the academic research response to the developing SARS-CoV-2 pandemic. The aim was to rapidly provide a curated dataset covering the acute immune response towards SARS-CoV-2 infection in humans, as it occurred during the first wave. The Immune Atlas was built as an open resource for broad research and educational purposes. It contains a presentation of the response evoked by different immune and inflammatory cells in defined naïve patient-groups as they presented with moderate and severe COVID-19 disease. The present Resource Article describes how the Karolinska KI/K COVID-19 Immune Atlas allow scientists, students, and other interested parties to freely explore the nature of the immune response towards human SARS-CoV-2 infection in an online setting.

Post-COVID-19 fatigue: the contribution of cognitive and neuropsychiatric symptoms.

Fatigue in its many forms of physical, mental, and psychosocial exhaustion is a common symptom of post-COVID-19 condition, also known as "Long COVID." Persistent fatigue in COVID-19 patients is frequently accompanied by cognitive dysfunction and neuropsychiatric symptoms; however, less is known about the relationships between these components of post-COVID-19 condition and fatigue itself. Consequently, the present study sought to (1) distinguish the types of fatigue experienced by participants, and (2) investigate whether cognitive deficits across various domains and neuropsychiatric conditions predicted these different types of fatigue. The study included 136 COVID-19 patients referred for neuropsychological evaluation due to cognitive complaints 8 months on average after SARS-CoV-2 infection. Measures included self-reported fatigue (physical, cognitive, and psychosocial), neuropsychiatric questionnaires (assessing symptoms of depression, anxiety, apathy, and executive functioning), a comprehensive neuropsychological assessment, and self-reported quality of life and everyday functioning. Results showed that reports of clinical significant fatigue were pervasive in our sample (82.3% of participants), with physical fatigue rated highest on average relative to the subscale maximum. Elevated levels of apathy, anxiety, and executive dysfunction in neuropsychiatric measures along with executive and attentional difficulties on cognitive tests were found to be consistently important predictors among different types of fatigue. This implicates both cognitive and neuropsychiatric symptoms as predictors of fatigue in post-COVID-19 condition, and stresses the importance of a holistic approach in assessing and considering potential treatment for COVID-19 patients experiencing fatigue.

SARS-CoV-2 Nsp13 encodes for an HLA-E-stabilizing peptide that abrogates inhibition of NKG2A-expressing NK cells.

Natural killer (NK) cells are innate immune cells that contribute to host defense against virus infections. NK cells respond to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in vitro and are activated in patients with acute coronavirus disease 2019 (COVID-19). However, by which mechanisms NK cells detect SARS-CoV-2-infected cells remains largely unknown. Here, we show that the Non-structural protein 13 of SARS-CoV-2 encodes for a peptide that is presented by human leukocyte antigen E (HLA-E). In contrast with self-peptides, the viral peptide prevents binding of HLA-E to the inhibitory receptor NKG2A, thereby rendering target cells susceptible to NK cell attack. In line with these observations, NKG2A-expressing NK cells are particularly activated in patients with COVID-19 and proficiently limit SARS-CoV-2 replication in infected lung epithelial cells in vitro. Thus, these data suggest that a viral peptide presented by HLA-E abrogates inhibition of NKG2A+ NK cells, resulting in missing self-recognition.

SARS-CoV-2 Nsp13 encodes for an HLA-E-stabilizing peptide that abrogates inhibition of NKG2A-expressing NK cells

Natural killer (NK) cells eliminate virus-infected cells. Hammer et al. show that SARS-CoV-2 encodes for a peptide that does not bind to an inhibitory receptor of NK cells, thereby facilitating NK cell activation. This missing self recognition could enable NK cells to detect and kill SARS-CoV-2-infected cells.

Broad anti-SARS-CoV-2 antibody immunity induced by heterologous ChAdOx1/mRNA-1273 vaccination.

Heterologous prime-boost immunization strategies have the potential to augment COVID-19 vaccine efficacy. We longitudinally profiled severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike (S)-specific serological and memory B cell (MBC) responses in individuals who received either homologous (ChAdOx1:ChAdOx1) or heterologous (ChAdOx1:mRNA-1273) prime-boost vaccination. Heterologous messenger RNA (mRNA) booster immunization induced higher serum neutralizing antibody and MBC responses against SARS-CoV-2 variants of concern (VOCs) compared with that of homologous ChAdOx1 boosting. Specificity mapping of circulating B cells revealed that mRNA-1273 boost immunofocused ChAdOx1-primed responses onto epitopes expressed on prefusion-stabilized S. Monoclonal antibodies isolated from mRNA-1273-boosted participants displayed overall higher binding affinities and increased breadth of reactivity against VOCs relative to those isolated from ChAdOx1-boosted individuals. Overall, the results provide molecular insight into the enhanced quality of the B cell response induced after heterologous mRNA booster vaccination.

High-dimensional profiling reveals phenotypic heterogeneity and disease-specific alterations of granulocytes in COVID-19.

Since the outset of the COVID-19 pandemic, increasing evidence suggests that the innate immune responses play an important role in the disease development. A dysregulated inflammatory state has been proposed as a key driver of clinical complications in COVID-19, with a potential detrimental role of granulocytes. However, a comprehensive phenotypic description of circulating granulocytes in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-infected patients is lacking. In this study, we used high-dimensional flow cytometry for granulocyte immunophenotyping in peripheral blood collected from COVID-19 patients during acute and convalescent phases. Severe COVID-19 was associated with increased levels of both mature and immature neutrophils, and decreased counts of eosinophils and basophils. Distinct immunotypes were evident in COVID-19 patients, with altered expression of several receptors involved in activation, adhesion, and migration of granulocytes (e.g., CD62L, CD11a/b, CD69, CD63, CXCR4). Paired sampling revealed recovery and phenotypic restoration of the granulocytic signature in the convalescent phase. The identified granulocyte immunotypes correlated with distinct sets of soluble inflammatory markers, supporting pathophysiologic relevance. Furthermore, clinical features, including multiorgan dysfunction and respiratory function, could be predicted using combined laboratory measurements and immunophenotyping. This study provides a comprehensive granulocyte characterization in COVID-19 and reveals specific immunotypes with potential predictive value for key clinical features associated with COVID-19.

Key factors affecting people's unwillingness to be confined during the COVID-19 pandemic in Spain: a large-scale population study.

Population confinements have been one of the most widely adopted non-pharmaceutical interventions (NPIs) implemented by governments across the globe to help contain the spread of the SARS-CoV-2 virus. While confinement measures have been proven to be effective to reduce the number of infections, they entail significant economic and social costs. Thus, different policy makers and social groups have exhibited varying levels of acceptance of this type of measures. In this context, understanding the factors that determine the willingness of individuals to be confined during a pandemic is of paramount importance, particularly, to policy and decision-makers. In this paper, we study the factors that influence the unwillingness to be confined during the COVID-19 pandemic by the means of a large-scale, online population survey deployed in Spain. We perform two types of analyses (logistic regression and automatic pattern discovery) and consider socio-demographic, economic and psychological factors, together with the 14-day cumulative incidence per 100,000 inhabitants. Our analysis of 109,515 answers to the survey covers data spanning over a 5-month time period to shed light on the impact of the passage of time. We find evidence of pandemic fatigue as the percentage of those who report an unwillingness to be in confinement increases over time; we identify significant gender differences, with women being generally less likely than men to be able to sustain long-term confinement of at least 6 months; we uncover that the psychological impact was the most important factor to determine the willingness to be in confinement at the beginning of the pandemic, to be replaced by the economic impact as the most important variable towards the end of our period of study. Our results highlight the need to design gender and age specific public policies, to implement psychological and economic support programs and to address the evident pandemic fatigue as the success of potential future confinements will depend on the population's willingness to comply with them.

A Review of Spatiotemporal Models for Count Data in R Packages. A Case Study of COVID-19 Data

Spatiotemporal models for count data are required in a wide range of scientific fields, and they have become particularly crucial today because of their ability to analyze COVID-19-related data. The main objective of this paper is to present a review describing the most important approaches, and we monitor their performance under the same dataset. For this review, we focus on the three R-packages that can be used for this purpose, and the different models assessed are representative of the two most widespread methodologies used to analyze spatiotemporal count data: the classical approach and the Bayesian point of view. A COVID-19-related case study is analyzed as an illustration of these different methodologies. Because of the current urgent need for monitoring and predicting data in the COVID-19 pandemic, this case study is, in itself, of particular importance and can be considered the secondary objective of this work. Satisfactory and promising results have been obtained in this second goal. With respect to the main objective, it has been seen that, although the three models provide similar results in our case study, their different properties and flexibility allow us to choose the model depending on the application at hand.

SARS-CoV-2-specific humoral and cellular immunity persists through 9 months irrespective of COVID-19 severity at hospitalisation.

OBJECTIVES: Humoral and cellular immunity to SARS-CoV-2 following COVID-19 will likely contribute to protection from reinfection or severe disease. It is therefore important to characterise the initiation and persistence of adaptive immunity to SARS-CoV-2 amidst the ongoing pandemic. METHODS: Here, we conducted a longitudinal study on hospitalised moderate and severe COVID-19 patients from the acute phase of disease into convalescence at 5 and 9 months post-symptom onset. Utilising flow cytometry, serological assays as well as B cell and T cell FluoroSpot assays, we assessed the magnitude and specificity of humoral and cellular immune responses during and after human SARS-CoV-2 infection. RESULTS: During acute COVID-19, we observed an increase in germinal centre activity, a substantial expansion of antibody-secreting cells and the generation of SARS-CoV-2-neutralising antibodies. Despite gradually decreasing antibody levels, we show persistent, neutralising antibody titres as well as robust specific memory B cell responses and polyfunctional T cell responses at 5 and 9 months after symptom onset in both moderate and severe COVID-19 patients. CONCLUSION: Our findings describe the initiation and, importantly, persistence of cellular and humoral SARS-CoV-2-specific immunological memory in hospitalised COVID-19 patients long after recovery, likely contributing towards protection against reinfection.

Aproximación a la respuesta comunitaria a la pandemia por COVID-19 de los equipos de Atención Primaria de Salud aragoneses

INTRODUCCIÓN: ¿cómo seguir trabajando la orientación y participación comunitaria en Atención Primaria durante la pandemia por COVID-19?. OBJETIVOS Y MÉTODOS: observar, describir, reflexionar y documentar aspectos relativos a la atención comunitaria en el momento actual de pandemia por COVID-19 en los equipos de Atención Primaria (EAP) de Aragón. Estudio exploratorio-descriptivo observacional transversal con enfoque cualitativo, con dos fases. 1ª: recopilación de experiencias comunitarias y localización de informantes clave. 2ª: descripción de acciones comunitarias. Análisis descriptivo y tipo DAFO. RESULTADOS: se detectaron 47 iniciativas. Participaron 11 expertas y 54 informantes clave. El 66,6% consideró el rol de los EAP como consultores/colaboradores. El 64,9% de las iniciativas contempló la diversidad. El 49,1% no sabía si valoraron diferencias por género. Destacaron la importancia de lo comunitario para superar la crisis y la cooperación y coordinación con la comunidad e instituciones locales. DISCUSIÓN: protocolos con orientación biomédica, miedo e incertidumbre por la COVID-19 dificultaron el desarrollo de iniciativas comunitarias;frente a esto, fue clave la trayectoria comunitaria previa de los EAP, el trabajo en equipo, con especial relevancia el de las trabajadoras sociales, y su motivación. La participación del EAP como colaborador refuerza la importancia del liderazgo compartido. Son necesarios espacios colaborativos, apoyo institucional y coordinación intersectorial. CONCLUSIÓN: durante la pandemia, las comunidades deben ser parte de la respuesta;la orientación comunitaria de los EAP es clave. Es preciso visibilizar, acompañar y reforzar el trabajo comunitario y estimular la coordinación con Salud Pública INTRODUCTION: How to continue working on community guidance and participation in Primary Care during the COVID-19 pandemic?. OJECTIVES AND METHODS: To observe, report, reflect and document autonomous community experiences of Aragonese Primary Care Teams (PCT) during the COVID-19 pandemic. A two-phase exploratory-descriptive observational, cross-sectional study with a qualitative approach. Phase 1: compilation of experiences in community health and location of key informants. Phase 2: description of community actions. Descriptive and SWOT analysis. RESULTS: A total of 47 initiatives were detected;11 experts and 54 key informants took part. A total of 66.6% considered the role of the PCT as consultants or collaborators;64.9% of initiatives considered diversity. A total of 49.1% did not know whether they evaluated differences by sex. They highlighted the importance of the community to overcome the crisis, and cooperation and coordination with community and local institutions. DISCUSSION: Protocols with biomedical guidance, fear and uncertainty due to COVID-19 hindered development of community initiatives. In light of this, the previous community trajectory of PCTs, teamwork with special relevance of social workers and their motivation were fundamental. PCT involvement as a partner strengthens the importance of shared leadership. Collaborative spaces, institutional support and intersectoral coordination are all necessary. CONCLUSION: During the pandemic, communities must be part of the response;PCT community guidance is essential. Visibility, working alongside and strengthening community work and stimulating public health coordination are all necessary requirements

Innate lymphoid cell composition associates with COVID-19 disease severity.

OBJECTIVES: The role of innate lymphoid cells (ILCs) in coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is unknown. Understanding the immune response in COVID-19 could contribute to unravel the pathogenesis and identification of treatment targets. Here, we describe the phenotypic landscape of circulating ILCs in COVID-19 patients and identified ILC phenotypes correlated to serum biomarkers, clinical markers and laboratory parameters relevant in COVID-19. METHODS: Blood samples collected from moderately (n = 11) and severely ill (n = 12) COVID-19 patients, as well as healthy control donors (n = 16), were analysed with 18-parameter flow cytometry. Using supervised and unsupervised approaches, we examined the ILC activation status and homing profile. Clinical and laboratory parameters were obtained from all COVID-19 patients, and serum biomarkers were analysed with multiplex immunoassays. RESULTS: Innate lymphoid cells were largely depleted from the circulation of COVID-19 patients compared with healthy controls. Remaining circulating ILCs revealed decreased frequencies of ILC2 in severe COVID-19, with a concomitant decrease of ILC precursors (ILCp) in all patients, compared with controls. ILC2 and ILCp showed an activated phenotype with increased CD69 expression, whereas expression levels of the chemokine receptors CXCR3 and CCR4 were significantly altered in ILC2 and ILCp, and ILC1, respectively. The activated ILC profile of COVID-19 patients was associated with soluble inflammatory markers, while frequencies of ILC subsets were correlated with laboratory parameters that reflect the disease severity. CONCLUSION: This study provides insights into the potential role of ILCs in immune responses against SARS-CoV-2, particularly linked to the severity of COVID-19.

Characteristics, complications and outcomes among 1549 patients hospitalised with COVID-19 in a secondary hospital in Madrid, Spain: a retrospective case series study.

OBJECTIVES: To describe demographic, clinical, radiological and laboratory characteristics, as well as outcomes, of patients admitted for COVID-19 in a secondary hospital. DESIGN AND SETTING: Retrospective case series of sequentially hospitalised patients with confirmed SARS-CoV-2, at Infanta Leonor University Hospital (ILUH) in Madrid, Spain. PARTICIPANTS: All patients attended at ILUH testing positive to reverse transcriptase-PCR on nasopharyngeal swabs and diagnosed with COVID-19 between 1 March 2020 and 28 May 2020. RESULTS: A total of 1549 COVID-19 cases were included (median age 69 years (IQR 55.0-81.0), 57.5% men). 78.2% had at least one underlying comorbidity, the most frequent was hypertension (55.8%). Most frequent symptoms at presentation were fever (75.3%), cough (65.7%) and dyspnoea (58.1%). 81 (5.8%) patients were admitted to the intensive care unit (ICU) (median age 62 years (IQR 51-71); 74.1% men; median length of stay 9 days (IQR 5-19)) 82.7% of them needed invasive ventilation support. 1393 patients had an outcome at the end of the study period (case fatality ratio: 21.2% (296/1393)). The independent factors associated with fatality (OR; 95% CI): age (1.07; 1.06 to 1.09), male sex (2.86; 1.85 to 4.50), neurological disease (1.93; 1.19 to 3.13), chronic kidney disease (2.83; 1.40 to 5.71) and neoplasia (4.29; 2.40 to 7.67). The percentage of hospital beds occupied with COVID-19 almost doubled (702/361), with the number of patients in ICU quadrupling its capacity (32/8). Median length of stay was 9 days (IQR 6-14). CONCLUSIONS: This study provides clinical characteristics, complications and outcomes of patients with COVID-19 admitted to a European secondary hospital. Fatal outcomes were similar to those reported by hospitals with a higher level of complexity.

Expansion of SARS-CoV-2-Specific Antibody-Secreting Cells and Generation of Neutralizing Antibodies in Hospitalized COVID-19 Patients.

Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), emerged in late 2019 and has since become a global pandemic. Pathogen-specific Abs are typically a major predictor of protective immunity, yet human B cell and Ab responses during COVID-19 are not fully understood. In this study, we analyzed Ab-secreting cell and Ab responses in 20 hospitalized COVID-19 patients. The patients exhibited typical symptoms of COVID-19 and presented with reduced lymphocyte numbers and increased T cell and B cell activation. Importantly, we detected an expansion of SARS-CoV-2 nucleocapsid protein-specific Ab-secreting cells in all 20 COVID-19 patients using a multicolor FluoroSpot Assay. Out of the 20 patients, 16 had developed SARS-CoV-2-neutralizing Abs by the time of inclusion in the study. SARS-CoV-2-specific IgA, IgG, and IgM Ab levels positively correlated with SARS-CoV-2-neutralizing Ab titers, suggesting that SARS-CoV-2-specific Ab levels may reflect the titers of neutralizing Abs in COVID-19 patients during the acute phase of infection. Last, we showed that IL-6 and C-reactive protein serum concentrations were higher in patients who were hospitalized for longer, supporting the recent observations that IL-6 and C-reactive protein could be used as markers for COVID-19 severity. Altogether, this study constitutes a detailed description of clinical and immunological parameters in 20 COVID-19 patients, with a focus on B cell and Ab responses, and describes tools to study immune responses to SARS-CoV-2 infection and vaccination.