Disease severity related to VOC dominance in unvaccinated SARS-CoV-2 positive adults without risk factors in Sweden

Although the emerging SARS-CoV-2 variants of concern (VOC) have shown increasing transmissibility, their role for causing severe disease has not been fully clarified. Here, we studied changes in rates of hospitalisation and severe illness (subjection to high-flow nasal oxygen or admission to an intensive care unit during hospital stay) among all (n=685 891) unvaccinated SARS-CoV-2 positive adults without risk factors in Sweden from November 2020 to September 2021. After adjustment for age, sex, and socio-economic factors, and with November 2020 (non-VOC period) as reference, the odds ratios (OR) for hospitalisation were 1.6-1.7 in March-May 2021 (Alpha VOC dominance) and 2.4-3.0 in June-September 2021 (Delta VOC dominance), and the ORs for severe illness were 1.8-2.1 in March-May 2021 and 3.1-4.7 in June-September 2021. This study shows that unvaccinated adults without risk factors, have had a gradually increased risk for hospital admission and severe illness when infected with the Alpha and Delta VOCs, respectively.

Second wave mortality among patients hospitalised for COVID-19 in Sweden: a nationwide observational cohort study

BackgroundDuring the first pandemic wave, a substantial decline in mortality was seen among hospitalised COVID-19 patients. We aimed to study if the decreased mortality continued during the second wave, using data compiled by the Swedish National Board of Health and Welfare. MethodRetrospective nationwide observational study of all patients hospitalised in Sweden between March 1st and December 31st, 2020, with SARS-CoV-2 RNA positivity 14 days before to 5 days after admission and a discharge code for COVID-19. Outcome was 60-day all-cause mortality. Poisson regression was used to estimate the relative risk (RR) for death by month of admission, adjusting for age, sex, socio-economic data, comorbidity, care dependency, and country of birth. FindingsA total of 32 452 patients were included. December had the highest number of admissions/month (n=8253) followed by April (n=6430). The 60-day crude mortality decreased from 24{middle dot}7% (95% CI, 23{middle dot}0%-26{middle dot}5%) for March to 10{middle dot}4% (95% CI, 8{middle dot}9%-12{middle dot}1%) for July-September (as reported previously), later increased to 19{middle dot}9% (95% CI, 19{middle dot}1-20{middle dot}8) for December. RR for 60-day death for December (reference) was higher than those for June to November (RR ranging from 0{middle dot}74 to 0{middle dot}89; 95% CI <1 for all months). SARS-CoV-2 variants of concern were only sporadically found in Sweden before January 2021. InterpretationThe decreased mortality of hospitalised COVID-19 patients after the first wave turned and increased during the second wave. Focused research is urgent to describe if this increase was caused by a high load of patients, management and treatment, viral properties, or other factors. Research in contextO_ST_ABSEvidence before this studyC_ST_ABSDuring the first pandemic wave, a substantial decline in mortality was seen among hospitalised COVID-19 patients in many countries. As the reason for this decline has not been clarified, no one could foresee how mortality would change during forthcoming waves. Added valueThis retrospective nationwide study of all patients hospitalised for COVID-19 in Sweden from March to December 2020 showed that the gradual decrease in mortality seen in the first pandemic wave was followed by an increased crude and adjusted 60-day all-cause mortality during the second wave. This increase in mortality occurred although the standard-of-care recommendations for hospitalised COVID-19 patients did not change in Sweden during the second half of 2020. Implications of all the available evidenceWhile improved standard-of-care was believed to be an important factor for the decrease in mortality during the first pandemic wave, the increasing mortality during the second wave has no apparent explanation. As the currently known virus variants of concern occurred only sporadically in Sweden before January 2021, they were most likely not involved. Focused research is urgent to describe if this increase in mortality was caused by a high load of patients, management and treatment factors, viral properties, or other circumstances

Longitudinal characterization of humoral and cellular immunity in hospitalized COVID-19 patients reveal immune persistence up to 9 months after infection

BackgroundInsights into early, specific humoral and cellular responses to infection with SARS-CoV-2, as well as the persistence and magnitude of resulting immune memory is important amidst the ongoing pandemic. The combination of humoral and cellular immunity will most likely contribute to protection from reinfection or severe disease. MethodsHere, we conducted a longitudinal study on hospitalized moderate and severe COVID-19 patients from the acute phase of disease into convalescence at five- and nine-months post symptom onset. Utilizing 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 memory during and after human SARS-CoV-2 infection. FindingsDuring acute COVID-19, we observed an increase in germinal center activity, a substantial expansion of antibodysecreting cells, and the generation of SARS-CoV-2-neutralizing antibodies. Despite gradually decreasing antibody levels, we show persistent, neutralizing antibody titers as well as robust specific memory B cell responses and polyfunctional T cell responses at five- and nine-months after symptom onset in both moderate and severe COVID-19 patients. Long-term SARS-CoV-2 specific responses were marked by preferential targeting of spike over nucleocapsid protein. ConclusionsOur findings describe the initiation and, importantly, persistence of cellular and humoral SARS-CoV-2 specific immunological memory in hospitalized COVID-19 patients long after recovery, likely contributing towards protection against reinfection.

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 key driver of clinical complications in COVID-19, with a potential detrimental role of granulocytes. However, a comprehensive phenotypic description of circulating granulocytes in 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 multi-organ 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. SignificanceAccumulating evidence shows that granulocytes are key modulators of the immune response to SARS-CoV-2 infection and their dysregulation could significantly impact COVID-19 severity and patient recovery after virus clearance. In the present study, we identify selected immune traits in neutrophil, eosinophil and basophil subsets associated to severity of COVID-19 and to peripheral protein profiles. Moreover, computational modeling indicates that the combined use of phenotypic data and laboratory measurements can effectively predict key clinical outcomes in COVID-19 patients. Finally, patient-matched longitudinal analysis shows phenotypic normalization of granulocyte subsets 4 months after hospitalization. Overall, in this work we extend the current understanding of the distinct contribution of granulocyte subsets to COVID-19 pathogenesis.

Decline in mortality among hospitalised covid-19 patients in Sweden: a nationwide observational study

OBJECTIVEIt is important to know if mortality among hospitalised covid-19 patients has changed as the pandemic has progressed. The aim of this study was to describe the dynamics of mortality among patients hospitalised for covid-19 in a nationwide study. DESIGNNationwide observational cohort study of all patients hospitalised in Sweden 1 March to 30 June 2020 with SARS-CoV-2 RNA positivity 14 days before to 5 days after admission, and a discharge code for covid-19. SETTINGAll hospitals in Sweden. PARTICIPANTS15 761 hospitalised patients with covid-19, with data compiled by the Swedish National Board of Health and Welfare. MAIN OUTCOME MEASURESOutcome was 60-day all-cause mortality. Patients were stratified according to month of hospital admission. Poisson regression was used to estimate the relative risk of death by month of admission, adjusting for pre-existing conditions, age, sex, care dependency, and severity of illness (Simplified Acute Physiology, version 3), for patients in intensive care units (ICU). RESULTSThe overall 60-day mortality was 17.8% (95% confidence interval (CI), 17.2% to 18.4%), and it decreased from 24.7% (95% CI, 23.0% to 26.5%) in March to 13.3% (95% CI, 12.1% to 14.7%) in June. Adjusted relative risk (RR) of death was 0.56 (95% CI, 0.51 to 0.63) for June, using March as reference. Corresponding RR for patients not admitted to ICU and those admitted to ICU were 0.60 (95% CI, 0.53 to 0.67) and 0.61 (95% CI, 0.48 to 0.79), respectively. The proportion of patients admitted to ICU decreased from 19.5% (95% CI, 17.9% to 21.0%) in the March cohort to 11.0% (95% CI, 9.9% to 12.2%) in the June cohort. CONCLUSIONSThere was a gradual decline in mortality from March to June 2020 in Swedish hospitalised covid-19 patients, which was independent of pre-existing conditions, age, and sex. Future research is needed to explain the reasons for this decline. The changing covid-19 mortality should be taken into account when management and results of studies from the first pandemic wave are evaluated.

Innate lymphoid cell composition associates with COVID-19 disease severity

ObjectivesThe 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. To describe the phenotypic landscape of circulating ILCs in COVID-19 patients and to identify ILC phenotypes correlated to serum biomarkers, clinical markers, and laboratory parameters relevant in COVID-19. MethodsBlood samples collected from moderately (n=11) and severely ill (n=12) COVID-19 patients as well as healthy control donors (n=16), were analyzed 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 analyzed with multiplex immunoassays. ResultsILCs were largely depleted from the circulation of COVID-19 patients compared with healthy controls. Remaining circulating ILCs from patients revealed increased frequencies of ILC2 in moderate COVID-19, with a concomitant decrease of ILC precursors (ILCp), as 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. ConclusionThis study provides insights into the potential role of ILCs in immune responses against SARS-CoV-2, particularly linked to the severity of COVID-19.

MAIT cell activation and dynamics associated with COVID-19 disease severity and outcome

Severe COVID-19 is characterized by excessive inflammation of the lower airways. The balance of protective versus pathological immune responses in COVID-19 is incompletely understood. Mucosa-associated invariant T (MAIT) cells are antimicrobial T cells that recognize bacterial metabolites, and can also function as innate-like sensors and mediators of antiviral responses. Here, we investigated the MAIT cell compartment in COVID-19 patients with moderate and severe disease, as well as in convalescence. We show profound and preferential decline in MAIT cells in circulation of patients with active disease paired with strong activation, as well as significant MAIT cell enrichment and pro-inflammatory IL-17A bias in the airways. Unsupervised analysis identified MAIT cell CD69high and CXCR3low immunotypes associated with poor clinical outcome. MAIT cell levels normalized in the convalescent phase, consistent with dynamic recruitment to the tissues and subsequent release with disease resolution. These findings indicate that MAIT cells are engaged in the immune response against SARS-CoV-2 and suggest their involvement in COVID-19 immunopathogenesis. One sentence summaryMAIT cells are strongly activated by SARS-CoV-2 infection in a manner associated with disease severity and outcome, they decline in blood, are enriched in the airways as a prominent IL-17A expressing subset, and dynamically recover in circulation during convalescence.

Perturbations in the mononuclear phagocyte landscape associated with COVID-19 disease severity

Monocytes and dendritic cells are crucial mediators of innate and adaptive immune responses during viral infection, but misdirected responses by these cells might contribute to immunopathology. A comprehensive map of the mononuclear phagocyte (MNP) landscape during SARS-CoV-2 infection and concomitant COVID-19 disease is lacking. We performed 25-color flow cytometry-analysis focusing on MNP lineages in SARS-CoV-2 infected patients with moderate and severe COVID-19. While redistribution of monocytes towards intermediate subset and decrease in circulating DCs occurred in response to infection, severe disease associated with appearance of Mo-MDSC-like cells and a higher frequency of pre-DC2. Furthermore, phenotypic alterations in MNPs, and their late precursors, were cell-lineage specific and in select cases associated with severe disease. Finally, unsupervised analysis revealed that the MNP profile, alone, could identify a cluster of COVID-19 non-survivors. This study provides a reference for the MNP response to clinical SARS-CoV-2 infection and unravel myeloid dysregulation associated with severe COVID-19.

Natural killer cell activation related to clinical outcome of COVID-19

Understanding innate immune responses in COVID-19 is important for deciphering mechanisms of host responses and interpreting disease pathogenesis. Natural killer (NK) cells are innate effector lymphocytes that respond to acute viral infections, but might also contribute to immune pathology. Here, using 28-color flow cytometry, we describe a state of strong NK cell activation across distinct subsets in peripheral blood of COVID-19 patients, a pattern mirrored in scRNA-seq signatures of lung NK cells. Unsupervised high-dimensional analysis identified distinct immunophenotypes that were linked to disease severity. Hallmarks of these immunophenotypes were high expression of perforin, NKG2C, and Ksp37, reflecting a high presence of adaptive NK cell expansions in circulation of patients with severe disease. Finally, arming of CD56bright NK cells was observed in course of COVID-19 disease states, driven by a defined protein-protein interaction network of inflammatory soluble factors. This provides a detailed map of the NK cell activation-landscape in COVID-19 disease.