Highly resolved spatial transcriptomics for detection of rare events in cells

Single-cell spatial transcriptomics technologies leveraged the potential to transcriptionally landscape sophisticated reactions in cells. Current methods to delineate such complex interplay lack the flexibility in rapid target adaptation and are particularly restricted in detecting rare transcripts. We developed a multiplex single-cell RNA In-situ hybridization technique, called Molecular Cartography (MC) that can be easily tailored to specific applications and, by providing unprecedented sensitivity, specificity and resolution, is particularly suitable in tracing rare events at a subcellular level. Using a SARS-CoV-2 infection model, MC allows the discernment of single events in host-pathogen interactions, dissects primary from secondary responses, and illustrates differences in antiviral signaling pathways affected by SARS-CoV-2, simultaneously in various cell types.

Potential contributors to increased pulmonary embolism hospitalizations during the Covid-19 pandemic

BackgroundAfter the first Covid-19 infection wave, a constant increase of pulmonary embolism (PE) hospitalizations not linked with active PCR-confirmed Covid-19 has been observed but potential contributors to this observation are unclear. Therefore, we analyzed associations between changes in PE hospitalizations and (1) the incidence of non-Covid-19 pneumonia, (2) the use of computed tomography pulmonary angiography (CTPA), (3) volume depletion and (4) preceding Covid-19 infection numbers in Germany. MethodsClaims data of Helios hospitals in Germany were used and consecutive cases with a hospital admission between May 6 and December 15, 2020 (PE surplus period) were analyzed and compared to corresponding periods covering the same weeks in 2016-2019 (control period). We analyzed the number of PE cases in the target period with multivariable Poisson general linear mixed models (GLMM) including (a) cohorts of 2020 versus 2016- 2019, (b) the number of cases with pneumonia, (c) CTPA, and (d) volume depletion and adjusted for age and sex. In order to associate the daily number of PE cases in 2020 with the number of preceding SARS-CoV-2 infections in Germany, we calculated the average number of daily infections (divided by 10,000) occurring 14 up to 90 days with increasing window sizes before PE cases and modelled the data with Poisson regression. ResultsThere were 2,404 PE hospitalizations between May 6 and December 15, 2020 as opposed to 2,112 - 2,236 (total 8,717) in the corresponding 2016 - 2019 control periods. (crude rate ratio [CRR] 1.10, 95% CI 1.05 - 1.15, P<0.01). Using multivariable Poisson GLMM adjusted for age, sex and volume depletion, PE cases were significantly associated with the number of cases with pneumonia (CRR 1.09, 95 % CI 1.07-1.10, P<0.01), and with CTPA (CRR 1.10, 95 % CI 1.09-1.10, P<0.01). The increase of PE cases in 2020 compared with the control period remained significant (CRR 1.07, 95 % CI 1.02-1.12, P<0.01) when controlling for those factors. In the 2020 cohort, number of preceding average daily Covid-19 infections were associated with increased PE case incidence in all investigated windows, i.e. including preceding infections from 14 to 90 days. The best model (log likelihood -576) was with a window size of 4 days, i.e. average Covid-19 infections 14 - 17 days before PE hospitalization had a risk of 1.20 (95 % CI 1.12- 1.29, P<0.01). ConclusionsThere is an increase in PE cases since early May 2020 compared to corresponding periods in 2016 - 2019. This surplus was significant even when controlling for changes in potential modulators such as demographics, volume depletion, non-Covid-19 pneumonia, CTPA use and preceding Covid-19 infections. Future studies are needed (1) to investigate a potential causal link for increased risk of delayed PE with preceding SARS-CoV-2 infection, and (2) to define optimal screening for SARS-CoV-2 in patients presenting with pneumonia and PE.

Hospitalizations, resource use and outcomes of acute pulmonary embolism in Germany during the Covid-19 pandemic - Emergence of different phenotypes of thrombotic disease?

BackgroundThere is discussion evolving around the emergence of different phenotypes of Covid-19-associated thromboembolic disease, i.e. acute pulmonary embolism vs pulmonary thrombosis and different phenotypes of in situ thrombosis. With this study, we wish to provide hospitalization, treatment and in-hospital outcome data for pulmonary embolism during the 2020 Covid-19 pandemic and a corresponding 2016 - 2019 control period. MethodsWe performed a retrospective analysis of claims data of Helios hospitals in Germany. Consecutive cases with a hospital admission between January 1 and December 15, 2020 and pulmonary embolism as primary discharge diagnosis were analyzed and compared to a corresponding period covering the same weeks in 2016 - 2019. ResultsAs previously reported for other emergent medical conditions, there was a hospitalization deficit coinciding with the 1st pandemic wave. Beginning with the 12-week interval May 6 - July 28, there was a stable surplus of hospital admissions in 2020. During this surplus period (May 6 - December 15, 2020), there were 2,449 hospitalizations including 45 PCR-confirmed Covid-19 cases (1.8%) as opposed to 8,717 in 2016 - 2019 (IRR 1.12, 95% CI 1.07 - 1.18, P<0.01). When excluding Covid-19 cases IRR was 1.10 (95% CI 1.05 - 1.15, P<0.01). While overall comorbidities expressed as weighted AHRQ Elixhauser Comorbidity Index (14.1 {+/-} 10.1 vs. 13.9 {+/-}10.3, P=0.28), the presence of thrombosis (46.1 vs 45.4%, P=0.55) and surgery (3.8 vs. 4.3%, P=0.33) were comparable, coagulopathy (3.3 vs 4.5%, P=0.01) and metastatic cancer (3.0 vs 4.0%, P=0.03) as contributing factors were less frequently observed during the 2020 surplus. Interventional treatments (thrombolytic therapy, thrombectomy or inferior vena cava filter placement) were less frequently used (4.7 vs 6.6%, OR 0.72, 95% CI 0.58 - 0.89, P< 0.01). Similarly, intensive care (35.1 vs 38.8%, OR 0.83, 95% CI 0.75 - 0.92, P< 0.01) and mechanical ventilation utilization (7.2 vs 8.1%, OR 0.88, 95% CI 0.74 - 1.04, P=0.14) as well as in-hospital-mortality rates (7.8 vs 9.8%, OR 0.76, 95% CI 0.64 - 0.90, P< 0.01) were lower in 2020 compared with 2016 - 2019. This was associated with a shorter length of hospital stay (6.4 {+/-}5.4 vs. 7.2 {+/-}5.7 days, P< 0.01) during the 2020 surplus period. ConclusionsOnly a minority of cases were associated with PCR-confirmed Covid-19 but this does not rule out preceding or undetected SARS-CoV-2 infection. Although there is a shift towards milder disease course, the increased incidence of hospitalizations for pulmonary embolism requires immediate attention, close surveillance and further studies.

Hospitalizations for emergency-sensitive conditions in Germany during the Covid-19 pandemic - Insights from the German-wide Helios hospital network

BackgroundWhile there are numerous reports that describe emergency care during the early Covid-19 pandemic, there is scarcity of data for later stages. This study analyzes hospitalization rates for 37 emergency-sensitive conditions in the largest German-wide hospital network during different pandemic phases. MethodsUsing claims data of 80 hospitals, consecutive cases between January 1 and November 17, 2020 were analyzed and compared to a corresponding period in 2019. Incidence-rate ratios (IRR) comparing the both periods were calculated using Poisson regression to model the number of hospitalizations per day. ResultsThere was a hospitalization deficit between March 12 and June 13, 2020 (coinciding with the 1st pandemic wave) with 32,807 hospitalizations as opposed to 39,379 in 2019 (IRR 0.83, 95% CI 0.82 - 0.85, P<0.01). During the following period (June 14 to November 17, 2020, including the start of 2nd wave), hospitalizations were reduced from 63,799 in 2019 to 59,910 in 2020, but this reduction was not that pronounced (IRR 0.94, 95% CI 0.93 - 0.95, P<0.01). There was an increase in hospitalizations for acute myocardial infarction, aortic aneurism/dissection and pulmonary embolism after the 1st wave during which hospitalizations had been reduced for those conditions. In contrast, hospitalizations for sepsis, pneumonia, obstructive pulmonary disease, and intracranial injuries were reduced during the entire pandemic. ConclusionsThere was an overall reduction of hospitalizations for emergency-sensitive conditions in Germany during the Covid-19 pandemic with heterogeneous effects on different disease categories. The increase of hospitalizations for acute myocardial infarction, aortic aneurism/dissection and pulmonary embolism is an alarming signal that requires attention and further studies. KEY MESSAGESO_ST_ABSWhat is already known on this subjectC_ST_ABSO_LIThere has been a reduction in emergency room visits and hospital admissions for several emergent medical and surgical conditions during the early Covid-19 pandemic (1st wave). C_LI What this study addsO_LIUsing claims data of 80 German-wide Helios hospitals, we found an overall reduction of hospitalizations for emergency-sensitive conditions in Germany during the Covid-19 pandemic until mid November 2020 with heterogeneous effects on different disease categories. While hospitalizations for sepsis, pneumonia, obstructive pulmonary disease, and intracranial injuries were reduced during the entire pandemic. There was an alarming increase of hospitalizations for acute myocardial infarction, aortic aneurism/dissection and pulmonary embolism after the 1st wave. C_LI