Exploring the Spatial Relative Risk of COVID-19 in Berlin-Neukölln.

Identifying areas with high and low infection rates can provide important etiological clues. Usually, areas with high and low infection rates are identified by aggregating epidemiological data into geographical units, such as administrative areas. This assumes that the distribution of population numbers, infection rates, and resulting risks is constant across space. This assumption is, however, often false and is commonly known as the modifiable area unit problem. This article develops a spatial relative risk surface by using kernel density estimation to identify statistically significant areas of high risk by comparing the spatial distribution of address-level COVID-19 cases and the underlying population at risk in Berlin-Neukölln. Our findings show that there are varying areas of statistically significant high and low risk that straddle administrative boundaries. The findings of this exploratory analysis further highlight topics such as, e.g., Why were mostly affluent areas affected during the first wave? What lessons can be learned from areas with low infection rates? How important are built structures as drivers of COVID-19? How large is the effect of the socio-economic situation on COVID-19 infections? We conclude that it is of great importance to provide access to and analyse fine-resolution data to be able to understand the spread of the disease and address tailored health measures in urban settings.

Performance of 20 rapid antigen detection tests to detect SARS-CoV-2 B.1.617.2 (Delta) and B.1.1.529 (Omicron) variants using a clinical specimen panel from January 2022, Berlin, Germany.

BackgroundThere are conflicting reports on the performance of rapid antigen detection tests (RDT) in the detection of the SARS-CoV-2 Omicron (B.1.1.529) variant; however, these tests continue to be used frequently to detect potentially contagious individuals with high viral loads.AimThe aim of this study was to investigate comparative detection of the Delta (B.1.617.2) and Omicron variants by using a selection of 20 RDT and a limited panel of pooled combined oro- and nasopharyngeal clinical Delta and Omicron specimens.MethodsWe tested 20 CE-marked RDT for their performance to detect SARS-CoV-2 Delta and Omicron by using a panel of pooled clinical specimens collected in January 2022 in Berlin, Germany.ResultsWe observed equivalent detection performance for Delta and Omicron for most RDT, and sensitivity was widely in line with our previous pre-Delta/Omicron evaluation. Some variation for individual RDT was observed either for Delta vs Omicron detection, or when compared with the previous evaluation, which may be explained both by different panel sizes resulting in different data robustness and potential limitation of batch-to-batch consistency. Additional experiments with three RDT using non-pooled routine clinical samples confirmed comparable performance to detect Delta vs Omicron. Overall, RDT that were previously positively evaluated retained good performance also for Delta and Omicron variants.ConclusionOur findings suggest that currently available RDT are sufficient for the detection of SARS-CoV-2 Delta and Omicron variants.

High variability of COVID-19 case fatality rate in Germany.

BACKGROUND: During the first wave of the COVID-19 pandemic a high case fatality rate (CFR) was noticed worldwide including also Germany where the first European cases have been observed. The WHO recommended immediate intubation for patients with dyspnoea which has since been revised after reviewing the initial clinical outcome. The objective of this study is to analyze CFR and assess if there is an advantage of a more conservative management of COVID-19 induced hypoxemia. METHODS: PCR confirmed COVID-19 infections and death counts were obtained for all German districts from 27 Jan 2020 until 15 Feb 2021 using official reports of Robert Koch Institute Berlin, Germany. A moving average CFRt was constructed by dividing disease related deaths two weeks after a given index day by the number of infections two weeks prior to that date. In addition to a local comparison also mortality outcomes in other German speaking countries were compared. RESULTS: The mean CFR is estimated to be 2.92% based on 71.965 fatalities and 2.465.407 cases. There was a large regional scattering of CFRs across the German districts. Differences of the mortality pattern were observed also at state level and preserved across different sex and age groups while being largely independent of case numbers. Although Munich city had higher infection rates, more patients died during the first wave in Hamburg (OR 1.6, 95% CI 1.3-1.9) which was mirrored also by higher death risk at Hamburg intensive care units (OR 2.0, 95% CI 1.3-3.1). While the majority of Munich hospitals favoured a conservative management of hypoxemia including high flow nasal cannula (HFNC), Hamburg hospitals followed a more aggressive scheme of early mechanical ventilation (MV). Austria and Switzerland experienced higher CFRs than Germany during the first wave but after changing their treatment guidelines, both countries experienced lower CFRs during the second wave. CONCLUSION: Using retrospective public health data, different case fatality rates have been observed across Germany. A more conservative management of COVID-19 induced Adult Respiratory Distress Syndrome (ARDS) is justified also by epidemiological data.

Psychiatric presentations and admissions during the first wave of Covid-19 compared to 2019 in a psychiatric emergency department in Berlin, Germany: a retrospective chart review.

BACKGROUND: Most studies agree that the Covid-19 pandemic and the subsequent lockdown had a negative impact on mental health. On the other hand, international studies have shown that psychiatric emergency departments (pED) experienced a decrease in presentations and admissions. METHODS: Retrospective chart review of all pED presentations and admissions during the first wave of Covid-19 pandemic in Germany (Covid-19 period: 3/2/20 to 05/24/20) in a psychiatric hospital in Berlin compared to 1 year earlier (pre-Covid-19 period). Descriptive statistics and logistic regression were performed. RESULTS: We observed no statistical significant changes in overall pED presentations and overall hospital admissions during the Covid-19 period compared to the pre-Covid-19 period (813 vs. 894, - 9.1%, p = 0.064 and (363 vs. 437, - 16.9%, p = 0.080 respectively). In the subgroup analysis, less patients with depressive disorders (p = 0.035) and with personality disorders (p = 0.002) presented to the pED, a larger number of presentations with schizophrenia was observed (p = 0.020). In the Covid-19 period, less patients with substance use disorder and paranoid schizophrenia were admitted to the hospital via the pED than in the pre-Covid-19 period (p = 0.035 and p = 0.006, respectively). Bed capacity was reduced in the Covid-19 period by - 32.8% (p <  0.001). Presentations in police custody were 13.7% (p = 0.029) higher during the Covid-19 compared to pre-Covid-19 period, with higher rates in female presentations (p = 0.008) and suicide attempts (p = 0.012) and less hospital admissions (p = 0.048). Logistic regression analyses revealed that positive predictors for pED presentation during Covid-19 period were police custody (p <  0.001), being redirected from another hospital (p <  0.001), suicide attempt (p = 0.038), suicidal thoughts (p = 0.004), presentation with paranoid schizophrenia (p = 0.001) and bipolar and manic disorders (p = 0.004), negative predictors were hospital admission (p <  0.001), depressive disorders (p = 0.021) and personality disorders (p <  0.001). CONCLUSIONS: A larger number of presentations in police custody during the Covid-19 period may represent untreated medical needs. This was seen predominantly in female patients, suggesting this subgroup might have suffered particularly under lockdown measures. Patients with paranoid schizophrenia were the only subgroup, which increased in absolute numbers, also suggesting a particular lockdown effect. Reduced bed capacity due to infection curbing measures is suggestive to have played an important role in augmenting the threshold for hospital admissions.

Analysis of two choir outbreaks acting in concert to characterize long- range transmission risks through SARS-CoV-2, Berlin, Germany, 2020.

BACKGROUND: Superspreading events are important drivers of the SARS-CoV-2 pandemic and long-range (LR) transmission is believed to play a major role. We investigated two choir outbreaks with different attack rates (AR) to analyze the contribution of LR transmission and highlight important measures for prevention. METHODS: We conducted two retrospective cohort studies and obtained demographic, clinical, laboratory and contact data, performed SARS-CoV-2 serology, whole genome sequencing (WGS), calculated LR transmission probabilities, measured particle emissions of selected choir members, and calculated particle air concentrations and inhalation doses. RESULTS: We included 65 (84%) and 42 (100%) members of choirs 1 and 2, respectively, of whom 58 (89%) and 10 (24%) became cases. WGS confirmed strain identity in both choirs. Both primary cases transmitted presymptomatically. Particle emission rate when singing was 7 times higher compared to talking. In choir 1, the median concentration of primary cases' emitted particles in the room was estimated to be 8 times higher, exposure at least 30 minutes longer and room volume smaller than in choir 2, resulting in markedly different estimated probabilities for LR transmission (mode: 90% vs. 16%, 95% CI: 80-95% vs. 6-36%). According to a risk model, the first transmission in choir 1 occurred likely after 8 minutes of singing. CONCLUSIONS: The attack rate of the two choirs differed significantly reflecting the differences in LR transmission risks. The pooled proportion of cases due to LR transmission was substantial (81%; 55/68 cases) and was facilitated by likely highly infectious primary cases, high particle emission rates, and indoor rehearsing for an extended time. Even in large rooms, singing of an infectious person may lead to secondary infections through LR exposure within minutes. In the context of indoor gatherings without mask-wearing and waning or insufficient immunity, these results highlight the ongoing importance of non-pharmaceutical interventions wherever aerosols can accumulate.

High genetic diversity of Babesia canis (Piana & Galli-Valerio, 1895) in a recent local outbreak in Berlin/ Brandenburg, Germany.

Canine babesiosis caused by Babesia canis (Piana & Galli-Valerio, 1895) is emerging in new regions in Europe since its vector Dermacentor reticulatus (Fabricius, 1794) is expanding its geographic range. In the Berlin/Brandenburg area in northeast Germany, D. reticulatus is highly abundant but in the past only one autochthonous B. canis infection was reported. Since 2015, autochthonous cases were occasionally diagnosed but numbers increased since autumn 2019. The aim of the study was to genotype autochthonous canine Babesia spp. infections from Berlin/Brandenburg. Between 04/2015 and 01/2022, 46 dogs with acute babesiosis were presented to the small animal clinic (one dog was infected twice resulting in 47 samples). There were 32 dogs that had never left Berlin/Brandenburg and 14 others that had not left the region in the 6 weeks prior to disease onset. PCRs targeting the 18S rRNA and the Bc28.1 merozoite surface antigen were positive in 47 and 42 samples, respectively. Sequencing of cloned PCR products identified all samples as B. canis with 17 18S rRNA and 12 Bc28.1 haplotypes. Based on network analysis for 18S rRNA sequences and a previously described polymorphic dinucleotide, samples were assigned to two distinct clusters. One contained 31 and the other 16 samples. Using network analysis, the Bc28.1 haplotypes could also be separated into two clusters differing by at least five polymorphisms. Analyses of sequences from multiple clones indicated the presence of up to five 18S rRNA and eight Bc28.1 haplotypes and thus high parasite variability in an individual host. The genetic diversity could suggest that the parasites in the region have multiple origins, but diversity in individual dogs and dog populations from endemic regions is unknown. The suitability of both markers for genotyping is questionable due to potential intragenomic diversity for the rRNA and high intergenomic variability for the Bc28.1 marker.

Melanomversorgung während eines Jahres Pandemie in Berlin: abnehmende Terminstornierungen trotz zunehmender Besorgnis über COVID-19.

HINTERGRUND UND ZIELE: Die COVID-19-Pandemie stellt für Krebspatienten eine große Herausforderung dar. Unser Ziel war es, ihren Einfluss auf die Behandlung und auf Arzttermine von Melanompatienten nach einem Jahr Pandemie zu untersuchen. PATIENTEN UND METHODIK: Melanompatienten, die im Vivantes Hauttumorzentrum in Berlin behandelt wurden, beantworteten eine postalische Umfrage zu Pandemie-bedingten Änderungen ihrer Melanomversorgung. Einflussfaktoren auf Terminänderungen wurden mit deskriptiven Analysen und multivariater logistischer Regression untersucht. Daten nach einem Jahr Pandemie wurden mit Daten nach der ersten Welle verglichen. ERGEBNISSE: Von den 366 Teilnehmern (57,7 % Männer; Durchschnittsalter 69,2 Jahre, Rücklaufquote: 36,1 %) berichteten 38 (10,1 %) über verschobene oder verpasste Arzttermine, meist auf eigenen Wunsch (71,1 %) aus Angst vor COVID-19 (52,6 %). Eine aktuelle Therapie war mit einem geringeren Risiko, Termine zu verpassen, assoziiert (Odds Ratio [OR]: 0,194, p = 0,002), höheres Alter (OR: 1,037, p = 0,039), längere Krankheitsdauer (OR: 1,007, p = 0,028) und ein höherer Schulabschluss (OR: 2,263, p = 0,043) mit höherer Wahrscheinlichkeit. Von den 177 Patienten, die aktuell eine Therapie erhielten, erfuhren nur 1,7 % Pandemie-bedingte Behandlungsänderungen. Die Besorgnis über COVID-19 war nach einem Jahr Pandemie signifikant größer als nach der ersten Welle, die Zahl der verpassten Arzttermine jedoch niedriger. SCHLUSSFOLGERUNGEN: Pandemie-bedingte Änderungen waren in unserer Kohorte selten und nahmen trotz zunehmender Besorgnis mit der Zeit ab.

Psychosocial Wellbeing of Schoolchildren during the COVID-19 Pandemic in Berlin, Germany, June 2020 to March 2021.

The COVID-19 pandemic and related restrictions have affected the wellbeing of schoolchildren worldwide, but the extent and duration of specific problems are still not completely understood. We aimed to describe students' psychosocial and behavioral parameters and associated factors during the COVID-19 pandemic in Berlin, Germany. Our longitudinal study included 384 students from 24 randomly selected Berlin primary and secondary schools, assessing psychosocial wellbeing at four time points between June 2020 and March 2021. We analyzed temporal changes in the proportions of anxiety, fear of infection, reduced health-related quality of life (HRQoL), physical activity and social contacts, as well as sociodemographic and economic factors associated with anxiety, fear of infection and HRQoL. During the observation period, the presence of anxiety symptoms increased from 26.2% (96/367) to 34.6% (62/179), and fear of infection from 28.6% (108/377) to 40.6% (73/180). The proportion of children with limited social contacts (<1/week) increased from 16.4% (61/373) to 23.5% (42/179). Low physical activity (<3 times sports/week) was consistent over time. Low HRQoL was observed among 44% (77/174) of children. Factors associated with anxiety were female sex, increasing age, secondary school attendance, lower household income, and the presence of adults with anxiety symptoms in the student´s household. Fear of infection and low HRQoL were associated with anxiety. A substantial proportion of schoolchildren experienced unfavorable psychosocial conditions during the COVID-19 pandemic in 2020/2021. Students from households with limited social and financial resilience require special attention.

Melanoma care during one year pandemic in Berlin: decreasing appointment cancellations despite increasing COVID-19 concern.

BACKGROUND AND OBJECTIVES: The COVID-19 pandemic poses a great challenge for cancer patients. Our aim was to assess its influence on treatment and appointments of melanoma patients after one year of pandemic. METHODS: Melanoma patients treated in the Vivantes Skin Cancer Centre in Berlin, Germany completed a postal survey on pandemic-related alterations in melanoma care. Impact factors on changes of appointments were examined with descriptive analyses and multivariate logistic regression. Data after one year of pandemic were compared to those after its first wave. RESULTS: Among 366 participants (57.7 % males; mean age 69.2 years, response rate: 36.1 %), 38 (10.1 %) reported postponed or missed appointments, mostly on their own demand (71.1 %) due to fear of COVID-19 (52.6 %). Current treatment was associated with a lower risk of changing appointments (Odds Ratio [OR]: 0.194, p = 0.002), higher age (OR: 1.037, p = 0.039), longer disease duration (OR: 1.007, p = 0.028), and higher school degree (OR: 2.263, p = 0.043) with higher probability. Among 177 patients currently receiving therapy, only 1.7 % experienced pandemic-related treatment alterations. Concern about COVID-19 was significantly higher after one year of pandemic than after its first wave, but the number of missed appointments was lower. CONCLUSIONS: Pandemic-related changes were rare in our cohort and decreased over time despite increasing concern.

Effects of COVID-19 Restriction Policies on Urban Heat Islands in Some European Cities: Berlin, London, Paris, Madrid, and Frankfurt.

The present study investigates the effects of policies restricting human activities during the COVID-19 epidemic on the characteristics of Night Land Surface Temperature (NLST) and Night Urban Heat Islands (NUHI) in five major European cities. In fact, the focus of this study was to explore the role of anthropogenic factors in the formation and intensity of NUHI. The effect of such factors was uncontrollable before the COVID-19 outbreak on the global scale and in a real non-laboratory environment. In this study, two indices, the concentration of Nitrogen dioxide (NO2) and Nighttime Lights (NL), were used as indicators of the number of anthropogenic activities. The data were collected before the COVID-19 outbreak and after its prevalence in 2019-2020. A Paired samples t-test and a Pearson correlation were used to examine the differences or significant relationships between the variables and indicators studied throughout the two periods. The results of the study confirmed a direct and significant relationship between NO2 and NL indices and the NUHI and NLST variables; however, using strict restrictions during the COVID-19 pandemic, the NO2 and NL indices decreased seriously, leading to significant changes in the characteristics of the NUHI and NLST in the five cities. This study has some implications for urban planners and politicians, e.g., the environmental impacts of changing the nature and level of anthropogenic activities can greatly affect the pattern and intensity of the Urban Heat Islands (UHIs) (as a serious environmental challenge).

SARS-CoV-2 infection among educational staff in Berlin, Germany, June to December 2020.

BackgroundSARS-CoV-2 infections in preschool and school settings potentially bear occupational risks to educational staff.AimWe aimed to assess the prevalence of SARS-CoV-2 infection in teachers and preschool educators and at identifying factors associated with infection.MethodsWe analysed cross-sectional data derived from 17,448 voluntary, PCR-based screening tests of asymptomatic educational staff in Berlin, Germany, between June and December 2020 using descriptive statistics and a logistic regression model.ResultsParticipants were largely female (73.0%), and median age was 41 years (range: 18-78). Overall, SARS-CoV-2 infection proportion was 1.2% (95% CI: 1.0-1.4). Proportion of positive tests in educational staff largely followed community incidence until the start of the second pandemic wave, when an unsteady plateau was reached. Then, the proportion of positive tests in a (concurrent) population survey was 0.9% (95% CI: 0.6-1.4), 1.2% (95% CI: 0.8-1.8) in teachers and 2.6% (95% CI: 1.6-4.0) in preschool educators. Compared with teachers, increased odds of infection were conferred by being a preschool educator (adjusted odds ratio (aOR): 1.6; 95% CI: 1.3-2.0) and by contact with a SARS-CoV-2 infected individual outside of work (aOR: 3.0; 95% CI: 1.5-5.5). In a step-wise backward selection, the best set of associated factors with SARS-CoV-2 infection involved age, occupation, and calendar week.ConclusionsThese results indicate that preschool educators bear increased odds of SARS-CoV-2 infection compared with teachers. At the same time, the private environment appeared to be a relevant source of SARS-CoV-2 infection for educational staff in 2020.

A Retrospective Outbreak Investigation of a COVID-19 Case Cluster in a Berlin Kindergarten, November 2020.

While SARS-CoV-2 infection activity in German kindergartens during the first year of the pandemic appeared to be overall low, outbreaks did occur. We retrospectively investigated an outbreak in November and December 2020 in a Berlin kindergarten participating in the Berlin Corona School and Kindergarten Study (BECOSS). Interviews were conducted with affected families regarding symptomatology, contact persons and possible sources of infection, as well as relevant information on the conditions on-site and infection prevention measures. A chronology of the outbreak was elaborated, and based on data on contacts and symptoms, we mapped the most likely chains of infection. Overall, 24 individuals, including ten educators, seven children, and seven household members, were infected with SARS-CoV-2 in a four-week time interval. Courses of infection ranged from asymptomatic to severe, with children less affected by symptoms. Viral spread within the facility seemed to occur mainly through kindergarten staff, while children primarily transmitted infections within their families. Interviewees reported that hygiene measures were not always adhered to inside the facility. To prevent outbreaks in kindergartens, especially in the light of current and newly emerging viral variants of concern, strict compliance to hygiene rules, staff vaccinations against SARS-CoV-2, and immediate reaction to suspected cases by quarantining and frequent testing seem reasonable measures.

Characterization of COVID-19 outbreaks in three nursing homes during the first wave in Berlin, Germany.

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) belongs to the coronavirus family and is characterized by its high transmission competence. Elderly COVID-19 patients are at significantly higher risk of severe course of disease and death. Therefore, outbreaks in nursing homes are particularly challenging for facility managers and health authorities. Here, we report three outbreaks of COVID-19 related to nursing homes (NH01.a, NH02 and NH03) with almost 1000 affected individuals during the first COVID-19 wave in Berlin, Germany. The occurrence of cases and the measures taken were analyzed retrospectively. In all three outbreaks, the index persons were nursing home employees or volunteers. Measures taken were quarantine of contacts, close-meshed tests, separation of the affected housing unit, suspension of admission, ban on visiting, and equipping staff with personal protective equipment, of which there was a shortage in Germany at the beginning of the pandemic. A court-ordered quarantine became necessary for three residents of NH01.a due to cognitive disabilities. In total, 61 persons were tested positive for SARS-CoV-2 in NH01.a, ten persons in NH02, and sixteen persons in NH03. Seventeen patients (27.9%) of NH01.a and three patients (18.8%) of NH03 were referred to hospital. Of all confirmed cases, thirteen (21.3%) related to NH01.a and four (25.0%) related to NH03 died as a result of the infection. Besides one 82 year old volunteer, all deceased persons were residents aged between 66 and 98. Our results emphasize the importance of a previously developed containment and cluster strategy for nursing homes. Due to the particular vulnerability of the residents, immediate action, close cooperation and communication between the facility management, residents, visitors and the health authorities are essential in the case of confirmed COVID-19 cases in healthcare facilities.

Plasma Proteome Fingerprints Reveal Distinctiveness and Clinical Outcome of SARS-CoV-2 Infection.

BACKGROUND: We evaluated how plasma proteomic signatures in patients with suspected COVID-19 can unravel the pathophysiology, and determine kinetics and clinical outcome of the infection. METHODS: Plasma samples from patients presenting to the emergency department (ED) with symptoms of COVID-19 were stratified into: (1) patients with suspected COVID-19 that was not confirmed (n = 44); (2) non-hospitalized patients with confirmed COVID-19 (n = 44); (3) hospitalized patients with confirmed COVID-19 (n = 53) with variable outcome; and (4) patients presenting to the ED with minor diseases unrelated to SARS-CoV-2 infection (n = 20). Besides standard of care diagnostics, 177 circulating proteins related to inflammation and cardiovascular disease were analyzed using proximity extension assay (PEA, Olink) technology. RESULTS: Comparative proteome analysis revealed 14 distinct proteins as highly associated with SARS-CoV-2 infection and 12 proteins with subsequent hospitalization (p < 0.001). ADM, IL-6, MCP-3, TRAIL-R2, and PD-L1 were each predictive for death (AUROC curve 0.80-0.87). The consistent increase of these markers, from hospital admission to intensive care and fatality, supported the concept that these proteins are of major clinical relevance. CONCLUSIONS: We identified distinct plasma proteins linked to the presence and course of COVID-19. These plasma proteomic findings may translate to a protein fingerprint, helping to assist clinical management decisions.

A longitudinal study on symptom duration and 60-day clinical course in non-hospitalised COVID-19 cases in Berlin, Germany, March to May, 2020.

BackgroundDetailed information on symptom duration and temporal course of patients with mild COVID-19 was scarce at the beginning of the COVID-19 pandemic.AimWe aimed to determine the longitudinal course of clinical symptoms in non-hospitalised COVID-19 patients in Berlin, Germany.MethodsBetween March and May 2020, 102 confirmed COVID-19 cases in home isolation notified in Berlin, Germany, were sampled using total population sampling. Data on 25 symptoms were collected during telephone consultations (a maximum of four consultations) with each patient. We collected information on prevalence and duration of symptoms for each day of the first 2 weeks after symptom onset and for day 30 and 60 after symptom onset.ResultsMedian age was 35 years (range 18-74), 57% (58/102) were female, and 37% (38/102) reported having comorbidities. During the first 2 weeks, most common symptoms were malaise (94%, 92/98), headache (71%, 70/98), and rhinitis (69%, 68/98). Malaise was present for a median of 11 days (IQR 7-14 days) with 35% (34/98) of cases still reporting malaise on day 14. Headache and muscle pain mostly occurred during the first week, whereas dysosmia and dysgeusia mostly occurred during the second week. Symptoms persisted in 41% (39/95) and 20% (18/88) of patients on day 30 and 60, respectively.ConclusionOur study shows that a significant proportion of non-hospitalised COVID-19 cases endured symptoms for at least 2 months. Further research is needed to assess the frequency of long-term adverse health effects in non-hospitalised COVID-19 patients.

Predicting the effects of COVID-19 related interventions in urban settings by combining activity-based modelling, agent-based simulation, and mobile phone data.

Epidemiological simulations as a method are used to better understand and predict the spreading of infectious diseases, for example of COVID-19. This paper presents an approach that combines a well-established approach from transportation modelling that uses person-centric data-driven human mobility modelling with a mechanistic infection model and a person-centric disease progression model. The model includes the consequences of different room sizes, air exchange rates, disease import, changed activity participation rates over time (coming from mobility data), masks, indoors vs. outdoors leisure activities, and of contact tracing. It is validated against the infection dynamics in Berlin (Germany). The model can be used to understand the contributions of different activity types to the infection dynamics over time. It predicts the effects of contact reductions, school closures/vacations, masks, or the effect of moving leisure activities from outdoors to indoors in fall, and is thus able to quantitatively predict the consequences of interventions. It is shown that these effects are best given as additive changes of the reproduction number R. The model also explains why contact reductions have decreasing marginal returns, i.e. the first 50% of contact reductions have considerably more effect than the second 50%. Our work shows that is is possible to build detailed epidemiological simulations from microscopic mobility models relatively quickly. They can be used to investigate mechanical aspects of the dynamics, such as the transmission from political decisions via human behavior to infections, consequences of different lockdown measures, or consequences of wearing masks in certain situations. The results can be used to inform political decisions.

A Novel 29-Messenger RNA Host-Response Assay From Whole Blood Accurately Identifies Bacterial and Viral Infections in Patients Presenting to the Emergency Department With Suspected Infections: A Prospective Observational Study.

OBJECTIVES: The rapid diagnosis of acute infections and sepsis remains a serious challenge. As a result of limitations in current diagnostics, guidelines recommend early antimicrobials for suspected sepsis patients to improve outcomes at a cost to antimicrobial stewardship. We aimed to develop and prospectively validate a new, 29-messenger RNA blood-based host-response classifier Inflammatix Bacterial Viral Non-Infected version 2 (IMX-BVN-2) to determine the likelihood of bacterial and viral infections. DESIGN: Prospective observational study. SETTING: Emergency Department, Campus Benjamin Franklin, Charité-Universitätsmedizin Berlin, Germany. PATIENTS: Three hundred twelve adult patients presenting to the emergency department with suspected acute infections or sepsis with at least one vital sign change. INTERVENTIONS: None (observational study only). MEASUREMENTS AND MAIN RESULTS: Gene expression levels from extracted whole blood RNA was quantified on a NanoString nCounter SPRINT (NanoString Technologies, Seattle, WA). Two predicted probability scores for the presence of bacterial and viral infection were calculated using the IMX-BVN-2 neural network classifier, which was trained on an independent development set. The IMX-BVN-2 bacterial score showed an area under the receiver operating curve for adjudicated bacterial versus ruled out bacterial infection of 0.90 (95% CI, 0.85-0.95) compared with 0.89 (95% CI, 0.84-0.94) for procalcitonin with procalcitonin being used in the adjudication. The IMX-BVN-2 viral score area under the receiver operating curve for adjudicated versus ruled out viral infection was 0.83 (95% CI, 0.77-0.89). CONCLUSIONS: IMX-BVN-2 demonstrated accuracy for detecting both viral infections and bacterial infections. This shows the potential of host-response tests as a novel and practical approach for determining the causes of infections, which could improve patient outcomes while upholding antimicrobial stewardship.