SARS-CoV-2, the cause of COVID19, has caused a pandemic that has infected more than 80 M and killed more than 1.6 M persons worldwide. In the US as of December 2020, it has infected more than 32 M people while causing more than 570,000 deaths. As the pandemic persists, there has been a public demand to reopen schools and university campuses. To consider these demands, it is necessary to rapidly identify those individuals infected with the virus and isolate them so that disease transmission can be stopped. In the present study, we examined the sensitivity of the Quidel Rapid Antigen test for use in screening both symptomatic and asymptomatic individuals at the University of Arizona from June to August 2020. A total of 885 symptomatic and 1551 asymptomatic subjects were assessed by antigen testing and real-time PCR testing. The sensitivity of the test for both symptomatic and asymptomatic persons was between 82 and 90%, with some caveats. In less than one year, the novel coronavirus, SARS-CoV-2, the causative agent of COVID-19, has jumped from animals to humans, causing a pandemic that has infected more than 80 M and killed more than 12 M persons worldwide. In the US alone, as of February 2021, it has infected more than 32 M people while causing approximately 570,000 deaths [Tracking and tracing efforts that are required to establish the identity of secondary infections depend on the rapid identification of the primary infected person to limit viral spread. The source of infection must be isolated and quarantined so they may be observed and treated as necessary. Viral testing strategies must be specific for the disease, sensitive to low (possibly asymptomatic) viral loads and return results to those responsible in as short a time as possible . TypicalThere are other testing options, however, that may be sufficiently sensitive and disease-specific to achieve the rapid identification of infected patients and facilitate early isolation and contact tracing. Such tests may be able to compensate for reduced sensitivity as compared to PCR testing by being amenable to multiple rounds of testing combined with the rapid return of results within minutes to hours. As long as these alternative testing approaches are safe, easy to perform and inexpensive, there could be significant advantages. If these tests are capable of being self-administered and include the return of results documentation, then such tests might become a preferred choice when screening large populations of individuals in a high throughput manner.FDA EUA Application) but these results were not based on testing large numbers of “real-world” samples.Such a testing strategy became commercially available from Quidel, Inc.  to analyze subjects for the presence of the SARS-CoV-2 viral antigen Ag) . The assIn the present study, we examined the sensitivity of the Quidel Rapid Ag test for use in screening both symptomatic and asymptomatic individuals in the student and staff community at the University of Arizona from June to August 2020. After test validation, a total of 885 symptomatic and 1551 asymptomatic subjects were assessed by both antigen testing and real-time PCR (RT-PCR or PCR) testing performed side-by-side at the same time on the same patient.All human subjects in the study were students, faculty, or staff at the University of Arizona. Participation was voluntary. Symptomatic subjects were tested within 5 days of symptom onset. Asymptomatic subjects were asked to volunteer for testing as a screen for return to campus activities, and none had symptoms of infection or had been exposed to anyone with symptoms. All testing was performed by CLIA and/or CAP-accredited laboratories under the standard of care. An institutional review determined that the study did not require consent as long as all data was de-identified upon receipt and that all data pertaining to this study were de-identified prior to publication. All collections were performed between June and August 2020. In addition, a small number of COVID-19-positive patients from the local university ICU provided samples as part of the initial validation studies of the assay (with consent).Rapid antigen (Ag) testing specimens were collected using foam swabs provided by the manufacturer. Dry anterior nasal collections were self-performed for both nostrils under supervision. Dry swabs were placed in a barcoded 15 mL conical tube, kept in an insulated cooler to maintain 65–80 °F (18–27 °C) and transported within 60 min of collection to the laboratory. PCR specimens were collected from one nostril using CDC-approved nasopharyngeal (NP) swabs  with medical assistance. The swab was then placed in a VMT transport buffer and brought to the laboratory for testing within 60 min. NP and Ag nasal specimens were collected in that order at the same time from individuals in this study. Tested subjects were classified as being antigen-positive/PCR-positive, antigen-negative/PCR-negative, antigen-positive/PCR-negative or antigen-negative/PCR-positive based on the combination of test results.https://www.cdc.gov/coronavirus/2019-ncov/lab/virus-requests.html) (accessed on 1 February 2021) [PCR testing utilized a CDC-approved primer set with a detected/not detected cut-off of 40 cycles (CDC 2019-Novel Coronavirus (2019-nCoV) Real-Time RT-PCR Diagnostic Panel  ordered through Integrated DNA Technologies, Inc. (IDT): Catalog #2019-nCoVEUA-01 Diagnostic Panel Box #1; (ry 2021) ,7. TestsThe Quidel Sofia 2 SARS antigen FIA test displayed a digital readout as positive or negative based on the ratio of relative fluorescence units to background in an LFT  assay termed the S/CO  ratio . Ratios The sensitivity and specificity of the rapid Ag assay were initially assessed by performing rapid antigen testing using three types of biospecimens: “spiked” positive and negative samples provided by Quidel, Inc.; samples obtained from suspected, symptomatic, critically ill patients admitted to intensive care units; and samples obtained from asymptomatic campus students and staff . AnterioA select group of initially asymptomatic patients from the validation studies who tested positive during the validation studies were followed and tested for an additional 1–2 weeks using the rapid antigen test and PCR test as before. As shown in To explore the limits of the rapid antigen assay, 885 students and staff presenting at university campus health were tested, including both those exposed to the virus  and those symptomatic with cough, fever, aches, etc. were tested. As shown in Based on these findings, further analyses were performed to examine the role of PCR cycle time  in the detection of the virus by the rapid antigen test. It was observed that symptomatic patients displayed lower cycle thresholds in the PCR analysis see  regardle(88%) symptomatic subjects and 6 out of 7 (86%) asymptomatic subjects with cycle times below 30 being both Ag and PCR test concordant. These analyses confirmed the conclusions implied in The results observed in and contagious with cycle thresholds under 30. That is, in symptomatic individuals the Ag test is very sensitive, while in asymptomatic individuals the Ag test detected less than half of those who had been infected with SARS-CoV-2 but identified 86% of those who were contagious and likely to spread the virus. In addition, based on the findings, a slightly higher false-negative rate for asymptomatic persons with the rapid antigen test could be overcome if one were to perform antigen testing a minimum of three times a week. Repeated testing could reduce to less than one percent the chance that any individual who is truly positive is missed by the antigen test [Overall results from the rapid antigen and PCR tests were generally concordant for these two large groups of individuals on the university campus, regardless of symptomology, when PCR ct were 30 cycles or less. Of note, asymptomatic subjects had higher underlying PCR cycle thresholds regardless of whether they were antigen-positive or negative, which has also been reported in a previous study . Possiblgen test .Interestingly, more than half of all subjects who presented at Campus Health with COVID-19 symptoms during the study period did not test positive for SARS-CoV-2 by either a rapid antigen or PCR test, a noteworthy and cautionary finding in and of itself. This finding also helps to explain the lower-than-expected positivity rates in the symptomatic population. Our observations seem to indicate that compared with the rapid antigen test the PCR test detects viral loads that may be 200-fold lower, which may not be biologically relevant in terms of infectivity/contagiousness . Recent


Liquid crystals are promising molecular materials in the application of lubrication. Herein, the microscale solid superlubricity is accomplished by the construction of uniform and ordered self-assembly of several liquid crystals. The self-assembly structures on a highly oriented pyrolytic graphite (HOPG) surface are explicitly revealed by using scanning tunneling microscopy (STM). Meanwhile, the nanotribological performance of the self-assemblies are measured by using atomic force microscopy (AFM), revealing ultralow friction coefficients lower than 0.01. The interaction energies are calculated by density functional theory (DFT) method, indicating the positive correlation between friction coefficients and interaction strength. The effort on the self-assembly and superlubricity of liquid crystals could enhance the understanding of the nanotribological mechanism and benefit the further application of liquid crystals as lubricants. All the solutions and assembly samples were prepared under ambient conditions.The self-assembly structures of liquid crystals were characterized using a Nanoscope IIIA system  under ambient conditions. And the theoretical calculations were performed using DFT-D scheme provided by DMol3 code. Further characterization and calculation details can be seen in the The microscopic friction forces of different liquid crystal systems were measured using an MFP-3D AFM  at room temperature. To eliminate the solvent effect on the friction forces, the measurements were conducted at the gas-solid interface after the solvent was evaporated. The silicon CSG10 probe with a rectangular cantilever  was used. All the friction pairs are silicon probe (CSG10)—sample (assembly on HOPG). The selection of probe and loads were optimized after several attempts of friction experiments to get stable and repeatable data. It should be mentioned that the genuine normal and lateral factors need to be calibrated before each measurement. The normal photodetector sensitivity was calculated from the slope of the force curve obtained on a hard substrate. The normal spring constant was estimated from the power spectral density of thermal noise fluctuations under ambient conditions , in which the linear arrangement of bright rods could be observed. However, the arranging patterns of two adjacent rows are quite different, in which the bright rods are loose-packed in one row and close-packed in the neighbor row. Further details of assembly structure can be observed in the high resolution STM image, as shown in a = 7.9 ± 0.1 nm, b = 5.8 ± 0.1 nm, and α = 105 ± 1°.−1 Å−2) is lowest, which means that the interaction strength is the strongest among four assembly systems.The unit cell parameters and interaction energies of LC-amide-1 at high concentration are calculated with the DFT method based on the STM observation to further analyze the self-assembly structure. The calculated unit cell parameters (as shown in −3 M) and low concentration (10−4 M), LC-amide-2, LC-ester and HOPG are presented as a function of the applied load. For these five systems, friction forces increased linearly with the load. In comparison, the friction forces of LC-amide-1 at low concentration, LC-amide-2 and LC-ester are similar, while the friction forces of LC-amide-1 at high concentration are approximately twice larger. The friction-load data are linearly fitted to acquire friction coefficient, which can be defined as the slope of the linear fitting curve, as labeled in At present, the tribological research on liquid crystals is mainly conducted at macroscale. To investigate the nanotribological performance, the friction forces of liquid crystals, including self-assembly mentioned above and three other self-assemblies in our previous research (Tan S. et al., As mentioned above, the interaction strength of LC-amide-1 at high concentration is the strongest among all the self-assemblies. Considering that the friction coefficient of LC-amide-1 at high concentration is also the highest, it seems that the nanotribological properties are related to the interaction strength. Therefore, to better understand such correlation, the experimental friction coefficient and theoretical total energy per unit area of four liquid crystal self-assembly systems are summarized in In summary, the self-assembly structures and superlubrication properties of liquid crystals are investigated at the molecular level. The STM characterization indicates that Lc-amide-1 molecules can form a totally different assembly structures at higher concentration. More importantly, the microscale superlubricity of liquid crystals on HOPG surface is successfully achieved. The DFT calculation reveals the positive correlation between the friction coefficient and the interaction strength. From an energy point of view, the energy dissipation in frictional process derives from the continuous breaking and reforming of the physical bonds. This work of superlubricity and self-assembly of liquid crystals could enhance our understanding of the interface friction mechanisms at nanoscale and provide a promising strategy to explore the further applications of liquid crystals in lubrication.The raw data supporting the conclusions of this article will be made available by the authors, without undue reservation.ST completed the STM and AFM characterization under the guidance of YL and QZ. JT synthesized all the liquid crystals under the guidance of HX. WL completed the DFT calculation. HS provided the help of STM experiments. BT and HJ provided the help of calculation and synthesis. The manuscript was written through contributions of all authors. All authors have given approval to the final version of the manuscript.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.


Since the beginning of March 2020, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has been the cause of millions of deaths worldwide. The need to better define the pathogenesis of coronavirus disease 19 (Covid-19) as well as to provide the correct statistical records concerning deaths related to this virus, inevitably involves the role of forensic pathology and routine autopsy practice. Currently, some data on macroscopic and microscopic features in autopsies performed in suspected Covid-19 cases are reported in the literature. The persistence of SARS-CoV-2 in cadavers has not yet been elucidated and only a few reports have emphasized the importance of evaluating the Virus RNA in post-mortem tissues. In this preliminary study, we observed that SARS-CoV-2 survives in multiple cadaver tissues many days after death despite some extreme conditions of post-mortem body preservation. The results of this on-going analysis could help improve the safety of working practices for pathologists as well as understanding the possible interaction between microbiological agents and the cadaver tissue’s supravital reactions. SARS-CoV-2 has caused millions of deaths worldwide. Globally, new COVID-19 cases and deaths have continued to increase to approximately 4.6 million new cases and about 79 000 new deaths every week. This brings the cumulative number to over 75 million reported cases and 1.6 million deaths globally since the start of the pandemic  and Middle East Respiratory Syndrome [MERS] coronaviruses) that have appeared over the last 20 years –13. The According to the World Health Organization (WHO), the transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) between individuals is through inhalation of sizeable respiratory droplets, fomites, and proximity with infected persons and facets . AlthougFor this reason, the Italian Ministry of Health issued a recommendation that in principle discourages the performing of autopsies on COVID-19 related bodies . HoweverAccording to the relevant literature, the majority of the microorganisms responsible for death also have a shorter life-span after the death of the host and therefore infection risk is minimized . The higNonetheless, there is the possibility of an increase in the chances of disease transmission with direct exposure to body fluids and invasive procedures on the cadaver, such as procedures that generate droplets or aerosols , 24. SofThe SARS-CoV-2 virus has strong persistence in the external environment, especially at low temperatures. Kampf et al. supported the claim that human coronaviruses on inanimate surfaces could still be contagious at room temperature for about nine days . HoweverAccording to a study on the resistance of severe acute respiratory syndrome coronavirus , the virIn a study conducted by Riddell et al. survival rates of SARS-CoV-2 were determined at different temperatures on common surfaces . The autPagat et al. argued that heat (autoclave) and hypochlorites are effective in the decontamination of SARS-CoV , while oIn human inanimate bodies, a report by Camero stated that people who had passed away from the novel COVID-19 might still be contagious for hours or days . In a seIn consideration, therefore, of the potential relevance of data generated by analysis of material obtained from post-mortem examination, adopting the stricter safety procedures, we performed 5 complete autopsies with the main objective of verifying SARS-CoV-2 persistence in individuals whose death resulted from COVID-19 and whose cadavers were refrigerated at a temperature of -15° for a time interval between the moment of death and the autopsy which varied between 22 and 27 days. One of them had previously been buried for 5 days.Our study demonstrates that a large amount of virus, which has a multiorgan distribution thanks to its tropism for many human organs and tissues, may remain in deceased people infected with SARS-CoV-2, and the survival time of the virus may even be prolonged in refrigerated cadavers thanks to its resistance to cold environments.Thus, the performance of autopsies on infectious COVID-19 bodies could be catastrophic for forensic pathologists and mortuary workers if the cadavers are not properly handled. As a rule in the COVID-19 pandemic, some invasive procedures in standard pathology autopsies, especially those methods that produce tiny-particles (such as using an oscillating saw or cleansing of intestines) should be discouraged. However, if it is necessary to perform any of the above procedures, full protection with necessary personal protective equipment (PPE) is vital , 35, 36.In the light of the current COVID-19 pandemic, it is pertinent to ensure that COVID-19 safety protocols and standard operating procedures recommended for cadaveric dissections are strictly followed –40. BesiThe results of our study demonstrate that personal protection of examiners and disinfection of dissecting rooms, surroundings, and instruments should be taken seriously to avoid examiners being infected due to inadequate protection or careless operation.At the same time, as the remains of patients who have died of COVID-19 may have a large amount of the virus, the prevention of infected bodies being accessible to relatives and speeding up the post-mortal procedures for burial is thoroughly justified.Our study demonstrates that SARS-CoV-2 infection is characterized by a multiorgan distribution as this coronavirus has a tropism for many human organs and tissues. Nevertheless, such multiorgan distribution in cadaver tissues does not mean that infected people had developed the disease during their lifetime, nor is it related to disease severity. For this reason, matching molecular investigation results with any detectable anatomical damage by histological analyses of infected tissues is essential, and this is the subject of an ongoing study by the authors. Certainly, the ubiquitous post-mortem presence of SARS-CoV-2 even a long time after death and also in bodies subjected to burial and/or refrigeration is an extraordinary result, demonstrating the high resistance of this coronavirus to uncomfortable environmental conditions.However, these results must be treated with caution, not only because positive molecular investigations for coronaviruses are not automatically diagnostic of coronavirus disease, but also and above all because they do not always define the main cause of death. Therefore, without contextual histological investigations or when the results of histological investigations are compromised by partial cadaveric decomposition or by advanced putrefaction, the positivity of post-mortem molecular analyses should not lead pathologists to conclude that COVID-19 was the cause of death, especially due to the consequences that such improper conclusions could have in medico-legal disputes.The SARS-CoV-2 virus has strong persistence in the external environment, especially at low temperatures, and it could still be contagious on inanimate surfaces.A large amount of virus may remain in deceased people infected with SARS-CoV-2 even a long time after death and also in bodies subjected to burial and/or refrigeration. The survival time of the virus may even be prolonged in refrigerated cadavers thanks to its resistance to cold environments.The ubiquitous post-mortem presence of SARS-CoV-2 RNA demonstrates that SARS-CoV-2 infection is characterized by a multiorgan distribution, thanks to virus tropism for many human organs and tissues.The suspected risk to health professionals of COVID-19 infection from an individual whose death resulted from COVID-19 should not be overlooked.


The neurophysiological footprint of brain activity after cardiac arrest and during near-death experience (NDE) is not well understood. Although a hypoactive state of brain activity has been assumed, experimental animal studies have shown increased activity after cardiac arrest, particularly in the gamma-band, resulting from hypercapnia prior to and cessation of cerebral blood flow after cardiac arrest. No study has yet investigated this matter in humans. Here, we present continuous electroencephalography (EEG) recording from a dying human brain, obtained from an 87-year-old patient undergoing cardiac arrest after traumatic subdural hematoma. An increase of absolute power in gamma activity in the narrow and broad bands and a decrease in theta power is seen after suppression of bilateral hemispheric responses. After cardiac arrest, delta, beta, alpha and gamma power were decreased but a higher percentage of relative gamma power was observed when compared to the interictal interval. Cross-frequency coupling revealed modulation of left-hemispheric gamma activity by alpha and theta rhythms across all windows, even after cessation of cerebral blood flow. The strongest coupling is observed for narrow- and broad-band gamma activity by the alpha waves during left-sided suppression and after cardiac arrest. Albeit the influence of neuronal injury and swelling, our data provide the first evidence from the dying human brain in a non-experimental, real-life acute care clinical setting and advocate that the human brain may possess the capability to generate coordinated activity during the near-death period. Near-death experience (NDE) has been reported in situations where the brain transitions toward death. Subjective descriptions of this phenomenon are described as intense and surreal and include a panoramic life review with memory recalls, transcendental and out-of-body experiences with dreaming, hallucinations and a meditative state . The neuThe classic view of a hypoactive brain during the near-death phase has been challenged by recent evidence demonstrating end-of-life electrical surges (ELES) . In rodeAn 87-year-old male presented to the emergency department after a fall. Initially, his Glasgow Coma Scale (GCS) was 15, however, he rapidly deteriorated to a GCS of 10 (E3V2M5) with anisocoria  and bilateral reaction to light. Corneal and gag reflexes were preserved. The CT scan demonstrated bilateral acute subdural hematomas (SDH), with a larger mass effect on the left side  with a 2-s epoch size and 1 s overlapping each epoch . Epochs Phase-amplitude coupling is measured by the mean vector length modulation index , which qCoherence between pairs of electrodes belonging to different regions was measured by their magnitude-squared coherence. This measure calculates the normalized magnitude-squared of the cross-spectrum of two signals at each frequency. The estimation of coherence was obtained using the tool mscohere.m . The tool was applied to pairs of EEG signals of distinct electrodes segmented in 2-s epochs with 1 s overlapping each epoch as previously shown . CoherenTo investigate oscillatory changes during NDE, we analyzed neuronal oscillations from EEG recordings obtained during the transition period to death. We analyzed four time windows of interest: (1.) The interictal interval (II) window captures activity from 385 to 415 s after the clinical seizure. (2.) The left suppression (LS) window targets global spectral power from 510 to 540 s at the midpoint between suppression of left and bilateral hemispheric activity. (3.) The bilateral suppression (BS) window spans an interval between suppression of bilateral hemispheric activity and clinical cardiac arrest from 690 to 720 s. (4.) The final window includes the post-cardiac arrest (post-CA) period from 810 to 840 s at the midpoint between cardiac arrest and the end of the EEG recording. A timeline with these windows is shown in 2, II absolute γBB: 0.04μV2, BS absolute γNB: 0.14μV2, BS absolute γBB: 0.2μV2). This increment is also identified for the relative power of narrow and broad-band gamma, the percentage of power in such bands compared to the total power summed across all bands considered . On the contrary, the relative power spectrum reveals an increase of relative gamma power activity when compared to the interictal interval (Absolute . A surge2) to LS (1.80 μV2) and a further decay in the post-CA period (0.84 μV2) , while the sole change in the relative theta band is seen after bilateral activity suppression . A summary of all absolute and relative spectral power values across all investigated bands is provided in In addition, a prominent decline is seen in the delta-band from the interictal interval period  and broadband gamma  by the phase of alpha band activity during the suppression of left hemispheric activity (LS). A summary of all modulation indices for phase-amplitude coupling across all investigated bands is provided in Phase-amplitude cross-frequency coupling has been used to determine the strength with which the phase of one frequency band modulates the amplitude of another . This tyCoherence analysis between different electrodes was also used to estimate frequency-resolved dependencies across EEG signals. We report continuous EEG recording from a human brain across the transition period to death. The spectral analysis revealed a surge in absolute gamma power after suppression of neuronal activity in both hemispheres, followed by a marked decrease after cardiac arrest. In relative terms, the percentage gamma power over the total signal power is also increased after bilateral suppression together with a reduction of theta rhythms. After cardiac arrest, the relative amount of gamma power increased compared to the interictal interval, while a reduction of delta, beta, alpha and absolute gamma waves was identified. Cross-frequency coupling revealed strong modulation of the low- and broad gamma power by the alpha band. Inter-regional coherence analysis showed that after cardiac arrest, a reduction in global coherence occurred for the slower frequency bands while the coherence for faster bands was unchanged or slightly enhanced for narrow-band gamma. Together, these findings suggest that an intricate interplay between low- and high-frequency bands takes place after gradual cessation of cerebral activity and lasts into the period when cerebral blood flow is ceased (post cardiac arrest).The findings we report here are similar to the alterations in neuronal activity that have been observed in rodents, where an increase of low gamma band frequencies was observed 10–30 s after cardiac arrest . Our datin vitro slice preparations  and white matter damage can influence rhythmic brain activity . Post-inarations . Second,arations  and an iarations . Third, arations  and psycarations , openingarations . Fifth, arations  and in hDespite these caveats, the overall similarity in oscillatory changes between the highly controlled experimental rodent study and the present work suggests that the brain may pass through a series of stereotyped activity patterns during death. It may ultimately be difficult to assess this in a physiological environment, since gathering such data from “healthy-subjects” is impossible by definition. We do not anticipate death in healthy subjects and therefore could not obtain uninterrupted recordings in the near-death phase in anything other than from circumstances involving pathological conditions in acute care hospital settings.The original contributions presented in the study are included in the article/Ethical review and approval was not required for the study on human participants in accordance with the local legislation and institutional requirements. The patients/participants provided their written informed consent to participate in this study.RV, MR, RL, AL, JN, and AZ wrote the manuscript. RV, MR, TK, FM-A, and AZ analyzed data. CS, KY, MS, MF, and CH provided data and revised the manuscript. All authors contributed to the article and approved the submitted version.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher.


The severe acute respiratory syndrome coronavirus (SARS-CoV-2) is a highly transmittable virus which causes the novel coronavirus disease (COVID-19). Monocyte distribution width (MDW) is an in-vitro hematological parameter which describes the changes in monocyte size distribution and can indicate progression from localized infection to systemic infection. In this study we evaluated the correlation between the laboratory parameters and available clinical data in different quartiles of MDW to predict the progression and severity of COVID-19 infection.A retrospective analysis of clinical data collected in the Emergency Department of Rashid Hospital Trauma Center-DHA from adult individuals tested for SARS-CoV-2 between January and June 2020. The patients (n = 2454) were assigned into quartiles based on their MDW value on admission. The four groups were analyzed to determine if MDW was an indicator to identify patients who are at increased risk for progression to sepsis.Our data showed a significant positive correlation between MDW and various laboratory parameters associated with SARS-CoV-2 infection. The study also revealed that MDW ≥ 24.685 has a strong correlation with poor prognosis of COVID-19.Monitoring of monocytes provides a window into the systemic inflammation caused by infection and can aid in evaluating the progression and severity of COVID-19 infection.The online version contains supplementary material available at 10.1186/s12879-021-07016-4. The severe acute respiratory syndrome coronavirus (SARS-CoV-2) is a highly transmittable virus which causes the novel coronavirus disease COVID-19) that has affected over 131 million people worldwide and has caused 2.85 million deaths globally as of April 5th, 2021. The most common clinical presentation of this disease includes fever, dry cough and fatigue. However, in a subset of COVID-19 patients, severe outcomes such as viral sepsis are seen. Sepsis is a life-threatening systemic illness which can result in dysregulated immune responses leading to organ dysfunction and a leading cause of mortality [9 that haTo date, several biomarkers have been identified as early markers to evaluate inflammation and disease outcomes such as C-reactive protein, creatinine and D-dimer . In respIn this study, we retrospectively analyzed the clinical and biological characteristics of the COVID-19 infected patients and investigated the ability of MDW to predict at an earlier time the disease severity, in comparison with other biomarkers. We also investigated the correlation between routine laboratory parameters in different quartiles of MDW values to evaluate the usefulness of this value in predicting disease outcomes.This is a retrospective cohort study, which includes all adult individuals (≥ 18 years old) tested for SARS-CoV-2 in the Emergency Department—Rashid Hospital Trauma Center of DHA between January and June 2020. We included only the laboratory-confirmed cases, as the diagnosis was performed by real-time reverse transcriptase-polymerase chain reaction (RT-PCR) conducted on a nasopharyngeal swab of the patient according to the World Health Organization (WHO) guidance.Salama using a standardized data collection form, which is a modified version of the WHO/International Severe Acute Respiratory and Emerging Infection Consortium case record form for severe acute respiratory infections , serum biochemical test  in addition to some inflammatory markers . Frequency of examinations was determined according to the disease progress. For hospitalized patients, nasopharyngeal swab specimens were obtained for SARS-CoV-2 RT-PCR re-examination every other day after clinical remission of symptoms, including fever, cough, and dyspnea. Repeat RT-PCR tests were performed for SARS-CoV-2 done in patients confirmed to have COVID-19 infection to show viral clearance before hospital discharge or discontinuation of isolation as per national guidelines at the time of this study.The MDW, which was measured in this study using Beckman Coulter DxH 900 analyzer, is an additional parameter that was recorded in the data collection form. MDW values were compared among the studied groups to determine its usefulness as an indicator to identify patients who are at increased risk for progression to sepsis.Data were presented as mean and standard deviation for continuous variables and frequency  for categorical variables. For all statistical analyses and tests, SPSS was used . The normality test for all groups was done by Shapiro–Wilk tests using SPSS, and sig. of all independent variables > 0.05 means that all groups were normally distributed. To assess the differences between COVID-19 patients different groups based on MDW, ANOVA: analysis of variance used to identify and compare variances among groups for the continuous variables and Chi-square test was used for the categorical variables. P value < 0.05 had been considered significant.From January to June 2020, 2899 patients were tested positive for SARS-CoV-2 in the Emergency Department of Rashid Hospital Trauma Center of DHA. Only positive COVID-19 patients who had no comorbidities were selected for further analysis (n = 2454) as demonstrated in Fig. As presented in Table The results of the current study indicated significant positive correlation between MDW and COVID inflammation markers including C-reactive protein (CRP) , lactate dehydrogenase (LDH) , Ferritin , and Procalcitonin  as shown in Table Based on the MDW value, the patients were divided into quartiles with approximately equal numbers of patients assigned to each of the four groups as follows: Q1 , Q2 , Q3  and Q4 . These findings are concurrent with the fact that COVID-19 is associated with mild thrombocytopenia that is linked with more severe disease and mortality as SARS-CoV-2 can alter platelet number, form, and function , 32. AlsThis study has limitation for being a single-institution study and focused on adults COVID-19 patients. Nevertheless, the interesting about the study is the investigation, for the first time, the correlation between routine laboratory parameters in different quartiles of MDW values and the use of large sample size to support the findings precision. The MDW correlation with different inflammation markers involved in the cytokine storm induced by SARS-CoV-2, such as Interlukin-6 (IL6) and granulocyte colony-stimulating factor (GCSF), is a focal point for future research to increase our understanding of the MDW as a novel sepsis indicator in COVID-19 patients. Further study to investigate the MDW relationship with the clinical evolution of the patients is suggested to make the prognostic value of MDW in disease progress.To conclude, MDW can be predictor of poor outcome in patients presenting to the emergency setting with COVID-19. Interventions and specific therapeutics to target macrophage activation may be useful in mitigating adverse outcomes in these populations and manage the inflammatory response in COVID-19, preventing progressing to sepsis and multiorgan failure.Additional file 1: Appendix 1. WHO/International Severe Acute Respiratory and Emerging Infection Consortium case record form for severe acute respiratory infections, which is used to develop data collection form for the current study.


Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-associated coronavirus disease 2019 (COVID-19) pandemic has been the subject of a large number of studies in recent times. Here, starting from the evidence that in Italy, the areas with the lowest number of COVID-19 cases were those with the highest incidence of malaria in the early 1900's, we explore possible inverse relationships between malaria and COVID-19. Indeed, some genetic variants, which have been demonstrated to give an advantage against malaria, can also play a role in the incidence and severity of SARS-CoV-2 infections . To verify this scientific hypothesis, we here use public data from whole-genome sequencing (WGS) experiments to extrapolate the genetic information of 46 world populations with matched COVID-19 data. In particular, we focus on 47 genes, including ACE2 and genes which have previously been reported to play a role in malaria. Only common variants (>5%) in at least 30% of the selected populations were considered, and, for this subset, we correlate the intra-population allele frequency with the COVID-19 data (cases/million inhabitants), eventually pinpointing meaningful variants in 6 genes. This study allows us to distinguish between positive and negative correlations, i.e., variants whose frequency significantly increases with increasing or decreasing COVID-19 cases. Finally, we discuss the possible molecular mechanisms associated with these variants and advance potential therapeutic options, which may help fight and/or prevent COVID-19. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-associated coronavirus disease 2019 (COVID-19) has gripped the world in a pandemic, challenging its healthcare infrastructure, economy, and culture. In the last months, the epidemic moved from Europe to other parts of the World, growing very rapidly in Latin America, USA, and India. In Africa, the impact of COVID-19 is worrying the whole world due to the precariousness of the healthcare system with limited financial resources and scarcity of solid infrastructures and trained health workers  . DiffereThe ACE2 gene is located on the X chromosome and several single-nucleotide polymorphisms (SNPs) within the ACE2 gene have been reported. For instance, the ACE2 rs2106809 T allele in intron 1 has been associated with reduced expression of the ACE2 enzyme . A recenThe observations on ACE2 polymorphism suggest that a genetic predisposition could be worth to be investigated with the final objective to discover other common variations in the genome that could explain the low incidence of COVID-19 in areas where malaria is endemic. Indeed, while SARS-CoV-2 has infected humanity for only less than a year, for tens of thousands of years humans have been confronted with the pathogens responsible for malaria, and therefore natural selection has promoted the genetic variants of greater resistance to the disease.Based on these preliminary observations, here we first evaluate whether the spread of SARS-CoV-2 infection in the Italian regions is actually different in relation to the historical presence of malaria. Then, we investigate a list of genes linked to positive/negative responses to malaria, using whole genome sequencing (WGS) data from different populations scattered around the world. Only variants with allele frequency (AF) > 5% in at least 30% of the selected populations were considered. For this subset, we subsequently correlate the intra-population allele frequency with the COVID-19 data (cases/million inhabitants) in the first wave (from the beginning of the pandemic to 13th July 2020). In this way, we could identify positive and negative correlations, i.e., variants whose frequency significantly increases with increasing or decreasing COVID-19 cases, hence discovering putative genetic links between malaria and COVID-19. These genetic variants led subsequently us to investigate novel mechanisms, which may help more in-depth understanding the physiopathology and the complexity of COVID-19. Studying these molecular mechanisms, we eventually propose potential novel therapeutic options to combat and/or prevent the spread of SARS-CoV-2 infections.The incidence of malaria at the beginning of 20th century in Italy was reported as the number of deaths for malaria per million inhabitants in 1910, based on the Italian National Report on Causes of deaths  and the Whole-genome genotyping data of 969 worldwide healthy people from 54 diverse human populations were obtained from the Human Genome Diversity (HGDP) project as VCF files . COVID-1The analysis of Italian provinces and worldwide populations started with COVID-19 data collected in the so-called “first wave,” i.e., from the beginning of the pandemic until mid-July 2020. In order to confirm the results obtained from the “first wave,” COVID-19 cases between 1st November 2020 and 15th February 2021, known as “second wave,” were also considered.Forty-seven genes were considered in the present study. In particular, in addition to the ACE2 gene we selected (i) all the genes reported in Online Mendelian Inheritance in Man (OMIM) database  as relat6 inhabitants and (i) malaria prevalence in Italy , (ii) AF of the variants in each population . This test assesses the monotonic relationship (whether linear or not) between two variables and is less sensitive to the presence of outliers.The Spearman's correlation has been used to compute the correlation between COVID-19 cases/10p-values were obtained using the Benjamini & Hochberg method implemented in p.adjust R function. All the analyses were performed in R.To correct for multiple testing, FDR adjusted Haploview  was usedp = 5.4E-10) has been found. Indeed, COVID-19 distribution is clear, with Northern Italy far more affected than Southern Italy. Sicily and Sardinia, along with other regions in Southern Italy, have the lowest number of registered cases, whereas most of Northern Italy is greatly affected by SARS-CoV-2. Interestingly enough, the percentage of COVID-19 cases in Ferrara and Rovigo is much lower than in the rest of the North, and these areas were historically marshy, with a high incidence of malaria  were further investigated and classified based on their positive or negative correlation with COVID-19 cases.42,978 variants at the 47 genes selected see  were useGiven the similar allele frequency of many variants throughout the populations, we performed a linkage disequilibrium (LD) analysis to identify blocks of variants in LD and we selected the tag SNVs in LD that could capture the other alleles, leading to a final number of 25 and 16 representative SNVs for positive and negative correlations, respectively . All theTo focus on SNVs with a potential effect of gene expression, the GTEx database was interrogated to filter variants which were eQTLs. Excepted for the two variants in ACE2, all the other variants in the same gene were in LD and could be, therefore, considered together . Only onAmong the variants whose frequency positively correlates with COVID-19 cases, we identified (i) two variants at FCGR2A gene which may potentially decrease the expression of FCGR2C and HSPA7, (ii) one variant in IRF1 gene which may upregulate SLC22A, (iii) a variant in ADORA2B which increases the mRNA expression of CENPV gene in lung, and (iv) 9 variants in GYPB (see below).Variants with inverse correlation with COVID-19 cases include a variant in ABO which increases the expression of its transcript, and the two unrelated variants in ACE2 which may potentially increase the expression of PIR mRNA in both lung and blood.Particular attention must be paid to the variants of GYPB. Actually, some of these variants positively correlate with COVID-19 cases and increase the expression of GYPE. Others that negatively correlate with COVID-19 determine a reduction in the transcripts of FREM and GYPE. This contradiction can be interpreted by assuming that variants positively correlated with the cases of disease induce an increase in protein expression, exerting their putative risk effect for COVID-19. Conversely, the negatively correlated, and therefore protective variants, exert their effect by decreasing FREM expression, rather than decreasing GYPE.SNVs in SPTB gene were not considered, since they resulted associated both positively and negatively with COVID-19 cases, all with eQTL with positive slopes. Variants thus selected are reported in p-value 1.2E-5). Similarly, the significant trend between allele frequencies and COVID-19 cases worldwide observed for the 8 SNVs in the first wave was corroborated by the data from the second wave (Spearman FDR ranges from 1.6E-04 to 3.3E-09).The analysis of the correlation between Italian COVID-19 cases and deaths for malaria was also performed with the COVID-19 cases in the second wave (1st November 2020–15th February 2021), and we confirmed the correlation already observed  was more limited in the provinces where malaria was endemic at the beginning of the 20th century. Indeed, a highly significant inverse correlation emerged between COVID-19 cases and malaria mortality in 1910. A possible confounding factor could derive from the fact that the spread of SARS-CoV-2 is slightly greater in the northern Italian regions, while the malaria was endemic especially in the coasts of central and southern Italy. However, it is interesting to note that in some areas, such as in the provinces of Ferrara and Rovigo, located in the Po river delta and areas of malarial endemic, the spread of SARS-CoV-2 is much lower than in the neighboring provinces. These data have led to the hypothesis that some genetic variants, positively selected because of advantage against malaria, could also confer greater resistance to SARS-CoV-2 infection and thus explain the lower spread of the virus in the malarial areas.A bioinformatic analysis of public worldwide WGS data led to the final identification of variants in 6 malaria related genes, whose frequency is significantly associated to the incidence of COVID-19 cases. Indeed, some of these genes have already been identified by case control studies as associated with COVID-19, while for the others a direct evidence for a role in SARS-CoV-2 infections or in the progression/severity of COVID-19 has never been reported in the literature.We are aware that several factors could affect our observations. First, given the lack of genomic data from COVID-19 cases in malarial regions, we leveraged allele frequencies from healthy populations worldwide to highlight significant trends between MAF of variants in malarial genes and the prevalence of SARS-COV-2. In particular, variants from whole genome sequencing come from the Human Genome Diversity Project (HGDP) where, for each population, the approximate geographical place of origin was indicated by its latitude and longitude. Similarly, COVID-19 cases downloaded from the John Hopkins repository were annotated with latitude and longitude. We matched populations with similar coordinates in both datasets and, in cases where two populations were geographically very close, the COVID-19 or genetic data were aggregated in order to guarantee a geographical correspondence as reliable as possible. The final set used for downstream analysis consists of 46 populations for which both data were available. This approach does not take into account differences within countries  but we aimed at discovering global trends across populations worldwide. Although this is an indirect approach, several promising variants have emerged. Second, some of the subpopulations had a small sample size. Although they contribute to the estimate of the global genetic variability, the AF may not be representative of the population they belong to. The availability of multiple populations, and the use of a robust correlation, which is less sensitive to outliers, should mitigate this issue. Finally, in this study, we focused on the time frame corresponding to the first wave of pandemic (until mid-July 2020), however, the selected significant correlations were corroborated by the data from the second wave (Nov 2020-Feb 2021). Despite these issues, several variants passed all the filtering steps and were eventually selected.In the following, we report on a possible link with SARS-CoV-2 infections, also in terms of molecular mechanisms and potential therapeutic options.Several epidemiological analyses revealed that blood group O is associated with a lower risk of SARS-CoV infection . Using aThese results gathered for SARS-CoV are consistent with recent observations with SARS-CoV-2. Li et al. have recently published “Association between ABO blood groups and risk of SARS-CoV-2 pneumonia” , an obseHisto-blood group ABO system transferase is an enzyme with glycosyltransferase activity, which is encoded by the ABO gene in humans. ABO determines the ABO blood group of an individual by modifying the oligosaccharides on cell surface glycoproteins. In our study, we observed that the intron variant rs8176725 of ABO determined an increase in histo-blood group ABO system transferase expression and correlated negatively with COVID-19 cases. This is consistent with the previous reported observations revealing that blood group O was associated with a low risk of SARS-CoV and SARS-CoV-2 infections and that ABO natural antibodies can block the interaction between S protein and ACE2.P. Falciparum infection among individuals with blood group A, B, AB, or non-O compared with blood group O. However, the difference in the level of P. Falciparum parasitaemia was not significant among individuals with blood group A or non-O compared with blood group O. Blood group A likely promotes increased severity of disease through mechanisms dependent on rosetting and cytoadhesion  represent a small gene family localized on chromosome 4q28-q31 that encodes the major red cell membrane glycophorins, GPA and GPB, and GPE. Glycophorins play an important role in the invasion of red blood cells (RBCs) by malaria parasite. The glycophorin gene cluster has a complex pattern of gene conversion and structural variation, and selective pressure due to pathogens, including malaria, has contributed to induce diversity in this region . HoweverFREM3 (FRAS1-related extracellular matrix protein 3) is a gene located near GYPE and encodes an extracellular matrix protein that is required for maintaining the integrity of the skin epithelium and the differentiated state of renal epithelia. Although FREM3 apparently is not correlated with malaria and COVID-19, a recent study has demonstrated a link between a variant of FREM3 (rs186873296) and malaria . People If the role of GYPB as a protective factor against malarial infection, either directly or through FREM3, is sufficiently clarified, there are no data in the literature in relation to SARS-CoV-2 infection. GYPB rs6840234 decreases the expression of both glycophorin B and FREM3, and how this effect can protect against virus infection remains to be elucidated.We observed two intron-variants of ACE2 gene that were negatively correlated with COVID-19 cases. These variants (rs4646120 and rs1978124) were able to increase the mRNA expression of PIR, a gene encoding the enzyme quercetin 2,3-dioxygenase, which is involved in the degradation of quercetin by a dioxygenase reaction. ACE2 and PIR are two genes located on X-chromosome and are co-regulated by “double elite” enhancers. The co-regulation of ACE2 and PIR represents an important step during SARS-CoV-2 infections. Actually, after interaction between SARS-CoV-2 and the ACE2 receptor, this complex is internalized with a marked ACE2 depletion in cell surface. ACE2 is an essential protein under feedback regulation to restore protein expression. Thus, ACE2 depletion is followed by an upregulation of ACE2 gene transcription. ACE2 gene lies in a co-regulated cluster with PIR and VEGFD, sharing “double-elite” enhancers, implying homeostatic host responses . ACE2 geQuercetin 2,3-dioxygenase encoded by PIR converts the “antioxidant” quercetin to quinone, with a semiquinone radical intermediate, which reacts with oxygen to generate reactive oxygen species (ROS) superoxide O2·– and H2O2 . This caWe identified an intron variant in IRF1 gene (rs17622656) that positively correlated with COVID-19. Interferon regulatory factor 1 (IRF1) was the first member of the interferon regulatory transcription factor family identified. IRF1 regulates expression of target genes by binding to an interferon stimulated response element (ISRE) in their promoters. Several reports suggest that IFN-α and IFN-γ can co-operatively inhibit some virus replication including SARS-CoV, and IRF-1 plays a key role in this process . ConversThe observation that leukocytes, including monocytes and lymphocytes, are enriched in carnitines first suggested that carnitine may regulate the immune response . A reducRecently, particular attention has been focused on IFN genes and those that regulate them. It is unknown whether rs17622656 negatively regulates IRF1, which in turn would act downstream on the IRF genes. If this effect was demonstrated, the positive correlation with COVID-19 cases would be explainable. In line with this hypothesis, there are findings demonstrating the presence of mutations in type I IFN-related genes in patients with life-threatening COVID-19 pneumonia .ADORA2B encodes for an adenosine receptor. We found 2 introns variants (rs4646120 and rs1978124) of ADORA2B which correlated with COVID-19. These variants decrease protein expression in the lung. The activity of this adenosine receptor is mediated by G proteins which activate adenylyl cyclase. Adenosine is an endogenous ligand for four different adenosine receptor subtypes . Increased concentrations of adenosine were found in ascites of MethA sarcoma or in culture medium of 3LL Lewis lung carcinoma growing under hypoxic conditions. Adenosine and its analogs efficiently inhibited the cytotoxic activity of LAK cells. In fact, intratumor adenosine impairs the ability of lymphokine-activated killer (LAK) cells to kill tumor cells. It is possible to hypothesize that a decrease in ADOR2B may decrease the NK response toward cells infected with SARS-CoV-2, although there are no experimental studies that can confirm this hypothesis .Alternatively, ADORA2B could directly affect lung function. In fact, there are many instances where acute lung injury (ALI) resolves spontaneously through endogenous pathways that help to control excessive lung inflammation. Previous studies have implicated the extracellular signaling molecule adenosine and signaling events through the A2B adenosine receptor in lung protection. In this context, alveolar epithelial A2B adenosine receptor signaling contributes to lung protection. Thus, variants that induce a decrease in ADORA2B in the lung may be risk factors for the evolution of SARS-CoV-2 infection .We found that the frequency of intron variants rs72717040 and rs17400517 of FCGR2A correlated with the frequency of COVID-19. This gene encodes one member of a family of immunoglobulin Fc receptor genes found on the surface of many immune response cells. The protein encoded by this gene is a cell surface receptor found on phagocytic cells such as macrophages and neutrophils and is involved in the process of phagocytosis and clearing of immune complexes. It has also been associated with severe malaria in Gambia and in Kenia .The polymorphisms of FCGR2A exert a downregulation effect for both the FCGR2C and HSPA7 genes. The protein encoded by the first gene is again a receptor for the Fc region of complexed immunoglobulins gamma and is involved in a variety of effector and regulatory functions such as phagocytosis of immune complexes and modulation of antibody production by B-cells. HSPA7 is a pseudogene, member of Heat Shock Protein Family A (Hsp70). It is unclear how a decrease in FCGR2C can affect SARS-CoV-2 infection, and there is no association data between this gene and COVID-19. It is possible to hypothesize that its decrease in the lung and in phagocytic cells could reduce the effectiveness of the immune response to the virus.It is also interesting to note that other polymorphisms in FCGR2A have been associated with Kawasaki disease , 54. ThiThe present study demonstrates that some genetic variants selected to be protective against malaria may also play a role in the severity of SARS-CoV-2 infections. After identifying the genes known to be associated with malaria, we focused on those variants related to the frequency of COVID-19, both directly and inversely. After further skimming, we pinpointed six genes, representing a possible link between malaria and COVID-19. Indeed, for some of these, there is already direct evidence of implication with SARS-CoV-2 infection or with the evolution of COVID-19, such as ABO (blood groups) and ACE2 (a key human receptor for SARS-CoV-2). For other genes, there are interesting hypotheses for their role on COVID-19, as in IRF1 and ADORA2B. Finally, for the genes GYPB and FCGR2A, further investigations are needed to confirm an association with COVID-19 along with molecular studies to shed light on the mechanisms responsible for higher/lower incidence of SARS-CoV-2 infections.Among the genetic outcomes, the one related to the uptake of carnitine particularly attracted our attention. Carnitine is actually responsible for maintaining a high level of the immune response, and a lower level of this amino acid can negatively impact lymphocytes and monocytes. Therefore, we point to L-carnitine (or its prodrug acetyl-L-carnitine) as a possible dietary supplement to improve the immune response and combat/prevent COVID-19. A clinical trial to study the role of carnitine in addition to the standard of care has recently been launched.We want to conclude that the COVID-19 pandemic was rather brutal, particularly in the initial steps, forcing the health systems to concentrate all energy on the hospitals' emergency. This hampered the possibility to plan the collection of biological samples from COVID-19 patients for subsequent genomics and/or other analyses. Furthermore, to carry out a malaria-COVID-19 correlation study, one would have needed to find biological samples from malarial areas, along with clinical information on the malarial patient's history. All these steps are currently planned and will represent the subject matter of subsequent studies in the field (which are currently ongoing), where the present genetic variants will be confirmed. New ones will likely be disclosed to shed further light on the biological and genetic mechanisms of this complex infection, responsible for the current worldwide pandemic. Finally, possible links may emerge among variants in the human and viral genome, as intensive programs of high throughput sequencing are currently ongoing worldwide.Despite being rather different, malaria and COVID-19 may show some commonalities, mainly related to genetic variants present in populations living in malaria-endemic regions. In particular, starting from the evidence that in Italy, the areas with the lowest number of COVID-19 cases were those with the highest incidence of malaria, we here analyze genomic data from a May 2020 database. We filter the database for ACE2 and variants that are connected to malaria, pointing eventually to 47 genes. Further focusing only on those variants statistically relevant, we ultimately identify 6 genes that could be responsible for major susceptibility (or major resistance) to malaria. Surprisingly enough, these variants are also statistically related to higher/lower incidence/severity of SARS-CoV-2 infections. Among others, we identified genetic variants connected to blood group O, to a reduced expression of the ACE2 receptor (the entry point of SARS-CoV-2 into the human body), and to a decreased uptake of carnitine, an amino acid that plays a key role in the immune system response to infections. In conclusion, this study sheds further light on the genetic and molecular mechanisms responsible for the high/low impact of COVID-19. It points to a possible dietary supplement (L-carnitine) as a therapeutic adjuvant in treating SARS-CoV-2 infections.ftp://ngs.sanger.ac.uk/production/hgdp (WGS data) and https://github.com/CSSEGISandData/COVID-19/tree/master/csse_covid_19_data/csse_covid_19_daily_reports (COVID-19 data).Publicly available datasets were analyzed in this study. These data can be found at: MR drafted the manuscript, performed the analysis, and analyzed the results. PU designed the pipeline, performed the bioinformatic analysis, and analyzed the results. AA and MT analyzed the results. AC conceived the study, analyzed the results, and wrote the manuscript. All authors contributed to manuscript revision, read, and approved the submitted version.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.


Mw 8.3 outer-rise earthquake along the Japan Trench. Dispersive (Boussinesq) calculations predicted significant frequency dispersion in the 1933 tsunami. The dispersive tsunami deformation offshore produced tsunami inundation heights that were about 10% larger than those predicted by non-dispersive (long-wave) calculations. The dispersive tsunami calculations simulated the observed tsunami inundation heights better than did the non-dispersive tsunami calculations. Contrary to conventional practice, we conclude that dispersive calculations are essential when preparing deterministic hazard maps for outer-rise tsunamis.Although tsunamis are dispersive water waves, hazard maps for earthquake-generated tsunamis neglect dispersive effects because the spatial dimensions of tsunamis are much greater than the water depth, and dispersive effects are generally small. Furthermore, calculations that include non-dispersive effects tend to predict higher tsunamis than ones that include dispersive effects. Although non-dispersive models may overestimate the tsunami height, this conservative approach is acceptable in disaster management, where the goal is to save lives and protect property. However, we demonstrate that offshore frequency dispersion amplifies tsunamis caused by outer-rise earthquakes, which displace the ocean bottom downward in a narrow area, generating a dispersive short-wavelength and pulling-dominant (water withdrawn) tsunami. We compared observational evidence and calculations of tsunami for a 1933  Mw 9.1)4 that ruptured the plate boundary between the Indian, the Australian, and the Eurasian plates, caused massive damage across vast coastal regions around the Indian Ocean and run-ups as high as 50 m above sea level5. Although the Japan Meteorological Agency immediately issued a tsunami warning following the 2011 Mw 9.0 interplate earthquake in the Japan Trench subduction zone9, the ensuing tsunami killed about 20,000 people. Mori et al.10 measured a maximum tsunami run-up of 40.4 m at Aneyoshi in Iwate in northeastern Japan. Tsunami disasters of this kind are too frequent worldwide to list them all, but they include the 2010 Maule (Chile)11, the 2013 Solomon12, and the 2018 Palu tsunamis (Indonesia)13. Mitigating tsunami disasters is thus an enormous global issue.Sudden seafloor displacements by earthquakes and submarine landslides displace the overlying water column, generating tsunamis. The great 2004 Indian Ocean tsunami, following the Sumatra earthquake  was smaller than that observed during the 2011 Tohoku earthquake . The 1933 earthquake, however, produced a large tsunami that caused severe damage comparable that of the 2011 Tohoku tsunami. The maximum run-up of the 1933 tsunami reached 28.7 m and about 3,000 people died18. Another famous example of an interplate/outer-rise earthquake pair occurred in the Kuril Trench; the 2006 M 8.3 Kuril interplate earthquake was followed by the 2007 M 8.1 Kuril outer-rise earthquake 2 months later25. The 1977 Mw 8.2 Sumba earthquake was one of the most powerful outer-rise normal-faulting events ever recorded27. In 2012, a large intraplate earthquake (Mw 8.6) occurred in the subducting plate off the source region of the 2004 Sumatra earthquake30. Although the focal mechanism of that event indicates strike-slip fault motion, it may have changed from pure normal faulting because of the characteristic geological setting or the state of pre-accumulated stresses. Accordingly, intraplate earthquakes in a subducting plate can be activated by neighboring large interplate earthquakes. However, an outer‐rise earthquake corresponding to the 2011 Tohoku earthquake has yet to occur in the Japan Trench subduction zone. Although a Mw 7.6 outer-rise normal faulting earthquake occurred about 40 min after the 2011 main shock, its magnitude was much smaller than that of the main shock.Other large earthquakes generated tsunamis in the Japan Trench subduction zone in 1896 and 1933. The 1896 35 are the most basic element in mitigating tsunami disasters, showing tsunami risks such as expected inundation area, flow depth, and arrival time. Because hazard maps also indicate locations and accessible evacuation routes, they are useful for rapid evacuations during tsunami disasters. Authorities in many tsunami-prone regions have already prepared deterministic tsunami hazard maps and disseminated them to residents. The construction of a deterministic tsunami hazard map consists of defining a set of potential tsunami source models that incorporate the maximum tsunami size expected based on geophysical knowledge of a region or the maximum tsunami size the region has ever experienced. These tsunami source models are then used in numerical simulations. Because tsunami propagation depends on water depth, the accuracy of the bathymetric and topographic data control prediction accuracy. For tsunami propagation and inundation calculations, the Navier-Stokes equations, the universal governing equations of fluid flow, can be used to accurately predict seawater motions during tsunamis. But seawater can be treated as an incompressible and non-viscous fluid. Also, a tsunami can be approximated by a long-wave because the fault length for a great tsunami is several hundred kilometers, whereas the ocean depth is only about 5 km. Accordingly, the long-wave  theory36 is adequately accurate for constructing deterministic tsunami hazard maps. The calculation requirements for solving the long-wave equations are small enough so that a personal computer can be used to solve the equations.Here, we model possible future tsunamis that might be caused by a large outer-rise earthquake that could follow the 2011 Tohoku event. Tsunami hazard maps38 to improve the accuracy of the tsunami calculations. Because the phase velocity of a gravity wave in a dispersive model depends on water depth and wavelength, wave dispersion cannot be neglected for some classes of tsunami sources that have short wavelengths. In general, dispersion delays the short-wavelength component of tsunamis, forms wave trains, and reduces the maximum water height40. High-angle normal faults in the subducting plate cause outer-rise earthquakes under the deep ocean. The earthquakes deform the ocean bottom by subsidence in a narrow area, resulting in the generation of a pulling-dominant (water withdrawn), short-wavelength tsunami. Therefore, dispersion in an outer-rise tsunami is not negligible, as has been observed by bottom pressure gauges in the deep ocean where nonlinear effects on tsunami propagation are small43. However, the effects of dispersion are often neglected in tsunami hazard maps because of the high computational costs associated with dispersive tsunami calculations. Compared to dispersive calculations, non-dispersive (long-wave) calculations also tend to overpredict tsunami heights in our estimations  terms into the long-wave equationsons Fig. a and pre41 constructed outer-rise fault models, estimated initial sea surface displacement, and calculated tsunami propagation. The fault models were based on high-resolution bathymetric surveys, as well as active and passive seismic observations51. The survey results showed that the upper edges of outer-rise faults reach the seafloor, have dip angles of 45–75°, and that the thickness of the seismogenic zone for normal faulting is about 40 km. Using an earthquake scaling law52 and these survey results, Baba et al.41 proposed 33 possible outer-rise faults in the Japan Trench. Because these predictions include uncertainties, they also tested variations of the predictions resulting from uncertainties in the assumed parameters. This study expands on the results of Baba et al.41, which assumed a rigidity of 50 GPa, which is too small considering S-wave velocity  and κ is the geometric standard deviation indicating the variance of K54. We applied the same procedure to evaluate several previously proposed fault models of the 1933 Showa-Sanriku earthquake55 (models 34–38 in Table 55 was in good agreement with the observed inundation data (K = 1.03 and κ = 1.50). Figure K and κ for all fault models presented in Table 55 adjusted the fault parameters to predict the observed 1933 tsunami, we implemented the tsunami calculations using a completely forward-looking method. We conclude that our tsunami prediction procedures, including the method to construct the fault models, are appropriate for predicting tsunamis caused by future outer-rise earthquakes in the Japan Trench.The outer-rise tsunamis were calculated from the 33 fault models by solving the nonlinear long-wave (non-dispersive) equations in a finite difference scheme. Fault model 10 (K = 0.97 and κ = 1.49). The decrease in K from 1.09 to 0.97 indicates that the tsunami inundation heights in the dispersive calculations were about 10% larger than those in the non-dispersive calculations, resulting in better agreement with the observed data.We recalculated the outer-rise tsunamis from fault models 9, 10, 34, 36, and 38 Table  using thSurprisingly, the dispersive calculations amplified the tsunami inundation heights in the coastal region by about 10%. This amplification is a result of the characteristic shape of the initial sea surface displacement by outer-rise earthquakes. Outer-rise earthquakes on high-angle normal faults cause a narrow band of subsidence as the initial tsunamigenic deformation. Figure The difference in phase velocity between the initial and later parts of the tsunami wave causes shoaling, which increases the height of the water wave that propagates over the region from the deep ocean to the coast Movie . The firTo evaluate dispersive deformation of the outer-rise tsunamis, in Fig. 20 and 3621  to evaluate the difference between the non-dispersive and dispersive models. The results show that the tsunami inundation heights of the two models are almost the same at the observed points of the 1933 tsunami (errors are about 0.5%). The wavelength of tsunamis generated by the interplate earthquakes is within the valid range of the long-wave approximation, so we can ignore the effect of tsunami dispersion for the great interplate earthquakes when making tsunami hazard maps. However, for tsunamis that travel across the ocean, the effect of dispersion becomes important over their long propagation distances56.The question arises of whether non-dispersive equations underestimate tsunamis from interplate earthquakes. Therefore, we performed the same analysis for an ideal interplate earthquake  equations36 and nonlinear dispersive equations38. The time integrations were solved using JAGURS62, open-source software that solves either the non-dispersive or dispersive equations with a nested algorithm using a leapfrog, staggered-grid, finite-difference method.We performed tsunami calculations using the following procedure. Vertical crustal displacement at the seafloor was calculated assuming that the crust is a homogeneous elastic half-space63 (GtTM), which compiles open-source data around Japan to make 2 arc-sec gridded data. We resampled the GtTM to make a nested grid system consisting of 18 arc-sec, 6 arc-sec, and 2 arc-sec grids  in our comparisons. The total number of points to compare was 670 (Fig. 54K and κ for all of the calculated tsunamis in this study to find the best-fit fault model for the 1933 Showa-Sanriku earthquake. We also compared the calculated and observed tsunami waveforms at the tide gauge stations (Fig. 19. If the tide gauges were on land in our computational bathymetric data, we shifted the tide gauge location to the nearest sea point (Table We compared the calculated and observed tsunami heights from the 1933 Showa-Sanriku tsunami in the Japan tsunami trace database compiled by Tohoku University and the Nuclear Regulation Authority670 Fig. . If the ons Fig. . The obsnt Table .Supplementary Information 1.Supplementary Information 2.Supplementary Information 3.


During the SARS-CoV-2 pandemic a mass casualty incident of ambulatory patients occurred at the COVID-19 rapid response infrastructure (CRRI) facility at the University Hospital of Cologne (UHC). We report the development of a patient-centred mobile-device solution to support efficient management of the facility, triage of patients and rapid delivery of test results.The UHC-Corona Web Tool (CWT) was developed as a web-based software useable on each patient’s smartphone. It provides, among others, a self-reported medical history including type and duration of symptoms and potential risk contacts and links all retrieved information to the digital patient chart via a QR code. It provides scheduling of outpatient appointments and automated transmission of SARS-CoV-2 test results.The UHC-CWT was launched on 9 April 2020. It was used by 28,652 patients until 31 August 2020. Of those, 15,245  consulted the CRRI, representing 43,1% of all CRRI patients during the observed period.There were 8304  specifications concerning travel history and 17,145  indications of ≥1 symptom of SARS-CoV-2 infection. The most frequently indicated symptoms were sore throat , headache , common cold  and cough  while 11,057  patients did not report any symptoms. After implementation of the UHC-CWT, the amount of patient contacts per physician rose from 38 to 98,7 per day. The personnel for communication of test results were reduced from four on seven days to one on five days.The UHC-CWT is an effective digital solution for management of large numbers of outpatients for SARS-CoV-2 testing.The online version contains supplementary material available at 10.1186/s12879-021-06249-7. From the end of February 2020 onwards, many patients were seen at the emergency department as well as the COVID-19 rapid response infrastructure (CRRI) facility of the University Hospital of Cologne (UHC) in context of the SARS-CoV-2 pandemic . In addiThis mass influx of ambulatory patients demanded a drastic increase of efficiency for up-front triage of patients, consultations and rapid communication of test results while ascertaining constant quality.To reduce consultation time to a reasonable minimum, a paper-based questionnaire on prior medical history was distributed to waiting patients. The questionnaire was available in several languages and updated on a daily basis to include new findings, such as newly declared high-risk areas or newly identified symptoms of COVID-19 such as olfactory or taste disorders –8. This It soon became evident, that a digital approach was needed to support this overwhelming situation.The following goals were set: enabling patients to take their own medical history, embedding the Web Tool into the IT system of the CRRI and the automated communication of negative SARS-CoV-2-PCR results.Scrum method. The Scrum method entailed the setting of a time frame , in this case two weeks, in which the product increment was developed. In preparation of the Sprint, requirements were defined and prioritized. In the course of the Sprint, a continuous exchange between development team and users took place. By the end of the Sprint, as many defined requirements as possible should be met and the product should be finalized.The rapidly changing epidemiological situation required a continuously flexible software development in a limited time frame. Definition of the process flow and legal review of applicable data security and privacy requirements as well as development of texts for automated electronic notifications took place simultaneously. The development of the UHC Corona Web Tool  was conducted in accordance with principles of agile software development using the The electronic patient chart regularly used by UHC in the clinical information system (CIS) ORBIS®  and SAP-SE  were linked with the patient chart of the UHC Corona Web Tool.The UHC Corona Web Tool was announced via internet, signage on the hospital campus as well as the mobile CRRI. A smartphone call to the UHC hotline automatically initiates a SMS with a link being sent to the caller. The link opens the UHC Corona Web Tool on the smartphone browser. Once the patient has agreed to the data privacy terms, he/she can provide his/her personal medical history Fig. . The WebAll features can be used via any standard internet browser on an ordinary smartphone and do not require installation of an additional app.The self-reported medical history (MH) conducted through the UHC Corona Web Tool records the type and duration of symptoms, risk contacts, stays in high risk-areas, underlying diseases and prognostic factors. The questionnaire was answered before entering the CRRI.Robert Koch Institute (RKI) were applied, whilst taking into account further epidemiological and clinical criteria [During the subsequent physician consultation, the patient was supposed to show the MH to the physician who evaluated the indication for SARS-CoV-2 testing via nasopharyngeal swab. Current recommendations of the German Centre for Disease Control, the criteria , 10.A negative SARS-CoV-2-PCR test result was communicated within seconds via an automatically dispatched SMS right after validation of the PCR test result by a UHC virologist. A data link between the virologic laboratory and the UHC Corona Web Tool allowed for this notification. Positive test results were communicated via a telephone call consultation conducted by a physician Fig. . AdditioThe utilization of the UHC Corona Web Tool does not require an external login into a patient file, nor does it require access to a hospital’s IT system. All user interaction is conducted via SMS using the individual’s phone number. No personal information is shared or made available online at any given time. According to the technical state of the art, compromise of the data through third parties is therefore not possible. The informed consent to use anonymized data is actively given by the user during the administrative process in the UHC Web Tool. A revocation of consent is possible via the data safety officer of the UHC.Informed consent was obtained from all subjects  regarding the anonymized scientific evaluation of their reported data. This study and all methods were carried out in accordance with the declaration of Helsinki. The data was completely anonymized before analysis, therefore ethics approval by the ethics committee of the University Hospital of Cologne was waived.The data generated through the implementation of the UHC Corona Web Tool concerning symptoms, risk contacts and SARS-CoV-2 test results was analysed in a descriptive manner. A possible influence of the increased usage of the UHC Corona Web Tool on efficiency in the consultation was assessed by quantitatively analysing the patient contact per physician. The cut-off date of the here presented data is 31 August 2020.The first operational version of the UHC Corona Web Tool was completed in one sprint. In a following internal test phase, further requirements were evaluated. After three weeks of development, the Web Tool was launched on 9 April 2020. Since project initiation, the methodology for further development has remained the same. This method entails an update conducted every two weeks regarding additional user functions as well as updates necessitated by the epidemiological situation.Geographically, the CRRI’s catchment area includes the adjacent neighbourhoods as well as other areas within and around the city of Cologne, Germany. The number of patients per region  can be found in Fig. Since the establishment of the CRRI, a total of 35,378 ambulatory patients were seen until 31 August 2020 and 36,214 nasopharyngeal swabs for SARS-CoV-2-PCR tests were conducted in this time period. The discrepancy in results is due to multiple testing of some individual patients. On average, 1263 patients per week over the described period were seen. Prior to the implementation of the UHC Corona Web Tool 1150 patients per week were seen. After implementation of the UHC Corona Web Tool, 27,515 patients were seen in the CRRI (1310 per week on average) (Table completely. This resulted in 8304 (29.0%) data entries on travel information and 487 (1.7%) data entries on potential risk contacts with SARS-CoV-2 positive persons. The latter entry option was excluded from the 27th calendar week onwards due to users’ inaccurate data entry and additional potential confounders. Overall, 17,145 (59.8%) of patients reported symptoms. The most common symptoms were: sore throat (60.0%), headache (50.7%), common flu-like symptoms (45.1%) and cough (42.6%). The remaining 11,057 patients (40.2%) reported no symptoms at all  filled out the questionnaire on medical history 15,245 users of the of the UHC Corona Web Tool (53.2%) visited the CRRI in person. Of these, 12,228 patients (80.3%) underwent SARS-CoV-2-PCR testing via nasopharyngeal swab. 52 tests (0.43%) were positive and 12,172 were negative for SARS-CoV-2  Patients with contact to a SARS-CoV-2 positive tested person 2.) symptomatic and 3.) asymptomatic patients. This triage is carried out before the patient enters the CRRI. This procedure prevents possible transmissions of the virus in the CRRI site itself , 16. In By using a web-based approach, time pressure on patients reporting their medical history is avoided which can increase accuracy and validity of the medical history. Through storage of the fourteen-day-long symptoms log on the patient’s smartphone, the documentation of the development of symptoms is easily accessible and may help to facilitate contact tracing by public healthcare institutions. In line with other research, the most common symptoms suggestive of SARS-CoV-2 infection in the described cohort were: common cold, cough, headache and sore throat . AccordiThe percentage of UHC Web Tool users who subsequently underwent SARS-CoV-2 testing was low in comparison to all patients consulted at the CRRI. Especially UHC employees received multiple tests, which led to an increase in the overall rate of tests. These employees, however, did not use the UHC Corona Web Tool as often. It is possible, that the increase in efficiency is due to stricter evaluation regarding test indications updated by the RKI as well as due to the implementation of the UHC Corona Web Tool .not using the UHC Corona Web Tool was not compromised, however, this aspect was not analysed qualitatively in the margin of this study. The UHC Corona Web Tool is continuously updated due to the dynamic of the COVID-19 pandemic. This may limit the structured and comparative analysis of the data in the future, e.g. by adding additional items to the survey and thereby causing biases. The here described data from mid-April to August represents a low incidence period of SARS-CoV-2 in Germany. Lack of internet connection, data leakage and other technical issues could cause lack of utilization of the UHC Corona Web Tool, e.g. patients who presented more than once to the CRRI were sent the same text message concerning a negative test result several times which lead to confusion. This error was resolved within one week.Our approach certainly has limitations. The usage of the UHC Corona Web Tool is voluntary. Since older patients do not use smartphones as frequently, the population that uses the UHC Corona Web Tool differs from the groups at risk of severe SARS-CoV-2 infection . In our Software like the UHC Corona Web Tool can provide detailed and anonymized data for analysis of the development of infections in a scientific context . The utiThe UHC Corona Web Tool facilitated SARS-CoV-2 testing by increasing patient contacts per physician. Also, the personnel required to communicate test results was reduced. Software like the UHC Corona Web Tool can support the collection of data to analyse developments in infectious diseases. Web-based applications open up new perspectives for our future healthcare systems, especially in regard to future pandemics. The UHC Corona Web Tool represents an effective digital solution for the overall management from admission right through to the test result for large scale testing of ambulatory patients during the COVID-19 pandemic.Additional file 1 Fig. A1. Exemplary screenshot of UHC Corona Web Tool (in German). Fig. A2a-d. Distributions of postal codes (place of residence) of outpatients of the UHC CRRI from February 25th until August 31st, 2020.