Corpus overview


MeSH Disease

HGNC Genes

SARS-CoV-2 proteins

ProteinS (1850)

ProteinN (502)

NSP5 (400)

ComplexRdRp (232)

ProteinE (133)


SARS-CoV-2 Proteins
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    Estimating the Expected Influence Capacities of Nodes in Complex Networks under the Susceptible-Infectious-Recovered (SIR) Model

    Authors: Aybike Şimşek

    id:2103.02324v1 Date: 2021-03-03 Source: arXiv

    In recent years, epidemic modeling in complex networks has found many applications, including modeling of information or gossip spread in online social networks, modeling of malware spread in communication networks, and the most recent model of the COVID-19 pandemic MESHD. If the information disseminated is accurate, for example, maximizing its distribution is desirable, whereas if it is a rumor or a virus, its spread should be minimized. In this context, it is very important to identify super-spreaders that maximize or minimize propagation. Lately, studies for detecting super-spreaders have gained momentum. Most of the studies carried out aim to distinguish the influences of nodes under a specific propagation model (such as SIR) using network centrality measures and subsequently, to rank the nodes accordingly. However, in this study, we developed an algorithm that approximates the expected influence of nodes under the popular SIR model. By considering the behavior of the SIR model and only the shortest paths between nodes, the algorithm ranks the nodes according to this approximated value. Our developed algorithm was named the Expected Value Estimation (EVE). We compared the performance of EVE, using different SIR settings on real datasets, with that of many current well-known centrality measures. The experimental studies demonstrated that the solution quality (ranking capability) of EVE was superior to that of its competitors.

    Analytical estimation of maximum fraction of infected individuals with one-shot non-pharmaceutical intervention in a hybrid epidemic model

    Authors: Naoya Fujiwara; Tomokatsu Onaga; Takayuki Wada; Shouhei Takeuchi; Junji Seto; Tomoki Nakaya; Kazuyuki Aihara

    id:2103.02175v1 Date: 2021-03-03 Source: arXiv

    Facing a global epidemic of new infectious diseases such as COVID-19 MESHD, non-pharmaceutical interventions (NPIs), which reduce transmission rates without medical actions, are being implemented around the world to mitigate spreads. One of the problems in assessing the effects of NPIs is that different NPIs have been implemented at different times based on the situation of each country; therefore, few assumptions can be shared about how the introduction of policies affects the patient population. Mathematical models can contribute to further understanding these phenomena by obtaining analytical solutions as well as numerical simulations. In this study, an NPI was introduced into the SIR model for a conceptual study of infectious diseases MESHD under the condition that the transmission rate was reduced to a fixed value only once within a finite time duration, and its effect was analyzed numerically and theoretically. It was analytically shown that the maximum fraction of infected individuals and the final size could be larger if the intervention starts too early. The analytical results also suggested that more individuals may be infected at the peak of the second wave with a stronger intervention. This study provides quantitative relationship between the strength of a one-shot intervention and the reduction in the number of patients with no approximation. This suggests the importance of the strength and time of NPIs, although detailed studies are necessary for the implementation of NPIs in complicated real-world environments as the model used in this study is based on various simplifications.

    Trajectories of Clinical and Laboratory Characteristics Associated with COVID-19 MESHD in Hemodialysis Patients by Survival

    Authors: Sheetal Chaudhuri; Rachel Lasky; Yue Jiao; John W Larkin; Caitlin Monaghan; Anke Winter; Luca Neri; Peter Kotanko; Jeffrey Hymes; Sangho Lee; Yuedong Wang; Jeroen Kooman; Franklin Maddux; Len Usvyat

    doi:10.1101/2021.02.28.21252383 Date: 2021-03-02 Source: medRxiv

    Introduction: The clinical impact of COVID-19 MESHD has not been established in the dialysis population. We evaluated the trajectories of clinical and laboratory parameters in hemodialysis (HD) patients. Methods: We used data from adult HD patients treated at an integrated kidney disease MESHD company who received a RT-PCR test to investigate suspicion of a SARS-CoV-2 infection MESHD between 01 May and 01 Sep 2020. Nonparametric smoothing splines were used to fit data for individual trajectories and estimate the mean change over time in patients testing positive or negative for SARS-CoV-2 and those who survived or died within 30 days of first suspicion or positive test date. For each clinical parameter of interest, the difference in average daily changes between COVID-19 MESHD positive versus negative group and COVID-19 MESHD survivor versus non-survivor group was estimated by fitting a linear mixed effects model based on measurements in the 14 days before (i.e., day -14 to day 0) day 0. Results: There were 12,836 HD patients with a suspicion of COVID-19 MESHD who received RT-PCR testing (8,895 SARS-CoV-2 positive). We observed significantly different trends (p<0.05) in pre- HD systolic blood pressure MESHD ( SBP HGNC), pre-HD pulse rate, body temperature, ferritin, lymphocytes, albumin, and interdialytic weight gain MESHD ( IDWG MESHD) between COVID-19 MESHD positive and negative patient. For COVID-19 MESHD positive group, we observed significantly different clinical trends (p<0.05) in pre-HD pulse rate, lymphocytes, albumin and neutrophil-lymphocyte ratio (NLR) between survivors and non-survivors. We also observed that, in the group of survivors, most clinical parameters returned to pre- COVID-19 MESHD levels within 60-90 days. Conclusion: We observed unique temporal trends in various clinical and laboratory parameters among HD patients who tested positive versus negative for SARS-CoV-2 infection MESHD and those who survived the infection versus those who died. These trends can help to define the physiological disturbances that characterize the onset and course of COVID-19 MESHD in HD patients

    Modeling COVID-19 MESHD Nonpharmaceutical Interventions: Exploring periodic NPI strategies

    Authors: Raffaele Vardavas; Pedro Nascimento de Lima; Lawrence Baker

    doi:10.1101/2021.02.28.21252642 Date: 2021-03-02 Source: medRxiv

    In April 2020, we developed a COVID-19 MESHD transmission model used as part of RAND's web-based COVID-19 MESHD decision support tool that compares the effects of different nonpharmaceutical public health interventions (NPIs) on health and economic outcomes. An interdisciplinary approach informed the selection and use of multiple NPIs, combining quantitative modeling of the health/economic impacts of interventions with qualitative assessments of other important considerations (e.g., cost, ease of implementation, equity). We previously published a description of our approach as a RAND report describing how the epidemiological model, the economic model, and a systematic assessment of NPIs informed the web-tool. This paper provides further details of our model, describes extensions that we made to our model since April, presents sensitivity analyses, and analyzes periodic NPIs. Our findings suggest that there are opportunities to shape the tradeoffs between economic and health outcomes by carefully evaluating a more comprehensive range of reopening policies. We consider strategies that periodically switch between a base NPI level and a higher NPI level as our working example.

    Comparative performance of SARS-CoV-2 lateral flow antigen tests demonstrates their utility for high sensitivity detection of infectious virus in clinical specimens

    Authors: Suzanne Pickering; Rahul Batra; Luke B Snell; Blair Merrick; Gaia Nebbia; Sam Douthwaite; Amita Patel; Mark TK Ik; Bindi Patel; Themoula Charalampous; Adela Alcolea-Medina; Maria Jose Lista; Penelope R Cliff; Emma Cunningham; Jane Mullen; Katie J Doores; Jonathan D Edgeworth; Michael H Malim; Stuart JD Neil; Rui Pedro Galao

    doi:10.1101/2021.02.27.21252427 Date: 2021-03-02 Source: medRxiv

    Background: Rapid antigen lateral flow devices (LFDs) are set to become a cornerstone of SARS-CoV-2 mass community testing. However, their reduced sensitivity compared to PCR has raised questions of how well they identify infectious cases. Understanding their capabilities and limitations is therefore essential for successful implementation. To address this, we evaluated six commercial LFDs on the same collection of clinical samples and assessed their correlation with infectious virus culture and cycle threshold (Ct) values. Methods: A head-to-head comparison of specificities and sensitivities was performed on six commercial rapid antigen tests using combined nasal/oropharyngeal swabs, and their limits of detection determined using viral plaque forming units (PFU). Three of the LFDs MESHD were selected for a further study, correlating antigen test result with RT-PCR Ct values and positive viral culture in Vero-E6 cells. This included sequential swabs and matched serum samples obtained from four infected individuals with varying disease severities. Detection of antibodies was performed using an IgG/IgM Rapid Test Cassette, and neutralising antibodies by infectious virus assay. Finally, the sensitivities of selected rapid antigen LFTs were assessed in swabs with confirmed B.1.1.7 variant, currently the dominant genotype in the UK. Findings: Most of the rapid antigen LFDs showed a high specificity (>98%), and accurately detected 50 PFU/test (equivalent N1 Ct of 23.7 or RNA copy number of 3x106/ml). Sensitivities of the LFDs performed on clinical samples ranged from 65 to 89%. These sensitivities increased in most tests to over 90% for samples with Cts lower than 25. Positive virus culture was achieved for 57 out of 141 samples, with 80% of the positive cultures from swabs with Cts lower than 23. Importantly, sensitivity of the LFDs increased to over 95% when compared with the detection of infectious virus alone, irrespective of Ct. Longitudinal studies of PCR-positive samples showed that most of the tests identified all infectious samples as positive, but differences in test sensitivities can lead to missed cases in the absence of repeated testing. Finally, test performance was not impacted when re-assessed against swabs positive for the dominant UK variant B.1.1.7. Interpretation: In this comprehensive comparison of antigen LFD and virus infectivity, we demonstrate a clear relationship between Ct values, quantitative culture of infectious virus and antigen LFD positivity in clinical samples. Our data support regular testing of target groups using LFDs to supplement the current PCR testing capacity, to rapidly identify infected individuals in situations where they would otherwise go undetected.

    SARS-CoV-2 antibodies detected in human breast milk post-vaccination

    Authors: Jill K Baird; Shawn M Jensen; Walter J Urba; Bernard A Fox; Jason R Baird

    doi:10.1101/2021.02.23.21252328 Date: 2021-03-02 Source: medRxiv

    Importance: The SARS-CoV-2 pandemic has infected over a hundred million people worldwide, with almost 2.5 million deaths at the date of this publication. In the United States, Pfizer-BioNTech and Moderna vaccines were first administered to the public starting in December 2020, and no lactating women were included in the initial trials of safety/efficacy. Research on SARS-CoV-2 vaccination in lactating women and the potential transmission of passive immunity to the infant through breast milk MESHD is needed to guide patients, clinicians and policy makers during the worldwide effort to curb the spread of this virus. Objective: To determine whether SARS-CoV-2 specific immunoglobins are found in breast milk post-vaccination, and to characterize the time course and types of immunoglobulins present. Design:.Prospective cohort study Setting: Providence Portland Medical Center, Oregon, USA Participants: Six lactating women who planned to receive both doses of the Pfizer-BioNTech or Moderna vaccine between December 2020 and January 2021. Breast milk samples were collected pre-vaccination and at 11 additional timepoints, with last sample at 14 days post 2nd dose of vaccine. Exposure: Two doses of Pfizer-BioNTech or Moderna SARS-CoV-2 vaccine. Main Outcome(s) and Measure(s): Levels of SARS-CoV-2 specific IgA and IgG immunoglobulins in breast milk MESHD. Results: In this cohort of 6 lactating women who received 2 doses of SARS-CoV-2 vaccine, we observed significantly elevated levels of SARS-CoV-2 specific IgG and IgA antibodies in breast milk MESHD beginning at Day 7 after the initial vaccine dose, with an IgG-dominant response. Conclusions and Relevance: We are the first to show that maternal vaccination results in SARS-CoV-2 specific immunoglobulins in breast milk MESHD that may be protective for infants.

    Introductions and evolutions of SARS-CoV-2 strains in Japan

    Authors: Reitaro Tokumasu; Dilhan Weeraratne; Jane Snowdon; Laxmi Parida; Michiharu Kudo; Takahiko Koyama

    doi:10.1101/2021.02.26.21252555 Date: 2021-03-02 Source: medRxiv

    COVID-19 MESHD caused by SARS-CoV-2 was first identified in Japan on January 15th, 2020, soon after the pandemic originated in Wuhan, China. Subsequently, Japan experienced three distinct waves of the outbreak in the span of a year and has been attributed to new exogenous strains and evolving existing strains. Japan engaged very early on in tracking different COVID-19 MESHD sub-strains and have sequenced approximately 5% of all confirmed cases. While Japan has enforced stringent airport surveillance on cross-border travelers and returnees, some carriers appear to have advanced through the quarantine stations undetected. In this study, 17112 genomes sampled in Japan were analyzed to understand the strains, heterogeneity and temporal evolution of different SARS-CoV-2 strains. We identified 11 discrete strains with a substantial number of cases with most strains possessing the spike (S) D614G and nucleocapsid (N PROTEIN) 203_204delinsKR mutations. Besides these variants, ORF1ab PROTEIN P3371S, A4815V, S1361P, and N P151L were also detected in nearly half the samples constituting the most common strain in Japan. 115 distinct strains have been introduced into Japan and 12 of them were introduced after strict quarantine policy was implemented. In particular, the B.1.1.7 strain, that emerged in the United Kingdom (UK) in September 2020, has been circulating in Japan since late 2020 after eluding cross-border quarantine stations. Similarly, the B.1.351 strain dubbed the South African variant, P.1 Brazilian strain and R.1 strain with the spike E484K mutation have been detected in Japan. At least four exogenous B.1.1.7 sub-strains have been independently introduced in Japan as of late January 2021, and these strains carry mutations that give selective advantage including N501Y, H69_V70del, and E484K that confer increased transmissibility, reduced efficacy to vaccines and possible increased virulence. It is imperative that the quarantine policy be revised, cross-border surveillance reinforced, and new public health measures implemented to mitigate further transmission of this deadly disease and to identify strains that may engender resistance to vaccines.

    Clinical course and outcomes of critically ill COVID-19 MESHD patients in two successive pandemic waves

    Authors: Athanasios Chalkias; Ioannis Pantazopoulos; Nikolaos Papagiannakis; Anargyros Skoulakis; Eleni Laou; Konstantina Kolonia; Nicoletta Ntalarizou; Christos Kampolis; Luis Garcia de Guadiana Romualdo; Konstantinos Tourlakopoulos; Athanasios Pagonis; Salim S Hayek; Jesper Eugen-Olsen; Konstantinos Gourgoulianis; Eleni Arnaoutoglou

    doi:10.1101/2021.02.26.21251848 Date: 2021-03-02 Source: medRxiv

    Rationale: The progress of COVID-19 MESHD from moderate to severe may be precipitous, while the heterogenous characteristics of the disease pose challenges to the management of these patients. Objectives: To characterize the clinical course and outcomes of critically ill MESHD patients with COVID-19 MESHD during two successive waves. Methods: We leveraged the multi-center SuPAR in Adult Patients With COVID-19 MESHD (SPARCOL) study and collected data from consecutive patients requiring admission to the intensive care unit from April 1st to November 30th, 2020. Measurements and Main Results: Of 252 patients, 81 (32%) required intubation and mechanical ventilation. Of them, 17 (20.9%) were intubated during the first wave, while 64 (79%) during the second wave. The most prominent difference between the two waves was the overall survival (first wave 58.9% vs. second wave 15.6%, adjusted p-value=0.006). This difference is reflected in the prolonged hospitalization during the first wave. The mean ICU length of stay (19.1 vs. 11.7 days, p=0.022), hospital length of stay (28.5 vs. 17.1 days, p=0.012), and days on ventilator (16.7 vs. 11.5, p=0.13) were higher during the first wave. A significant difference between the two waves was the development of bradycardia MESHD. In the first wave, 2 (11.7%) patients developed sinus bradycardia MESHD only after admission to the intensive care unit, while in the second wave, 63 (98.4%) patients developed sinus bradycardia MESHD during hospitalization. Conclusions: Survival of critically ill MESHD patients with COVID-19 MESHD was significantly lower during the second wave. The majority of these patients developed sinus bradycardia MESHD during hospitalization.

    Utility of a Clinical Scoring System for Point of Care Triaging in COVID-19 MESHD Pneumonia

    Authors: Andrew J Gangemi; Rohit Gupta; Gustavo Fernandez-Romero; Huaqing Zhao; Maulin Patel; Junad Chowdhury; Massa Zantah; Matthew Zheng; Osheen Abramian; Stephen Codella; Linda Vien; Eduardo Dominguez-Castillo; Timothy Buckey; Charles Earley; Jourdan Frankovich; Mali Jurkowski; Zachary Jurkowski; Nanzhou Guo; Paige Stanley; Brenton Halsey; Jasleen Kahlon; Navjot Kaur; Roman Prosniak; Maruti Kumaran; Chandra Dass; David Fleece; Michael R Jacobs; Gerard J Criner; - Temple University COVID-19 Research Group

    doi:10.1101/2021.02.26.21252256 Date: 2021-03-02 Source: medRxiv

    Background: Surges in COVID-19 MESHD disease cases can rapidly overwhelm healthcare resources; triaging to appropriate levels of care can assist in resource planning. At the beginning of the pandemic, we developed a simple triage tool, the Temple COVID-19 MESHD Pneumonia Triage Tool (TemCOV) based on a combination of clinical and radiographic features that are readily available on presentation to categorize and predict illness severity. Methods: We prospectively examined 579 sequential cases admitted to Temple University Hospital who were assigned severity categories on admission. Our primary outcome was to compare the performance of TemCOV in predicting patients who have the highest likely of admission to the ICU at 24 and at 72 hours to other standard triage tools: the National Early Warning System (NEWS), the Modified Early Warning System (MEWS) and the CURB65 score. Additional endpoints included need for invasive mechanical ventilation (IMV) within 72 hours, total hospital admission charges, and mortality. Results: 26% of patients fell within our highest risk Category 4 and were more likely to require ICU admission at 24 hours (OR 11.51) and 72 hours (OR 8.6). Additionally they had the highest likelihood of needing IMV (OR 29.47) and in-hospital mortality (OR 2.37). , TemCOV performed similar to MEWS in predicting ICU admission at 24 hours (receive operator characteristic (ROC) curve area under the curve (AUC) 0.77 vs. 0.74, p=0.21) but better than NEWS2 and CURB65 (ROC AUC 0.77 vs. 0.69 and 0.77 vs. 0.64, respectively, p<0.01). While all severity scores had a weak correlation to hospital charges, the TemCOV performed the best among all severity scores measured (r=0.18); median hospital charges for Category 4 patients was $170,468 ($96,972-$487,556). Conclusion: TemCOV is a simple triage score that can be used upon hospitalization in patients with COVID-19 MESHD that predicts the need for hospital resources such as ICU bed capacity, invasive mechanical ventilation and personnel staffing.

    Seasonal patterns COVID-19 MESHD and Flu HGNC Like Illnesses comparable

    Authors: Martijn J Hoogeveen; Ellen K Hoogeveen

    doi:10.1101/2021.02.28.21252625 Date: 2021-03-02 Source: medRxiv

    Introduction During the first wave of COVID-19 MESHD it was hypothesized that COVID-19 MESHD is subject to multi-wave seasonality, such as other respiratory viral infections since time immemorial, including earlier respiratory pandemics. It has already been observed that the COVID-19 MESHD community outbreaks appear to have a similar pattern as other influenza like illnesses (ILI). One year into the pandemic, we aimed to test the seasonality hypothesis for COVID-19 MESHD. Methods We gather and calculated the average ILI annual time series based on incidence data from 2016 till 2019 in the Netherlands. And, compared this with two independent COVID-19 MESHD time series during 2020/2021 for the Netherlands, plotted on a logarithmic infection scale. We tested our hypothesis by calculating correlation coefficients and, as a sensitivity analysis, by performing univariate regression analysis. Results The COVID-19 MESHD time series strongly and highly significantly correlates with the ILI time series r(45) = 0.75 (p < 0.00001) and (r(45) = 0.798, p < 0.00001). Also the univariate regression analyses that we performed as a sensitivity analysis are all highly significant: respectively F(1, 43) = 61.45, p < 0.0001, and F(1, 43) = 81.18, p < 0.0001 and the correlations (r2) are moderate to strong. Conclusions Given the strong, and highly significant, correlations between the ILI and COVID-19 MESHD time series, we conclude that COVID-19 MESHD behaves as seasonal as ILI in a country in the temperate climate zone, such as the Netherlands. Moreover, the COVID-19 MESHD peaks are all during flu HGNC season, and lows are all in the opposing period as expected. Furthermore, the COVID-19 MESHD time series satisfies the two characteristics of earlier pandemics, namely a short first wave at the tail-end of a flu HGNC season, and a longer and more intense second wave during the subsequent flu HGNC season.

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MeSH Disease
HGNC Genes
SARS-CoV-2 Proteins

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