ABSTRACT
Objective: To investigate the significance of the detection results of different types of samples in the clinical diagnosis and treatment of new coronavirus pneumonia (COVID-19) and the prevention and control of epidemic situation.
ABSTRACT
With the outbreak of COVID-19, how to mitigate and suppress its spread is a big issue to the government. Department of public health need powerful models to model and predict the trend and scale of such pandemic. And models that could evaluate the effect of the public policy are also essential to the fight with the COVID-19. A main limitation of existing models is that they can only evaluate the policy by calculating $R_0$ after infection happens instead of giving observable index. To tackle this, based on the transmission character of the COVID-19, we preposed a novel framework Spatial-Temporal-Susceptible-Infected-Removed (STSIR) model. In particular, we merged both intra-city and inter-city mobility index with the traditional SIR dynamics and make it a dynamic system. And we proved that the STSIR system is a closed system which makes the system self-consistent. And finally we proposed a Multi-Stage Simulated Annealing (MSSA) algorithm to find optimal parameter of the system. In our experiments, based on Baidu Mobility dataset, and China pandemic dataset provided by Dingxiangyuan, our model can effectively predict the total scale of the pandemic and also gives clear policy analysis with observable index.
Subject(s)
COVID-19ABSTRACT
We present the extension of the Tinker-HP package (Lagard\`ere et al., Chem. Sci., 2018,9, 956-972) to the use of Graphics Processing Unit (GPU) cards to accelerate molecular dynamics simulations using polarizable many-body force fields. The new high-performance module allows for an efficient use of single- and multi-GPU architectures ranging from research laboratories to modern supercomputer centers. After detailing an analysis of our general scalable strategy that relies on OpenACC and CUDA, we discuss the various capabilities of the package. Among them, the multi-precision possibilities of the code are discussed. If an efficient double precision implementation is provided to preserve the possibility of fast reference computations, we show that a lower precision arithmetic is preferred providing a similar accuracy for molecular dynamics while exhibiting superior performances. As Tinker-HP is mainly dedicated to accelerate simulations using new generation point dipole polarizable force field, we focus our study on the implementation of the AMOEBA model. Testing various NVIDIA platforms including 2080Ti, 3090, V100 and A100 cards, we provide illustrative benchmarks of the code for single- and multi-cards simulations on large biosystems encompassing up to millions of atoms. The new code strongly reduces time to solution and offers the best performances to date obtained using the AMOEBA polarizable force field. Perspectives toward the strong-scaling performance of our multi-node massive parallelization strategy, unsupervised adaptive sampling and large scale applicability of the Tinker-HP code in biophysics are discussed. The present software has been released in phase advance on GitHub in link with the High Performance Computing community COVID-19 research efforts and is free for Academics (see https://github.com/TinkerTools/tinker-hp).
Subject(s)
COVID-19ABSTRACT
Objective To investigate the epidemiological characteristics, clinical features, treatment and short-term prognosis of SARS-CoV-2 infection in children.Methods A retrospective analysis was conducted in children with SARS-CoV-2 admitted to twelve hospitals in eight cities in Hunan province, China, from January 26, 2020 to June 30, 2020.Results A total of 48 children were enrolled in this study. 11 cases (23%) were asymptomatic, 15 cases (31%) were mild, 20 cases (42%) were moderate, and 2 cases (4%) were severe. No children were critical requiring intensive care. The most common symptom was fever (42%), cough (40%), fatigue (17%) and diarrhea (10%). The total peripheral blood leukocytes count decreased in two case (4%), Lymphocytopenia was present in 5 cases (10%). There were abnormal chest CT changes in 22 children (46%), including 15 (68%) with patchy ground glass opacity. In addition to supportive treatment, 41 children (85%) received antiviral therapy, 11 patients and (23%) were treated with antibiotics, 2 children (4%) were treated with methylprednisolone and IVIG. There was no death occurred.Conclusions Most children with SARS CoV-2 infection in Hunan province were asymptomatic, mild or moderate. Severe cases are rare. Close family contact was the main route of infection. The younger the age, the less obvious symptoms for children might be. Epidemiological history, nucleic acid test and chest imaging were important tools for the diagnosis in children.
Subject(s)
Lymphopenia , Fever , Severe Acute Respiratory Syndrome , Fatigue , DiarrheaABSTRACT
Today, we are all threatened by an unprecedented pandemic: COVID-19. How different is it from other coronaviruses? Will it be attenuated or become more virulent? Which animals may be its original host? In this study, we analyzed 377 publicly available complete genome sequences for the COVID-19 virus, the previously known flu-causing coronaviruses (HCov-229E, HCov-OC43, HCov-NL63 and HCov-HKU1) and the lethal, pathogenic P3/P4 viruses, SARS, MERS, Victoria, Lassa, Yamagata, Ebola, and Dengue. We found strong similarities between the current circulating COVID-19 and SARS and MERS, as well as COVID-19 in rhinolophines and pangolins. On the contrary, COVID-19 shares little similarity with the flu-causing coronaviruses and the other P3/P4 viruses. Strikingly, we observed divergence of COVID-19 strains isolated from human hosts has steadily increased from December 2019 to March 2020, suggesting COVID-19 is actively evolving in human hosts. From all existing human COVID-19 genome sequences, we calculated the first common model that represents the shared sequences of the human COVID-19 strains, which provides important information for vaccine and antibody development. Geographic and time-course analysis of the evolutionary trees of the human COVID-19 reveals possibly heterogeneous evolutional paths among strains from 21 countries. This finding has important implications to the management of COVID-19 and the development of vaccines.
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COVID-19ABSTRACT
The COVID-19 pandemic is spreading rapidly, highlighting the urgent need for an efficient approach to rapidly develop therapeutics and prophylactics against SARS-CoV-2. We describe here the development of a phage-displayed single-domain antibody library by grafting naive CDRs into framework regions of an identified human germline IGHV allele. This enabled the isolation of high-affinity single-domain antibodies of fully human origin. The panning using SARS-CoV-2 RBD and S1 as antigens resulted in the identification of antibodies targeting five types of neutralizing or non-neutralizing epitopes on SARS-CoV-2 RBD. These fully human single-domain antibodies bound specifically to SARS-CoV-2 RBD with subnanomolar to low nanomolar affinities. Some of them were found to potently neutralize pseudotyped and live virus, and therefore may represent promising candidates for prophylaxis and therapy of COVID-19. This study also reports unique immunogenic profile of SARS-CoV-2 RBD compared to that of SARS-CoV and MERS-CoV, which may have important implications for the development of effective vaccines against SARS-CoV-2.
Subject(s)
COVID-19 , Severe Acute Respiratory SyndromeABSTRACT
Today, we are all threatened by an unprecedented pandemic: COVID-19. How different is it from other coronaviruses? Will it be attenuated or become more virulent? Which animals may be its original host? In this study, we analyzed 377 publicly available complete genome sequences for the COVID-19 virus, the previously known flu-causing coronaviruses (HCov-229E, HCov-OC43, HCov-NL63 and HCov-HKU1) and the lethal, pathogenic P3/P4 viruses, SARS, MERS, Victoria, Lassa, Yamagata, Ebola, and Dengue. We found strong similarities between the current circulating COVID-19 and SARS and MERS, as well as COVID-19 in rhinolophines and pangolins. On the contrary, COVID-19 shares little similarity with the flu-causing coronaviruses and the other P3/P4 viruses. Strikingly, we observed divergence of COVID-19 strains isolated from human hosts has steadily increased from December 2019 to March 2020, suggesting COVID-19 is actively evolving in human hosts. From all existing human COVID-19 genome sequences, we calculated the first common model that represents the shared sequences of the human COVID-19 strains, which provides important information for vaccine and antibody development. Geographic and time-course analysis of the evolutionary trees of the human COVID-19 reveals possibly heterogeneous evolutional paths among strains from 21 countries. This finding has important implications to the management of COVID-19 and the development of vaccines.
Subject(s)
COVID-19ABSTRACT
Today, we are all threatened by an unprecedented pandemic: COVID-19. How different is it from other coronaviruses? Will it be attenuated or become more virulent? Which animals may be its original host? In this study, we collected and analyzed nearly thirty thousand publicly available complete genome sequences for COVID-19 virus from 79 different countries, the previously known flu-causing coronaviruses (HCov-229E, HCov-OC43, HCov-NL63 and HCov-HKU1) and the lethal, pathogenic viruses, SARS, MERS, Victoria, Lassa, Yamagata, Ebola, and Dengue. We found strong similarities between the current circulating COVID-19 and SARS and MERS, as well as COVID-19 in rhinolophines and pangolins. On the contrary, COVID-19 shares little similarity with the flu-causing coronaviruses and the other known viruses. Strikingly, we observed that the divergence of COVID-19 strains isolated from human hosts has steadily increased from December 2019 to May 2020, suggesting COVID-19 is actively evolving in human hosts. In this paper, we first propose a novel MLCS algorithm NP-MLCS1 for the big sequence analysis, which can calculate the common model for COVID-19 complete genome sequences to provide important information for vaccine and antibody development. Geographic and time-course analysis of the evolution trees of the human COVID-19 reveals possible evolutional paths among strains from 79 countries. This finding has important implications to the management of COVID-19 and the development of vaccines and medications.