Your browser doesn't support javascript.
Show: 20 | 50 | 100
Results 1 - 20 de 76
Filter
1.
Viruses ; 14(7)2022 06 23.
Article in English | MEDLINE | ID: covidwho-1964114

ABSTRACT

The spike protein (S) plays a crucial role in porcine epidemic diarrhea virus (PEDV) infection and induces neutralizing antibodies. Mutations of the S protein are supposed to provide the main antigenic shift leading to the antigenic escape of PEDVs. It is therefore a significant question how much accumulation of antigenic shift could lead to the antigenic escape of the variant PEDV. To provide an answer in the study, B cell epitopes (BCEs) on the S protein of the PEDV vaccine strain CV777 (SCV777) and variant strain SD2014 (SSD2014) were mapped using biosynthetic peptides and rabbit anti-PEDV S serum. Seventy-nine and 68 linear BCEs were identified from SCV777 and SSD2014, respectively. While 66.2% of the BCEs of SSD2014 could be recognized by anti-SCV777 serum and 67.1% of SCV777 BCEs could be recognized by anti-SSD2014 serum, more than 40% of the BCEs identified using anti-SCV777 serum on SCV777 could not be recognized by anti-SSD2014 serum and vice versa. The completely shared BCEs took low percentages of 29.4% and 25.3% for SSD2014 and SCV777, respectively. These results indicate a low conservation of antigenicity of the S protein compared to a relatively high amino acid sequence similarity of 92.2% between the two strains. The study provided a BCE shift reference of PEDV antigenic escape and surveillance control.


Subject(s)
Coronavirus Infections , Porcine epidemic diarrhea virus , Swine Diseases , Animals , Antibodies, Neutralizing , Epitope Mapping , Epitopes, B-Lymphocyte , Porcine epidemic diarrhea virus/genetics , Rabbits , Spike Glycoprotein, Coronavirus , Swine
2.
Diagnostic Microbiology and Infectious Disease ; : 115766, 2022.
Article in English | ScienceDirect | ID: covidwho-1936296

ABSTRACT

The COVID-19 pandemic has necessitated the rapid expansion of laboratories that conduct SARS-CoV-2 tests. A provincial external quality assessment (EQA) scheme on SARS-CoV-2 tests was organized by Zhejiang Provincial CDC to assess the accuracy of the tests in individual CDC municipal and county laboratories in Zhejiang Province, China. Three positive samples in high, medium, and low concentrations, respectively, were prepared using the serial dilutions from the culture with the viral titer concentration of 1×106.3 TCID50/ml, and one negative sample were included. A total of 93 laboratories participated, contributing results from 36 distinct combinations of nucleic acid extraction methods and PCR reagents. There was 100% concordance among all laboratories for all EQA samples, and no false-positive or false-negative results were observed. The EQA survey provides confidence in the identification of infected individuals or asymptomatic populations and assurance for clinical and public health decision-making based on test results.

3.
Viruses ; 14(6)2022 06 06.
Article in English | MEDLINE | ID: covidwho-1911617

ABSTRACT

Porcine epidemic diarrhea virus (PEDV) belongs to the genus Alphacoronavirus of the family Coronaviridae that causes severe diarrhea and high mortality in neonatal suckling piglets. Currently, there is no effective medication against this pathogen. Cepharanthine (CEP), tetrandrine (TET), and fangchinoline (FAN) are natural bis-benzylisoquinoline alkaloids with anti-inflammatory, antitumor, and antiviral properties. Here, we first found that CEP, TET, and FAN had anti-PEDV activity with IC50 values of 2.53, 3.50, and 6.69 µM, respectively. The compounds could block all the processes of viral cycles, but early application of the compounds before or during virus infection was advantageous over application at a late stage of virus replication. FAN performed inhibitory function more efficiently through interfering with the virus entry and attachment processes or through attenuating the virus directly. CEP had a more notable effect on virus entry. With the highest SI index of 11.8 among the three compounds, CEP was chosen to carry out animal experiments. CEP in a safe dosage of 11.1 mg/kg of body weight could reduce viral load and pathological change of piglet intestinal tracts caused by PEDV field strain challenge, indicating that CEP efficiently inhibited PEDV infection in vivo. All of these results demonstrated that the compounds of bis-benzylisoquinoline alkaloids could inhibit PEDV proliferation efficiently and had the potential of being developed for PED prevention and treatment.


Subject(s)
Benzylisoquinolines , Coronavirus Infections , Porcine epidemic diarrhea virus , Swine Diseases , Animals , Benzylisoquinolines/pharmacology , Coronavirus Infections/drug therapy , Coronavirus Infections/pathology , Coronavirus Infections/veterinary , Diarrhea , Swine , Swine Diseases/pathology
4.
- IMPACC group; Al Ozonoff; Joanna Schaenman; Naresh Doni Jayavelu; Carly E. Milliren; Carolyn S. Calfee; Charles B. Cairns; Monica Kraft; Lindsey R. Baden; Albert C. Shaw; Florian Krammer; Harm Van Bakel; Denise Esserman; Shanshan Liu; Ana Fernandez Sesma; Viviana Simon; David A. Hafler; Ruth R. Montgomery; Steven H. Kleinstein; Ofer Levy; Christian Bime; Elias K. Haddad; David J. Erle; Bali Pulendran; Kari C. Nadeau; Mark M. Davis; Catherine L. Hough; William B. Messer; Nelson I. Agudelo Higuita; Jordan P. Metcalf; Mark A. Atkinson; Scott C. Brakenridge; David B. Corry; Farrah Kheradmand; Lauren I. R. Ehrlich; Esther Melamed; Grace A. McComsey; Rafick Sekaly; Joann Diray-Arce; Bjoern Peters; Alison D. Augustine; Elaine F. Reed; Kerry McEnaney; Brenda Barton; Claudia Lentucci; Mehmet Saluvan; Ana C. Chang; Annmarie Hoch; Marisa Albert; Tanzia Shaheen; Alvin Kho; Sanya Thomas; Jing Chen; Maimouna D. Murphy; Mitchell Cooney; Scott Presnell; Leying Guan; Jeremy Gygi; Shrikant Pawar; Anderson Brito; Zain Khalil; James A. Overton; Randi Vita; Kerstin Westendorf; Cole Maguire; Slim Fourati; Ramin Salehi-Rad; Aleksandra Leligdowicz; Michael Matthay; Jonathan Singer; Kirsten N. Kangelaris; Carolyn M. Hendrickson; Matthew F. Krummel; Charles R. Langelier; Prescott G. Woodruff; Debra L. Powell; James N. Kim; Brent Simmons; I.Michael Goonewardene; Cecilia M. Smith; Mark Martens; Jarrod Mosier; Hiroki Kimura; Amy Sherman; Stephen Walsh; Nicolas Issa; Charles Dela Cruz; Shelli Farhadian; Akiko Iwasaki; Albert I. Ko; Evan J. Anderson; Aneesh Mehta; Jonathan E. Sevransky; Sharon Chinthrajah; Neera Ahuja; Angela Rogers; Maja Artandi; Sarah A.R. Siegel; Zhengchun Lu; Douglas A. Drevets; Brent R. Brown; Matthew L. Anderson; Faheem W. Guirgis; Rama V. Thyagarajan; Justin Rousseau; Dennis Wylie; Johanna Busch; Saurin Gandhi; Todd A. Triplett; George Yendewa; Olivia Giddings; Tatyana Vaysman; Bernard Khor; Adeeb Rahman; Daniel Stadlbauer; Jayeeta Dutta; Hui Xie; Seunghee Kim-Schulze; Ana Silvia Gonzalez-Reiche; Adriana van de Guchte; Holden T. Maecker; Keith Farrugia; Zenab Khan; Joanna Schaenman; Elaine F. Reed; Ramin Salehi-Rad; David Elashoff; Jenny Brook; Estefania Ramires-Sanchez; Megan Llamas; Adreanne Rivera; Claudia Perdomo; Dawn C. Ward; Clara E. Magyar; Jennifer Fulcher; Yumiko Abe-Jones; Saurabh Asthana; Alexander Beagle; Sharvari Bhide; Sidney A. Carrillo; Suzanna Chak; Rajani Ghale; Ana Gonzales; Alejandra Jauregui; Norman Jones; Tasha Lea; Deanna Lee; Raphael Lota; Jeff Milush; Viet Nguyen; Logan Pierce; Priya Prasad; Arjun Rao; Bushra Samad; Cole Shaw; Austin Sigman; Pratik Sinha; Alyssa Ward; Andrew - Willmore; Jenny Zhan; Sadeed Rashid; Nicklaus Rodriguez; Kevin Tang; Luz Torres Altamirano; Legna Betancourt; Cindy Curiel; Nicole Sutter; Maria Tercero Paz; Gayelan Tietje-Ulrich; Carolyn Leroux; Jennifer Connors; Mariana Bernui; Michele Kutzler; Carolyn Edwards; Edward Lee; Edward Lin; Brett Croen; Nicholas Semenza; Brandon Rogowski; Nataliya Melnyk; Kyra Woloszczuk; Gina Cusimano; Matthew Bell; Sara Furukawa; Renee McLin; Pamela Marrero; Julie Sheidy; George P. Tegos; Crystal Nagle; Nathan Mege; Kristen Ulring; Vicki Seyfert-Margolis; Michelle Conway; Dave Francisco; Allyson Molzahn; Heidi Erickson; Connie Cathleen Wilson; Ron Schunk; Trina Hughes; Bianca Sierra; Kinga K. Smolen; Michael Desjardins; Simon van Haren; Xhoi Mitre; Jessica Cauley; Xiofang Li; Alexandra Tong; Bethany Evans; Christina Montesano; Jose Humberto Licona; Jonathan Krauss; Jun Bai Park Chang; Natalie Izaguirre; Omkar Chaudhary; Andreas Coppi; John Fournier; Subhasis Mohanty; M. Catherine Muenker; Allison Nelson; Khadir Raddassi; Michael Rainone; William Ruff; Syim Salahuddin; Wade L. Schulz; Pavithra Vijayakumar; Haowei Wang; Elsio Wunder Jr.; H. Patrick Young; Yujiao Zhao; Miti Saksena; Deena Altman; Erna Kojic; Komal Srivastava; Lily Q. Eaker; Maria Carolina Bermudez; Katherine F. Beach; Levy A. Sominsky; Arman Azad; Juan Manuel Carreno; Gagandeep Singh; Ariel Raskin; Johnstone Tcheou; Dominika Bielak; Hisaaki Kawabata; Lubbertus CF Mulder; Giulio Kleiner; Laurel Bristow; Laila Hussaini; Kieffer Hellmeister; Hady Samaha; Andrew Cheng; Christine Spainhour; Erin M. Scherer; Brandi Johnson; Amer Bechnak; Caroline R. Ciric; Lauren Hewitt; Bernadine Panganiban; Chistopher Huerta; Jacob Usher; Erin Carter; Nina Mcnair; Susan Pereira Ribeiro; Alexandra S. Lee; Evan Do; Andrea Fernandes; Monali Manohar; Thomas Hagan; Catherine Blish; Hena Naz Din; Jonasel Roque; Samuel S. Yang; Amanda E. Brunton; Peter E. Sullivan; Matthew Strnad; Zoe L. Lyski; Felicity J. Coulter; John L. Booth; Lauren A. Sinko; Lyle Moldawer; Brittany Borrensen; Brittney Roth-Manning; Li-Zhen Song; Ebony Nelson; Megan Lewis-Smith; Jacob Smith; Pablo Guaman Tipan; Nadia Siles; Sam Bazzi; Janelle Geltman; Kerin Hurley; Giovanni Gabriele; Scott Sieg; Matthew C. Altman; Patrice M. Becker; Nadine Rouphael.
Preprint in English | medRxiv | ID: ppmedrxiv-22273396

ABSTRACT

BackgroundBetter understanding of the association between characteristics of patients hospitalized with coronavirus disease 2019 (COVID-19) and outcome is needed to further improve upon patient management. MethodsImmunophenotyping Assessment in a COVID-19 Cohort (IMPACC) is a prospective, observational study of 1,164 patients from 20 hospitals across the United States. Disease severity was assessed using a 7-point ordinal scale based on degree of respiratory illness. Patients were prospectively surveyed for 1 year after discharge for post-acute sequalae of COVID-19 (PASC) through quarterly surveys. Demographics, comorbidities, radiographic findings, clinical laboratory values, SARS-CoV-2 PCR and serology were captured over a 28-day period. Multivariable logistic regression was performed. FindingsThe median age was 59 years (interquartile range [IQR] 20); 711 (61%) were men; overall mortality was 14%, and 228 (20%) required invasive mechanical ventilation. Unsupervised clustering of ordinal score over time revealed distinct disease course trajectories. Risk factors associated with prolonged hospitalization or death by day 28 included age [≥] 65 years (odds ratio [OR], 2.01; 95% CI 1.28-3.17), Hispanic ethnicity (OR, 1.71; 95% CI 1.13-2.57), elevated baseline creatinine (OR 2.80; 95% CI 1.63-4.80) or troponin (OR 1.89; 95% 1.03-3.47), baseline lymphopenia (OR 2.19; 95% CI 1.61-2.97), presence of infiltrate by chest imaging (OR 3.16; 95% CI 1.96-5.10), and high SARS-CoV2 viral load (OR 1.53; 95% CI 1.17-2.00). Fatal cases had the lowest ratio of SARS-CoV-2 antibody to viral load levels compared to other trajectories over time (p=0.001). 589 survivors (51%) completed at least one survey at follow-up with 305 (52%) having at least one symptom consistent with PASC, most commonly dyspnea (56% among symptomatic patients). Female sex was the only associated risk factor for PASC. InterpretationIntegration of PCR cycle threshold, and antibody values with demographics, comorbidities, and laboratory/radiographic findings identified risk factors for 28-day outcome severity, though only female sex was associated with PASC. Longitudinal clinical phenotyping offers important insights, and provides a framework for immunophenotyping for acute and long COVID-19. FundingNIH RESEARCH IN CONTEXTO_ST_ABSEvidence before this studyC_ST_ABSWe did a systematic search of the PubMed database from January 1st, 2020 until April 24th, 2022 using the search terms: "hospitalized" AND "SARS-CoV-2" OR "COVID-19" AND "Pro-spective" AND "Antibody" OR "PCR" OR "long term follow up" and applying the following filters: "Multicenter Study" AND "Observational Study". No language restrictions were applied. While clinical, laboratory, and radiographic features associated with severe COVID-19 in hospitalized adults have been described, description of the kinetics of SARS-CoV-2 specific assays available to clinicians (e.g. PCR and binding antibody) and their integration with other variables is scarce for both short and long term follow up. The current literature is comprised of several studies with small sample size, cross-sectional design with laboratory data typically only recorded at a single point in time (e.g., on admission), limited clinical characteristics, variable duration of follow up, single-center setting, retrospective analyses, kinetics of either PCR or antibody testing but not both, and outcomes such as death or, mechanical ventilation that do not allow delineation of variations in clinical course. Added value of this studyIn our large longitudinal multicenter cohort, the description of outcome severity, was not limited to survival versus death, but encompassed a clinical trajectory approach leveraging longitudinal data based on time in hospital, disease severity by ordinal scale based on degree of respiratory illness, and presence or absence of limitations at discharge. Fatal COVID-19 cases had the lowest ratio of antibody to viral load levels over time as compared to non-fatal cases. Integration of PCR cycle threshold and antibody values with demographics, baseline comorbidities, and laboratory/radiographic findings identified additional risk factors for outcome severity over the first 28 days. However, female sex was the only variable associated with persistence of symptoms over time. Persistence of symptoms was not associated with clinical trajectory over the first 28 days, nor with antibody/viral loads from the acute phase. Implications of all the available evidenceThe described calculated ratio (binding IgG/PCR Ct value) is unique compared to other studies, reflecting host pathogen interactions and representing an accessible approach for patient risk stratification. Integration of SARS-CoV-2 viral load and binding antibody kinetics with other laboratory as well as clinical characteristics in hospitalized COVID-19 patients can identify patients likely to have the most severe short-term outcomes, but is not predictive of symptom persistence at one year post-discharge.

5.
Nano Res ; 15(6): 5510-5516, 2022.
Article in English | MEDLINE | ID: covidwho-1877966

ABSTRACT

Developing convenient and accurate SARS-CoV-2 antigen test and serology test is crucial in curbing the global COVID-19 pandemic. In this work, we report an improved indium oxide (In2O3) nanoribbon field-effect transistor (FET) biosensor platform detecting both SARS-CoV-2 antigen and antibody. Our FET biosensors, which were fabricated using a scalable and cost-efficient lithography-free process utilizing shadow masks, consist of an In2O3 channel and a newly developed stable enzyme reporter. During the biosensing process, the phosphatase enzymatic reaction generated pH change of the solution, which was then detected and converted to electrical signal by our In2O3 FETs. The biosensors applied phosphatase as enzyme reporter, which has a much better stability than the widely used urease in FET based biosensors. As proof-of-principle studies, we demonstrate the detection of SARS-CoV-2 spike protein in both phosphate-buffered saline (PBS) buffer and universal transport medium (UTM) (limit of detection [LoD]: 100 fg/mL). Following the SARS-CoV-2 antigen tests, we developed and characterized additional sensors aimed at SARS-CoV-2 IgG antibodies, which is important to trace past infection and vaccination. Our spike protein IgG antibody tests exhibit excellent detection limits in both PBS and human whole blood ((LoD): 1 pg/mL). Our biosensors display similar detection performance in different mediums, demonstrating that our biosensor approach is not limited by Debye screening from salts and can selectively detect biomarkers in physiological fluids. The newly selected enzyme for our platform performs much better performance and longer shelf life which will lead our biosensor platform to be capable for real clinical diagnosis usage. Electronic Supplementary Material: Supplementary material (materials and methods for device fabrication, functionalization of In2O3 devices, photographs of the liquid gate measurement setup, mobilities of the nine devices labeled in Fig. 1(b), family curves of I DS-V DS with the liquid gate setup and current change after bubbling the substrate solution (current vs. time curve for S1 antigen detection)) is available in the online version of this article at 10.1007/s12274-022-4190-0.

6.
Cancer Med ; 2022 May 31.
Article in English | MEDLINE | ID: covidwho-1866511

ABSTRACT

INTRODUCTION: Cancer patients may be susceptible to poorer outcomes in COVID-19 infection owing to the immunosuppressant effect of chemotherapy/radiotherapy and cancer growth, along with the potential for nosocomial transmission due to frequent hospital admissions. METHODS: This was a population-based retrospective cohort study of COVID-19 patients who presented to Hong Kong public hospitals between 1 January 2020 and 8 December 2020. The primary outcome was a composite endpoint of requirement for intubation, ICU admission and 30-day mortality. RESULTS: The following study consisted of 6089 COVID-19 patients (median age 45.9 [27.8.1-62.7] years; 50% male), of which 142 were cancer subjects. COVID-19 cancer patients were older at baseline and tended to present with a higher frequency of comorbidities, including diabetes mellitus, hypertension, chronic obstructive pulmonary disease, ischemic heart disease, ventricular tachycardia/fibrillation and gastrointestinal bleeding (p < 0.05). These subjects also likewise tended to present with higher serum levels of inflammatory markers, including D-dimer, lactate dehydrogenase, high sensitivity troponin-I and C-reactive protein. Multivariate Cox regression showed that any type of cancer presented with an almost four-fold increased risk of the primary outcome (HR: 3.77; 95% CI: 1.63-8.72; p < 0.002) after adjusting for significant demographics, Charlson comorbidity index, number of comorbidities, past comorbidities and medication history. This association remained significant when assessing those with colorectal (HR: 5.07; 95% CI: 1.50-17.17; p < 0.009) and gastrointestinal malignancies (HR: 3.79; 95% CI: 1.12-12.88; p < 0.03), but not with lung, genitourinary, or breast malignancies, relative to their respective cancer-free COVID-19 counterparts. CONCLUSIONS: COVID-19 cancer patients are associated with a significantly higher risk of intubation, ICU admission and/or mortality.

8.
J Infect Dev Ctries ; 16(2): 283-290, 2022 02 28.
Article in English | MEDLINE | ID: covidwho-1744872

ABSTRACT

INTRODUCTION: The high development of tourism is considered a factor that facilitates the global spread of infectious diseases. The association between tourism and the epidemic of coronavirus diseases 2019 (COVID-19) remains unclear. METHODOLOGY: We retrieved the data of COVID-19 in 178 countries/territories from the Center for Systems Science and Engineering at Johns Hopkins University. Data on tourism indicators were collected from the World Tourism Organization. We used Spearman's correlation analysis to explore the association between tourism and the epidemic of COVID-19. RESULTS: We find that international tourism expenditure, international tourism receipts, international tourist arrivals, and international tourism exports were significantly correlated with the total number of cases (rs=0.86, rs=0.79, rs=0.80, rs=0.81, respectively), the daily growth of cases of COVID-19 (rs=0.84, rs=0.76, rs=0.78, rs=0.78, respectively), and the number of cases (per million persons) (rs=0.52, rs=0.53, rs=0.36, rs=0.53, respectively) (p < 0.0001 for all), especially in places with high-income. Tourism as percentage of exports was slightly associated with the total number of cases and the daily growth of cases (rs=-0.33, rs=-0.33) (p < 0.0001 for both). CONCLUSIONS: The clinical and public health care providers must realize the potential for the transmission of infections across regions and put more effort to prevent and respond to future infections.


Subject(s)
COVID-19 , Communicable Diseases , COVID-19/epidemiology , Humans , Tourism , Travel
9.
PLoS Comput Biol ; 18(3): e1009892, 2022 03.
Article in English | MEDLINE | ID: covidwho-1731577

ABSTRACT

Emerging clinical evidence suggests that thrombosis in the microvasculature of patients with Coronavirus disease 2019 (COVID-19) plays an essential role in dictating the disease progression. Because of the infectious nature of SARS-CoV-2, patients' fresh blood samples are limited to access for in vitro experimental investigations. Herein, we employ a novel multiscale and multiphysics computational framework to perform predictive modeling of the pathological thrombus formation in the microvasculature using data from patients with COVID-19. This framework seamlessly integrates the key components in the process of blood clotting, including hemodynamics, transport of coagulation factors and coagulation kinetics, blood cell mechanics and adhesive dynamics, and thus allows us to quantify the contributions of many prothrombotic factors reported in the literature, such as stasis, the derangement in blood coagulation factor levels and activities, inflammatory responses of endothelial cells and leukocytes to the microthrombus formation in COVID-19. Our simulation results show that among the coagulation factors considered, antithrombin and factor V play more prominent roles in promoting thrombosis. Our simulations also suggest that recruitment of WBCs to the endothelial cells exacerbates thrombogenesis and contributes to the blockage of the blood flow. Additionally, we show that the recent identification of flowing blood cell clusters could be a result of detachment of WBCs from thrombogenic sites, which may serve as a nidus for new clot formation. These findings point to potential targets that should be further evaluated, and prioritized in the anti-thrombotic treatment of patients with COVID-19. Altogether, our computational framework provides a powerful tool for quantitative understanding of the mechanism of pathological thrombus formation and offers insights into new therapeutic approaches for treating COVID-19 associated thrombosis.


Subject(s)
COVID-19/complications , Microvessels/physiopathology , Thrombosis/physiopathology , Thrombosis/virology , Anticoagulants , Blood Coagulation , Computational Biology , Humans , Models, Biological , SARS-CoV-2
10.
EuropePMC; 2020.
Preprint in English | EuropePMC | ID: ppcovidwho-323625

ABSTRACT

Electric vehicles (EVs) represent a major path for global decarbonization, improvement of air quality and promotion of renewable energy. To tackle the COVID-19 pandemic, China imposed full lockdowns and thorough travel restrictions. This event represents an unprecedented inadvertent geoengineering experiment in vehicle emissions, emulating transition to EVs. Here we novelly exploited observations of air quality during the full lockdown to constrain predictions of a comprehensive chemical transport model. Large traffic flux reductions were near-linearly linked to reductions of NO 2 and PM 2.5 (correlation = 0.491 ~ 0.626). Extrapolating to a full conversion to EV results in a large reduction of PM 2.5 (30 ~ 70%) in most of central and south eastern China. A smaller reduction of PM 2.5 (10 ~ 20%) in Beijing and Tianjin was achievable due to the presence of major industrial emission sources which cause haze at a regional scale. The potential reductions in NO 2 were 40 ~ 90% in most of the megacities. At this present crossroads of policy, our findings reveal timely evidence supporting the transition towards renewable energy.Funding: This study is supported by the Department of Science and Technology of China (No. 2016YFC0202702, 2018YFC0213506 and 2018YFC0213503), National Research Program for Key Issues in Air Pollution Control in China (No. DQGG0107) and National Natural Science Foundation of China (No. 21577126, 41561144004, 21625701). Pengfei Li is supported by Initiation Fund for Introducing Talents of Hebei Agricultural University (412201904) and Youth Top Fund of Universities in Hebei Province (BJ2020032). Conflict of Interest: Authors declare no competing interests.

11.
EuropePMC; 2021.
Preprint in English | EuropePMC | ID: ppcovidwho-322525

ABSTRACT

Background: Serosurvalence is crucial in estimating the range of SARS-CoV-2 infections, predicting the possibility of another wave, and decide on a vaccination strategy. To understand the herd immunity after the COVID-19 pandemic, the seroprevalence was measured in 3062 individuals with or without COVID-19. Methods: : The levels of SARS-CoV-2 antibody IgM and IgG were measured by the immuno-colloidal gold method. Results: : The mean seroprevalence for IgM and IgG in all participants was 2.81% and 7.51%, respectively. The positive rate of IgG was significantly higher in women than in men (P<0.05). The highest positive rate of IgM was observed in 41-60 years of age (3.49%), while the highest seroprevalence for IgG was observed in persons >60 years of age (8.61%). The positive rates of IgM and IgG in the convalescent patients were 31.82% and 77.27%, respectively, which was significantly higher than individuals with suspected syndromes or individuals without any clinical signs (P<0.01). Seroprevalence for IgG in medical staff was markedly higher than those in residents. The seroprevalence in patients with various comorbidity was no significant difference (P>0.05). Conclusions: : The low positive rate of the SARS-CoV-2 IgM and NA test indicated that the SARS-CoV-2 outbreak is subsiding after three months, and the possibility of reintroduction of the virus from an unidentified natural reservoir is low. Seroprevalence provides the information for humoral immunity and vaccine in the future.

12.
EuropePMC; 2020.
Preprint in English | EuropePMC | ID: ppcovidwho-315663

ABSTRACT

Developing conversational agents to interact with patients and provide primary clinical advice has attracted increasing attention due to its huge application potential, especially in the time of COVID-19 Pandemic. However, the training of end-to-end neural-based medical dialogue system is restricted by an insufficient quantity of medical dialogue corpus. In this work, we make the first attempt to build and release a large-scale high-quality Medical Dialogue dataset related to 12 types of common Gastrointestinal diseases named MedDG, with more than 17K conversations collected from the online health consultation community. Five different categories of entities, including diseases, symptoms, attributes, tests, and medicines, are annotated in each conversation of MedDG as additional labels. To push forward the future research on building expert-sensitive medical dialogue system, we proposes two kinds of medical dialogue tasks based on MedDG dataset. One is the next entity prediction and the other is the doctor response generation. To acquire a clear comprehension on these two medical dialogue tasks, we implement several state-of-the-art benchmarks, as well as design two dialogue models with a further consideration on the predicted entities. Experimental results show that the pre-train language models and other baselines struggle on both tasks with poor performance in our dataset, and the response quality can be enhanced with the help of auxiliary entity information. From human evaluation, the simple retrieval model outperforms several state-of-the-art generative models, indicating that there still remains a large room for improvement on generating medically meaningful responses.

13.
EuropePMC; 2021.
Preprint in English | EuropePMC | ID: ppcovidwho-315588

ABSTRACT

Medical imaging technologies, including computed tomography (CT) or chest X-Ray (CXR), are largely employed to facilitate the diagnosis of the COVID-19. Since manual report writing is usually too time-consuming, a more intelligent auxiliary medical system that could generate medical reports automatically and immediately is urgently needed. In this article, we propose to use the medical visual language BERT (Medical-VLBERT) model to identify the abnormality on the COVID-19 scans and generate the medical report automatically based on the detected lesion regions. To produce more accurate medical reports and minimize the visual-and-linguistic differences, this model adopts an alternate learning strategy with two procedures that are knowledge pretraining and transferring. To be more precise, the knowledge pretraining procedure is to memorize the knowledge from medical texts, while the transferring procedure is to utilize the acquired knowledge for professional medical sentences generations through observations of medical images. In practice, for automatic medical report generation on the COVID-19 cases, we constructed a dataset of 368 medical findings in Chinese and 1104 chest CT scans from The First Affiliated Hospital of Jinan University, Guangzhou, China, and The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China. Besides, to alleviate the insufficiency of the COVID-19 training samples, our model was first trained on the large-scale Chinese CX-CHR dataset and then transferred to the COVID-19 CT dataset for further fine-tuning. The experimental results showed that Medical-VLBERT achieved state-of-the-art performances on terminology prediction and report generation with the Chinese COVID-19 CT dataset and the CX-CHR dataset. The Chinese COVID-19 CT dataset is available at https://covid19ct.github.io/.

14.
EuropePMC; 2020.
Preprint in English | EuropePMC | ID: ppcovidwho-315208

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread widely from China to the world. Although the viral genome has been well characterized, the evolutionary origin and global transmission dynamics of SARS-CoV-2 remain poorly investigated. To address this, we retrieved 313 SARS-CoV-2 genomes from the GISAID database (https://www.gisaid.org), from which 99 genomes generated from original clinical specimens with exact collection dates from 16 countries were selected and enrolled for Bayesian phylodynamic analysis. Here we show that the time to the Most Recent Common Ancestor (tMRCA) of SARS-CoV-2 is Dec 11, 2019 (95%HPD, Nov 21 - Dec 24). Two clades of global circulating strains of SARS-CoV-2 were suggested by Bayesian Maximum Clade Credibility (MCC) tree. The USA circulating strains of SARS-CoV-2 seemed to be from both of the two clades, the UK and Australia circulating strains were from Clade 1, the circulating strains in Singapore, Japan, Germany, France, and Italy were from Clade 2. Although we have not found any obvious bottle-neck-effect from the Bayesian Skyline Plot of the viral population dynamics reconstruction, a sharp reduction of the lower 95% HPD of the relative genetic diversity was observed from Feb 5, 2020, suggesting a possible initiation of a bottle-neck-effect. Thirteen (6 synonymous and 7 non-synonymous) mutations in the viral genome were observed, including two clade-specific mutations (C8782T and T1844C in Clade 1 rather than Clade 2) and eleven sub-clade specific mutations. All of the observed mutations occurred in the USA circulating strains, except one mutation T18488C only occurred in the UK circulating strains. A non-synonymous mutation in the 3’-UTR was also observed, suggesting an altered RNA replication capacity of SARS-CoV-2. We thus came to the conclusion that continuous evolution occurred in almost all regions of the SARS-CoV-2 genome and potentially in a country-specific manner. Further efforts on monitoring the genomic mutations of SARS-CoV-2 from different countries are recommended.

15.
EuropePMC;
Preprint in English | EuropePMC | ID: ppcovidwho-328888

ABSTRACT

Background: Medical microbiology and medical immunology are required introductory courses for second-year dentistry students. It is essential to find suitable teaching methods after the outbreak of COVID-19 to implement the call for "stop class, but not stop teaching and not stop learning." Methods We mainly used Rain Classroom for online teaching and QQ Group Classroom to support education during this particular period. Result We assessed the effectiveness of this special period instruction by analyzing anonymous questionnaires and final exam results. The anonymous questionnaire showed that most of the students were satisfied with this online instruction and found it very helpful in answering their questions and solving their problems. The final exam results showed that teaching in 2020 was no worse than teaching in 2019 and better in terms of pass rate. Teaching in 2021 was worse than in 2020, but there was a breakthrough in the highest score. Conclusion These data suggest that online teaching during the epidemic had an impact on teaching effectiveness. Most students are satisfied with online teaching, but some students' grades are affected, which may be related to the fact that some students were not comfortable with blended teaching or online teaching. We share our experiences and reflections on online and blended teaching of medical immunology and medical microbiology courses during the epidemic, hoping that it will be helpful for other teachers to teach.

16.
Environ Chem Lett ; 20(1): 59-69, 2022.
Article in English | MEDLINE | ID: covidwho-1680976

ABSTRACT

Despite large decreases of emissions of air pollution during the coronavirus disease 2019 (COVID-19) lockdown in 2020, an unexpected regional severe haze has still occurred over the North China Plain. To clarify the origin of this pollution, we studied air concentrations of fine particulate matter (PM2.5), NO2, O3, PM10, SO2, and CO in Beijing, Hengshui and Baoding during the lockdown period from January 24 to 29, 2020. Variations of PM2.5 composition in inorganic ions, elemental carbon and organic matter were also investigated. The HYSPLIT model was used to calculate backward trajectories and concentration weighted trajectories. Results of the cluster trajectory analysis and model simulations show that the severe haze was caused mainly by the emissions of northeastern non-stopping industries located in Inner Mongolia, Liaoning, Hebei, and Tianjin. In Beijing, Hengshui and Baoding, the mixing layer heights were about 30% lower and the maximum relative humidity was 83% higher than the annual averages, and the average wind speeds were lower than 1.5 m s-1. The concentrations of NO3 -, SO4 2-, NH4 +, organics and K+ were the main components of PM2.5 in Beijing and Hengshui, while organics, K+, NO3 -, SO4 2-, and NH4 + were the main components of PM2.5 in Baoding. Contrary to previous reports suggesting a southerly transport of air pollution, we found that northeast transport caused the haze formation. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10311-021-01314-8.

17.
Am J Infect Control ; 50(5): 516-524, 2022 05.
Article in English | MEDLINE | ID: covidwho-1676380

ABSTRACT

BACKGROUND: Face masks from worldwide satisfy different standards during the COVID-19 pandemic, which led to the public misunderstanding of the concepts. METHODS: We systematically evaluated the quality of face masks provided by different companies according to multi-national standards, including EN 149-2001+A1: 2009, GB 2626-2019 and NIOSH 42 CFR Part 84-2019, focusing particularly on the particulate filtration efficiency (PFE) and respiratory resistance performance. RESULTS: Three types of masks (planar, folding and cup type masks) were measured based on different standard protocols. The results indicated that the PFE of the mask decreased in sequence of folding mask ≈ cup type mask > planar mask. The respiratory resistance of the masks ranked as follows: cup type mask > folding mask> planar mask. Overall, when PFE was used as the quality indicator, all the masks have a higher chance of meeting criteria of the EN149-2001+A1:2009, followed by the stricter standard set by the GB2626-2019 and NIOSH 42 CFR Part84-2019. Conversely, the respiratory resistance of the masks fulfilled the highest requirement of the EN149-2001+A1:2009 standard, while it is easier to satisfied the standard of GB 2626-2019 and NIOSH 42 CFR Part 84-2019. CONCLUSIONS: We believe that our study provides effective guidance for customers worldwide to choose proper face masks under different epidemic situations.


Subject(s)
COVID-19 , COVID-19/prevention & control , Filtration , Humans , Pandemics/prevention & control , Respiratory System
18.
J Food Biochem ; 46(5): e14085, 2022 05.
Article in English | MEDLINE | ID: covidwho-1673175

ABSTRACT

SARS-CoV-2 wreaks havoc around the world, triggering the COVID-19 pandemic. It has been confirmed that the endoribonuclease NSP15 is crucial to the viral replication, and thus identified as a potential drug target against COVID-19. The NSP15 protein was used as the target to conduct high-throughput virtual screening on 30,926 natural products from the NPASS database to identify potential NSP15 inhibitors. And 100 ns molecular dynamics simulations were performed on the NSP15 and NSP15-NPC198199 system. In all, 10 natural products with high docking scores with NSP15 protein were obtained, among which compound NPC198199 scored the highest. The analysis of the binding mode between NPC198199 and NSP15 found that NPC198199 would form H-bond interactions with multiple key residues at the catalytic site. Subsequently, a series of post-dynamics simulation analyses (including RMSD, RMSF, PCA, DCCM, RIN, binding free energy, and H-bond occupancy) were performed to further explore inhibitory mechanism of compound NPC198199 on NSP15 protein at the molecular level. The research strongly indicates that the 10 natural compounds screened can be used as potential inhibitors of NSP15, and provides valuable information for the subsequent drug discovery of anti-SARS-CoV-2. PRACTICAL APPLICATIONS: Natural products play an important role in the treatment of many difficult diseases. In this study, high-throughput virtual screening technology was used to screen the natural product database to obtain potential inhibitors against endoribonuclease NSP15. The binding mechanism between natural products and NSP15 was investigated at the molecular level by molecular dynamics technology so that it is expected to become candidate drugs for the treatment of SARS-CoV-2. We hope that our research can provide new clue to combat COVID-19 and overcome the epidemic situation as soon as possible.


Subject(s)
Antiviral Agents , Biological Products , Endoribonucleases , SARS-CoV-2 , Viral Nonstructural Proteins , Antiviral Agents/chemistry , Antiviral Agents/pharmacology , Biological Products/pharmacology , COVID-19/drug therapy , Endoribonucleases/antagonists & inhibitors , Humans , Molecular Docking Simulation , Molecular Dynamics Simulation , SARS-CoV-2/drug effects , Viral Nonstructural Proteins/antagonists & inhibitors
19.
Biophys J ; 120(14): 2828-2837, 2021 07 20.
Article in English | MEDLINE | ID: covidwho-1606137

ABSTRACT

The cell surface receptor Neuropilin-1 (Nrp1) was recently identified as a host factor for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) entry. The Spike protein of SARS-CoV-2 is cleaved into two segments, the S1 (residues (res.) 1-685) and the S2 (res. 686-1273) domains by furin protease. Nrp1 predominantly binds to the C-terminal RRAR amino acid motif (res. 682-685) of the S1 domain. In this study, we firstly modeled the association of an Nrp1 protein (consisting of domains a2-b1-b2) with the Spike protein. Next, we studied the separation of S2 from the S1 domain, with and without Nrp1 bound, by utilizing molecular dynamics pulling simulations. During the separation, Nrp1 stabilizes the S1 C-terminal region (res. 640-685) and thereby assists the detachment of S2 N-terminal region (res. 686-700). Without Nrp1 bound, S1 tends to become stretched, whereas the bound Nrp1 stimulates an earlier separation of S2 from the S1 domain. The liberated S2 domain is known to mediate the fusion of virus and host membranes; thus, Nrp1 likely increases virus infectivity by facilitating the S1 and S2 separation. We further analyzed the possible topological structure of the SARS-CoV-2 Spike protein when bound with Nrp1 and angiotensin-converting enzyme 2 (ACE2). Understanding of such an Nrp1-assisted viral infection opens the gate for the generation of protein-protein inhibitors, such as antibodies, which could attenuate the infection mechanism and protect certain cells in a future Nrp1-ACE2 targeted combination therapy.

20.
BMC Infect Dis ; 22(1): 10, 2022 Jan 04.
Article in English | MEDLINE | ID: covidwho-1608186

ABSTRACT

BACKGROUND: Serosurveillance is crucial in estimating the range of SARS-CoV-2 infections, predicting the possibility of another wave, and deciding on a vaccination strategy. To understand the herd immunity after the COVID-19 pandemic, the seroprevalence was measured in 3062 individuals with or without COVID-19 from the clinic. METHODS: The levels of SARS-CoV-2 antibody IgM and IgG were measured by the immuno-colloidal gold method. A fusion fragment of nucleocapsid and spike protein was detected by a qualitative test kit with sensitivity (89%) and specificity (98%). RESULTS: The seroprevalence rate for IgM and IgG in all outpatients was 2.81% and 7.51%, respectively. The sex-related prevalence rate of IgG was significantly higher (P < 0.05) in women than men. The highest positive rate of IgM was observed in individuals < 20 years of age (3.57%), while the highest seroprevalence for IgG was observed in persons > 60 years of age (8.61%). Positive rates of IgM and IgG in the convalescent patients were 31.82% and 77.27%, respectively, which was significantly higher than individuals with suspected syndromes or individuals without any clinical signs (P < 0.01). Seroprevalence for IgG in medical staff was markedly higher than those in residents. No significant difference of seroprevalence was found among patients with different comorbidities (P > 0.05). CONCLUSIONS: The low positive rate of the SARS-CoV-2 IgM and nucleic acid (NA) test indicated that the SARS-CoV-2 outbreak is subsiding after 3 months, and the possibility of reintroduction of the virus from an unidentified natural reservoir is low. Seroprevalence provides information for humoral immunity and vaccine in the future.


Subject(s)
COVID-19 , SARS-CoV-2 , Antibodies, Viral , Communicable Disease Control , Female , Humans , Immunoglobulin G , Immunoglobulin M , Male , Pandemics , Seroepidemiologic Studies
SELECTION OF CITATIONS
SEARCH DETAIL