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1.
EuropePMC; 2022.
Preprint in English | EuropePMC | ID: ppcovidwho-335878

ABSTRACT

The long-term consequences of coronavirus disease 2019 (COVID-19) on brain physiology and function are not yet well understood. From the recently described NeuroCOVID-19 study, we examined cerebral blood flow (CBF) in 50 participants recruited to one of two groups: 1) adults who previously self-isolated at home due to COVID-19 (n = 39;116.5 ± 62.2 days since positive diagnosis), or 2) controls who experienced flu-like symptoms but had a negative COVID-19 diagnosis (n = 11). Participants underwent arterial spin labeling magnetic resonance imaging at 3 T to yield measures of CBF. Voxel-wise analyses of CBF were performed to assess for between-group differences, after controlling for age and sex. Relative to controls, the COVID-19 group exhibited decreased CBF in the thalamus, orbitofrontal cortex, and regions of the basal ganglia. Within the COVID-19 group, CBF differences in occipital and parietal regions were observed between those with (n = 11) and without (n = 28) self-reported on-going fatigue. These results suggest long-term changes in brain physiology in adults across the post-COVID-19 timeframe. Moreover, CBF may aid in understanding the heterogeneous symptoms of the post-COVID-19 condition. Future longitudinal studies are needed to further characterize the consequences of COVID-19 on the brain.

2.
BMC Cardiovasc Disord ; 22(1): 194, 2022 04 26.
Article in English | MEDLINE | ID: covidwho-1817181

ABSTRACT

BACKGROUND: COVID-19 affects healthcare resource allocation, which could lead to treatment delay and poor outcomes in patients with acute myocardial infarction (AMI). We assessed the impact of the COVID-19 pandemic on AMI outcomes. METHODS: We compared outcomes of patients admitted for acute ST-elevation MI (STEMI) and non-STEMI (NSTEMI) during a non-COVID-19 pandemic period (January-February 2019; Group 1, n = 254) and a COVID-19 pandemic period (January-February 2020; Group 2, n = 124). RESULTS: For STEMI patients, the median of first medical contact (FMC) time, door-to-balloon time, and total myocardial ischemia time were significantly longer in Group 2 patients (all p < 0.05). Primary percutaneous intervention was performed significantly more often in Group 1 patients than in Group 2 patients, whereas thrombolytic therapy was used significantly more often in Group 2 patients than in Group 1 patients (all p < 0.05). However, the rates of and all-cause 30-day mortality and major adverse cardiac event (MACE) were not significantly different in the two periods (all p > 0.05). For NSTEMI patients, Group 2 patients had a higher rate of conservative therapy, a lower rate of reperfusion therapy, and longer FMC times (all p < 0.05). All-cause 30-day mortality and MACE were only higher in NSTEMI patients during the COVID-19 pandemic period (p < 0.001). CONCLUSIONS: COVID-19 pandemic causes treatment delay in AMI patients and potentially leads to poor clinical outcome in NSTEMI patients. Thrombolytic therapy should be initiated without delay for STEMI when coronary intervention is not readily available; for NSTEMI patients, outcomes of invasive reperfusion were better than medical treatment.


Subject(s)
COVID-19 , Myocardial Infarction , Non-ST Elevated Myocardial Infarction , ST Elevation Myocardial Infarction , Humans , Myocardial Infarction/diagnosis , Myocardial Infarction/epidemiology , Myocardial Infarction/therapy , Non-ST Elevated Myocardial Infarction/diagnosis , Non-ST Elevated Myocardial Infarction/therapy , Pandemics , ST Elevation Myocardial Infarction/diagnosis , ST Elevation Myocardial Infarction/epidemiology , ST Elevation Myocardial Infarction/therapy , Time Factors , Treatment Outcome
3.
Cell ; 185(7): 1117-1129.e8, 2022 Mar 31.
Article in English | MEDLINE | ID: covidwho-1682965

ABSTRACT

Game animals are wildlife species traded and consumed as food and are potential reservoirs for SARS-CoV and SARS-CoV-2. We performed a meta-transcriptomic analysis of 1,941 game animals, representing 18 species and five mammalian orders, sampled across China. From this, we identified 102 mammalian-infecting viruses, with 65 described for the first time. Twenty-one viruses were considered as potentially high risk to humans and domestic animals. Civets (Paguma larvata) carried the highest number of potentially high-risk viruses. We inferred the transmission of bat-associated coronavirus from bats to civets, as well as cross-species jumps of coronaviruses from bats to hedgehogs, from birds to porcupines, and from dogs to raccoon dogs. Of note, we identified avian Influenza A virus H9N2 in civets and Asian badgers, with the latter displaying respiratory symptoms, as well as cases of likely human-to-wildlife virus transmission. These data highlight the importance of game animals as potential drivers of disease emergence.


Subject(s)
Animals, Wild/virology , Communicable Diseases, Emerging/virology , Disease Reservoirs , Mammals/virology , Virome , Animals , China , Phylogeny , Zoonoses
4.
Sustain Cities Soc ; 80: 103753, 2022 May.
Article in English | MEDLINE | ID: covidwho-1665461

ABSTRACT

Indoor transmission of COVID-19 is highly probable. Multiple sources have verified that the SARS-CoV-2 can be detected within toilets, and people can be infected in restrooms. There is a huge gap in the coronavirus transmission mechanism in restrooms. Understanding it can help to flatten the curve of the infected cases as well as prevent other viruses transmitted through the sewage or human body fluid. Previous studies have shown how simple actions in daily life (coughing, sneezing, or toilet flushing) contribute to virus transmission. This paper visually and quantitatively demonstrates that male urination, which is also a daily action, can agitate virus particles within the toilet and raise them, which may be the main promoter of cross-infection of COVID-19 in restrooms. Adopting numerical and experimental methods, we demonstrate that male urination can cause strong turbulent flow with an averaged urine impinging velocity of 2.3 m/s, which can act as an agitator to raise the virus particles. The climbing velocity of the airflow can be 0.75-1.05 m/s. The observed upwards flow will disturb and spread any lurking virus particles (not limited to SARS-CoV-2). Experiments demonstrated that the concentration of the airborne particle could be tripled during male urination. Corresponding precautions are offered as well to prepare the public to act properly when and after using facilities in restrooms for preventing emerging and re-emerging pandemics not limited to the current COVID-19, contributing to the sustainability of human society.

5.
Mol Biol Evol ; 39(2)2022 02 03.
Article in English | MEDLINE | ID: covidwho-1594013

ABSTRACT

The ongoing SARS (severe acute respiratory syndrome)-CoV (coronavirus)-2 pandemic has exposed major gaps in our knowledge on the origin, ecology, evolution, and spread of animal coronaviruses. Porcine epidemic diarrhea virus (PEDV) is a member of the genus Alphacoronavirus in the family Coronaviridae that may have originated from bats and leads to significant hazards and widespread epidemics in the swine population. The role of local and global trade of live swine and swine-related products in disseminating PEDV remains unclear, especially in developing countries with complex swine production systems. Here, we undertake an in-depth phylogeographic analysis of PEDV sequence data (including 247 newly sequenced samples) and employ an extension of this inference framework that enables formally testing the contribution of a range of predictor variables to the geographic spread of PEDV. Within China, the provinces of Guangdong and Henan were identified as primary hubs for the spread of PEDV, for which we estimate live swine trade to play a very important role. On a global scale, the United States and China maintain the highest number of PEDV lineages. We estimate that, after an initial introduction out of China, the United States acted as an important source of PEDV introductions into Japan, Korea, China, and Mexico. Live swine trade also explains the dispersal of PEDV on a global scale. Given the increasingly global trade of live swine, our findings have important implications for designing prevention and containment measures to combat a wide range of livestock coronaviruses.


Subject(s)
Coronavirus , Porcine epidemic diarrhea virus , Swine Diseases , Animals , China , Pandemics , Phylogeny , Phylogeography , Porcine epidemic diarrhea virus/genetics , Swine , Swine Diseases/epidemiology , United States
6.
CMAJ Open ; 9(4): E1114-E1119, 2021.
Article in English | MEDLINE | ID: covidwho-1547694

ABSTRACT

BACKGROUND: The detailed extent of neuroinvasion or deleterious brain changes resulting from COVID-19 and their time courses remain to be determined in relation to "long-haul" COVID-19 symptoms. Our objective is to determine whether there are alterations in functional brain imaging measures among people with COVID-19 after hospital discharge or self-isolation. METHODS: This paper describes a protocol for NeuroCOVID-19, a longitudinal observational study of adults aged 20-75 years at Sunnybrook Health Sciences Centre in Toronto, Ontario, that began in April 2020. We aim to recruit 240 adults, 60 per group: people who contracted COVID-19 and were admitted to hospital (group 1), people who contracted COVID-19 and self-isolated (group 2), people who experienced influenza-like symptoms at acute presentation but tested negative for COVID-19 and self-isolated (group 3, control) and healthy people (group 4, control). Participants are excluded based on premorbid neurologic or severe psychiatric illness, unstable cardiovascular disease, and magnetic resonance imaging (MRI) contraindications. Initial and 3-month follow-up assessments include multiparametric brain MRI and electroencephalography. Sensation and cognition are assessed alongside neuropsychiatric assessments and symptom self-reports. We will test the data from the initial and follow-up assessments for group differences based on 3 outcome measures: MRI cerebral blood flow, MRI resting state fractional amplitude of low-frequency fluctuation and electroencephalography spectral power. INTERPRETATION: If neurophysiologic alterations are detected in the COVID-19 groups in our NeuroCOVID-19 study, this information could inform future research regarding interventions for long-haul COVID-19. The study results will be disseminated to scientists, clinicians and COVID-19 survivors, as well as the public and private sectors to provide context on how brain measures relate to lingering symptoms.


Subject(s)
Brain/physiopathology , COVID-19/complications , Patient Discharge , Adult , Aged , Brain/diagnostic imaging , COVID-19/diagnostic imaging , COVID-19/physiopathology , Electroencephalography/methods , Female , Hospitalization , Hospitals , Humans , Longitudinal Studies , Magnetic Resonance Imaging/methods , Male , Middle Aged , Ontario , Patient Isolation/methods , SARS-CoV-2 , Young Adult
7.
[Unspecified Source]; 2020.
Preprint in English | [Unspecified Source] | ID: ppcovidwho-292775

ABSTRACT

The SARS-CoV-2 pandemic led to the closure of nearly all K-12 schools in the United States of America in March 2020. Although reopening K-12 schools for in-person schooling is desirable for many reasons, officials also understand that risk reduction strategies and detection of cases must be in place to allow children to safely return to school. Furthermore, the consequences of reclosing recently reopened schools are substantial and impact teachers, parents, and ultimately the educational experience in children. Using a stratified Susceptible-Exposed-Infected-Removed model, we explore the influences of reduced class density, transmission mitigation (such as the use of masks, desk shields, frequent surface cleaning, or outdoor instruction), and viral detection on cumulative prevalence. Our model predicts that a combination of all three approaches will substantially reduce SARS-CoV-2 prevalence. The model also shows that reduction of class density and the implementation of rapid viral testing, even with imperfect detection, have greater impact than moderate measures for transmission mitigation.

8.
Nature ; 595(7869): 713-717, 2021 07.
Article in English | MEDLINE | ID: covidwho-1287812

ABSTRACT

After the first wave of SARS-CoV-2 infections in spring 2020, Europe experienced a resurgence of the virus starting in late summer 2020 that was deadlier and more difficult to contain1. Relaxed intervention measures and summer travel have been implicated as drivers of the second wave2. Here we build a phylogeographical model to evaluate how newly introduced lineages, as opposed to the rekindling of persistent lineages, contributed to the resurgence of COVID-19 in Europe. We inform this model using genomic, mobility and epidemiological data from 10 European countries and estimate that in many countries more than half of the lineages circulating in late summer resulted from new introductions since 15 June 2020. The success in onward transmission of newly introduced lineages was negatively associated with the local incidence of COVID-19 during this period. The pervasive spread of variants in summer 2020 highlights the threat of viral dissemination when restrictions are lifted, and this needs to be carefully considered in strategies to control the current spread of variants that are more transmissible and/or evade immunity. Our findings indicate that more effective and coordinated measures are required to contain the spread through cross-border travel even as vaccination is reducing disease burden.


Subject(s)
COVID-19/transmission , COVID-19/virology , SARS-CoV-2/isolation & purification , COVID-19/epidemiology , COVID-19/prevention & control , Europe/epidemiology , Genome, Viral/genetics , Humans , Incidence , Locomotion , Phylogeny , Phylogeography , SARS-CoV-2/classification , SARS-CoV-2/genetics , SARS-CoV-2/pathogenicity , Time Factors , Travel/statistics & numerical data
9.
PLoS One ; 16(5): e0251242, 2021.
Article in English | MEDLINE | ID: covidwho-1236586

ABSTRACT

The SARS-CoV-2 pandemic led to closure of nearly all K-12 schools in the United States of America in March 2020. Although reopening K-12 schools for in-person schooling is desirable for many reasons, officials understand that risk reduction strategies and detection of cases are imperative in creating a safe return to school. Furthermore, consequences of reclosing recently opened schools are substantial and impact teachers, parents, and ultimately educational experiences in children. To address competing interests in meeting educational needs with public safety, we compare the impact of physical separation through school cohorts on SARS-CoV-2 infections against policies acting at the level of individual contacts within classrooms. Using an age-stratified Susceptible-Exposed-Infected-Removed model, we explore influences of reduced class density, transmission mitigation, and viral detection on cumulative prevalence. We consider several scenarios over a 6-month period including (1) multiple rotating cohorts in which students cycle through in-person instruction on a weekly basis, (2) parallel cohorts with in-person and remote learning tracks, (3) the impact of a hypothetical testing program with ideal and imperfect detection, and (4) varying levels of aggregate transmission reduction. Our mathematical model predicts that reducing the number of contacts through cohorts produces a larger effect than diminishing transmission rates per contact. Specifically, the latter approach requires dramatic reduction in transmission rates in order to achieve a comparable effect in minimizing infections over time. Further, our model indicates that surveillance programs using less sensitive tests may be adequate in monitoring infections within a school community by both keeping infections low and allowing for a longer period of instruction. Lastly, we underscore the importance of factoring infection prevalence in deciding when a local outbreak of infection is serious enough to require reverting to remote learning.


Subject(s)
COVID-19/transmission , Contact Tracing/methods , Pandemics , Population Surveillance/methods , Schools , Adolescent , Child , Humans , Models, Theoretical , United States
10.
Eur Radiol ; 31(10): 7342-7352, 2021 Oct.
Article in English | MEDLINE | ID: covidwho-1184662

ABSTRACT

OBJECTIVES: To investigate the association between longitudinal total pulmonary infection volume and volume ratio over time and clinical types in COVID-19 pneumonia patients. METHODS: This retrospective review included 367 patients with COVID-19 pneumonia. All patients underwent CT examination at baseline and/or one or more follow-up CT. Patients were categorized into two clinical types (moderate and severe groups). The severe patients were matched to the moderate patients via propensity scores (PS). The association between total pulmonary infection volume and volume ratio and clinical types was analyzed using a generalized additive mixed model (GAMM). RESULTS: Two hundred and seven moderate patients and 160 severe patients were enrolled. The baseline clinical and imaging variables were balanced using PS analysis to avoid patient selection bias. After PS analysis, 172 pairs of moderate patients were allocated to the groups; there was no difference in the clinical and CT characteristics between the two groups (p > 0.05). A total of 332 patients, including 396 CT scans, were assessed. The impact of total pulmonary infection volume and volume ratio with time was significantly affected by clinical types (p for interaction = 0.01 and 0.01, respectively) using GAMM. Total pulmonary infection volume and volume ratio of the severe group increased by 14.66 cm3 (95% confidence interval [CI]: 3.92 to 25.40) and 0.45% (95% CI: 0.13 to 0.77) every day, respectively, compared to that of the moderate group. CONCLUSIONS: Longitudinal total pulmonary infection volume and volume ratio are independently associated with the clinical types of COVID-19 pneumonia. KEY POINTS: • The impact of total pulmonary infection volume and volume ratio over time was significantly affected by the clinical types (p for interaction = 0.01 and 0.01, respectively) using the GAMM. • Total pulmonary infection volume and volume ratio of the severe group increased by 14.66 cm3 (95% CI: 3.92 to 25.40) and 0.45% (95% CI: 0.13 to 0.77) every day, respectively, compared to that of the moderate group.


Subject(s)
COVID-19 , Pneumonia , Humans , Lung/diagnostic imaging , Propensity Score , Retrospective Studies , SARS-CoV-2
11.
Nat Commun ; 12(1): 814, 2021 02 05.
Article in English | MEDLINE | ID: covidwho-1065864

ABSTRACT

On the basis of Covid-19-induced pulmonary pathological and vascular changes, we hypothesize that the anti-vascular endothelial growth factor (VEGF) drug bevacizumab might be beneficial for treating Covid-19 patients. From Feb 15 to April 5, 2020, we conducted a single-arm trial (NCT04275414) and recruited 26 patients from 2-centers (China and Italy) with severe Covid-19, with respiratory rate ≥30 times/min, oxygen saturation ≤93% with ambient air, or partial arterial oxygen pressure to fraction of inspiration O2 ratio (PaO2/FiO2) >100 mmHg and ≤300 mmHg, and diffuse pneumonia confirmed by chest imaging. Followed up for 28 days. Among these, bevacizumab plus standard care markedly improves the PaO2/FiO2 ratios at days 1 and 7. By day 28, 24 (92%) patients show improvement in oxygen-support status, 17 (65%) patients are discharged, and none show worsen oxygen-support status nor die. Significant reduction of lesion areas/ratios are shown in chest computed tomography (CT) or X-ray within 7 days. Of 14 patients with fever, body temperature normalizes within 72 h in 13 (93%) patients. Relative to comparable controls, bevacizumab shows clinical efficacy by improving oxygenation and shortening oxygen-support duration. Our findings suggest bevacizumab plus standard care is highly beneficial for patients with severe Covid-19. Randomized controlled trial is warranted.


Subject(s)
Bevacizumab/therapeutic use , COVID-19/drug therapy , SARS-CoV-2/drug effects , Aged , Angiogenesis Inhibitors/therapeutic use , Body Temperature/drug effects , COVID-19/virology , China , Female , Fever/prevention & control , Humans , Italy , Male , Middle Aged , SARS-CoV-2/physiology , Treatment Outcome
12.
Respiration ; 100(2): 116-126, 2021.
Article in English | MEDLINE | ID: covidwho-1044350

ABSTRACT

BACKGROUND: There is still no clinical evidence available to support or to oppose corticosteroid treatment for coronavirus disease 2019 (COVID-19) pneumonia. OBJECTIVE: To investigate the efficacy and safety of corticosteroid given to the hospitalized patients with COVID-19 pneumonia. METHODS: This was a prospective, multicenter, single-blind, randomized control trial. Adult patients with COVID-19 pneumonia who were admitted to the general ward were randomly assigned to either receive methylprednisolone or not for 7 days. The primary end point was the incidence of clinical deterioration 14 days after randomization. RESULTS: We terminated this trial early because the number of patients with COVID-19 pneumonia in all the centers decreased in late March. Finally, a total of 86 COVID-19 patients underwent randomization. There was no difference of the incidence of clinical deterioration between the methylprednisolone group and control group (4.8 vs. 4.8%, p = 1.000). The duration of throat viral RNA detectability in the methylprednisolone group was 11 days (interquartile range, 6-16 days), which was significantly longer than that in the control group (8 days [2-12 days], p = 0.030). There were no significant differences between the 2 groups in other secondary outcomes. Mass cytometry discovered CD3+ T cells, CD8+ T cells, and NK cells in the methylprednisolone group which were significantly lower than those in the control group after randomization (p < 0.05). CONCLUSIONS: From this prematurely closed trial, we found that the short-term early use of corticosteroid could suppress the immune cells, which may prolong severe acute respiratory syndrome coronavirus 2 shedding in patients with COVID-19 pneumonia. TRIAL REGISTRATION: ClinicalTrials.gov, NCT04273321.


Subject(s)
COVID-19/drug therapy , Glucocorticoids/therapeutic use , Hospitalization , Methylprednisolone/therapeutic use , Pharynx/chemistry , RNA, Viral/isolation & purification , Virus Shedding , Adult , Aged , Anti-Bacterial Agents/therapeutic use , Antiviral Agents/therapeutic use , CD3 Complex , CD8-Positive T-Lymphocytes , COVID-19/blood , COVID-19/therapy , COVID-19/transmission , COVID-19 Nucleic Acid Testing , Disease Progression , Early Medical Intervention , Extracorporeal Membrane Oxygenation , Female , Humans , Killer Cells, Natural , Lymphocyte Count , Male , Middle Aged , Oxygen Inhalation Therapy , Patients' Rooms , Pharynx/virology , Proportional Hazards Models , Respiration, Artificial , SARS-CoV-2 , Single-Blind Method , T-Lymphocyte Subsets , T-Lymphocytes , Time Factors , Treatment Outcome
13.
J Clin Lab Anal ; 35(1): e23643, 2021 Jan.
Article in English | MEDLINE | ID: covidwho-891884

ABSTRACT

BACKGROUND: We aimed to evaluate the analytical performance of five commercial RT-PCR kits (Genekey, Daan, BioGerm, Liferiver, and Yaneng) commonly used in China, since such comparison data are lacking. METHODS: A total of 20 COVID-19 confirmed patients and 30 negative nasopharyngeal swab specimens were analyzed by five kits. The detection ability of five RT-PCR kits was evaluated with 5 concentration gradients diluted by a single positive sample. The limit of detection was evaluated by N gene fragment solid standard. Two positive clinical specimens were used to evaluate the repeatability and imprecision. Finally, we used six human coronaviruses plasmid and four respiratory pathogens plasmid to check for cross-reactivity. RESULTS: The positive detection rate was 100% for Genekey, Daan, and BioGerm,and 90% for Liferiver and Yaneng in 20 clinical SARS-CoV-2 infection. The coincidence rate of five kits in 10 negative samples was 100%. The detection rate of target genes for Daan, BioGerm, Liferiver, and Yaneng was 100% from Level 1 to Level 3. In Level 4, only Daan detection rate was 100%. In Level 5, five kits presented poor positive rate. The limit of detection declared by each manufacturer was verified. The repeatability for target genes was less than 5% and so did the total imprecision. There is no cross-reactivity of five kits with six human coronaviruses and four respiratory pathogens for ORF1ab and N gene. CONCLUSIONS: Five RT-PCR kits assessed in this study showed acceptable analytical performance characteristics and are useful tools for the routine diagnosis of SARS-CoV-2.


Subject(s)
COVID-19 Testing/methods , Reverse Transcriptase Polymerase Chain Reaction/methods , SARS-CoV-2/genetics , Humans , Limit of Detection , Nasopharynx/virology , Polyproteins/genetics , Reproducibility of Results , Viral Proteins/genetics
14.
Phys Fluids (1994) ; 32(8): 081703, 2020 Aug 01.
Article in English | MEDLINE | ID: covidwho-729022

ABSTRACT

A virus-laden particle movement from urinal flushing is simulated. Similar to the toilet-induced flushing, results indicate that the trajectory of the particles triggered by the urinal flushing manifests an external spread type. Even more alarmingly, the particle can reach 0.84 m (man's thigh) in 5.5 s when compared with the diffusion performance of the toilet-induced one (around 0.93 m in 35 s). A more violent climbing tendency is discovered in this Letter. Wearing masks should be made mandatory in public washrooms, and anti-diffusion improvements of facilities in public washrooms are urgently needed, especially in the current "SARS-CoV-2" crisis.

15.
Eur Radiol ; 30(12): 6888-6901, 2020 Dec.
Article in English | MEDLINE | ID: covidwho-631855

ABSTRACT

OBJECTIVES: To develop and validate a radiomics model for predicting 2019 novel coronavirus (COVID-19) pneumonia. METHODS: For this retrospective study, a radiomics model was developed on the basis of a training set consisting of 136 patients with COVID-19 pneumonia and 103 patients with other types of viral pneumonia. Radiomics features were extracted from the lung parenchyma window. A radiomics signature was built on the basis of reproducible features, using the least absolute shrinkage and selection operator method (LASSO). Multivariable logistic regression model was adopted to establish a radiomics nomogram. Nomogram performance was determined by its discrimination, calibration, and clinical usefulness. The model was validated in 90 consecutive patients, of which 56 patients had COVID-19 pneumonia and 34 patients had other types of viral pneumonia. RESULTS: The radiomics signature, consisting of 3 selected features, was significantly associated with COVID-19 pneumonia (p < 0.05) in both training and validation sets. The multivariable logistic regression model included the radiomics signature and distribution; maximum lesion, hilar, and mediastinal lymph node enlargement; and pleural effusion. The individualized prediction nomogram showed good discrimination in the training sample (area under the receiver operating characteristic curve [AUC], 0.959; 95% confidence interval [CI], 0.933-0.985) and in the validation sample (AUC, 0.955; 95% CI, 0.899-0.995) and good calibration. The mixed model achieved better predictive efficacy than the clinical model. Decision curve analysis demonstrated that the radiomics nomogram was clinically useful. CONCLUSIONS: The radiomics model derived has good performance for predicting COVID-19 pneumonia and may help in clinical decision-making. KEY POINTS: • A radiomics model showed good performance for prediction 2019 novel coronavirus pneumonia and favorable discrimination for other types of pneumonia on CT images. • A central or peripheral distribution, a maximum lesion range > 10 cm, the involvement of all five lobes, hilar and mediastinal lymph node enlargement, and no pleural effusion is associated with an increased risk of 2019 novel coronavirus pneumonia. • A radiomics model was superior to a clinical model in predicting 2019 novel coronavirus pneumonia.


Subject(s)
Betacoronavirus , Coronavirus Infections/diagnosis , Nomograms , Pneumonia, Viral/diagnosis , Tomography, X-Ray Computed/methods , Adult , Aged , Aged, 80 and over , COVID-19 , China/epidemiology , Coronavirus Infections/epidemiology , Cross-Sectional Studies , Female , Humans , Male , Middle Aged , Pandemics , Pneumonia, Viral/epidemiology , ROC Curve , Retrospective Studies , SARS-CoV-2 , Young Adult
16.
Phys Fluids (1994) ; 32(6): 065107, 2020 Jun 01.
Article in English | MEDLINE | ID: covidwho-613396

ABSTRACT

Currently, a novel coronavirus named "SARS-CoV-2" is spreading rapidly across the world, causing a public health crisis, economic losses, and panic. Fecal-oral transmission is a common transmission route for many viruses, including SARS-CoV-2. Blocking the path of fecal-oral transmission, which occurs commonly in toilet usage, is of fundamental importance in suppressing the spread of viruses. However, to date, efforts at improving sanitary safety in toilet use have been insufficient. It is clear from daily experience that flushing a toilet generates strong turbulence within the bowl. Will this flushing-induced turbulent flow expel aerosol particles containing viruses out of the bowl? This paper adopts computational fluid dynamics to explore and visualize the characteristics of fluid flow during toilet flushing and the influence of flushing on the spread of virus aerosol particles. The volume-of-fluid (VOF) model is used to simulate two common flushing processes (single-inlet flushing and annular flushing), and the VOF-discrete phase model (DPM) method is used to model the trajectories of aerosol particles during flushing. The simulation results are alarming in that massive upward transport of virus particles is observed, with 40%-60% of particles reaching above the toilet seat, leading to large-scale virus spread. Suggestions concerning safer toilet use and recommendations for a better toilet design are also provided.

17.
Eur Radiol ; 30(11): 6139-6150, 2020 Nov.
Article in English | MEDLINE | ID: covidwho-436953

ABSTRACT

OBJECTIVES: To investigate whether meaningful subgroups sharing the CT features of patients with COVID-19 pneumonia could be identified using latent class analysis (LCA) and explore the relationship between the LCA-derived subgroups and clinical types. METHODS: This retrospective review included 499 patients with confirmed COVID-19 pneumonia between February 11 and March 8, 2020. Subgroups sharing the CT features were identified using LCA. Univariate and multivariate logistic regression models were utilized to analyze the association between clinical types and the LCA-derived subgroups. RESULTS: Two radiological subgroups were identified using LCA. There were 228 subjects (45.69%) in class 1 and 271 subjects (54.31%) in class 2. The CT findings of class 1 were smaller pulmonary infection volume, more peripheral distribution, more GGO, more maximum lesion range ≤ 5 cm, a smaller number of lesions, less involvement of lobes, less air bronchogram, less dilatation of vessels, less hilar and mediastinal lymph node enlargement, and less pleural effusion than the CT findings of class 2. Univariate analysis demonstrated that older age, therapy, presence of fever, presence of hypertension, decreased lymphocyte count, and increased CRP levels were significant parameters associated with an increased risk for class 2. Multivariate analyses revealed that the patients with clinically severe type disease had a 1.97-fold risk of class 2 than the patients with clinically moderate-type disease. CONCLUSIONS: The demographic and clinical differences between the two radiological subgroups based on the LCA were significantly different. Two radiological subgroups were significantly associated with clinical moderate and severe types. KEY POINTS: • Two radiological subgroups were identified using LCA. • Older age, therapy, presence of fever, presence of hypertension, decreased lymphocyte count, and increased CRP levels were significant parameters with an increased risk for class 2 defined by LCA. • Patients with clinically severe type had a 1.97-fold higher risk of class 2 defined by LCA in comparison with patients showing clinically moderate-type disease.


Subject(s)
Betacoronavirus , Coronavirus Infections/diagnostic imaging , Coronavirus Infections/pathology , Latent Class Analysis , Pneumonia, Viral/diagnostic imaging , Pneumonia, Viral/pathology , Tomography, X-Ray Computed/methods , COVID-19 , Coronavirus Infections/physiopathology , Cross-Sectional Studies , Female , Humans , Lung/diagnostic imaging , Lung/pathology , Lung/physiopathology , Male , Middle Aged , Pandemics , Pneumonia, Viral/physiopathology , Retrospective Studies , SARS-CoV-2 , Severity of Illness Index
18.
Mol Biol Evol ; 37(9): 2641-2654, 2020 09 01.
Article in English | MEDLINE | ID: covidwho-260310

ABSTRACT

The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has shown once again that coronavirus (CoV) in animals are potential sources for epidemics in humans. Porcine deltacoronavirus (PDCoV) is an emerging enteropathogen of swine with a worldwide distribution. Here, we implemented and described an approach to analyze the epidemiology of PDCoV following its emergence in the pig population. We performed an integrated analysis of full genome sequence data from 21 newly sequenced viruses, along with comprehensive epidemiological surveillance data collected globally over the last 15 years. We found four distinct phylogenetic lineages of PDCoV, which differ in their geographic circulation patterns. Interestingly, we identified more frequent intra- and interlineage recombination and higher virus genetic diversity in the Chinese lineages compared with the USA lineage where pigs are raised in different farming systems and ecological environments. Most recombination breakpoints are located in the ORF1ab gene rather than in genes encoding structural proteins. We also identified five amino acids under positive selection in the spike protein suggesting a role for adaptive evolution. According to structural mapping, three positively selected sites are located in the N-terminal domain of the S1 subunit, which is the most likely involved in binding to a carbohydrate receptor, whereas the other two are located in or near the fusion peptide of the S2 subunit and thus might affect membrane fusion. Finally, our phylogeographic investigations highlighted notable South-North transmission as well as frequent long-distance dispersal events in China that could implicate human-mediated transmission. Our findings provide new insights into the evolution and dispersal of PDCoV that contribute to our understanding of the critical factors involved in CoVs emergence.


Subject(s)
Coronavirus Infections/veterinary , Coronavirus/genetics , Genome, Viral , Spike Glycoprotein, Coronavirus/genetics , Swine Diseases/epidemiology , Viral Proteins/genetics , Animals , Biological Evolution , China/epidemiology , Coronavirus/classification , Coronavirus/pathogenicity , Coronavirus Infections/epidemiology , Coronavirus Infections/transmission , Coronavirus Infections/virology , Genetic Variation , Genomics , Humans , Models, Molecular , Molecular Epidemiology , Open Reading Frames , Phylogeny , Phylogeography , Protein Structure, Secondary , Recombination, Genetic , Selection, Genetic , Spike Glycoprotein, Coronavirus/chemistry , Spike Glycoprotein, Coronavirus/metabolism , Swine/virology , Swine Diseases/transmission , Swine Diseases/virology , Viral Proteins/metabolism
19.
Trends Mol Med ; 26(5): 483-495, 2020 05.
Article in English | MEDLINE | ID: covidwho-11922

ABSTRACT

The recent outbreak of COVID-19 in Wuhan turned into a public health emergency of international concern. With no antiviral drugs nor vaccines, and the presence of carriers without obvious symptoms, traditional public health intervention measures are significantly less effective. Here, we report the epidemiological and virological characteristics of the COVID-19 outbreak. Originated in bats, 2019-nCoV/ severe acute respiratory syndrome coronavirus (SARS-CoV)-2 likely experienced adaptive evolution in intermediate hosts before transfer to humans at a concentrated source of transmission. Similarities of receptor sequence binding to 2019-nCoV between humans and animals suggest a low species barrier for transmission of the virus to farm animals. We propose, based on the One Health model, that veterinarians and animal specialists should be involved in a cross-disciplinary collaboration in the fight against this epidemic.


Subject(s)
Betacoronavirus , Coronavirus Infections/veterinary , Pneumonia, Viral/epidemiology , Pneumonia, Viral/virology , Animals , Betacoronavirus/genetics , COVID-19 , Chiroptera/virology , Coronavirus Infections/epidemiology , Coronavirus Infections/transmission , Coronavirus Infections/virology , Humans , Interdisciplinary Communication , Pandemics , Pneumonia, Viral/transmission , Receptors, Virus/genetics , SARS-CoV-2
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