Your browser doesn't support javascript.
Show: 20 | 50 | 100
Results 1 - 15 de 15
Filter
2.
Frontiers in Public Health ; 10, 2022.
Article in English | Web of Science | ID: covidwho-2022944

ABSTRACT

PurposeTo evaluate the volumetric change of COVID-19 lesions in the lung of patients receiving serial CT imaging for monitoring the evolution of the disease and the response to treatment. Materials and methodsA total of 48 patients, 28 males and 20 females, who were confirmed to have COVID-19 infection and received chest CT examination, were identified. The age range was 21-93 years old, with a mean of 54 +/- 18 years. Of them, 33 patients received the first follow-up (F/U) scan, 29 patients received the second F/U scan, and 11 patients received the third F/U scan. The lesion region of interest (ROI) was manually outlined. A two-step registration method, first using the Affine alignment, followed by the non-rigid Demons algorithm, was developed to match the lung areas on the baseline and F/U images. The baseline lesion ROI was mapped to the F/U images using the obtained geometric transformation matrix, and the radiologist outlined the lesion ROI on F/U CT again. ResultsThe median (interquartile range) lesion volume (cm(3)) was 30.9 (83.1) at baseline CT exam, 18.3 (43.9) at first F/U, 7.6 (18.9) at second F/U, and 0.6 (19.1) at third F/U, which showed a significant trend of decrease with time. The two-step registration could significantly decrease the mean squared error (MSE) between baseline and F/U images with p < 0.001. The method could match the lung areas and the large vessels inside the lung. When using the mapped baseline ROIs as references, the second-look ROI drawing showed a significantly increased volume, p < 0.05, presumably due to the consideration of all the infected areas at baseline. ConclusionThe results suggest that the registration method can be applied to assist in the evaluation of longitudinal changes of COVID-19 lesions on chest CT.

3.
PeerJ ; 10, 2022.
Article in English | PMC | ID: covidwho-2010486

ABSTRACT

Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the cause of coronavirus disease 2019 (COVID-19), has spread globally and is being surveilled with an international genome sequencing effort. Surveillance consists of sample acquisition, library preparation, and whole genome sequencing. This has necessitated a classification scheme detailing Variants of Concern (VOC) and Variants of Interest (VOI), and the rapid expansion of bioinformatics tools for sequence analysis. These bioinformatic tools are means for major actionable results: maintaining quality assurance and checks, defining population structure, performing genomic epidemiology, and inferring lineage to allow reliable and actionable identification and classification. Additionally, the pandemic has required public health laboratories to reach high throughput proficiency in sequencing library preparation and downstream data analysis rapidly. However, both processes can be limited by a lack of a standardized sequence dataset. Methods: We identified six SARS-CoV-2 sequence datasets from recent publications, public databases and internal resources. In addition, we created a method to mine public databases to identify representative genomes for these datasets. Using this novel method, we identified several genomes as either VOI/VOC representatives or non-VOI/VOC representatives. To describe each dataset, we utilized a previously published datasets format, which describes accession information and whole dataset information. Additionally, a script from the same publication has been enhanced to download and verify all data from this study. Results: The benchmark datasets focus on the two most widely used sequencing platforms: long read sequencing data from the Oxford Nanopore Technologies platform and short read sequencing data from the Illumina platform. There are six datasets: three were derived from recent publications;two were derived from data mining public databases to answer common questions not covered by published datasets;one unique dataset representing common sequence failures was obtained by rigorously scrutinizing data that did not pass quality checks. The dataset summary table, data mining script and quality control (QC) values for all sequence data are publicly available on GitHub: https://github.com/CDCgov/datasets-sars-cov-2. Discussion: The datasets presented here were generated to help public health laboratories build sequencing and bioinformatics capacity, benchmark different workflows and pipelines, and calibrate QC thresholds to ensure sequencing quality. Together, improvements in these areas support accurate and timely outbreak investigation and surveillance, providing actionable data for pandemic management. Furthermore, these publicly available and standardized benchmark data will facilitate the development and adjudication of new pipelines.

4.
Journal of Environmental and Occupational Medicine ; 38(6):624-630, 2021.
Article in Chinese | Scopus | ID: covidwho-1912212

ABSTRACT

[Background] The epidemic of coronavirus disease 2019 (COVID-19) seriously affects the psychological status of medical staff who directly face the risk of the disease. [Objective] This study investigates the prevalence and related factors of depression, anxiety, and insomnia among medical staff during the COVID-19 pandemic. [Methods] From February 13 to March 1, 2020, a network questionnaire survey was conducted among 482 medical staff selected by convenience sampling. A self-designed questionnaire was used to investigate the basic demographic information and COVID-19-related questions. The Patient Health Questionnaire-9 (PHQ-9), Generalized Anxiety Disorder-7 (GAD-7), and Insomnia Severity Index (ISI) were used to estimate the prevalence of depression, anxiety, and insomnia among the medical staff. Stepwise multiple linear regression analysis was performed with PHQ-9 score, GAD-7 score, and ISI score as dependent variables. Multivariate logistic regression analysis (forward-conditional method) on depression, anxiety, and insomnia as dependent variables was performed with basic demographic information and COVID-19-related questions as independent variables. [Results] Among the surveyed medical staff, the prevalence rates of depression, anxiety, and insomnia were 14.3%, 11.2%, and 23.2%, respectively. There were no significant differences in the prevalence rates among different age, gender, local risk level, and occupation groups and those aiding Hubei Province or not. The medical staff who directly contacted fever or diagnosed patients had more serious depression (b=1.73, 95%CI: 0.79-2.66) and insomnia (b=2.43, 95%CI: 1.48-3.39) and a higher risk of insomnia (OR=1.89, 95%CI: 1.21-2.96). The medical staff whose current protective measures cannot prevent infection had more serious depression (b=1.72, 95% CI: 0.65-2.80), anxiety (b=1.75, 95% CI: 0.76-2.75), and insomnia (b=1.73, 95% CI: 0.63-2.82), and had a higher risk of depression (OR=1.97, 95% CI: 1.11-3.49), anxiety (OR=3.00, 95%CI: 1.64-5.46), and insomnia (OR=1.79, 95%CI: 1.08-2.96). [Conclusion] During the COVID-19 epidemic, the risks of depression, anxiety, and insomnia among selected medical staff are increased compared with the non-epidemic period. Occupational exposure to high-risk groups and protective measures would significantly affect mental health of medical staff. © 2021, Shanghai Municipal Center for Disease Control and Prevention. All rights reserved.

5.
Embase; 2022.
Preprint in English | EMBASE | ID: ppcovidwho-337493

ABSTRACT

Background. Monitoring the emergence and spread of SARS-CoV-2 variants is an important public health objective. Travel restrictions, aimed to prevent viral spread, have major economic consequences and unclear effectiveness despite considerable research. We investigated the introduction and establishment of the Gamma variant in New York City (NYC) in 2021. Methods. We performed phylogeographic analysis on 15,967 Gamma sequences available on GISAID and sampled between March 10th through May 1st, 2021, to identify geographic sources of Gamma lineages introduced into NYC. We identified locally circulating Gamma transmission clusters and inferred the timing of their establishment in NYC. Findings. We identified 16 phylogenetically-distinct Gamma clusters established in NYC (cluster sizes ranged 2-108 genomes). Most of the NYC clusters were introduced from Florida and Illinois;only one was introduced from outside the United States (US). By the time the first Gamma case was reported by genomic surveillance in NYC on March 10th, the majority (57%) of circulating Gamma lineages had already been established in the city for at least two weeks. Interpretation. Despite the expansion of SARS-CoV-2 genomic surveillance in NYC, there was a substantial gap between Gamma variant introduction and establishment in January/February 2021, and its identification by genomic surveillance in March 2021. Although travel from Brazil to the US was restricted from May 2020 through the end of the study period, this restriction did not prevent Gamma from becoming established in NYC as most introductions occurred from domestic locations.

6.
J Clin Virol Plus ; 2(3): 100079, 2022 Aug.
Article in English | MEDLINE | ID: covidwho-1814680

ABSTRACT

Objectives: To examine the comparative stochasticity profile of six commercial SARS-CoV-2 nucleic acid amplification tests (NAATs) and how this may affect retesting paradigms. Methods: Commercial quality control (QC) material was serially diluted in viral transport media to create a panel covering 10-10,000 copies/ml. The panel was tested across six commercial NAATs. A subset of high cycle threshold results was retested on a rapid PCR assay to simulate retesting protocols commonly used to discriminate false positives. Results: Performance beyond the LOD differed among assays, with three types of stochasticity profiles observed. The ability of the rapid PCR assay to reproduce a true weak positive specimen was restricted to its own stochastic performance at the corresponding viral concentration. Conclusion: Stochastic performance of various NAATs overlap across low viral concentrations and affect retesting outcomes. Relying on retesting alone to discriminate false positives risk missing true positives even when a more sensitive assay is deployed for confirmatory testing.

7.
Infectious Microbes and Diseases ; 3(1):32-40, 2021.
Article in English | Scopus | ID: covidwho-1795002

ABSTRACT

Coronavirus disease 2019 (COVID-19) has spread throughout China. However, information about COVID-19 in cities and regions outside Wuhan is limited and the indicators that predict the length of hospital stay for patients with COVID-19 are unclear. Therefore, we collected clinical data from 47 patients with COVID-19 in Quanzhou City. The median age was 38 years [interquartile range (IQR): 31-50 years], and 24 (51%) were male. There were 8 mild, 36 moderate, and 3 severe/critical cases. The median interval from exposure to disease onset was 13 days (IQR: 8-18 days). The incidence of severe/critical cases was 33% (3/10) in patients with hypertension. Common symptoms included fever (83%), cough (77%), fatigue (40%), a sore, dry throat (28%), and diarrhea (21%). One patient (2%) developed respiratory distress syndrome on day 13 of inpatient treatment. Six patients had leukopenia, 17 had elevated C-reactive protein (CRP), and 8 had lymphocytopenia and elevated lactate dehydrogenase (LDH). The median length of hospitalization was 22 days (IQR: 16-30 days). Dynamic monitoring of LDH, CRP, and neutrophil-lymphocyte ratio predicted whether length of hospitalization would exceed 21 days. Most patients presented with mild and moderate disease. Patients with hypertension were more likely to become severe or critical. Dynamic monitoring of LDH, CRP, and neutrophil-lymphocyte ratio levels can help predict delayed discharge from the hospital. © 2022 Lippincott Williams and Wilkins. All rights reserved.

8.
Open Forum Infectious Diseases ; 8(SUPPL 1):S89, 2021.
Article in English | EMBASE | ID: covidwho-1746776

ABSTRACT

Background. Detection and surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants is of great public health importance. Broadly accessible and inexpensive assays are needed to enhance variant surveillance and detection globally. We developed and validated a single-reaction multiplex real-time RT-PCR (the Spike SNP assay) to detect specific mutations associated with variants of concern (VOC). Methods. A single primer pair was designed to amplify a 348 bp region of spike. Probes were initially designed with locked nucleic acids (LNAs) to increase probe melting temperature, shorten probe length, and specifically detect 417K, E484K, and N501Y (Figure). The assay was optimized and evaluated using characterized variant sample pools. Clinical evaluation was performed on a convenience set of residual nasopharyngeal swabs, and variant calls were confirmed by SARS-CoV-2 genomic sequencing in a subset of samples. Following the initial evaluation, unmodified probes (without LNAs) were designed to detect L452R, L452Q, and E484Q. Figure. Spike SNP distinguishes mutations occurring in different lineages (A-C). Representative results of variant detection a single Spike SNP run are shown for mutations in the codons for 4177K (A) and mutations that encode 484K (B) and 501Y (C). Curves show dilutions of the following variants: blue, BEI 52286 (wild type);pink B.1.1.7;purple, B1.525;and green, P.1. Variant pools were used for B.1.17, B.1.525, and P.1 strains. Curves are displayed for a given dilution in each channel and result interpretation is shown (D). Results. The lower limit of 95% detection was 2.46 to 2.48 log10 GE/mL for the three targets (~1-2 GE/reaction). Among 253 nasopharyngeal swabs with detectable SARS-CoV-2 RNA, the Spike SNP assay was positive in 238 (94.1%), including all samples with Ct values < 30 (220/220) for the N2 target and 18/33 samples with N2 Ct values ≥ 30. Results were confirmed by SARS-CoV-2 genomic sequencing in 50/50 samples (100%). Subsequent addition of the 452R probe did not affect performance for the original targets, and probes for 452Q and 484Q performed similarly to LNAmodified probes. Conclusion. The Spike SNP assay provides fast, inexpensive and sensitive detection of specific mutations associated with SARS-CoV-2 VOCs, and the assay can be quickly modified to detect new mutations in the receptor binding domain. Similar analytical performance of LNA-modified and unmodified probes presents options for future assay customization that balance the shorter probe length (LNAs) and increased accessibility (unmodified). The Spike SNP assay, if implemented across laboratories offering SARS-CoV-2 testing, could greatly increase capacity for variant detection and surveillance globally.

9.
Acta Chimica Sinica ; 80(1):80-88, 2022.
Article in Chinese | Scopus | ID: covidwho-1643837

ABSTRACT

The worldwide outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in the infection even death of people all over the world, which has gravely affected our daily life. Globalization of trade and convenient transportation immensely accelerate the propagation of the epidemic, which brings severe difficulties to prevent the epidemic. Therefore, rapid and accurate diagnosis of infected persons and screening of asymptomatic persons play an important role. At present, the most widely used method for the detection of SARS-CoV-2 is reverse transcription-polymerase chain reaction (RT-PCR), which still has some problems including complicated sample storage and transportation, complex operations and so on. These shortcomings cause the hindrances to achieve fast, simple, efficient diagnostic testing under the normalization of the epidemic. In the past few years, with the development of nanotechnology, bio-sensing methods based on nano photonics have become a research hotspot. Label-free optical methods have been widely explored for bio-sensing including virus detection, such as surface plasmon resonance (SPR), surface enhanced Raman scattering (SERS), whispering gallery mode (WGM) and colorimetry. These approaches offer available alternatives to improve the speed, sensitivity, and accuracy of optical bio-sensing, owing to the enhanced interaction between the nanostructure and the biomarkers. This review summarizes these nano photonics-based bio-sensing technologies for the detection of SARS-CoV-2. Moreover, the detection mechanism of biomarkers by nano photonics is explained, and the further development trends are discussed. In view of the difficulties in manufacturing nano photonics structures, a new strategy of large-area preparation of nano photonics structures using nano green printing technology is proposed, which provides theoretical and technical support for accurate and effective prevention and control of the epidemic diseases. © 2022 Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences.

10.
Clinical Toxicology ; 59(11):1101-1101, 2021.
Article in English | Web of Science | ID: covidwho-1490042
11.
Social Media and Society ; 7(3), 2021.
Article in English | Scopus | ID: covidwho-1463206

ABSTRACT

Vaccine hesitancy has been a growing public health issue, but during COVID-19, understanding vaccine hesitancy and promote vaccine favorability takes on a troubling immediacy. With the growing political polarization on scientific issues, the COVID-19 vaccine-related sentiment has recently been divided across ideological lines. This study aims to understand how vaccine favorability and specific vaccine-related concerns including possible side effects, distrust in medical professionals, and conspiratorial beliefs concerning COVID-19 vaccines were articulated and transmitted by Twitter users from opposing ideological camps and with different follower scopes. Using a combination of computational approaches, including supervised machine-learning and structural topic modeling, we examined tweets surrounding COVID-19 vaccination (N = 16,959) from 1 March to 30 June 2020. Results from linear mixed-effects models suggested that Twitter users high on conservative ideology and with a standard instead of large follower scope tend to express less favorable vaccine-related sentiments and talk more about vaccine side effects, distrust of medical professionals, and conspiracy theories. There is also an interaction effect where liberals with large follower scope expressed the least amount of distrust of medical professionals, whereas extreme conservatives expressed greater distrust for health professionals, regardless of their follower scope. Finally, structural topic modeling revealed distinct topical focuses among liberal and conservative users. Theoretical and practical implications for leveraging social media in effective health communication practice were discussed. © The Author(s) 2021.

12.
Eur Rev Med Pharmacol Sci ; 25(2): 1135-1145, 2021 Jan.
Article in English | MEDLINE | ID: covidwho-1082411

ABSTRACT

OBJECTIVE: To explore the different clinical and CT features distinguishing COVID-19 from H1N1 influenza pneumonia. PATIENTS AND METHODS: We compared two independent cohorts of COVID-19 pneumonia (n=405) and H1N1 influenza pneumonia (n=78), retrospectively. All patients were confirmed by RT-PCR. Four hundred and five cases of COVID-19 pneumonia were confirmed in nine hospitals of Zhejiang province, China from January 21 to February 20, 2020. Seventy-eight cases of H1N1 influenza pneumonia were confirmed in our hospital from January 1, 2017 to February 29, 2020. Their clinical manifestations, laboratory test results, and CT imaging characteristics were compared. RESULTS: COVID-19 pneumonia patients showed less proportions of underlying diseases, fever and respiratory symptoms than those of H1N1 pneumonia patients (p<0.01). White blood cell count, neutrophilic granulocyte percentage, C-reactive protein, procalcitonin, D-Dimer, and lactate dehydrogenase in H1N1 pneumonia patients were higher than those of COVID-19 pneumonia patients (p<0.05). H1N1 pneumonia was often symmetrically located in the dorsal part of inferior lung lobes, while COVID-19 pneumonia was unusually showed as a peripheral but non-specific lobe distribution. Ground glass opacity was more common in COVID-19 pneumonia and consolidation lesions were more common in H1N1 pneumonia (p<0.01). COVID-19 pneumonia lesions showed a relatively clear margin compared with H1N1 pneumonia. Crazy-paving pattern, thickening vessels, reversed halo sign and early fibrotic lesions were more common in COVID-19 pneumonia than H1N1 pneumonia (p<0.05). Pleural effusion in COVID-19 pneumonia was significantly less common than H1N1 pneumonia (p<0.01). CONCLUSIONS: Compared with H1N1 pneumonia in Zhejiang, China, the clinical manifestations of COVID-19 pneumonia were more concealed with less underlying diseases and slighter respiratory symptoms. The more common CT manifestations of COVID-19 pneumonia included ground-glass opacity with a relatively clear margin, crazy-paving pattern, thickening vessels, reversed halo sign, and early fibrotic lesions, while the less common CT manifestations of COVID-19 pneumonia included consolidation and pleural effusion.


Subject(s)
COVID-19/diagnostic imaging , COVID-19/epidemiology , Influenza A Virus, H1N1 Subtype/isolation & purification , Influenza, Human/diagnostic imaging , Influenza, Human/epidemiology , Tomography, X-Ray Computed/methods , Adult , Aged , Case-Control Studies , China/epidemiology , Cohort Studies , Female , Humans , Male , Middle Aged , Retrospective Studies
13.
Medicine in Drug Discovery ; : 100043-100043, 2020.
Article | WHO COVID | ID: covidwho-276398

ABSTRACT

There are two key needs in COVID-19 management: (i) to reduce SARS-CoV-2 viral infection rate;and (ii) to reduce death rate of those infected - the subject of this commentary. The current WHO estimated global mortality rate is 3.4% (March 2020) and the global death toll has now past 200,000 (April 2020). Without therapy the COVID-19 pandemic is escalating exponentially: from the first reported death in Wuhan China 10th January 2020, it took 91 days for the global death toll to pass 100,000 - then a further 16 days to reach 200,000. A vaccination program will take 1–2 years to roll out, once safety and efficacy is proven. Anti-virals are being sought mainly amongst repurposed drug candidates but also with combinatorial screening of libraries, for example to block virus binding angiotensin converting enzyme 2 (ACE2) - ACE2 providing the receptor on cells that allows viral entry. Cell-based approaches include stem cells and exosomes but these will never meet scale of need whilst also carrying risk of viral transmission if contaminated. Countries have introduced Population control with social distancing and lockdown to isolate individuals: this has reduced infectivity rate - “R” - where R denotes the average number of people an infected person will spread the illness to. But, after lockdown, the virus remains: the probability of R increasing again is high. The new danger is exit from lockdown. Here, leukaemia inhibitory factor (LIF) represents an untapped resource to boost the lung's own resistance to developing COVID-19 - reducing risk of severe disease as nations cautiously leave lockdown to return to normality.

15.
Med Drug Discov ; 5: 100019, 2020 Mar.
Article in English | MEDLINE | ID: covidwho-9529

ABSTRACT

Human coronavirus, hCoV-19, is highly pathogenic with severe pneumonia associated with rapid virus replication. Arising in Wuhan China December 2019, the current COVID-19 epidemic has rapidly grown with person-to-person infection expanding to become a global health emergency now on pandemic scale. Governments will not be able to minimise both deaths from COVID-19 and the economic impact of viral spread in mitigation of this current COVID-19 pandemic, according to Anderson et al. 2020 [1], Keeping mortality as low as possible will be the highest priority for individuals; hence governments must put in place measures to ameliorate the inevitable economic downturn. The current global picture shows small chains of transmission in many countries and large chains resulting in extensive spread in a few countries, such as Italy, Iran, South Korea, and Japan. Most countries are likely to have spread of COVID-19, at least in the early stages, before any mitigation measures have an impact. The scale of the problem is massive. Here I consider new approaches to improve patient's biological resistance to COVID-19 using stem cells, and how benefit might be scaled and simplified using synthetic stem cells to meet logistical needs within a short time frame.

SELECTION OF CITATIONS
SEARCH DETAIL