Early Chest CT Features of Patients with 2019 Novel Coronavirus (COVID-19) Pneumonia: Relationship to Diagnosis and Prognosis

Chen, Hui Juan; Qiu, Jie; Wu, Biao; Huang, Tao; Gao, Yunsuo; Wang, Zhen Ping; Chen, Yang; Chen, Feng

doi:10.21203/rs.3.rs-16702/v1

Cited by 3 publications

(2 citation statements)

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“…To investigate the common pathogenetic processes of cHubGs, we selected top five common GO terms for each of BPs, MFs and CCs, and KEGG pathways that are significantly enriched by cHubGs in at least two of three databases (see Table 3). Among them, the association of the detected BPs (inflammatory response, response to virus, regulation of inflammatory response, response to tumor necrosis factor, response to cytokine) with COVID-19 and IPF diseases were supported by several independent studies [60][61][62][63][64][65][66][67][68][69][70][71][72][73][74] . The SARS-CoV-2 infection is influenced by a severe inflammatory response with the release of a huge amount of cytokine storm known as pro-inflammatory cytokines.…”

Section: Discussionmentioning

confidence: 88%

“…The SARS-CoV-2 infection is influenced by a severe inflammatory response with the release of a huge amount of cytokine storm known as pro-inflammatory cytokines. A number of studies suggested that the cytokine storms are associated directly with multi-organ failure, lung injury and unfavorable prognosis of SARS-CoV-2 infections [60][61][62][63][64] . Within the respiratory tract, persistent inflammatory response underlies the pathogenesis of a number of chronic pulmonary diseases including pulmonary fibrosis, asthma and chronic obstructive pulmonary disease 65 .…”

Section: Discussionmentioning

confidence: 99%

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Bioinformatics-based investigation on the genetic influence between SARS-CoV-2 infections and idiopathic pulmonary fibrosis (IPF) diseases, and drug repurposing

Islam

Kibria

Hossen

et al. 2023

Sci Rep

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Some recent studies showed that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections and idiopathic pulmonary fibrosis (IPF) disease might stimulate each other through the shared genes. Therefore, in this study, an attempt was made to explore common genomic biomarkers for SARS-CoV-2 infections and IPF disease highlighting their functions, pathways, regulators and associated drug molecules. At first, we identified 32 statistically significant common differentially expressed genes (cDEGs) between disease (SARS-CoV-2 and IPF) and control samples of RNA-Seq profiles by using a statistical r-package (edgeR). Then we detected 10 cDEGs (CXCR4, TNFAIP3, VCAM1, NLRP3, TNFAIP6, SELE, MX2, IRF4, UBD and CH25H) out of 32 as the common hub genes (cHubGs) by the protein–protein interaction (PPI) network analysis. The cHubGs regulatory network analysis detected few key TFs-proteins and miRNAs as the transcriptional and post-transcriptional regulators of cHubGs. The cDEGs-set enrichment analysis identified some crucial SARS-CoV-2 and IPF causing common molecular mechanisms including biological processes, molecular functions, cellular components and signaling pathways. Then, we suggested the cHubGs-guided top-ranked 10 candidate drug molecules (Tegobuvir, Nilotinib, Digoxin, Proscillaridin, Simeprevir, Sorafenib, Torin 2, Rapamycin, Vancomycin and Hesperidin) for the treatment against SARS-CoV-2 infections with IFP diseases as comorbidity. Finally, we investigated the resistance performance of our proposed drug molecules compare to the already published molecules, against the state-of-the-art alternatives publicly available top-ranked independent receptors by molecular docking analysis. Molecular docking results suggested that our proposed drug molecules would be more effective compare to the already published drug molecules. Thus, the findings of this study might be played a vital role for diagnosis and therapies of SARS-CoV-2 infections with IPF disease as comorbidity risk.

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Section: Discussionmentioning

confidence: 88%

Section: Discussionmentioning

confidence: 99%

Bioinformatics-based investigation on the genetic influence between SARS-CoV-2 infections and idiopathic pulmonary fibrosis (IPF) diseases, and drug repurposing

Islam

Kibria

Hossen

et al. 2023

Sci Rep

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False-Negative Results of Initial Rt-PCR Assays for Covid-19: A Systematic Review

Arévalo-Rodríguez

Buitrago-Garcia

Simancas‐Racines

et al. 2020

Preprint

386

372

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Background: Cases with negative reverse transcription-polymerase chain reaction (RT-PCR) results at initial testing for suspicion of SARS-CoV-2 infection, and found to be positive in a subsequent test, are considered as RT-PCR false-negative cases. False-negative cases have important implications for COVID-19 management, isolation, and risk of transmission. We aimed to review and critically appraise evidence about the proportion of RT-PCR false-negatives at initial testing for COVID-19. Methods: We performed a systematic review and critical appraisal of literature with high involvement of stakeholders in the review process. We searched on MEDLINE, EMBASE, LILACS, the WHO database of COVID-19 publications, the EPPI-Centre living systematic map of evidence about COVID-19, and the living systematic review developed by the University of Bern (ISPM). Two authors screened and selected studies according to the eligibility criteria and collected data of included studies (no-independent verification). Risk of bias was assessed using the Quality Assessment of Diagnostic Accuracy Studies (QUADAS-2) tool. We calculated the false-negative proportion with the corresponding 95% CI using a multilevel mixed-effect logistic regression model using STATA 16. Certainty of the evidence about false-negative cases was rated using the GRADE approach for tests and strategies. The information is current up to 6 April 2020. Findings: Five studies enrolling 957 patients were included. All studies were affected by several biases and applicability concerns. Pooled estimation of false-negative proportion was 0.085 (95% CI= 0.034 to 0.196; tau-squared = 1.08; 95% CI= 0.27 to 8.28; p<0.001); however, this estimation is highly affected by unexplained heterogeneity, and its interpretation should be avoided. The certainty of the evidence was judged as very low, due to the risk of bias, indirectness, and inconsistency issues. Conclusions: The collected evidence has several limitations, including risk of bias issues, high heterogeneity, and concerns about its applicability. Nonetheless, our findings reinforce the need for repeated testing in patients with suspicion of SARS-Cov-2 infection given that up to 29% of patients could have an initial RT-PCR false-negative result. Systematic review registration: Protocol available on OSF website: https://osf.io/gp38w/

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False-negative results of initial RT-PCR assays for COVID-19: A systematic review

et al. 2020

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Background A false-negative case of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is defined as a person with suspected infection and an initial negative result by reverse transcription-polymerase chain reaction (RT-PCR) test, with a positive result on a subsequent test. False-negative cases have important implications for isolation and risk of transmission of infected people and for the management of coronavirus disease 2019 (COVID-19). We aimed to review and critically appraise evidence about the rate of RT-PCR false-negatives at initial testing for COVID-19. Methods We searched MEDLINE, EMBASE, LILACS, as well as COVID-19 repositories, including the EPPI-Centre living systematic map of evidence about COVID-19 and the Coronavirus Open Access Project living evidence database. Two authors independently screened and selected studies according to the eligibility criteria and collected data from the included studies. The risk of bias was assessed using the Quality Assessment of Diagnostic Accuracy Studies (QUADAS-2) tool. We calculated the proportion of false-negative test results using a multilevel mixed-effect logistic regression model. The certainty of the evidence about false-negative cases was rated using the GRADE approach for tests and strategies. All information in this article is current up to July 17, 2020. Results We included 34 studies enrolling 12,057 COVID-19 confirmed cases. All studies were affected by several risks of bias and applicability concerns. The pooled estimate of false-negative proportion was highly affected by unexplained heterogeneity (tau-squared = 1.39; 90% prediction interval from 0.02 to 0.54). The certainty of the evidence was judged as very low due to the risk of bias, indirectness, and inconsistency issues. Conclusions There is substantial and largely unexplained heterogeneity in the proportion of false-negative RT-PCR results. The collected evidence has several limitations, including risk of bias issues, high heterogeneity, and concerns about its applicability. Nonetheless, our findings reinforce the need for repeated testing in patients with suspicion of SARS-Cov-2 infection given that up to 54% of COVID-19 patients may have an initial false-negative RT-PCR (very low certainty of evidence). Systematic review registration Protocol available on the OSF website: https://tinyurl.com/vvbgqya.

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Early Chest CT Features of Patients with 2019 Novel Coronavirus (COVID-19) Pneumonia: Relationship to Diagnosis and Prognosis

Cited by 3 publications

References 0 publications

Bioinformatics-based investigation on the genetic influence between SARS-CoV-2 infections and idiopathic pulmonary fibrosis (IPF) diseases, and drug repurposing

Bioinformatics-based investigation on the genetic influence between SARS-CoV-2 infections and idiopathic pulmonary fibrosis (IPF) diseases, and drug repurposing

False-Negative Results of Initial Rt-PCR Assays for Covid-19: A Systematic Review

False-negative results of initial RT-PCR assays for COVID-19: A systematic review

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