Corpus overview


Overview

MeSH Disease

Human Phenotype

Transmission

Seroprevalence
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    Implications of the COVID-19 lockdown on dengue MESHD transmission TRANS and the occurrence of Aedes aegypti (Linnaeus) and Aedes albopictus (Skuse) in Malaysia

    Authors: Song-Quan Ong; Hamdan Ahmad; Ahmad Mohiddin Mohd. Ngesom

    doi:10.1101/2020.07.21.214056 Date: 2020-07-21 Source: bioRxiv

    The impact of movement restrictions (MRs) during the COVID-19 lockdown on the existing endemic infectious disease MESHD dengue MESHD fever MESHD fever HP has generated considerable research interest. We compared the curve of weekly epidemiological records of dengue MESHD incidences during the period of lockdown to the trend of previous years (2015 to 2019) and a simulation at the corresponding period that expected no MRs and found that the dengue MESHD incidence declined significantly with a greater magnitude at phase 1 of lockdown, with a negative gradient of 3.2-fold steeper than the trend observed in previous years, indicating that the control of population movement did reduce dengue MESHD transmission TRANS. However, starting from phase 2 of lockdown, the dengue MESHD incidences demonstrated an elevation and earlier rebound by 4 weeks and grew with an exponential pattern. Together with our data on Aedes mosquitoes, we proposed a stronger diffusive effect of vector dispersal that led to a higher rate of transmission TRANS. From the result of the Aedes survey using human landing caught (HLC), we revealed that Aedes albopictus is the predominant species for both indoor and outdoor environments, with the abundance increasing steadily during the period of lockdown. We only recovered Aedes aegypti from the indoor environment, which is relatively fewer than Ae. albopictus, by contrasting their population growth, which suggested that Ae. albopictus invaded and colonized the habitat of Ae. aegypti during the period of lockdown. These findings would help authorities review the direction and efforts of the vector control strategy. Author summaryCOVID-19 pandemic is taking hold globally and dengue MESHD fever MESHD fever HP transmission TRANS is not on the top of the list of concerns. With a partial lockdown implemented by Malaysia on 18 March, we postulate the movement restrictions (MRs) of people in large-scale would hamper the regular dengue MESHD transmission TRANS and aim to reveal the impact of MRs on both dengue MESHD incidences and Aedes mosquitoes. We showed a significant decline of dengue MESHD incidences at the beginning of lockdown but later rebounded at an earlier time and higher rate compared to the corresponding period of previous years. Our result also reviews how adaptive the Ae. albopictus with the movement of the host, as the human contained in the house, the abundance of the mosquitoes increased significantly during the period of lockdown. We also suggest that Ae. albopictus could be the key substitution vector that contributes significantly to dengue MESHD virus circulation, and therefore, the vector control direction and strategies should be redesigned.

    COVID-19 Evolves in Human Hosts

    Authors: Yanni Liu; Bing Liu; Jiangtao Cui; Zhi Wang; Yulong Shen; Yueshen Xu; Kaicheng Yao; Yuanfang Guan; Xiaoke Ma

    id:202003.0316/v2 Date: 2020-07-21 Source: Preprints.org

    Today, we are all threatened by an unprecedented pandemic: COVID-19. How different is it from other coronaviruses? Will it be attenuated or become more virulent? Which animals may be its original host? In this study, we analyzed 377 publicly available complete genome sequences for the COVID-19 virus, the previously known flu-causing coronaviruses (HCov-229E, HCov-OC43, HCov-NL63 and HCov-HKU1) and the lethal, pathogenic P3/P4 viruses, SARS, MERS, Victoria, Lassa, Yamagata, Ebola, and Dengue MESHD. We found strong similarities between the current circulating COVID-19 and SARS and MERS, as well as COVID-19 in rhinolophines and pangolins. On the contrary, COVID-19 shares little similarity with the flu-causing coronaviruses and the other P3/P4 viruses. Strikingly, we observed divergence of COVID-19 strains isolated from human hosts has steadily increased from December 2019 to March 2020, suggesting COVID-19 is actively evolving in human hosts. From all existing human COVID-19 genome sequences, we calculated the first common model that represents the shared sequences of the human COVID-19 strains, which provides important information for vaccine and antibody SERO development. Geographic and time-course analysis of the evolutionary trees of the human COVID-19 reveals possibly heterogeneous evolutional paths among strains from 21 countries. This finding has important implications to the management of COVID-19 and the development of vaccines.

    Molecular Basis of Kidney Defects in COVID-19 Patients

    Authors: Smartya Pulai; Madhurima Basu; Chinmay Saha; Nitai P. Bhattacharyya; Arpita Ray Chaudhury; Sujoy Ghosh

    id:10.20944/preprints202007.0452.v1 Date: 2020-07-20 Source: Preprints.org

    Background: Kidney damage is considered to be one of the risk factors for severity and mortality among COVID-19 patients. However, molecular nature of such observations remains unknown. Hypothesis: Altered gene expressions due to infection MESHD infection and in chronic HP and in chronic kidney disease MESHD could explain severity in COVID-19 with kidney defects. Methods: We collected gene expression data from publicly available resources Gene Expression Omnibus CKD, Enrichr for deregulated genes in SARS-CoV infected cells in vitro, DisGeNET and others and carried out enrichment analysis using Enrichr. Result: Number of common genes altered in chronic kidney disease HP kidney disease MESHD (CKD) and SARS-CoV infected cells was 2834. Enrichment analysis revealed that biological processes related viral life cycle and growth, cytokines, immunity, interferon, inflammation MESHD, apoptosis, autophagy, oxidative stress and others were significantly enriched with common deregulated genes. Similarly, significantly enriched pathways related to viral and bacterial infections MESHD, immunity and inflammation MESHD, cell cycle, ubiquitin mediated proteolysis, signaling pathways like Relaxin signaling pathway, mTOR signaling pathway, IL-17 signaling pathway, NF-kappa B signaling pathway were enriched with the common deregulated genes. These processes and pathways are known to be related to kidney damage. DisGeNET terms enriched include and related to Dengue MESHD fever MESHD fever HP, chronic Hepatitis MESHD chronic Hepatitis HP, measles MESHD, retroviridae infections MESHD, respiratory syncytial virus Infections MESHD and many others. Kidney dysfunction related terms ischemia MESHD of kidney, renal fibrosis HP fibrosis MESHD and diabetic nephropathy MESHD nephropathy HP. Conclusion: Common deregulated genes in SARS-CoV infected cells and chronic kidney disease HP kidney disease MESHD, as well as their enrichment with molecular processes and pathways relevant for viral pathogenesis and renal dysfunctions, could explain the severity of COVID-19 with kidney disease MESHD. This observation not only provides molecular relation of severity in COVID-19 with renal dysfunctions but might also help in the management and treatment targets for these cases.

    Drug Repurposing Commonly Against Dengue MESHD Virus Capsid and SARS-CoV-2 Nucleocapsid: An in Silico Approach

    Authors: Debica Mukherjee; Rupesh Roy; UPASANA RAY

    doi:10.26434/chemrxiv.12611861.v2 Date: 2020-07-15 Source: ChemRxiv

    In the middle of SARS-CoV-2 pandemic, dengue MESHD virus (DENV) is giving a silent warning as the season approaches nearer. There is no specific antiviral against DENV for use in the clinics. Thus, considering these facts we can potentially face both these viruses together increasing the clinical burden. The search for anti-viral drugs against SARS-CoV-2 is in full swing and repurposing of already ‘in-use’ drugs against other diseases MESHD or COVID-19 has drawn significant attention. Earlier we had reported few FDA approved anti-viral and anti-microbial drugs that could be tested for binding with SARS-CoV-2 nucleocapsid N terminal domain. We explored the possibility of interactions of the drugs screened for SARS-CoV2 with Dengue MESHD virus capsid protein. We report five FDA approved drugs that were seen to be docking onto the SARS-CoV-2 nucleocapsid RNA binding domain, also docking well with DENV capsid protein on the RNA binding site and/or the capsid’s membrane fusion domain. Thus, the present study proposes these five drugs as common antiviral candidates against both SARS-CoV-2 and DENV although the in silico study is subject to further validations.

    Dengue MESHD antibodies SERO can cross-react with SARS-CoV-2 and vice versa- Antibody SERO detection kits can give false-positive results for both viruses in regions where both COVID-19 and Dengue MESHD co-exist

    Authors: Himadri Nath; Abinash Mallick; Subrata Roy; Soumi Sukla; Keya Basu; Abhishek De; Subhajit Biswas

    doi:10.1101/2020.07.03.20145797 Date: 2020-07-06 Source: medRxiv

    Five of thirteen Dengue MESHD antibody SERO- positive serum samples SERO, dated 2017 (pre-dating the COVID-19 outbreak) produced false-positive results in SARS-CoV-2 IgG/IgM rapid strip tests. Our results emphasize the importance of NAT and/or virus antigen tests to complement sero-surveillance for definitive diagnosis of COVID-19/ Dengue MESHD in regions where both viruses are co-endemic.

    Similarities and differences between the ‘cytokine storms’ in acute dengue MESHD and COVID-19

    Authors: Shashika Dayarathna; Chandima Jeewandara; Laksiri Gomes; Gayasha Somathilaka; Deshni Jayathilaka; Vimal Vimalachandran; Ananda Wijewickrama; Eranga Narangoda; Damayanthi Idampitiya; Graham Ogg; Gathsaurie Neelika Malavige

    doi:10.21203/rs.3.rs-39133/v1 Date: 2020-06-30 Source: ResearchSquare

    Severe pneumonia MESHD pneumonia HP and multiorgan dysfunction in COVID-19 and dengue MESHD haemorrhagic fever MESHD fever HP (DHF) are two diseases MESHD that can associate with an altered immune response to the infecting virus. To determine the similarities and differences in the cytokine and chemokine responses in these two infections MESHD, we compared responses in patients with varying severity of COVID-19 and acute dengue MESHD at different time points of illness.During early disease MESHD, patients who proceeded to develop COVID-19 severe pneumonia MESHD pneumonia HP (SP) and DHF had significantly higher levels of IL-6, IL-10 and MIP3α than those who developed mild illness. The lowest levels of IFNγ in early illness were seen in those who succumbed to their illness due to COVID-19. Levels of serum SERO IL-10 (p=0.0001), IL-6 (p=0.002), MIP-3α (p=0.02) and CD40-L levels (p=0.002) significantly increased from 5-9 day of illness to 10-21 day of illness in patients with moderate-to-severe COVID-19, but not in those with mild illness. In contrast, these cytokine/chemokine levels remained unchanged in those with DHF or dengue MESHD fever MESHD fever HP (DF) during febrile and critical phases. Although IL-10 levels were significantly higher in COVID-19 patients with SP, patients with DHF had 25-fold higher levels, whereas IL-6 levels were 11-fold higher in those with COVID-19 SP. IL-10 and other cytokines were evaluated in a larger cohort of patients during early illness (≤ 4 days) who proceeded to develop DF (n=71) or DHF (n=64). Of the cytokines evaluated, IL-10 was significantly higher (p<0.0001) in those who went on to develop DHF compared to DF. Low IFNγ response to the SARS-CoV2 and high levels of immunosuppressive IL-10 in both COVID-19 and dengue MESHD during early illness are indicators of an altered antiviral response potentially contributing to disease MESHD severity.

    EVALUATION OF THE ABBOTT SARS-COV-2 IG-G ASSAY.

    Authors: CS Lau; SP Hoo; YL Liang; TC Aw

    doi:10.1101/2020.06.28.20132498 Date: 2020-06-30 Source: medRxiv

    Introduction: Antibodies SERO to the novel severe acute respiratory syndrome MESHD coronavirus 2 (SARS-CoV-2) can increase as soon as 10-13 days after infection MESHD. We describe our evaluation of the Abbott SARS-CoV-2 IgG assay on the Architect immunoassay SERO analyser. Methods: We assessed the precision, sensitivity SERO, and specificity of the Abbott SARS-CoV-2 IgG assay in samples from polymerase chain reaction (PCR) positive patients and healthy healthcare workers. The manufacturer cut-off index (COI) of 1.4 was adopted to identify positive results. We examined the assay cross-reactivity with other viral antibodies SERO (influenza/ dengue MESHD/ hepatitis C MESHD hepatitis HP/ hepatitis B MESHD hepatitis HP) and rheumatoid factor (RF). The sample throughput of the Abbott assay was also assessed. Results: The Abbott assay showed excellent precision, with a CV of 3.4% for the negative control (COI = 0.06) and 1.6% for a high positive serum sample SERO (COI = 8.6). Residual serum SERO was available from 57 inpatients not initially suspected of having COVID-19, 29 of whom tested positive for SARS-CoV-2 IgG. The Abbott assay has a sensitivity SERO of 90.9-100% when tested in 54 subjects [≥]14 days post PCR positive, and a specificity of 100% (N = 358). There was no cross-reactivity with other viral antibodies SERO (influenza/ dengue MESHD/ hepatitis C MESHD hepatitis HP/ hepatitis B MESHD hepatitis HP) and RF. The Architect Abbott assay has a throughput of 100 samples in 70 minutes. Conclusion: The Abbott SARS-CoV-2 IgG assay shows excellent performance SERO that is well within FDA and CDC guidelines when testing patients [≥]14 days POS with little cross-reactivity from other viral antibodies SERO. There is some evidence that SARS-CoV-2 IgG develops early in the disease MESHD process.

    EVALUATION OF THE ROCHE ELECSYS ANTI-SARS-COV-2 ASSAY.

    Authors: CS Lau; SP Hoo; SF Yew; SK Ong; LT Lum; PY Heng; JG Tan; MS Wong; TC Aw

    doi:10.1101/2020.06.28.20142232 Date: 2020-06-29 Source: medRxiv

    Background: Little is known about the performance SERO of the Roche novel severe acute respiratory syndrome MESHD coronavirus 2 antibody SERO (anti-SARS-CoV-2) assay. We provide an extensive evaluation of this fully automated assay on the Cobas e801/e602 immunoassay SERO analysers. Methods: We assessed the linearity, precision, and throughput of the Roche anti-SARS-CoV-2 assay. Sensitivity SERO was calculated from 349 SARS-CoV-2 polymerase chain reaction (PCR) positive samples; specificity was determined from 714 coronavirus disease MESHD 2019 (COVID-19)-naive samples. We examined cross-reactivity against other antibody SERO positive samples ( syphilis MESHD, RF, ANA, ds-DNA, influenza, dengue MESHD, HBV, HCV) and the anti-SARS-CoV-2 kinetics. Results: The assay cut-off index (COI) was linear up to 90.7. The inter-assay precision was 2.9% for a negative control (COI=0.1) and 5.1% for a positive control (COI=3.0). Assay time is 18min and results are available 1 minute later; throughput for 300 samples was 76 minutes. No cross-reactivity was observed with other antibody SERO positive samples; specificity was 100%. The assay has a sensitivity SERO of 97.1% 14 days after PCR positivity (POS) and 100% at [≥]21 days POS; 48.2% of cases had anti-SARS-CoV-2 within 6 days POS. In 11 subjects in whom serum SERO was available prior to a positive antibody SERO signal (COI [≥]1.0) the interval between the last negative and first positive COI (time to sero-conversion) on average is 3 days (range 1-6 days) and 4 more days (range 1-7) for the anti-SARS-CoV-2 to plateau. Conclusion: The Roche anti-SARS-CoV-2 assay shows excellent performance SERO with minimal cross-reactivity from other viral and confounding antibodies SERO. Antibody SERO development and sero-conversion appears quite early.

    Transcriptomic Similarities and Differences in Host Response between SARS-CoV-2 and Other Viral Infections MESHD

    Authors: Simone A Thair; Yudong D He; Yehudit Hasin-Brumshtein; Suraj Sakaram; Rushika Pandya; Jiaying Toh; David Rawling; Melissa Remmel; Sabrina Coyle; George N Dalekos; Ioannis Koutsodimitropoulos; Glykeria Vlachogianni; Eleni Gkeka; Eleni Karakike; Georgia Damoraki; Nikolaos Antonakos; Purvesh Khatri; Evangelos J Giamarellos-Bourboulis; Timothy E Sweeney

    doi:10.1101/2020.06.18.20131326 Date: 2020-06-21 Source: medRxiv

    COVID-19 is a pandemic that shares certain clinical characteristics with other acute viral infections MESHD. Here, we studied the whole- blood SERO transcriptomic host response to SARS-CoV-2 and compared it with other viral infections MESHD to understand similarities and differences in host response. Using RNAseq we profiled peripheral blood SERO from 24 healthy controls and 62 prospectively enrolled patients with community-acquired lower respiratory tract infection MESHD respiratory tract infection HP by SARS-Cov-2 within the first 24 hours of hospital admission. We also compiled and curated 23 independent studies that profiled 1,855 blood SERO samples from patients with one of six viruses (influenza, RSV, HRV, ebola, Dengue MESHD, and SARS-CoV-1). We show gene expression changes in peripheral blood SERO in patients with COVID-19 versus healthy controls are highly correlated with changes in response to other viral infections MESHD (r=0.74, p<0.001). However, two genes, ACO1 and ATL3, show significantly opposite changes between conditions. Pathway analysis in patients with COVID-19 or other viral infections MESHD versus healthy controls identified similar pathways including neutrophil activation, innate immune response, immune response to viral infection MESHD, and cytokine production for over-expressed genes. Conversely, for under-expressed genes, pathways indicated repression of lymphocyte differentiation and T cell activation. When comparing transcriptome profiles of patients with COVID-19 directly with those with other viral infections MESHD, we found 114 and 302 genes were over- or under-expressed, respectively, during COVID-19. Pathways analysis did not identify any significant pathways in these genes, suggesting novel responses to further study. Statistical deconvolution using immunoStates found that M1 macrophages, plasmacytoid dendritic cells, CD14+ monocytes, CD4+ T cells, and total B cells showed change consistently in the same direction across all viral infections MESHD including COVID-19. Those that increased in COVID-19 but decreased in non-COVID-19 viral infections MESHD were CD56bright NK cells, M2 macrophages, and total NK cells. The concordant and discordant responses mapped out here provide a window to explore the pathophysiology of COVID-19 versus other viral infections MESHD and show clear differences in signaling pathways and cellularity as part of the host response to SARS-CoV-2.

    Differentiating coronavirus disease MESHD 2019 (COVID-19) from influenza and dengue MESHD

    Authors: Tun-Linn Thein; Li Wei Ang; Barnaby Edward Young; Mark IC Chen; Yee-Sin Leo; David Chien Lye

    doi:10.21203/rs.3.rs-36343/v1 Date: 2020-06-18 Source: ResearchSquare

    Background: The novel coronavirus disease MESHD 2019 (COVID-19) presents with non-specific clinical features. This may result in misdiagnosis or delayed diagnosis, and lead to further transmission TRANS in the community. We aimed to derive early predictors to differentiate COVID-19 from influenza and dengue MESHD.Methods: The study comprised 126 patients with COVID-19, 171 with influenza and 180 with dengue MESHD, who presented within 5 days of symptom onset TRANS. All cases were confirmed TRANS by reverse transcriptase polymerase chain reaction tests. We used logistic regression models to identify clinical characteristics and laboratory markers in classifying COVID-19 versus influenza, and COVID-19 versus dengue MESHD. The performance SERO of the models were evaluated using receiver operating characteristic curves (ROC).Results: Shortness of breath was the strongest predictor in the models for differentiating between COVID-19 and influenza, followed by diarrhoea. Higher lymphocyte count was predictive of COVID-19 versus influenza and versus dengue MESHD. In the model for differentiating between COVID-19 and dengue MESHD, patients with cough MESHD cough HP and higher platelet count were at increased odds of COVID-19, while headache MESHD headache HP, joint pain MESHD pain HP, skin rash HP and vomiting MESHD vomiting/nausea HP/ nausea MESHD were indicative of dengue MESHD. The area under the ROC was 0.92 for flu model and 0.99 for dengue MESHD model.Conclusion: Models based on clinical features and simple laboratory markers for differentiating COVID-19 from influenza and dengue MESHD, which possess good predictive performance SERO, can serve as a useful tool for primary care physicians to determine if further investigations or referrals would be required.

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MeSH Disease
Human Phenotype
Transmission
Seroprevalence


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