Dataset Information

The Omic Insights on Unfolding Saga of COVID-19.

ABSTRACT: The year 2019 has seen an emergence of the novel coronavirus named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing coronavirus disease of 2019 (COVID-19). Since the onset of the pandemic, biological and interdisciplinary research is being carried out across the world at a rapid pace to beat the pandemic. There is an increased need to comprehensively understand various aspects of the virus from detection to treatment options including drugs and vaccines for effective global management of the disease. In this review, we summarize the salient findings pertaining to SARS-CoV-2 biology, including symptoms, hosts, epidemiology, SARS-CoV-2 genome, and its emerging variants, viral diagnostics, host-pathogen interactions, alternative antiviral strategies and application of machine learning heuristics and artificial intelligence for effective management of COVID-19 and future pandemics.

SUBMITTER: Kaur A

PROVIDER: S-EPMC8564481 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature

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The Omic Insights on Unfolding Saga of COVID-19.

Kaur Arvinpreet A Chopra Mehak M Bhushan Mahak M Gupta Sonal S Kumari P Hima H Sivagurunathan Narmadhaa N Shukla Nidhi N Rajagopal Shalini S Bhalothia Purva P Sharma Purnima P Naravula Jalaja J Suravajhala Renuka R Gupta Ayam A Abbasi Bilal Ahmed BA Goswami Prittam P Singh Harpreet H Narang Rahul R Polavarapu Rathnagiri R Medicherla Krishna Mohan KM Valadi Jayaraman J Kumar S Anil A Chaubey Gyaneshwer G Singh Keshav K KK Bandapalli Obul Reddy OR Kavi Kishor Polavarapu Bilhan PB Suravajhala Prashanth P

Frontiers in immunology 20211020

The year 2019 has seen an emergence of the novel coronavirus named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing coronavirus disease of 2019 (COVID-19). Since the onset of the pandemic, biological and interdisciplinary research is being carried out across the world at a rapid pace to beat the pandemic. There is an increased need to comprehensively understand various aspects of the virus from detection to treatment options including drugs and vaccines for effective global m ...[more]

PMID: 34745097

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Project description:Using RNA-seq and high-resolution mass spectrometry we performed a comprehensive systems analysis on 128 plasma and leukocyte samples from hospitalized patients with or without COVID-19 (n=102 and 26 respectively) and with differing degrees of disease severity. We generated abundance measurements for over 17,000 transcripts, proteins, metabolites, and lipids and compiled them with clinical data into a curated relational database. This resource offers the unique opportunity to perform systems analysis and cross-ome correlations to both molecules and patient outcomes. In total 219 molecular features were mapped with high significance to COVID-19 status and severity, including those involved in processes such as complement system activation, dysregulated lipid transport, and B cell activation. In one example, we detected a trio of covarying molecules – citrate, plasmenyl-phosphatidylcholines, and gelsolin (GSN) – that offer both pathophysiological insight and potential novel therapeutic targets. Further, our data revealed in some cases, and supported in others, that several biological processes were dysregulated in COVID-19 patients including vessel damage, platelet activation and degranulation, blood coagulation, and acute phase response. For example, we observed that the coagulation-related protein, cellular fibronectin (cFN), was highly increased within COVID-19 patients and provide new evidence that the upregulated proteoform stems from endothelial cells, consistent with endothelial injury as a major activator of the coagulation cascade. The abundance of prothrombin, which is cleaved to form thrombin during clotting, was significantly reduced and correlated with severity and might help to explain the hyper coagulative environment of SARS-CoV-2 infection. From transcriptomic analysis of leukocytes, we concluded that COVID-19 patients with acute respiratory distress syndrome (ARDS) demonstrated a phenotype that overlapped with, but was distinct from, that found in patients with non-COVID-19-ARDS. To aid in the global efforts toward elucidation of disease pathophysiology and therapeutic development, we created a web-based tool with interactive visualizations allowing for easy navigation of this systems-level compendium of biomolecule abundance in relation to COVID-19 status and severity. Finally, we leveraged these multi-omic data to predict COVID-19 patient outcomes with machine learning, which highlighted the predictive power of these expansive molecular measurements beyond the standardized clinical estimate of 10-year survival Charlson score.

Project description:BackgroundChina is at the forefront of global efforts to develop COVID-19 vaccines and has five fast-tracked candidates at the final-stage, large-scale human clinical trials testing phase. Vaccine-promoting policymaking for public engagement is a prerequisite for social mobilization. However, making an informed and judicious choice is a dilemma for the Chinese government in the vaccine promotion context.ObjectiveIn this study, public opinions in China were analyzed via dialogues on Chinese social media, based on which Chinese netizens' views on COVID-19 vaccines and vaccination were investigated. We also aimed to develop strategies for promoting vaccination programs in China based on an in-depth understanding of the challenges in risk communication and social mobilization.MethodsWe proposed a novel behavioral dynamics model, SRS/I (susceptible-reading-susceptible/immune), to analyze opinion transmission paradigms on Chinese social media. Coupled with a meta-analysis and natural language processing techniques, the emotion polarity of individual opinions was examined in their given context.ResultsWe collected more than 1.75 million Weibo messages about COVID-19 vaccines from January to October 2020. According to the public opinion reproduction ratio (R0), the dynamic propagation of those messages can be classified into three periods: the ferment period (R01=1.1360), the revolution period (R02=2.8278), and the transmission period (R03=3.0729). Topics on COVID-19 vaccine acceptance in China include price and side effects. From September to October, Weibo users claimed that the vaccine was overpriced, making up 18.3% (n=899) of messages; 38.1% (n=81,909) of relevant topics on Weibo received likes. On the contrary, the number of messages that considered the vaccine to be reasonably priced was twice as high but received fewer likes, accounting for 25.0% (n=53,693). In addition, we obtained 441 (47.7%) positive and 295 (31.9%) negative Weibo messages about side effects. Interestingly, inactivated vaccines instigated more heated discussions than any other vaccine type. The discussions, forwards, comments, and likes associated with topics related to inactivated vaccines accounted for 53% (n=588), 42% (n=3072), 56% (n=3671), and 49% (n=17,940), respectively, of the total activity associated with the five types of vaccines in China.ConclusionsMost Chinese netizens believe that the vaccine is less expensive than previously thought, while some claim they cannot afford it for their entire family. The findings demonstrate that Chinese individuals are inclined to be positive about side effects over time and are proud of China's involvement with vaccine development. Nevertheless, they have a collective misunderstanding about inactivated vaccines, insisting that inactivated vaccines are safer than other vaccines. Reflecting on netizens' collective responses, the unfolding determinants of COVID-19 vaccine acceptance provide illuminating benchmarks for vaccine-promoting policies.

Dataset Information

The Omic Insights on Unfolding Saga of COVID-19.

Publications

The Omic Insights on Unfolding Saga of COVID-19.

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