Data science in unveiling COVID-19 pathogenesis and diagnosis: evolutionary origin to drug repurposing

Abstract

Motivation The outbreak of novel severe acute respiratory syndrome coronavirus (SARS-CoV-2, also known as COVID-19) in Wuhan has attracted worldwide attention. SARS-CoV-2 causes severe inflammation, which can be fatal. Consequently, there has been a massive and rapid growth in research aimed at throwing light on the mechanisms of infection and the progression of the disease. With regard to this data science is playing a pivotal role in in silico analysis to gain insights into SARS-CoV-2 and the outbreak of COVID-19 in order to forecast, diagnose and come up with a drug to tackle the virus. The availability of large multiomics, radiological, bio-molecular and medical datasets requires the development of novel exploratory and predictive models, or the customisation of existing ones in order to fit the current problem. The high number of approaches generates the need for surveys to guide data scientists and medical practitioners in selecting the right tools to manage their clinical data. Results Focusing on data science methodologies, we conduct a detailed study on the state-of-the-art of works tackling the current pandemic scenario. We consider various current COVID-19 data analytic domains such as phylogenetic analysis, SARS-CoV-2 genome identification, protein structure prediction, host–viral protein interactomics, clinical imaging, epidemiological research and drug discovery. We highlight data types and instances, their generation pipelines and the data science models currently in use. The current study should give a detailed sketch of the road map towards handling COVID-19 like situations by leveraging data science experts in choosing the right tools. We also summarise our review focusing on prime challenges and possible future research directions. Contact hguzzi@unicz.it, sroy01@cus.ac.in

Analyzing host-viral interactome of SARS-CoV-2 for identifying vulnerable host proteins during COVID-19 pathogenesis

“…Therefore, accurate molecular diagnosis of COVID-19 disease is essential by collecting the proper respiratory tract specimen ( Whetton et al, 2020 ; Ortuso et al, 2021 ). In this context, the integrated analysis ( Antonelli et al, 2019 ) of various data-sets, including clinical and imaging data, may explain, and hopefully predict, the longitudinal effects of SARS-CoV-2 infection ( Tang et al, 2020 ; Kumar Das et al, 2021 ). In particular, many independent projects throughout the world have focused on genomics and proteomics level ( Kumar Das et al, 2021 ), and then they integrated these data with clinical ones.…”

“…In this context, the integrated analysis ( Antonelli et al, 2019 ) of various data-sets, including clinical and imaging data, may explain, and hopefully predict, the longitudinal effects of SARS-CoV-2 infection ( Tang et al, 2020 ; Kumar Das et al, 2021 ). In particular, many independent projects throughout the world have focused on genomics and proteomics level ( Kumar Das et al, 2021 ), and then they integrated these data with clinical ones. These works have produced data about the infection's effect at a molecular scale, evidencing genes and proteins' role, such as the interactions among viral and human proteins.…”

BioNet: a large-scale and heterogeneous biological network model for interaction prediction with graph convolution

“…Kumar et al . [ 48 ] comprehensively analyzed the works and data tackling the COVID-19 pandemic and integrated heterogeneous COVID-19 data sources by various data processing methods, provided biomedical research and drug/vaccine designers with available systematic datasets, and computational biology and bioinformatics approaches.…”

Mutation-Induced Long-Range Allosteric Interactions in the Spike Protein Determine the Infectivity of SARS-CoV-2 Emerging Variants

“…However, such efforts are being seriously hindered by the rapid emergence of multiple SARS-CoV-2 variants—the causative agent of COVID-19. 1 − 3 There is now growing evidence that mutations that changed the antigenic phenotype of SARS-CoV-2 are capable of evading immune responses and attenuating the neutralizing effects of antibodies. 4 − 6 Recent studies further show that new variants are potentially evolving due to selective pressure exerted by convalescent plasma and mAb treatments.…”