HuCoPIA: An Atlas of Human vs. SARS-CoV-2 Interactome and the Comparative Analysis with Other Coronaviridae Family Viruses

Naveen Duhan; Rakesh Kaundal

doi:10.3390/v15020492

HuCoPIA: An Atlas of Human vs. SARS-CoV-2 Interactome and the Comparative Analysis with Other Coronaviridae Family Viruses

Viruses. 2023 Feb 10;15(2):492. doi: 10.3390/v15020492.

Authors

Naveen Duhan^{1

2}, Rakesh Kaundal^{1

2

3}

Affiliations

¹ Department of Plants, Soils, and Climate/Center for Integrated BioSystems, College of Agriculture and Applied Sciences, Utah State University, Logan, UT 84322, USA.
² Bioinformatics Facility, Center for Integrated BioSystems, College of Agriculture and Applied Sciences, Utah State University, Logan, UT 84322, USA.
³ Department of Computer Science, College of Science, Utah State University, Logan, UT 84322, USA.

Abstract

SARS-CoV-2, a novel betacoronavirus strain, has caused a pandemic that has claimed the lives of nearly 6.7M people worldwide. Vaccines and medicines are being developed around the world to reduce the disease spread, fatality rates, and control the new variants. Understanding the protein-protein interaction mechanism of SARS-CoV-2 in humans, and their comparison with the previous SARS-CoV and MERS strains, is crucial for these efforts. These interactions might be used to assess vaccination effectiveness, diagnose exposure, and produce effective biotherapeutics. Here, we present the HuCoPIA database, which contains approximately 100,000 protein-protein interactions between humans and three strains (SARS-CoV-2, SARS-CoV, and MERS) of betacoronavirus. The interactions in the database are divided into common interactions between all three strains and those unique to each strain. It also contains relevant functional annotation information of human proteins. The HuCoPIA database contains SARS-CoV-2 (41,173), SARS-CoV (31,997), and MERS (26,862) interactions, with functional annotation of human proteins like subcellular localization, tissue-expression, KEGG pathways, and Gene ontology information. We believe HuCoPIA will serve as an invaluable resource to diverse experimental biologists, and will help to advance the research in better understanding the mechanism of betacoronaviruses.

Keywords: MERS; SARS-CoV; SARS-CoV-2; human; protein-protein interactions.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Ascomycota*
COVID-19*
Coronaviridae*
Databases, Factual
Humans
SARS-CoV-2 / genetics

Grants and funding

The authors acknowledge the support to this study from the faculty start-up funds to RK from the Center for Integrated BioSystems (CIB)/Department of Plants, Soils, and Climate, USU. This research was also partially supported by Utah Agricultural Experiment Station (UAES) and approved as journal paper number 9659. The funding body did not play any role in the design of this study; the collection, analysis, or interpretation of data; or in the writing of this manuscript.