Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has a single-stranded RNA genome that encodes 14 open reading frames (ORFs), eight of which encode accessory proteins that allow the virus to infect the host and promote virulence. The genome expresses around 29 structural and nonstructural protein products. The accessory proteins of SARS-CoV-2 are not essential for virus replication but do affect viral release, stability, and pathogenesis and finally contribute to virulence. This paper has attempted the structure prediction and functional analysis of two such accessory proteins, 9b and ORF14, in the absence of experimental structures. Sequence analysis, structure prediction, functional characterization, and evolutionary analysis based on the UniProtKB reviewed the amino acid sequences of SARS-CoV-2 9b (P0DTD2) and ORF14 (P0DTD3) proteins. Modeling has been presented with the introduction of hybrid comparative and ab initio modeling. QMEANDisCo 4.0.0 and ProQ3 for global and local (per residue) quality estimates verified the structures as high quality, which may be attributed to structure-based drug design targets. Tunnel analysis revealed the presence of 1-2 highly active tunneling sites, perhaps which will able to provide certain inputs for advanced structure-based drug design or to formulate potential vaccines in the absence of a complete experimental structure. The evolutionary analysis of both proteins of human SARS-CoV-2 indicates close relatedness to the bat coronavirus. The whole-genome phylogeny indicates that only the new bat coronavirus followed by pangolin coronaviruses has a close evolutionary relationship with the novel SARS-CoV-2.
Highlights
Severe acute respiratory syndrome coronavirus 2 (SARSCoV-2) is a positive-sense, single-stranded RNA virus with a genome size of 29,903 nucleotides in length
The findings indicate that only the new bat coronavirus followed by pangolin coronaviruses have close evolutionary related with the novel SARS-CoV-2
The present study reported theoretical modeling, sequence-based, and structure-based functional characterization of two accessory protein-9b and ORF14 of SARS-CoV-2 p
Summary
Severe acute respiratory syndrome coronavirus 2 (SARSCoV-2) is a positive-sense, single-stranded RNA virus with a genome size of 29,903 nucleotides in length. The virus is the causative agent of coronavirus disease 2019 19) and is contagious through human-to-human transmission. Identified human CoVs that cause human disease include alphaCoVs hCoV-NL63 and hCoV-229E and the betaCoVs HCoV-OC43, HKU1, severe acute respiratory syndrome CoV (SARS-CoV), and Middle East respiratory syndrome CoV (MERS-CoV) [3]. Among the seven strains coronaviruses (CoVs) discovered so far, three strains proved to be highly pathogenic (SARS-CoV, MERS-CoV, and 2019-nCoV), which caused endemic to severe CoV disease [4, 5]. The SARS-CoV and MERS-CoV infections can result in life-threatening
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