SARS-Cov-2 ORF3a: Mutability and function

Abstract

In this study, analysis of changes of SARS-CoV-2 ORF3a protein during pandemic is reported. ORF3a, a conserved coronavirus protein, is involved in virus replication and release. A set of 70,752 high-quality SARS-CoV-2 genomes available in GISAID databank at the end of August 2020 have been scanned. All ORF3a mutations in the virus genomes were grouped according to the collection date interval and over the entire data set. The considered intervals were: start of collection-February, March, April, May, June, July and August 2020. The top five most frequent variants were examined within each collection interval. Overall, seventeen variants have been isolated. Ten of the seventeen mutant sites occur within the transmembrane (TM) domain of ORF3a and are in contact with the central pore or side tunnels. The other variant sites are in different places of the ORF3a structure. Within the entire sample, the five most frequent mutations are V13L, Q57H, Q57H + A99V, G196V and G252V. The same analysis identified 28 sites identically conserved in all the genome isolates. These sites are possibly involved in stabilization of monomer, dimer, tetramerization and interaction with other cellular components. The results here reported can be helpful to understand virus biology and to design new therapeutic strategies.

Keywords: Conserved sites; Mutated sites; ORF3a; Pore; Q57H; SARS-CoV-2.

Fig. 1

(A) ORF3a dimer represented as ribbon model. The two subunits are colored in orange and deep teal. Variant sites are labelled and the corresponding side chains reported as grey sticks. Transparent internal spheres indicate the transmembrane channel (yellow) and the tunnels connecting to the extracellular environment (green). (B) is rotated approximately 90° along the y axis with respect to (A). (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)

Fig. 2

ORF3a dimer represented as ribbon model. The two subunits are colored in orange and deep teal. Conserved sites are labelled and the corresponding side chains are reported as violet sticks. Transparent internal spheres indicate the transmembrane channel (yellow) and the tunnels connecting to the extracellular environment (green). (A) Trans-membrane domain; (B) extracellular domain. The protein is oriented as in Fig. 1A. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)

Fig. 3

Logo representation of the conservation of SARS-CoV-2 identical sites among other ORF3a from different Coronaviruses. X-axis numbering refers to the sequence positions in the ORF3a reference protein. Pile height is proportional to the information content of the site while letter height indicates frequency of the residue in the corresponding alignment column. Color indicates physical-chemical properties. The Logo was built using the alignment reported in Supplementary Fig. 2 using the site WebLogo. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)