Version 1
: Received: 3 July 2020 / Approved: 5 July 2020 / Online: 5 July 2020 (06:54:01 CEST)
Version 2
: Received: 29 October 2020 / Approved: 30 October 2020 / Online: 30 October 2020 (10:10:58 CET)
Martina Bianchi, Alessandra Borsetti, Massimo Ciccozzi, Stefano Pascarella,
SARS-Cov-2 ORF3a: Mutability and function,
International Journal of Biological Macromolecules,
Volume 170,
2021,
Pages 820-826,
ISSN 0141-8130,
https://doi.org/10.1016/j.ijbiomac.2020.12.142.
Martina Bianchi, Alessandra Borsetti, Massimo Ciccozzi, Stefano Pascarella,
SARS-Cov-2 ORF3a: Mutability and function,
International Journal of Biological Macromolecules,
Volume 170,
2021,
Pages 820-826,
ISSN 0141-8130,
https://doi.org/10.1016/j.ijbiomac.2020.12.142.
Martina Bianchi, Alessandra Borsetti, Massimo Ciccozzi, Stefano Pascarella,
SARS-Cov-2 ORF3a: Mutability and function,
International Journal of Biological Macromolecules,
Volume 170,
2021,
Pages 820-826,
ISSN 0141-8130,
https://doi.org/10.1016/j.ijbiomac.2020.12.142.
Martina Bianchi, Alessandra Borsetti, Massimo Ciccozzi, Stefano Pascarella,
SARS-Cov-2 ORF3a: Mutability and function,
International Journal of Biological Macromolecules,
Volume 170,
2021,
Pages 820-826,
ISSN 0141-8130,
https://doi.org/10.1016/j.ijbiomac.2020.12.142.
Abstract
In this study, the analysis of the changes of SARS-CoV-2 Orf3a protein during pandemic is reported. Orf3a, a conserved protein in the Coronaviruses, is involved in virus replication and release. A software workflow able to carry out a quick, systematic and repeatable screening of the SARS-CoV-2 genome isolates to detect protein mutations, was utilized to scan 70,752 high-quality SARS-CoV-2 genomes available in GISAID databank at the end of August 2020. 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.
Biology and Life Sciences, Biochemistry and Molecular Biology
Copyright:
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Received:
30 October 2020
Commenter:
Stefano Pascarella
Commenter's Conflict of Interests:
Author
Comment:
This manuscript is a "specialization" of the overview reported in the parent preprint. In fact, it focusses onto the protein ORF3a while applying the same methodology. Authorship has been changed to reflect the new contributions to the paper. The preprint has been submitted to a journal.
Commenter: Stefano Pascarella
Commenter's Conflict of Interests: Author