In silico Molecular Characterization and Phylogenetic Analyses of SARS-CoV-2 in Mediterranean Basin

Background: The novel human coronavirus disease COVID-19 has become the fifth reported pandemic since the global spread of 1918 flu and counted as the first documented coronavirus worldwide spread in the history. The COVID-19 was initially considered as a respiratory disease, but SARS-CoV-2 can lead to cause other serious complications.

Purpose: This study aimed to conduct phylogenetic analyses of the whole genome of SARS-CoV-2 strains isolated from infected humans in Mediterranean basin countries, Orf1ab gene, S gene, M gene, N gene and Orf3a gene sequences. In addition, the products of Orf1ab, S, M and N genes were also phylogenetically analyzed. Changes that occurred on the S-gene product of these SARS-CoV-2 strains were also detected.

Materials and Methods: The whole genome of SARS-CoV-2 isolates, the genes and the gene products (Accessed July 20, 2020) were recovered in Mediterranean basin countries were retrieved from GenBank Database previously available in National Center for Biotechnology Information (NCBI) using BLAST (Basic Local Alignment Search Tool) system. Analyses of these sequences were carried out using computer program MEGA6 software.

Results: The Phylogenetic analyses showed that Bat coronavirus RaTG13 isolate is more closely related to SARS-CoV-2 isolates than Pangolin coronaviruse isolates. The S gene product of this virus mediates entry into the host cell and has S1/S2 cleavage site containing multibasic amino acid sequence (PRRAR) which is not detected in other closely related coronaviruses. Many coronavirus strains that deposited in GenBank, showed that they have PRR sequence in Orf1ab gene product. Conclusion: we conclude that part of multibasic S1/S2 motif acquired by recombination or insertion. Theoretically, any coronavirus strain acquired this sequence becomes highly pathogenic to humans. The dominant mutation (79.3%) at S gene product level was 614D→G. The impact of mutations detected in S gene product on virus transmission, diagnosis, pathogenicity and strategies of antiviral therapy, should be rapidly assessed in further studies.