An in silico epitope-based peptide vaccine design against the 2019-nCoV,Egyptian Journal of Medical Human Genetics

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An in silico epitope-based peptide vaccine design against the 2019-nCoV
Egyptian Journal of Medical Human Genetics Pub Date : 2020-07-27 , DOI: 10.1186/s43042-020-00071-7
Olanrewaju Ayodeji Durojaye , Talifhani Mushiana , Samuel Cosmas , Glory Omini Ibiang , Mercy Omini Ibiang

Dear Editor, The 2019-nCoV is a novel SARS coronavirus which was first isolated from three individuals having pneumonia with connection to the Wuhan epidemic of the severe respiratory illness [1]. The 2019-nCoV shares a close relationship with the original SARS-CoV, and it is believed to exhibit a zoonotic property. Genomic analysis of the virus has shown that it clusters genetically with the Beta coronavirus genus, alongside two other strains derived from bat. It shares a 96% identity with other bat coronavirus samples (Bat Cov RaTG 13) at the whole genome level. Chinese researchers in February 2020 discovered the amino acid difference in specific parts of the human and pangolin virus genome sequences, however, whole-genome comparison between the pangolin coronavirus, and the 2019-nCoV found a maximum of 92% identical genetic materials, which has so far not been sufficient enough to confirm pangolins to be the viral intermediate host [2]. Vaccines have been produced to target several animal coronavirus diseases, which includes the canine coronavirus, the infectious bronchitis virus of birds, and feline coronavirus. Previous efforts aimed at the development of antiviral vaccines for the Coronaviridae family that majorly affects humans that have been targeted at the Middle East respiratory syndrome and severe acute respiratory syndrome coronavirus. The MERS and SARS vaccines have been tried in animal models and up till February 2020, there has been no cure or protective vaccine that has exhibited safety and efficacy in humans [3]. The historical immunotherapy consensus has been about the targeting of easily accessible antibody-binding extracellular antigens only. The reason for this is because the antibodies which are of higher molecular weight stop the antigens from gaining access to their intracellular targets through the crossing of the cell membrane. In consistence with this thought train, approved therapeutic antibody targets are mostly extracellular antigens [4]. Three broad approaches more recently have been used in intracellular antigen targeting. It is not impossible for normally intracellular antigens that become externalized to be targeted by antibodies or their derivatives in a disease state. It is also not impossible to engineer cell-penetrating antibodies or fragments of antibodies and even antibodies whose expression is intracellular, with the aid of gene therapy. Finally, cell surface MHC-I-binding antibodies can be generated (major histocompatibility complex class I) [5]. With reference to previous virus related in-silico vaccine design studies [6, 7], we designed a new potential vaccine candidate using the main proteinase of the 2019-nCoV as the target protein. The viral main proteinase coding sequence was mapped out from its full genome which has been made accessible for the public in the database of Genbank (https://www.ncbi. nlm.nih.gov/nuccore/MN908947.3?report=fasta) with the accession number “MN908947.3” (Additional file 1). The sequence which ranges from the 10055 to 10972 nucleotides of the viral genome was translated, and the amino acid sequence was used in the 3D structural homology protein model prediction. A total of 120 templates were found, and an initial HHblits profile was designed by making use of the outlined procedure in Remmert et al. [8]. In the vaccine development process, we engaged the BCEPred which

更新日期：2020-07-27

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