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Potential Peptide Targets for a COVID-19 Vaccine

Since the emergence of the COVID-19 outbreak, there is a great need to understand the molecular biology and immunogenicity of the SARS-CoV-2 virus to enable the development of potent vaccines. To help speed up vaccine development, Ahmed et al. identified a set of B cell and T cell epitopes. Epitopes identified are derived from structural proteins of SARS-CoV spike (S) and nucleocapsid (N) proteins and are identical to SARS-CoV-2 proteins.

For the T cell epitopes, the research group performed a population coverage analysis of the associated major histocompatibility complex (MHC) alleles. As a result the proposed set of epitopes are estimated to provide a broad coverage globally, including China. The assumption is that this screened set of epitopes helps to guide experimental efforts towards the development of vaccines against SARS-CoV-2. During the screening, a total of 120 whole-genome sequences of SARS-CoV-2 were downloaded on 21 February 2020 from the GISAID database and used for the analysis.

Coronaviruses are positive-sense single-stranded RNA viruses belonging to the family Coronaviridae.

The typical organization of the genome is as follows:

5'-leader-UTR-replicase-S(Spike)-E(Envelope)-M(Membrane)-N(Nucleocapsid)-3'-UTR-poly(A) tail.

The 3'-end of the virus genome contains accessory genes scattered between structural genes. Accessory proteins appear not to be needed for replication in tissue culture but to be important in viral pathogenesis. The synthesis of polypeptide 1ab (pp1ab) involves programmed ribosomal frameshifting during translation of open reading frame 1a (orf1a). Frame shifting results in a new reading frame that produces a trans-frame protein product. In coronaviruses, a fixed portion of the ribosomes translating orf1a change reading frame at a specific location now decoding information contained in orf1b. See structure of coronavius nCoV-2019-2020, now  SARS CoV-2.

Table 1:  SARS-CoV-derived T cell epitopes that are identical in SARS-CoV-2 for the N protein.

Protein

IEDB ID

Epitope

MHC Allele

MHC Allele Class

N

125100

 ILLNKHID

 HLA-A*02.01

I

N

1295

AFFGMSRIGMEVTPSGITW

N.A. 

N.A.

N

190494

MEVTPSGTWL

 HLA-B*40.01

I

N

21347

GMSRIGMEV

HLA-A*02.01

I

N

27182

ILLNKHIDA

HLA-A*02.01

I

N

2802

ALNTPKDHI

HLA-A*02.01

I

N

28371

IRQGTDYKHWPQIAQFA

N.A.

N.A.

N

31166

KHWPQIAQFAPSASAFF

N.A

N.A.

N

34851

LALLLLDRL

HLA-A*02.01

I

N

37473

LLLDRLNQL

HLA-A*02.01

II

N

37611

LLNKHIDAYKTFPPTEPK

N.A.

N.A.

N

38881

LQLPQGTTL

HLA-A*02.01

I

N

3957

AQFAPSASAFFGMSR

N.A.

I

N

3958

AQFAPSASAFFGMSRIGM

N.A.

N.A.

N

55683

RRPQGLPNNTASWFT

N.A.

I

N

74517

YKTFPPTEPKKDKKKK

N.A.

N.A.

 

Table 2:  SARS-CoV-derived T cell epitopes that are identical in SARS-CoV-2 for the S protein.

Protein

IEDB ID

Epitope

MHC Allele

MHC Allele Class

S

100048

GAALQIPFAMQMAYRF  

 HLA-DRA*01.01

HLA-DRB1*07.01

II

S

100300

MAYRFNGIGVTQNVLY

HLA-DRB1*04.01

II

S

100428

 QLIRAAEIRASANLAATK

HLA-DRB1*04.01

II

S

16156

FIAGLIAIV

 HLA-A*02.01

I

S

2801

ALNTLVKQL

HLA-A*02.01

I

S

 36724

 LITGRLQSL

HLA-A2

I

S

44814

NLNESLIDL

HLA-A*02.01

I

S

50311

QALNTLVKQLSSNFGAI

HLA-DRB1*04.01

II

S

54680

RLNEVAKNL

HLA-A*02.01

I

S

69657

VLNDILSRL

HLA-A*02.01

I

S

 

VVFLHVTYV

HLA-A*02.01

I


Reference

Ahmed SF, Quadeer AA, McKay MR.;  Preliminary Identification of Potential Vaccine Targets for the COVID-19 Coronavirus (SARS-CoV-2) Based on SARS-CoV Immunological Studies. Viruses. 2020 Feb 25;12(3). [PubMed]

Immune Epitope Database and Analysis Resource. A database that catalogs experimental data on antibody and T cell epitopes from humans, non-human primates, as well as other animal species in the context of infectious disease, allergy, autoimmunity and transplantation. [Link]

 Bio-Synthesis Inc. is pleased to offer a large variety of oligonucleotides and peptides for a number of research applications, including COVID 19 testing, analysis and vaccine development!

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