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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