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Article

SARS-CoV-2 Consensus-Sequence and Matching Overlapping Peptides Design for COVID19 Immune Studies and Vaccine Development

1
IrsiCaixa AIDS Research Institute-HIVACAT, Hospital Universitari Germans Trias i Pujol, 08916 Badalona, Spain
2
Faculty of Sciences and Technology, Universitat de Vic-Central de Catalunya (UVic-UCC), 08500 Vic, Spain
3
Faculty of Medicine, Universitat de Vic-Central de Catalunya (UVic-UCC), 08500 Vic, Spain
4
Germans Trias i Pujol Research Institute (IGTP), 08196 Barcelona, Spain
5
Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
*
Authors to whom correspondence should be addressed.
A.O. and M.N.-J. contributed equally to this paper.
J.G.P. and C.B. contributed equally to this paper.
Vaccines 2020, 8(3), 444; https://doi.org/10.3390/vaccines8030444
Received: 22 June 2020 / Revised: 28 July 2020 / Accepted: 31 July 2020 / Published: 6 August 2020
(This article belongs to the Section Vaccines against Infectious Diseases)
Synthetic antigens based on consensus sequences that represent circulating viral isolates are sensitive, time saving and cost-effective tools for in vitro immune monitoring and to guide immunogen design. When based on a representative sequence database, such consensus sequences can effectively be used to test immune responses in exposed and infected individuals at the population level. To accelerate immune studies in SARS-CoV-2 infection, we here describe a SARS-CoV-2 2020 consensus sequence (CoV-2-cons) which is based on more than 1700 viral genome entries in NCBI and encompasses all described SARS-CoV-2 open reading frames (ORF), including recently described frame-shifted and length variant ORF. Based on these sequences, we created curated overlapping peptide (OLP) lists containing between 1500 to 3000 peptides of 15 and 18 amino acids in length, overlapping by 10 or 11 residues, as ideal tools for the assessment of SARS-CoV-2-specific T cell immunity. In addition, CoV-2-cons sequence entropy values are presented along with variant sequences to provide increased coverage of the most variable sections of the viral genome. The identification of conserved protein fragments across the coronavirus family and the corresponding OLP facilitate the identification of T cells potentially cross-reactive with related viruses. This new CoV-2-cons sequence, together with the peptides sets, should provide the basis for SARS-CoV-2 antigen synthesis to facilitate comparability between ex-vivo immune analyses and help to accelerate research on SARS-CoV-2 immunity and vaccine development. View Full-Text
Keywords: COVID-19; SARS-CoV-2; consensus sequence; T cell immunity; overlapping peptides set COVID-19; SARS-CoV-2; consensus sequence; T cell immunity; overlapping peptides set
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MDPI and ACS Style

Olvera, A.; Noguera-Julian, M.; Kilpelainen, A.; Romero-Martín, L.; Prado, J.G.; Brander, C. SARS-CoV-2 Consensus-Sequence and Matching Overlapping Peptides Design for COVID19 Immune Studies and Vaccine Development. Vaccines 2020, 8, 444. https://doi.org/10.3390/vaccines8030444

AMA Style

Olvera A, Noguera-Julian M, Kilpelainen A, Romero-Martín L, Prado JG, Brander C. SARS-CoV-2 Consensus-Sequence and Matching Overlapping Peptides Design for COVID19 Immune Studies and Vaccine Development. Vaccines. 2020; 8(3):444. https://doi.org/10.3390/vaccines8030444

Chicago/Turabian Style

Olvera, Alex, Marc Noguera-Julian, Athina Kilpelainen, Luis Romero-Martín, Julia G. Prado, and Christian Brander. 2020. "SARS-CoV-2 Consensus-Sequence and Matching Overlapping Peptides Design for COVID19 Immune Studies and Vaccine Development" Vaccines 8, no. 3: 444. https://doi.org/10.3390/vaccines8030444

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