In silico detection of SARS-CoV-2 specific B-cell epitopes and validation in ELISA for serological diagnosis of COVID-19

Abstract

Rapid generation of diagnostics is paramount to understand epidemiology and to control the spread of emerging infectious diseases such as COVID-19. Computational methods to predict serodiagnostic epitopes that are specific for the pathogen could help accelerate the development of new diagnostics. A systematic survey of 27 SARS-CoV-2 proteins was conducted to assess whether existing B-cell epitope prediction methods, combined with comprehensive mining of sequence databases and structural data, could predict whether a particular protein would be suitable for serodiagnosis. Nine of the predictions were validated with recombinant SARS-CoV-2 proteins in the ELISA format using plasma and sera from patients with SARS-CoV-2 infection, and a further 11 predictions were compared to the recent literature. Results appeared to be in agreement with 12 of the predictions, in disagreement with 3, while a further 5 were deemed inconclusive. We showed that two of our top five candidates, the N-terminal fragment of the nucleoprotein and the receptor-binding domain of the spike protein, have the highest sensitivity and specificity and signal-to-noise ratio for detecting COVID-19 sera/plasma by ELISA. Mixing the two antigens together for coating ELISA plates led to a sensitivity of 94% (N = 80 samples from persons with RT-PCR confirmed SARS-CoV-2 infection), and a specificity of 97.2% (N = 106 control samples).

Cross-reactive and mono-reactive SARS-CoV-2 CD4+ T cells in prepandemic and COVID-19 convalescent individuals

“…In addition, 22 pre pandemic cryopreserved samples (samples collected before December 2019) were obtained from the Benaroya Research Institute Biorepository. The University of Washington cohort has been previously described [48,49] HLA typing was performed with OLERUP SSP typing kit according to the manufacturer's instruction or by sequencing at Scisco Genetics, Inc. (Seattle, WA).…”

T cell response to intact SARS-CoV-2 includes coronavirus cross-reactive and variant-specific components

“…The COVID-19 cohort has been described (7)(8)(9)(10). Subjects reporting SARS-CoV-2 detection and an illness compatible with COVID-19 were recruited.…”

“…The present report used PBMC from a cohort of coronavirus-19 (COVID-19) convalescent persons (7)(8)(9)(10) to begin to study T-cell responses to SARS-CoV-2 in the contexts of direct-and cross-presentation of complex viral antigens. Validation with proteome-covering full-length protein and peptide sets allowed definition and confirmation of many individual epitopes.…”

Untitled

“…Numerous efforts have been made in determining vaccine targets for SARS-CoV-2 using computational methods. These methods are based on B cell and T cell epitope prediction [7][8][9][10][11][12][13][14] and indeed extend beyond SARS-CoV-2 to encompass prediction of the pathogen-based immune response more generically [15][16][17][18][19] . In the current study, we explored this approach by investigating in silico the binding affinities of all linear 15-, 18and 22-amino acid long epitopes of S natural and its 5 variants (S D614G , S B.1.1.7 , S B.1.351 , S P.1 , S P.167.2 ) to 66 common HLA Class II alleles with global frequencies of ≥ 0.01.…”