Immunoinformatics and Pepscan strategies on the path of a peptide-based serological diagnosis of COVID19

Abstract

Several diagnostic tools have been developed for clinical and epidemiological assays. RT-PCR and antigen detection tests are more useful for diagnosis of acute disease, while antibody tests allow the estimation of exposure in the population. Currently, there is an urgent need for the development of diagnostic tests for COVID-19 that can be used for large-scale epidemiological sampling. Through a comprehensive strategy, potential 16 mer antigenic peptides suited for antibody-based SARS-CoV-2 diagnosis were identified. A systematic scan of the three structural proteins (S,N and M) and the non-structural proteins (ORFs) present in the SARS-CoV-2 virus was conducted through the combination of immunoinformatic methods, peptide SPOT synthesis and an immunoassay with cellulose-bound peptides (Pepscan). The Pepscan filter paper sheets with synthetic peptides were tested against pools of sera of COVID-19 patients. Antibody recognition showed a strong signal for peptides corresponding to the S, N and M proteins of SARS-CoV-2 virus, but not for the ORFs proteins. The peptides exhibiting higher signal intensity were found in the C -terminal region of the N protein. Several peptides of this region showed strong recognition with all three immunoglobulins in the pools of sera. The differential reactivity observed between the different immunoglobulin isotypes (IgA, IgM and IgG) within different regions of the S and N proteins, can be advantageous for ensuring accurate diagnosis of all infected patients, with different times of exposure to infection. Few peptides of the M protein showed antibody recognition and no recognition was observed for peptides of the ORFs proteins.

SARS-CoV-2 mRNA vaccine induces robust specific and cross-reactive IgG and unequal neutralizing antibodies in naive and previously infected people

“…SARS-CoV-2 nonstructural proteins such as open reading frame (ORF)-8 and ORF-3b (Alkhansa et al, 2021;Barik, 2021) have been identified as alternate antibody targets, which in combination may improve sensitivity for detecting previous SARS-CoV-2 infection. These and other non-spike viral epitopes (Lorenzo et al, 2021) constitute a promising strategy to distinguish past SARS-CoV-2 infection from vaccination.…”

Detecting anti–SARS-CoV-2 antibodies in urine samples: A noninvasive and sensitive way to assay COVID-19 immune conversion

“…SARS-CoV-2 has four structural proteins—spike (S), envelope (E), membrane (M), and nucleocapsid (N) proteins—and all of them have already been tested as antigens for COVID-19 diagnosis using recombinant proteins, synthetic peptides, and/or polypeptide chimeras ( 4 , 6 , 22 ). Although many diagnostic tests use the recombinant protein S as the antigen, ELISA-based assays using a recombinant N protein have also been widely used with high sensitivity to detect antibodies in mildly infected patients ( 21 , 23 ).…”

Challenges in Serologic Diagnostics of Neglected Human Systemic Mycoses: An Overview on Characterization of New Targets

“…There are several successful examples of the application of immunoinformatics in the identification/development of new diagnostic targets as described with COVID-19 [ 185 , 186 , 187 ], Schistosoma mansoni [ 188 ], Toxoplasma gondii [ 189 ] Fasciola hepatica [ 190 ], helminth [ 191 ] human brucellosis [ 192 ] and Leishmania [ 193 ]. In the context of systemic mycosis, the number of works is substantially limited, and this approach has been used combined with immunoproteomic analyses as described to Paracoccidioides complex [ 43 , 172 ], Sporothrix schenckii complex [ 159 ] and Cryptococcus gattii [ 158 ].…”