Transiently produced IgGs enable universal SARS-CoV-2 diagnosis and differentiation recent from past infections.

UNLABELLED: Early diagnosis and differentiating infected from vaccinated animals (DIVA) are the milestone in mitigation, control, and eradication of virus. However, the continuous evolution of new virus strains has hindered the success of many classical techniques, and no DIVA-compatible vaccines are available for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We here develop a universal diagnostic protein-peptide hybrid microarray (PPHM) for different SARS-CoV-2 strains infections and extend the DIVA concept to differentiate recently infected from historically vaccinated/infected hosts (DIVH) in the context of SARS-CoV-2 using in a single sample. First, we analyzed the amino acid sequence identities, which exceeded 96.6%, among the SARS-CoV-2 strains-Delta, Omicron, and New Omicron-and the wild strain. Based on this analysis, we identified a unique diagnostic combination for each of the three SARS-CoV-2 strains using the same peptide probes from the wild strain. Subsequently, we developed a diagnostic combination without regard to strain specificity, PPHMSARS-CoV-2, suitable for all three strains, demonstrating a specificity of 99.0% (99/100) and a sensitivity of 90.2% (175/194). Finally, we successfully achieved DIVH and classified 314 individuals to the classifications of uninfected (57/314, 18.2%), newly vaccinated or infected (5/314, 1.6%), recently infected (78/314, 24.8%), and historically vaccinated or infected (174/314, 55.4%) using PPHMSARS-CoV-2.

IMPORTANCE

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused global health concerns and led to economic losses reaching trillion dollars since 2019. Many diagnostic techniques are showing great success; for instance, nucleic acid amplification showed high specificity and sensitivity in SARS-CoV-2 infections. However, the results of these techniques can be affected by the continuous evolution of SARS-CoV-2 strains, and these techniques were not compatible with differentiating infected from vaccinated animals (DIVA). To circumvent these unfavorable outcomes, a novel strategy is imperative. In this study, we made an exciting discovery: transiently produced IgGs can be used not only for diagnosis and DIVA but also for differentiating recent infections from past infections (approximately 70 days after the occurrence of vaccination or infection). This protein-peptide hybrid microarray technique will have a positive impact on the mitigation and eradication of coronaviruses.