The current practice for diagnosis of COVID-19, based on SARS-CoV-2 PCR testing of pharyngeal or respiratory specimens in a symptomatic patient at high epidemiologic risk, likely underestimates the true prevalence of infection. Serologic methods can more accurately estimate the disease burden by detecting infections missed by the limited testing performed to date. We describe the validation of a coronavirus antigen microarray containing immunologically significant antigens from SARS-CoV-2, in addition to SARS-CoV, MERS-CoV, common human coronavirus strains, and other common respiratory viruses.
A comparison of antibody profiles detected on the array from control sera collected prior to the SARS-CoV-2 pandemic versus convalescent blood specimens from virologically confirmed COVID-19 cases demonstrates near-complete discrimination of these two groups, with improved performance from the use of antigen combinations that include both spike protein and nucleoprotein. This array can be used as a diagnostic tool, as an epidemiologic tool to more accurately estimate the disease burden of COVID-19, and as a research tool to correlate antibody responses with clinical outcome.
The antibody profiles of naïve individuals include high IgG reactivity to common cold coronaviruses with low-level cross-reactivity with S2 domains from SARS-CoV-2 and other epidemic coronaviruses, which is not surprising given the high degree of sequence homology and previously observed serologic cross-reactivity15 between S2 domains of betacoronaviruses, a group that includes SARS-CoV-2, SARS-CoV, MERS, and common cold coronaviruses HKU1 and OC43. This low-level cross-reactivity occurs in approximately 7% of unexposed individuals which leads to hypotheses regarding whether these individuals differ in COVID-19 susceptibility and outcomes. However, naïve individuals do not show cross-reactivity to other SARS-CoV-2 antigens. Even for the nucleocapsid protein, which also has high sequence homology between betacoronaviruses, cross-reactivity is only seen between SARS-CoV-2 and SARS-CoV and not with MERS-CoV or common cold coronaviruses. In addition, the quantitative difference between high antibody reactivity to SARS-CoV-2 S2 in the positive group and low-level antibody cross-reactivity in the negative group is large enough that these antigens still discriminate these groups with high significance.
This study also informs antigen selection and design for population surveillance and clinical diagnostic assays and vaccine development. The optimal assay to discriminate SARS-CoV-2 convalescent sera from pre-pandemic sera is a combination of 2 antigens that includes S2 and NP. As an individual antigen, the S2 demonstrates cross-reactivity with negative control sera which leads to low specificity, but this antigen adds predictive power when combined with the more specific NP antigen. The observation that unexposed individuals with antibodies to common cold coronaviruses do not show cross-reactivity to SARS-CoV-2 NP dispels concerns that the high sequence homology of this protein across betacoronaviruses would impair its performance as a diagnostic antigen. The low-level antibody cross-reactivity of a subset of unexposed ndividuals for SARS-CoV-2 spike protein containing S2 domain may not preclude its use as a diagnostic antigen given the large quantitative difference in antibody reactivity between positive and negative groups, but this cross-reactivity may influence response to vaccination with spike protein antigens containing the S2 domain in this subset of individuals.
A coronavirus antigen microarray containing a panel of antigens from SARS-CoV-2 in addition to other human coronaviruses was able to reliably distinguish convalescent plasma of PCR-positive COVID-19 cases from negative control sera collected prior to the pandemic. Antigen combinations including both spike protein and nucleoprotein demonstrated improved performance compared to each individual antigen.
Reference & Source information: https://www.biorxiv.org
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