Molecular basis of SARS-CoV-2 Omicron variant evasion from shared neutralizing antibody response (preprint)

A detailed understanding of the molecular features of the neutralizing epitopes developed by viral escape mutants is important for predicting and developing vaccines or therapeutic antibodies against continuously emerging SARS-CoV-2 variants. Here, we report three human monoclonal antibodies (mAbs) generated from COVID-19 recovered individuals during first wave of pandemic in India. These mAbs had publicly shared near germline gene usage and potently neutralized Alpha and Delta, but poorly neutralized Beta and completely failed to neutralize Omicron BA.1 SARS-CoV-2 variants. Structural analysis of these three mAbs in complex with trimeric spike protein showed that all three mAbs are involved in bivalent spike binding with two mAbs targeting class-1 and one targeting class-4 Receptor Binding Domain (RBD) epitope. Comparison of immunogenetic makeup, structure, and function of these three mAbs with our recently reported class-3 RBD binding mAb that potently neutralized all SARS-CoV-2 variants revealed precise antibody footprint, specific molecular interactions associated with the most potent multi-variant binding / neutralization efficacy. This knowledge has timely significance for understanding how a combination of certain mutations affect the binding or neutralization of an antibody and thus have implications for predicting structural features of emerging SARS-CoV-2 escape variants and to develop vaccines or therapeutic antibodies against these.

Nucleocapsid antigenemia is a marker of acute SARS-CoV-2 infection (preprint)

BackgroundReliable detection of SARS-CoV-2 infection is essential for diagnosis and treatment of disease as well as infection control and prevention during the ongoing COVID-19 pandemic. Existing nucleic acid tests do not reliably distinguish acute from resolved infection, as residual RNA is frequently detected in the absence of replication-competent virus. We hypothesized that viral nucleocapsid in serum or plasma may be a specific biomarker of acute infection that could enhance isolation and treatment strategies at an individualized level. MethodsSamples were obtained from a retrospective serological survey using a convenience sampling method from adult inpatient and outpatient encounters from January through March 2021. Samples were categorized along a timeline of infection (e.g. acute, late presenting, convalescent) based on timing of available SARS-CoV-2 testing and symptomatology. Nucleocapsid was quantified by digital immunoassay on the Quanterix HD-X platform. ResultsIn a large sample of 1860 specimens from 1607 patients, the highest level and frequency of antigenemia were observed in samples obtained during acute SARS-CoV-2 infection. Levels of antigenemia were highest in samples from seronegative individuals and in those with more severe disease. Using ROC analysis, we found that antigenemia exhibited up to 85.8% sensitivity and 98.6% specificity as a biomarker for acute COVID-19. ConclusionsNucleocapsid antigenemia is a sensitive and specific biomarker for acute SARS-CoV-2 infection and may aid in individualized assessment of SARS-CoV-2 infection resolution or persistence, although interpretation is limited by absence of a diagnostic gold standard for active infection.

Quantifying post-vaccination protective anti-SARS-CoV-2 IgG antibodies in blood and saliva with a fully automated, high throughput digital immunoassay (preprint)

Background: Antibodies induced by COVID-19 vaccination have been shown to wane over time. Current tests for assessing virus-neutralizing antibodies are complex and time-intensive. There is a need for a simple diagnostic test that measures levels of protective antibodies to help monitor immunity status. Method: Using a commercially available FDA-authorized semi-quantitative SARS-CoV-2 IgG test, we monitored the duration of the immune response in dried blood microsamples (DBS) and saliva to vaccination by 3 different vaccines across prospective cohorts of 8 COVID-19 naive and 29 COVID-19 recovered individuals over a six-month period. We correlated the results to a binding blockade assay validated to a live virus neutralization assay to validate the test for measurement of protective antibodies. Results: The immune response characteristics between the two mRNA vaccines were similar over the 6-month period in both the COVID-19 naive and recovered cohorts. IgG titers in DBS were generally 3-4 orders of magnitude higher than in saliva, and longitudinal profiles were highly correlated between the two matrices (Rm = 0.80). Median IgG concentrations post-vaccination declined to <10% neutralization capacity with all vaccines by six months. Conclusions: The potential of a simple, fully automated high throughput anti-SARS-CoV-2 IgG test to quantitatively measure protective antibodies in samples collected remotely or at the point of care was demonstrated. The IgG immune response and protective immunity was shown to decline significantly by six months.