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In silico antibody engineering for SARS-CoV-2 detection.

ABSTRACT: Engineered immunoglobulin-G molecules (IgGs) are of wide interest for the development of detection elements in protein-based biosensors with clinical applications. The strategy usually employed for the de novo design of such engineered IgGs consists on merging fragments of the three-dimensional structure of a native IgG, which is immobilized on the biosensor surface, and of an antibody with an exquisite target specificity and affinity. In this work conventional and accelerated classical molecular dynamics (cMD and aMD, respectively) simulations have been used to propose two IgG-like antibodies for COVID-19 detection. More specifically, the crystal structure of the IgG1 B12 antibody, which inactivates the human immunodeficiency virus-1, has been merged with the structure of the antibody CR3022 Fab tightly bounded to SARS-CoV-2 receptor-binding domain (RBD) and the structure of the S309 antibody Fab fragment complexed with SARS-CoV-2 RBD. The two constructed antibodies, named IgG1-CR3022 and IgG1-S309, respectively, have been immobilized on a stable gold surface through a linker. Analyses of the influence of both the merging strategy and the substrate on the stability of the two constructs indicate that the IgG1-S309 antibody better preserves the neutralizing structure than the IgG1-CR3022 one. Overall, results indicate that the IgG1-S309 is appropriated for the generation of antibody based sensors for COVID-19 diagnosis.

SUBMITTER: Marti D

PROVIDER: S-EPMC8496930 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:ObjectiveTo describe the frequency and timing of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibody detection in a convenience sample of skilled nursing facility (SNF) residents with and without confirmed SARS-CoV-2 infection.DesignRetrospective analysis of SNF electronic health records.SettingQualitative SARS-CoV-2 antibody test results were available from 81 SNFs in 16 states.ParticipantsSix hundred and sixty nine SNF residents who underwent both polymerase chain reaction (PCR) and antibody testing for SARS-CoV-2.MeasurementsPresence of SARS-CoV-2 antibodies following the first positive PCR test for confirmed cases, or first PCR test for non-cases.ResultsAmong 397 residents with PCR-confirmed infection, antibodies were detected in 4 of 7 (57.1%) tested within 7-14 days of their first positive PCR test; in 44 of 47 (93.6%) tested within 15-30 days; in 182 of 219 (83.1%) tested within 31-60 days; and in 110 of 124 (88.7%) tested after 60 days. Among 272 PCR negative residents, antibodies were detected in 2 of 9 (22.2%) tested within 7-14 days of their first PCR test; in 41 of 81 (50.6%) tested within 15-30 days; in 65 of 148 (43.9%) tested within 31-60 days; and in 9 of 34 (26.5%) tested after 60 days. No significant differences in baseline resident characteristics or symptoms were observed between those with versus without antibodies.ConclusionsThese findings suggest that vulnerable older adults can mount an antibody response to SARS-CoV-2, and that antibodies are most likely to be detected within 15-30 days of diagnosis. That antibodies were detected in a large proportion of residents with no confirmed SARS-CoV-2 infection highlights the complexity of identifying who is infected in real time. Frequent surveillance and diagnostic testing based on low thresholds of clinical suspicion for symptoms and/or exposure will remain critical to inform strategies designed to mitigate outbreaks in SNFs while community SARS-CoV-2 prevalence remains high.

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In silico antibody engineering for SARS-CoV-2 detection.

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