RESUMO
BackgroundThe emergence of recombinant viruses is a threat to public health. Recombination of viral variants may combine variant-specific features that together catalyze viral escape from treatment or immunity. The selective advantages of recombinant SARS-CoV-2 isolates over their parental lineages remain unknown. MethodsMulti-method amplicon and metagenomic sequencing of a clinical swab and the in vitro grown virus allowed for high-confidence detection of a novel recombinant variant. Mutational, phylogeographic, and structural analyses determined features of the recombinant genome and spike protein. Neutralization assays using infectious as well as pseudotyped viruses and point mutants thereof defined the recombinants sensitivity to a panel of monoclonal antibodies and sera from vaccinated and/or convalescent individuals. ResultsA novel Delta-Omicron SARS-CoV-2 recombinant was identified in an unvaccinated, immunosuppressed kidney transplant recipient treated with monoclonal antibody Sotrovimab. The recombination breakpoint is located in the spike N-terminal domain, adjacent to the Sotrovimab quaternary binding site, and results in a 5-Delta AY.45 and a 3-Omicron BA.1 mosaic spike protein. Delta and BA.1 are sensitive to Sotrovimab neutralization, whereas the Delta-Omicron recombinant is highly resistant to Sotrovimab, both with and without the RBD resistance mutation E340D. ConclusionsRecombination between circulating SARS-CoV-2 variants can functionally contribute to immune escape. It is critical to validate phenotypes of mosaic viruses and monitor immunosuppressed COVID-19 patients treated with monoclonal antibodies for the selection of recombinant and immune escape variants. (Funded by NYU, the National Institutes of Health, and others)
RESUMO
COVID-19 convalescent plasma (CCP) received approval for use under an Emergency Use Authorization by the FDA for treatment of seriously ill patients. Use of CCP units with a signal-to-cutoff ratio of [≥]12 using the Ortho VITROS SARS-CoV-2 IgG test (OVSARS2IgG) is authorized. Little is known about the relationship between this ratio and the neutralizing capacity of plasma/sera against genuine SARS-CoV-2 virus. We measured the neutralizing capacity of 981 samples from 196 CCP donors 7-119 days post initial donation (DPID). Neutralizing capacity was assessed for 50% (PRNT50) and 90% (PRNT90) reduction of infectious virus using the gold standard plaque reduction neutralization test (PRNT). Importantly, while 32.7%/79.5% (PRNT90/PRNT50) of donations met the FDA minimum titer of 1:80 initially, only 14.0%/48.8% (PRNT90/PRNT50) met this cut-off [≥]85 DPID. A subset of 91 donations were evaluated using the OVSARS2IgG and compared to PRNT titers for diagnostic accuracy. The correlation of OVSARS2IgG results to neutralizing capacity allowed extrapolation to CCP therapy efficacy results. CCP with OVSARS2IgG ratios in the therapeutically beneficial group had neutralizing titers of [≥]1:640 (PRNT50) and/or [≥]1:80 (PRNT90). This information provides a new basis for refining the recommended properties of CCP that is used to treat severe COVID-19.
