Complete Genome Sequences of Cluster S Mycobacteriophages Beelzebub, Raela, and RedRaider77

We isolated three mycobacteriophages that belong to cluster S, namely, Beelzebub, Raela, and RedRaider77. Annotation revealed a genome structure typical of cluster S phages, including an atypical location of two minor tail protein genes in the right arm of these viral genomes.

Limited Variation between SARS-CoV-2-Infected Individuals in Domain Specificity and Relative Potency of the Antibody Response against the Spike Glycoprotein

The spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is arranged as a trimer on the virus surface, composed of three S1 and three S2 subunits. Infected and vaccinated individuals generate antibodies against spike, which can neutralize the virus. Most antibodies target the receptor-binding domain (RBD) and N-terminal domain (NTD) of S1; however, antibodies against other regions of spike have also been isolated. The interhost variability in domain specificity and relative neutralization efficacy of the antibodies is still poorly characterized. To this end, we tested serum and plasma samples collected from 85 coronavirus disease 2019 (COVID-19) convalescent subjects. Samples were analyzed using seven immunoassays that employ different domains, subunits, and oligomeric forms of spike to capture the antibodies. Samples were also tested for their neutralization of pseudovirus containing SARS-CoV-2 spike and of replication-competent SARS-CoV-2. While the total amount of anti-spike antibodies produced varied among convalescent subjects, we observed an unexpectedly fixed ratio of RBD- to NTD-targeting antibodies. The relative potency of the response (defined as the measured neutralization efficacy relative to the total level of spike-targeting antibodies) also exhibited limited variation between subjects and was not associated with the overall amount of antispike antibodies produced. These studies suggest that host-to-host variation in the polyclonal response elicited against SARS-CoV-2 spike in early pandemic subjects is primarily limited to the quantity of antibodies generated rather than their domain specificity or relative neutralization potency. IMPORTANCE Infection by SARS-CoV-2 elicits antibodies against various domains of the spike protein, including the RBD and NTD of subunit S1 and against subunit S2. The antibody responses of different infected individuals exhibit different efficacies to inactivate (neutralize) the virus. Here, we show that the observed variation in the neutralizing activity of the antibody responses in COVID-19 convalescent subjects is caused by differences in the amounts of antibodies rather than their recognition properties or the potency of their antiviral activity. These findings suggest that COVID-19 vaccine strategies that focus on enhancing the overall level of the antibodies will likely elicit a more uniformly efficacious protective response.

Optimizing immunoassay-based selection of donors for COVID-19 convalescent plasma

COVID-19 convalescent plasma (CCP) is currently administered to hospitalized COVID-19 patients under an EAU by the FDA. CCP units are selected by commercially available ELISA quantification of anti-SARS-CoV-2 (SARS2) antibodies under the rationale that higher levels of anti-SARS2 antibodies correlate with higher neutralizing capabilities and thus greater efficacy. The validity of this selection process has yet to be investigated. We analyzed serum samples from 60 convalesced donors with PCR-confirmed COVID-19. Samples were analyzed using commercial SARS2 ELISAs (DiaSorin, Euroimmun, Ortho, and Roche) and a cell-based enzyme-linked immunosorbent assay (cbELISA) that detects antibodies against the native conformation of the SARS2 spike glycoprotein (GP). Sera were also tested for neutralizing activity against wild-type SARS2 and a pseudovirus expressing the SARS2 GP. Immunoassay and neutralization values were compared to determine the precision of each immunoassay to predict differing levels of neutralizing activity, and ability of each immunoassay to identify high neutralizing activity. Results of immunoassays that apply SARS2 GP as the antigen (DiaSorin, Euroimmun, Ortho, and cbELISA) correlated well with neutralization titers measured by wild-type SARS2 or SARS2 GP-pseudotyped virus as compared with assays using other SARS2 antigens (Roche; N protein). Differences in precision of these assays were evident when samples within the top quintile or decile of immunoassay values were analyzed, with DiaSorin and Ortho assays showing superior performance in predicting neutralizing capability. We hope this approach will assist in the selection of highly neutralizing CCP units that confer greater clinical efficacy.