Development of a SARS-CoV-2 emerging variant infectivity and immune evasion panel to quantify the efficacy of vaccine booster induced neutralizing antibodies.

Summary As the COVID19 pandemic and vaccine deployment continue there is an urgent need to monitor emerging variants for their infectivity and ability to escape both prior infection and vaccine induced neutralizing antibodies. Currently, there is no way to rapidly quantify emerging variants infectivity and immune evading capacity. The standard for quantifying viral infectivity involves the use of harvested viral isolates and performing quantitative plaque assays, which are tedious and time consuming. Additionally, the use of infectious SARS-CoV-2 requires high-level containment in BSL-3 facilities that limits its application in common clinical and research laboratories. Pseudoviruses have been widely used to model SARS-CoV-2 infectivity and antibody neutralization. Pseudoviruses, such as those derived from lentivirus and vesicular stomatitis virus, can mimic the entry process of SARS-CoV-2. However, these pseudovirions consist of mostly non-coronavirus structural proteins and require 2-3 days to generate results. Recently, a novel hybrid alphavirus-SARS-CoV-2 pseudovirion (HA-CoV-2) has been developed by the P.I. (Hetrick) for rapid (3-6 hours) and accurate quantification of viral infectivity and sensitivity to neutralizing antibodies. The HA-CoV-2 particle is a non-replicating SARS-CoV-2 virus-like particle (VLP) composed of only SARS-CoV-2 structural proteins (S, M, N, and E) and a RNA reporter genome derived from a fast expressing alphavirus vector. Our preliminary studies have demonstrated that the HA-CoV-2 assay can rapidly quantify the differences in neutralizing antibodies from vaccinated and previously infected individuals to specific SARS-CoV-2 variants. Virongy has recently licensed the HA-CoV-2 technology from George Mason University, and plans to develop commercial kits with panels of HA-CoV-2 particles that represent the SARS- CoV-2 variants currently in circulation with the greatest infectivity and potential for immune escape. As viral variants continue to emerge there is an urgent need to monitor the infectivity and evaluate the effectiveness of the vaccines on emerging variants. The HA-CoV-2 system would provide a robust platform for rapid and accurate quantification of viral variant infectivity and the neutralizing antibody response. We propose to develop a HA- CoV-2 pseudovirus-based panel to examine infectivity and neutralizing antibody response with two specific aims. Specific Aim 1 is to screen the 50 most prevalent SARS-CoV-2 variant spike proteins in circulation and identify the emerging variants with the highest infectivity using the HA-CoV-2 pseudovirus platform. Specific aim 2 is to conduct antibody neutralization assays of each COVID variant in circulation and determine the sensitivity of each variant to both vaccine and infection induced anti-serum and convalescent plasma. For this study the WHO International Standard and Reference Panel for anti-SARS-CoV-2 antibody will be screened along with a standard recombinant RBD antibody. Following the initial screening the top 5 variants will be selected to develop a commercial panel kit for vaccine and booster developers to evaluate the efficacy of their prophylactics. As part of this screening process Virongy plans to collaborate with John Hopkins university and other non-profit public health organizations to provide all the data acquired in this study. The HA-CoV-2 pseudovirus are currently marketed on Virongy’s company website (virongy.com) for research use only.