Discovery of highly potent small molecule pan-coronavirus fusion inhibitors (preprint)

The unprecedented pandemic of COVID-19, caused by a novel coronavirus, SARS-CoV-2, has led to massive human suffering, death, and economic devastation worldwide. The virus is mutating fast to more transmissible and infectious variants. The Delta variant (B.1.617.2), initially identified in India, and the omicron variant (BA.4 and BA.5) have spread worldwide. In addition, recently alarming antibody evasive SARS-CoV-2 subvariants, BQ and XBB, have been reported. These new variants may pose a substantial challenge to controlling the spread of this virus. Therefore, the continued development of novel drugs having pan-coronavirus inhibition to treat and prevent infection of COVID-19 is urgently needed. These drugs will be critically important in dealing with new pandemics that will emerge in the future. We report the discovery of several highly potent small molecule pan-coronavirus inhibitors. One of which, NBCoV63, showed low nM potency against SARS-CoV-2 (IC50: 55 nM), SARS-CoV (IC50: 59 nM), and MERS-CoV (IC50: 75 nM) in pseudovirus-based assays with excellent selectivity indices (SI: as high as > 900) demonstrating its pan-coronavirus inhibition. NBCoV63 showed equally effective antiviral potency against SARS-CoV-2 mutant (D614G) and several variants of concerns (VOCs) such as B.1.617.2 (Delta), B.1.1.529/BA.1 and BA.4/BA.5 (Omicron) and K417T/E484K/N501Y (Gamma). NBCoV63 also showed similar efficacy profiles to Remdesivir against authentic SARS-CoV-2 (Hong Kong strain) and two of its variants (Delta and Omicron) by plaque reduction in Calu3 cells. Additionally, we show that NBCoV63 inhibits virus-mediated cell-to-cell fusion in a dose-dependent manner. Furthermore, the Absorption, distribution, metabolism, and excretion (ADME) data of NBCoV63 demonstrated drug-like properties.

Seroprevalence of Anti-SARS-CoV-2 Antibodies in a Cohort of New York City Metro Blood Donors using Multiple SARS-CoV-2 Serological Assays: Implications for Controlling the Epidemic and Reopening. (preprint)

Projections of the stage of the Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2) pandemic and local, regional and national public health policies designed to limit the spread of the epidemic as well as reopen cities and states, are best informed by reproducible, high throughput, and statically credible antibody (Ab) assays. To date, a myriad of Ab tests, both available and authorized for emergency use by the FDA, has led to confusion rather than insight per se. The present study reports the results of a rapid, point-in-time 1,000-person cohort study using serial blood donors in the New York City metropolitan area (NYC) using multiple serological tests, including enzyme-linked immunosorbent assays (ELISAs) and high throughput serological assays (HTSAs). These were then tested and associated with assays for neutralizing Ab (NAb). Of the 1,000 NYC blood donor samples in late June and early July 2020, 12.1% and 10.9% were seropositive using the Ortho Total Ig and the Abbott IgG HTSA assays, respectively. These serological assays correlated with neutralization activity specific to SARS-CoV-2. The data reported herein suggest that seroconversion in this population occurred in approximately 1 in 8 blood donors from the beginning of the pandemic in NYC (considered March 1, 2020). These findings deviate with an earlier seroprevalence study in NYC showing 13.7% positivity. Collectively however, these data demonstrate that a low number of individuals have serologic evidence of infection during this first wave and suggest that the notion of herd immunity at rates of ~60% or higher are not near. Furthermore, the data presented herein show that the nature of the Ab-based immunity is not invariably associated with the development of NAb. While the blood donor population may not mimic precisely the NYC population as a whole, rapid assessment of seroprevalence in this cohort and serial reassessment could aid public health decision making.

Fluctuating High Throughput Serological Assay Results in Recurrent Convalescent Plasma Donors (preprint)

The clinical and scientific communities rely on serology testing to analyze the degree of antibody-mediated immunity afforded to recovered patients from SARS-CoV-2 infection. Neutralizing antibodies present in COVID-19 convalescent plasma (CCP) remains a practical therapy to treat COVID-19 patients requiring hospitalization. However, it remains unclear how long antibody levels persist in CCP donors after recovery. An accurate estimation of antibody kinetics in CCP donors provide an important observation to further define the extent of long-term immunity in recovered patient and simultaneously inform CCP collection processes in efforts to improve CCP dosing and therapeutic outcome. In this study, we analyzed 63 donors and measured antibody levels using two high throughput screening assays (HTSA) designed to detect antibodies targeting the spike protein (S1) and nucleocapsid protein (NP) of SARS-CoV-2 and monitored antibody levels between 2-8 consecutive donations. We show that anti-S1 antibody levels, as measured using the Ortho Total Ig HTSA, increased over time in repeat CCP donors while anti-NP antibody levels, as measured using the Abbott IgG HTSA, were unchanged or decreased over time. When we normalized these data, we found that both the absolute levels of anti-S1 antibodies and the ratio between S1 and NP antibodies tends to increase over time. These data have important implications for the convalescent donation process, patient protection from future infection and characterization of the SARS-CoV-2 immune response.

Low Seroprevalence of SARS-CoV-2 in Rhode Island Blood Donors Determined using Multiple Serological Assay Formats (preprint)

Epidemic projections and public health policies addressing Coronavirus disease (COVID)-19 have been implemented without data reporting on the seroconversion of the population since scalable antibody testing has only recently become available. We measured the percentage of severe acute respiratory syndrome- Coronavirus-2 (SARS-CoV-2) seropositive individuals from 2,008 blood donors drawn in the state of Rhode Island (RI). We utilized multiple antibody testing platforms, including lateral flow immunoassays (LFAs), enzyme-linked immunosorbent assays (ELISAs) and high throughput serological assays (HTSAs). We report than an estimated seropositive rate of RI blood donors of approximately 0.6% existed in April-May of 2020. These data imply that seroconversion, and thus infection, is likely not widespread within this population. Daily new case rates peaked in RI in late April 2020. We conclude that IgG LFAs and HTSAs are suitable to conduct seroprevalence assays in random populations. More studies will be needed using validated serological tests to improve the precision and report the kinetic progression of seroprevalence estimates.

Escape from neutralizing antibodies by SARS-CoV-2 spike protein variants (preprint)

Neutralizing antibodies elicited by prior infection or vaccination are likely to be key for future protection of individuals and populations against SARS-CoV-2. Moreover, passively administered antibodies are among the most promising therapeutic and prophylactic anti-SARS-CoV-2 agents. However, the degree to which SARS-CoV-2 will adapt to evade neutralizing antibodies is unclear. Using a recombinant chimeric VSV/SARS-CoV-2 reporter virus, we show that functional SARS-CoV-2 S protein variants with mutations in the receptor binding domain (RBD) and N-terminal domain that confer resistance to monoclonal antibodies or convalescent plasma can be readily selected. Notably, SARS-CoV-2 S variants that resist commonly elicited neutralizing antibodies are now present at low frequencies in circulating SARS-CoV-2 populations. Finally, the emergence of antibody-resistant SARS-CoV-2 variants that might limit the therapeutic usefulness of monoclonal antibodies can be mitigated by the use of antibody combinations that target distinct neutralizing epitopes.

Serological Analysis of New York City COVID19 Convalescent Plasma Donors (preprint)

Background: The development of neutralizing antibodies (NAbs) against SARS-CoV-2, following infection or vaccination, is likely to be critical for the development of sufficient population immunity to drive cessation of the COVID19 pandemic. A large number of serologic tests, platforms and methodologies are being employed to determine seroprevalence in populations to select convalescent plasmas for therapeutic trials, and to guide policies about reopening. However, these tests have substantially variable sensitivity and specificity, and their ability to quantitatively predict levels of NAbs is unknown. Methods: We determined levels of antibodies in convalescent plasma using commercially available SARS-CoV-2 detection tests and in-house ELISA assays and correlated those measurements with neutralization activity measured using pseudotyped virus particles, which offer the most informative assessment of antiviral activity of patient sera against viral infection. Findings: Our data show that a large proportion of convalescent plasma samples have modest antibody levels and that commercially available tests have varying degrees of accuracy in predicting neutralizing activity. Nevertheless, we found particular commercially available tests are capable of accurately measuring levels of antibodies that strongly correlate with neutralization assays. Interpretation: Our findings imply that SARS-CoV-2 convalescent plasma donors have a wide range of antibody concentrations. At present it is unclear how antibody acquisition, particularly for low titer individuals, might afford future immunity to SARS-CoV-2. Further research will be required to determine the minimum threshold of antibody and neutralization activity necessary to accurately predict immunity. Correlation of clinical antibody tests with neutralization activity in this study could serve as a valuable roadmap to guide the choice and interpretation of serological tests for SARS-CoV-2.