Equine Anti-SARS-CoV-2 Serum (ECIG) Binds to Mutated RBDs and N Proteins of Variants of Concern and Inhibits the Binding of RBDs to ACE-2 Receptor

Abstract

The COVID-19 pandemic caused by the severe acute syndrome virus 2 (SARS-CoV-2) has been around since November 2019. As of early June 2022, more than 527 million cases were diagnosed, with more than 6.0 million deaths due to this disease. Coronaviruses accumulate mutations and generate greater diversity through recombination when variants with different mutations infect the same host. Consequently, this virus is predisposed to constant and diverse mutations. The SARS-CoV-2 variants of concern/interest (VOCs/VOIs) such as Alpha (B.1.1.7), Beta (B.1.351), Gamma (B.1.1.28/P.1), Delta (B.1.617.2), and Omicron (B.1.1.529) have quickly spread across the world. These VOCs and VOIs have accumulated mutations within the spike protein receptor-binding domain (RBD) which interacts with the angiotensin-2 converting enzyme (ACE-2) receptor, increasing cell entry and infection. The RBD region is the main target for neutralizing antibodies; however, other notable mutations have been reported to enhance COVID-19 infectivity and lethality. Considering the urgent need for alternative therapies against this virus, an anti-SARS-CoV-2 equine immunoglobulin F(ab')₂, called ECIG, was developed by the Butantan Institute using the whole gamma-irradiated SARS-CoV-2 virus. Surface plasmon resonance experiments revealed that ECIG binds to wild-type and mutated RBD, S1+S2 domains, and nucleocapsid proteins of known VOCs, including Alpha, Gamma, Beta, Delta, Delta Plus, and Omicron. Additionally, it was observed that ECIG attenuates the binding of RBD (wild-type, Beta, and Omicron) to human ACE-2, suggesting that it could prevent viral entry into the host cell. Furthermore, the ability to concomitantly bind to the wild-type and mutated nucleocapsid protein likely enhances its neutralizing activity of SARS-CoV-2. We postulate that ECIG benefits COVID-19 patients by reducing the infectivity of the original virus and existing variants and may be effective against future ones. Impacting the course of the disease, mainly in the more vulnerable, reduces infection time and limits the appearance of new variants by new recombination.

Keywords: COVID-19; RBD; SPR; VOCs; equine serum; neutralizing antibodies; nucleocapsid.

Figure 1

Visual representation of the domain locations and the most common mutations. Abbreviations: NTD, N-terminal domain; RBD, receptor-binding domain; RBM, receptor-binding motif; SD, subdomain; S1/S2, the junction between the exposed S1 attachment domain and the partially buried S2 fusion domain.

Figure 2

Surface plasmon resonance analyses of ECIG binding to RBD, Spike S1+S2, and N proteins. (A) Binding of ECIG to wild-type and mutated RBD. (B) Binding of ECIG to Spike S1+S2 Gamma, Delta, and Omicron. (C) The binding of ECIG to wild-type N protein and N mut/del. Binding assays were performed with a BIAcore T200 biosensor instrument, with RBD, Spike, and N proteins immobilized on a CM5 sensor chip. Binding responses are represented in resonance units (RU). A running buffer was used as a negative control (0 μM). Results were evaluated by one-way ANOVA and showed statistical significance (p ≤ 0.05).

Figure 3

Surface plasmon resonance analysis of ECIG (showed in red symbols) in comparison to 34 sera samples from SARS-CoV-2 infected individuals (not vaccinated). All the samples were diluted at 1:10 v/v in HBS-EP. Binding assays were performed with a BIAcore T200 biosensor instrument, with RBD and N proteins immobilized on a CM5 sensor chip. Binding responses are represented in resonance units (RU). A running buffer was used as a negative control (0 μM).

Figure 4

Surface plasmon resonance analysis of (A) wild-type RBD, (B) RBD Beta, and (C) Omicron binding to ACE-2 in the presence and absence of ECIG. At their respective saturation concentration, wild-type RBD, RBD Beta, and RBD Omicron were pre-incubated with ECIG [1:10 v/v] for 1 hour at 37°C. These mixtures were then injected over the surface previously immobilized with ACE-2 to evaluate if ECIG alters SARS-CoV-2 RBD binding to ACE-2. The binding responses are represented in resonance units (RU). Running buffer was used as the negative control (0 μM). Results were evaluated by one-way ANOVA and showed statistical significance (p ≤ 0.05).