Measuring Neutralizing Antibodies to SARS-CoV-2 Using Lentiviral Spike-Pseudoviruses

The Importance of Antibody Titer Determination to the Effective Use of Convalescent Plasma

Convalescent Plasma (CP) has been used prophylactically and therapeutically over the past century to address a variety of infectious threats. Two tenets of the use of CP were clear from prior experience in the setting of other infectious outbreaks: (1) best results are obtained when CP is given early in the course of the disease, and (2) plasma containing high-titer neutralizing capacity is necessary to achieve optimal results. The magnitude of the COVID-19 pandemic along with the initial lack of effective therapeutic alternatives, combined with the relative safety of the approach of administration of CP, led to the initiation of an expanded access program (EAP) that ultimately provided CP to tens of thousands of individuals. When the program was initiated, no high-throughput assay was available for the determination of antibody titers, so antibody positive units were administered without regard to titer. With foresight regarding the need to ultimately determine such titers, samples from the CP units administered were retained and titers were determined retrospectively. An automated live-virus neutralization assay was ultimately selected for this purpose based on an evaluation of its accuracy and precision. Ultimately, an analysis performed in 13,794 individuals from the EAP for which clinical outcomes were known following the administration of single units of COVID-19 CP between the period of April and August 2020 indicated that higher titer COVID-19 CP was associated with a modest reduction in absolute mortality. The benefit observed was confined to individuals who were not intubated, and there was a trend toward a greater reduction in mortality using the highest SARS-CoV-2 neutralizing antibody-containing CP units. This experience during the COVID-19 pandemic is instructive for the future. To facilitate the production of CP that is likely to be most effective, high-throughput assays to determine neutralizing antibody titers need to be developed and implemented early during an outbreak to facilitate the identification and early administration of high-titer units.

Single-molecule imaging reveals allosteric stimulation of SARS-CoV-2 spike receptor binding domain by host sialic acid

Conformational dynamics of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike glycoprotein (S) mediate exposure of the binding site for the cellular receptor, angiotensin-converting enzyme 2 (ACE2). The N-terminal domain (NTD) of S binds terminal sialic acid (SA) moieties on the cell surface, but the functional role of this interaction in virus entry is unknown. Here, we report that NTD-SA interaction enhances both S-mediated virus attachment and ACE2 binding. Through single-molecule Förster resonance energy transfer imaging of individual S trimers, we demonstrate that SA binding to the NTD allosterically shifts the S conformational equilibrium, favoring enhanced exposure of the ACE2-binding site. Antibodies that target the NTD block SA binding, which contributes to their mechanism of neutralization. These findings inform on mechanisms of S activation at the cell surface.

Characterization of Entry Pathways, Species-Specific Angiotensin-Converting Enzyme 2 Residues Determining Entry, and Antibody Neutralization Evasion of Omicron BA.1, BA.1.1, BA.2, and BA.3 Variants

The SARS-CoV-2 Omicron variants were first detected in November 2021, and several Omicron lineages (BA.1, BA.2, BA.3, BA.4, and BA.5) have since rapidly emerged. Studies characterizing the mechanisms of Omicron variant infection and sensitivity to neutralizing antibodies induced upon vaccination are ongoing by several groups. In the present study, we used pseudoviruses to show that the transmembrane serine protease 2 (TMPRSS2) enhances infection of BA.1, BA.1.1, BA.2, and BA.3 Omicron variants to a lesser extent than ancestral D614G. We further show that Omicron variants have higher sensitivity to inhibition by soluble angiotensin-converting enzyme 2 (ACE2) and the endosomal inhibitor chloroquine compared to D614G. The Omicron variants also more efficiently used ACE2 receptors from 9 out of 10 animal species tested, and unlike the D614G variant, used mouse ACE2 due to the Q493R and Q498R spike substitutions. Finally, neutralization of the Omicron variants by antibodies induced by three doses of Pfizer/BNT162b2 mRNA vaccine was 7- to 8-fold less potent than the D614G. These results provide insights into the transmissibility and immune evasion capacity of the emerging Omicron variants to curb their ongoing spread. IMPORTANCE The ongoing emergence of SARS-CoV-2 Omicron variants with an extensive number of spike mutations poses a significant public health and zoonotic concern due to enhanced transmission fitness and escape from neutralizing antibodies. We studied three Omicron lineage variants (BA.1, BA.2, and BA.3) and found that transmembrane serine protease 2 has less influence on Omicron entry into cells than on D614G, and Omicron exhibits greater sensitivity to endosomal entry inhibition compared to D614G. In addition, Omicron displays more efficient usage of diverse animal species ACE2 receptors than D614G. Furthermore, due to Q493R/Q498R substitutions in spike, Omicron, but not D614G, can use the mouse ACE2 receptor. Finally, three doses of Pfizer/BNT162b2 mRNA vaccination elicit high neutralization titers against Omicron variants, although the neutralization titers are still 7- to 8-fold lower those that against D614G. These results may give insights into the transmissibility and immune evasion capacity of the emerging Omicron variants to curb their ongoing spread.