Researchers report isolation of potently neutralizing antibodies against highly transmissible SARS-CoV-2 variants

The ongoing coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), led to severe health and economic losses worldwide. Repeated clusters of mutations have led to the emergence of variants of the virus with higher transmissibility or immune evasion capabilities than the original virus, threatening the success of public health strategies to contain the spread of the virus.

Study: Extremely potent monoclonal antibodies neutralize Omicron and other SARS-CoV-2 variants. Image Credit: ktsdesign/Shutterstock

Successive replacements of the original Wuhan virus variant have occurred by the D614G, Alpha, Delta, and now Omicron, with the Beta and Gamma variants showing more localized spread.

The Omicron has caused spread at an unprecedented rate. It is being shown to resist neutralization by most, if not all, convalescent and therapeutic antibodies, as well as those elicited by the current COVID-19 vaccines. The large caseload has led to intensive research into prevention and treatment modalities of progressive disease, which causes severe or fatal outcomes. This extends to the search for broadly neutralizing antibodies that can counteract all known variants of the virus.

A recent preprint discusses using a combinatorial phage-display library approach to COVIID-19 antibodies. The application of this method to convalescent serum containing high titers of neutralizing antibodies led to the generation of highly potent broadly neutralizing monoclonal antibodies (mAb) against the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein, including many different variants with high transmissibility.

A preprint version of the study is available on the medRxiv* server while the article undergoes peer review.

What did the study show?

The approach used by the researchers in this study is different from the single B cell cloning approach used in most mAb sourcing experiments. The scientists isolated 18 mAbs with high neutralizing capacity against the virus, specifically with the RBD, and with little cross-competition except for two.

Most of them utilized the variable heavy chain and variable light chain genes VH1-2 and VH1-69, and VK1-39, respectively.

While heavy chain use is consistent with most earlier studies on SARS-CoV-2 antibodies, the pattern seen here is not typical of B cell repertoires in healthy individuals, which could indicate a propensity of certain germline B cell genes for the SARS-CoV-2 spike protein. The low levels of somatic hypermutation (SHM) in these antibodies also corroborate earlier studies that show little departure from germline configuration for antibodies to this virus, in particular.

They found seven mAbs that had potent neutralizing activity against the wild-type, Alpha, and Delta strains, but only four that also neutralized the immune-evading Beta variant.

One of the antibodies generated in this way is termed NE12. Its neutralizing potency was demonstrated against the Alpha and Delta variants of the virus, on a level that is on par with the ancestral strain, that is, at the picomolar level.

Another antibody, NA8, showed broad neutralizing capacity, showing picomolar activity against Beta and Omicron. Three other mAbs showed nanomolar activity against the Omicron variant as well.

Similar results were obtained by neutralization against the authentic SARS-CoV-2, using the wild-type and Beta variants. The most potent among these antibodies showed higher neutralizing capacity than currently used therapeutic monoclonal antibodies, namely, Lilly_CoV555 against the wild-type virus, which had four-fold or higher neutralizing levels. In addition, the latter showed no activity against the Beta variant.

Further, the researchers examined the ability of mAbs NE12 and NA8 to prevent and treat disease using the Syrian golden hamster animal model. At two doses, the animals were inoculated with a control set with wild-type or Beta variants of the virus. In the latter set, similar amounts of weight, >10% in both, were caused by both variants, which was prevented by treating the animals with either of these mAbs.

The viral load was less within the upper and lower respiratory tract tissues in the treated animals. Thus, NA8 protected the animals against two variants of the virus with different antigens, while NE12 protected them against the wild-type virus even at low doses.

In infected animals, too, post-inoculation treatment with these antibodies protected them against lethal or significant weight loss throughout the study, irrespective of infection with wild-type or Beta variant. However, mild weight loss was seen with the latter.

The next step was a structural study using cryo-electron microscopy (cryo-EM) to understand how these antibodies were configured to provide such ultrapotent neutralizing capacity. This showed that both the heavy and light chains disrupted binding to the RBD at different locations. This mechanism was confirmed by the competitive inhibition of binding on cells expressing the host receptor for the virus, the angiotensin-converting enzyme 2 (ACE2).

Mutations found in the Alpha and Delta variants are near or at the NE12 epitope and thus do not prevent their neutralization by the antibody. However, the E484K mutation of the Beta variant does block neutralization because it clashes with the binding heavy and light chain antibody residues. The case is similar for Omicron, with its multiple mutations in the RBD that prevent spike binding by the NE12 antibody.

In contrast, NA8 makes multiple contacts with the outer side of the RBD, reducing spike-ACE2 binding by 90%. Most of the variants tested here have mutations in residues outside the highly conserved NA8 epitope, except for L452 of the Delta variant, which explains why it has highly potent and broad neutralizing capacity against all of them. The structural analysis shows this epitope is on the outer side of the RBD, thus allowing it to bypass the mutations in the Beta and Omicron RBD.

This corroborates the observation that the rare antibodies capable of neutralizing B.1.351 recognize either the inner or the outer side of the RBD.”

What are the implications?

The combination of NE12 and NA8 has promising neutralizing potency against wild-type and variant strains of SARS-CoV-2 because their spectrum shows some differences in a complementary fashion. While the former is ultrapotent against wild-type, Alpha, and Delta, the latter has high potency against Beta and Omicron.

The ability of NA8 to neutralize the Beta strain is particularly impressive as this is among the most difficult to neutralize by currently available convalescent or therapeutic mAbs. NA8 also shows the ability to neutralize Omicron at picomolar levels, unlike the ineffectiveness of the mAbs used most commonly today for therapeutic purposes, namely, Lilly_CoV555, REGN10933, and REGN10987. While the mAb Sotrovimab does neutralize Omicron, its potency is far lower than that of NA8.

Potent and broadly neutralizing antibodies against conserved regions of the SARS-CoV-2 spike protein may play a key role against future variants of concern that evade immune control.”

*Important notice

medRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.