What’s New with Anti-SARS-CoV-2 Antibodies?

14 July, 2023

In the ongoing cat-and-mouse game between monoclonal antibody therapeutics and viral evolution, triumphs are sporadic and short-lived. Whether antibody therapies work to neutralize the SARS-CoV-2 virus is heavily affected by mutations in the spike protein of novel viral variants. After strong initial successes, almost all the available monoclonal antibody therapeutics now appear to have lost efficacy against the majority of circulating Omicron subvariants in the U.S., and their FDA EUAs have been revoked. No monoclonal antibody is currently approved in the U.S. for COVID-19 treatment, post-exposure prophylaxis or pre-exposure prophylaxis. Efforts are underway both to develop new antibody therapies (Yuan, May 2020) targeting epitopes that may be less changeable with variant evolution (e.g., ClinicalTrials.gov NCT05675943, NCT05648110) and to better understand the role of the non-neutralizing Fc effector function of existing monoclonal antibodies against evolving Omicron sublineages.

Intranasal SA-58 Shows Promising Human Results

Novel routes of administration other than intravenous are of interest with all COVID-19 therapeutics to avoid logistical and health system strain. A recent Chinese study (Song, December 2023) randomized participants (all healthy construction site workers) with known COVID exposure in the past 3 days to receive either placebo or SA58, a broad-spectrum monoclonal antibody against SARS-CoV-2 manufactured by Sinovac Life Sciences Company. SA58 is formulated as an intranasal spray and is reported to be fairly durable in neutralizing activity (though with slightly reduced efficacy against Omicron variants XBB and BA.2.75). The novel route of administration means that no detectable drug is present in the bloodstream, though it persists in the nasopharynx with a half-life of 12 to 27 hours.

The study took place over two weeks in late 2022, ending two days after China formally rolled back the country’s previously stringent “zero-COVID” pandemic restrictions. According to some estimates, this resulted in 250 million infections in the first 20 days of December 2022, accounting for almost a fifth of China’s 1.4-billion-person population and likely representing the largest global COVID outbreak to date.

The monoclonal spray was administered via one spray in each nostril on a given day of exposure every 3-4 hours for 5-6 administrations with a maximum 3 days of administration. Participants also self-collected daily nasopharyngeal/throat/nasal swabs for SARS-CoV-2 RT-PCR.

Laboratory-confirmed symptomatic COVID-19 developed in 7 of 824 participants (0.22 per 100 person-days) in the SA58 group vs. 14 of 299 (1.17 per 100 person-days) in the placebo group, resulting in an estimated efficacy of 80.82% (95%CI 52.41%−92.27%). There were 32 SARS-CoV-2 reverse transcriptase polymerase chain reaction (RT–PCR) positives (1.04 per 100 person-days) in the SA58 group vs. 32 (2.80 per 100 person-days) in the placebo group, resulting in an estimated efficacy of 61.83% (95%CI 37.50%−76.69%). (The study excluded from the efficacy analysis those 99 participants who tested positive for SARS-CoV-2 before or within the 24 hours after study product administration.)

Looking at just PCR positives regardless of symptoms, there was also a reduction in proportion of participants who were SARS-CoV-2 RT-PCR positive, from 32/299 in the placebo group (2.8 per 100 person-years) to 32/824 (1.04 per 100 person-years) in the SA58 arm (estimated efficacy of 61.83% [95% CI, 37.5%-76.69 %]).

These results raise the intriguing possibility of a self-administered therapeutic with no known problematic drug-drug interactions, delivered topically intranasally as a spray 5 to 6 times a day for 3 days following a known COVID exposure, with high efficacy at preventing symptomatic confirmed COVID-19 as well as reducing the likelihood of having SARS-CoV-2 virus recovered from the nasopharynx regardless of symptoms.

Of course, doing anything 5 to 6 times a day can be challenging, and interestingly, a previous study of SA58 among medical personnel in designated COVID-19 “fever hospitals” in Hohhot City, Inner Mongolia (preprint, not yet published), only recommended administering the nasal spray every 6 hours, 1 to 2 times per day, and still reported a 77% efficacy (however, that study required administration for a total of 30 days rather than 3 — our $0.02 is that anything that requires daily effort for a shorter period of time is generally more tolerable).

While preclinical studies of various intranasal monoclonal antibodies targeting SARS-CoV-2 in animals are rapidly accumulating and have demonstrated promise in challenge studies (Rompay, July 2021; Halwe, July 2021; Wang, January 2023; Zhang, January 2023; Seow, June 2023), the SA58 study represents one of the first positive efficacy studies in humans of an intranasal antiviral monoclonal antibody against SARS-CoV-2. Intranasal avenues could offer a safety benefit: It is rational to expect that therapeutics that are delivered to the primary reservoir of respiratory viruses (the nasopharynx) rather than systemically would have minimal systematic absorption and therefore avoid some of the systemic toxicities that can be seen with orally or intravenously delivered drugs. Indeed, the observed adverse events in the SA58 study were all mild and were observed at similar rates in the two arms, occurring in 25% and 22% of participants in the SA58 and placebo arms, respectively. Regardless, more options for method of delivery are always nice and are likely to increase uptake (as we have learned with contraception).

Another Novel Intranasal Approach: The Trimeric Sherpabody

One intranasally-administered monoclonal therapeutic approach detailed in a recent Nature article (Mäkelä, March 2023) uses a novel trimeric “sherpabody” (SH3 recombinant protein affinity). This represents part of a movement away from studying monoclonal antibodies towards working with smaller antibody fragments, including “nanobodies” (or the variable heavy chain region of heavy-chain antibodies). This could be a potentially more scalable, easier-to-manufacture approach, and nanobodies have shown promise at neutralizing SARS-CoV-2 in preclinical studies (Wrapp, May 2020; Xiang, December 2020; Xu, June 2021).

Sherpabodies are reportedly even easier to make and are small, scaffold-targeting proteins less than 60 amino acids in length that have an affinity for the SH3 domain on molecules in the body like phospholipase, tyrosine kinases and other adaptor proteins. They are known as “antibody mimetics,” molecules that can bind to antigens just like antibodies but are not produced by the body’s immune response and bear no structural similarity to antibodies.

The particular sherpabody under study in this paper, TriSb92, was designed to target a highly conserved region of the SARS-CoV-2 spike antigen receptor binding domain (RBD). It was chosen because of its strong binding to both the SARS-CoV-2 and SARS-CoV-1 RBD, suggesting a target that is likely to be conserved across many species of sarbecoviruses and many variants of SARS-CoV-2. It showed high (subnanomolar) potency against the virus’s ancestral strain (in vitro IC50 a remarkable 0.24nM), Beta, Delta, and Omicron BA.1, BA.5 variants of concern (IC50 of 0.11nM, 0.18nM, 0.08 nM, and 0.82nM, respectively). These results with live viruses were corroborated by testing it against pseudoviruses engineered to resemble emerging variants like BF.7, BQ.1.1 and XBB, and finding very similar inhibitory potency (IC50 of 0.18nM, 1.74 and 1.19, respectively).

The mechanism of neutralization was found to be that TriSb92 induces a change in the S2 subunit of the spike protein, not affecting viral attachment to cells, but preventing infection nonetheless. When TriSb92 was administered to mice intranasally and then challenged with intranasal SARS-CoV-2 (B.1.351 variant), there was complete absence of SARS-CoV-2 RNA in nasal mucosa or lungs of treated animals 2 days later at necropsy, whereas virus was detected throughout these anatomic areas of the control animals. This means it has efficacy as pre-exposure prophylaxis or perhaps early therapeutic efficacy in mice. And when a lethal dose of a pathogenic strain of SARS-CoV-2 was administered after intranasal TriSb92, all animals that got the sherpabody maintained their weight and survived, whereas all controls lost ≥15% of their body weight and were euthanized. And when they looked with cryogenic electron microscopy to see where exactly TriSb92 binds, it appeared to bind to a region next to the ACE2 binding site, and that binding region differs only by a single amino acid between SARS-CoV-2 and SARS-CoV-1! Highly conserved indeed, and it doesn’t appear to be further mutated even among the more recent Omicron variants. This is notably unlike certain monoclonal antibodies that target the ACE2 binding region itself and get knocked out by the mutations that frequently occur in this region. All said, a promising candidate to be sure, but experiments in humans are needed to be even surer.

Different Ways to Think About mAb Efficacy

Adding even more dimensionality to the horizon of monoclonal therapeutics for SARS-CoV-2 is the question of whether developed monoclonals may have efficacy that is mediated not by neutralizing capacity, but by non-neutralizing function — for example, elicitation of more potent Fc effector function.

In vitro data from cell culture experiments have consistently shown that sotrovimab has a vastly reduced ability to inhibit recent subvariants like BQ.1.1. But what about in an animal with an immune system? Preprint data suggests that the previously EUA-authorized (now revoked) monoclonal antibody sotrovimab continues to robustly bind all variants of Omicron including B.Q.1.1 and XBB.1, enhances Fc-dependent effector cell functions in the body’s defense against them and in fact retains the ability to neutralize them within living organisms.

[Immunology 101 interlude: What this means is that the constant, heavy chain “stalk” of the “Y”-shape that is an IgG antibody (known as the Fc region, whereas the “arms” of the Y are called the Fv and Fab regions and bind antigens) binds more strongly to Fc receptors on effector cells in the setting of sotrovimab. These effector cells (which can be NK cells, macrophages, monocytes and eosinophils), upon latching on, perform a variety of functions, including release of cytotoxins to zap and destroy the cell that is bound to the other end of the antibody.]

Sotrovimab was shown in the same preprint to protect mice that are challenged with latter-day Omicron variants such as BQ.1.1, and in another preprint, to protect hamsters against BQ.1.1.

A recent article followed up those findings, which were observed in mice, by challenging nonhuman primates with Omicron and examining whether sotrovimab protected the monkeys against infection with BQ.1.1 (Hérate, June 2023). It is important to remember that direct blocking or neutralizing activity by antibodies is just one of a wide array of mechanisms that result in antibody-mediated immune defense, or rather, that antibodies are not just lone-wolf assassins — they have henchmen and are part of a vast organized syndicate that, despite clues here and there, remains poorly understood. But back to the monkeys — three cynomolgus macaques, to be precise. They were given sotrovimab IV 96 hours before intranasal and intratracheal challenge with SARS-CoV-2 BQ.1.1. Pharmacokinetics showed that the monkeys had similar serum sotrovimab exposures as humans in the COMET-ICE trial. All of the control animals had viral RNA in tracheal and BAL fluid, but none of the three treated monkeys did (viral RNA was below the limit of detection in both trachea and BAL out to 10 days post-challenge [P=0.0238]). The conclusion of the authors was that sotrovimab may be considered for use in humans against BQ.1.1 if ritonavir-boosted nirmatrelvir cannot be used.

Now, we can quibble about the conclusion of anything definitive about human clinical treatment from monkey studies, but this work at the very least calls into question our ability to extrapolate prophylactic efficacy (or lack thereof) from in vitro experiments testing neutralization efficiency of developed monoclonal antibodies using pseudoviruses bearing variant S protein. It is worth remembering too that, like Walt Whitman, the Omicron sublineage itself contains multitudes within it (i.e., great heterogeneity — in fact, the variants that have emerged most recently to dominate the globe have been able to do so precisely because they have the largest number of S-protein mutations and are so different from original and early strains). It is likely the case that just as in vivo may not correlate precisely with in vitro, the neutralizing efficacy of a given therapeutic against one Omicron variant should perhaps not be assumed to apply to all Omicron variants, particularly once that therapeutic has been out of circulation for a while.

Does In Vitro Equal In Vivo?

Fragmented (and new-fangled!) antibodies aside, the pipeline is active for good old-fashioned anti-SARS-CoV-2 monoclonal antibodies, as demonstrated in a 2022 article describing the in vivo efficacy in mice of two mAbs — S309 (made by Vir, otherwise known as “sotrovimab’s cool dad,” as it is the parent compound of sotrovimab, formerly VIR-7831) and AZD7442 (made by AstraZeneca, also known as “Evusheld,” the combination of tixagevimab and cilgavimab) — against Omicron strains BA.1, BA.1.1 and BA.2 (Case, July 2022).

The S309 mAb binds a conserved epitode on the RBD of the spike protein separated from the RBM receiver, whereas the two mAbs in AZD7442 bind two different parts of the RBM. Neutralization curves in Vero-TMPRSS2 cells showed significant reduced potency (increased EC50) of slightly modified versions of these antibodies (with Fc substitutions to increase serum half-life and reduce Fc effector functions out of a desire to prevent antibody-dependent disease enhancement) against newer Omicron strains compared to the historical/ancestral SARS-CoV-2 WA1/2020 D614G strain (Loo, March 2022). While S309 retained neutralization efficacy against BA.1 and BA.1.1, it had less activity against BA.2, and AZD7442 had reduced efficacy against all the Omicron strains tested.

However, when it came to live transgenic mice that were bioengineered to express the ACE2 receptor and therefore were susceptible to COVID infection, a single intraperitoneal dose of the S309 mAb one day prior to intranasal challenge reduced BA.1, BA.1.1 and BA.2 viral loads in the lower respiratory infection, albeit to a lesser degree from BA.1, BA.1.1 and BA.2 than against D614G. For AZD7442, it reduced the burden of virus in the lower respiratory tract against BA.2 and D614G, but less efficiently reduced it for BA.1 and BA.1.1. Interestingly, AZD7442 had little impact on viral load in the nasopharynx, which makes sense given that other animal studies have shown that mAb concentrations in nasopharyngeal washes are 0.1% of the concentrations in serum (Cobb, March 2022). (Cue nasal sherpabodies!) Measurement of cytokines and chemokines in the lungs of treated mice were lower than in untreated mice, for the most part. Also, on histopathological analysis, untreated animals had evidence of pneumonia (airspace consolidations, infiltration of immune cells and fluid) whereas treated animals did not.

Intriguingly, the two mAbs seemed to have different mechanisms of action against the virus. The AZD7442 had a modified heavy chain that means it binds extremely poorly to Fc receptors and complement parts, and therefore, cannot summon its henchmen! It must work alone, and its efficacy boils down to virus neutralization and blocking virus from entering cells. However, S309 had no such modification, and was therefore likely able to use Fc effector function interactions to help kill virus. That is why the correlation between in vitro neutralization and in vivo protection was so much worse for S309 (R2 of 0.2264) than it was for AZD7442 (R2 of 0.9369) — because its efficacy was not defined solely by its neutralizing ability.

So what was the mechanism of S309’s viral killing? Well, when they jiggered with it a bit to modify its heavy chain too, and take away its ability to bid to Fc receptors, guess what? It was no longer able, in an assay of antibody-dependent cellular cytotoxicity, to zap virally infected cells via the summoning of natural killer cells or antibody-dependent cellular phagocytosis, whereas unmodified S309 was. And this was recapitulated in the mice, in whom the modified S309 antibody had only modest protective efficacy against ancestral strain and none against Omicron BA.1 or BA.2; it also had inflammatory cytokine and chemokine levels in lung that were just as high as in controls. All of this was supportive of the concept that the protection against viral infection afforded by S309 in vivo is achieved via Fc-mediated effector cell functions rather than direct neutralization.

Lastly, the authors tested therapeutic efficacy by giving first virus and then (one day later) both antibodies. Both S309 and AZD7442 for the most part reduced viral RNA in the upper and lower respiratory tracts of treated animals more than controls. The authors sum it up well when they say, “antibody countermeasure efficacy requires continued monitoring.” Stay tuned.

Horizon Scan

As Spock reminds us, “change is the essential process of all existence” — and this applies not only to viruses but also to the evolving tactics and strategies of those who hope to fight them.

Despite the well-documented issue of immunoevasion, the horizon appears bright for anti-SARS-CoV-2 monoclonals in a variety of formulations and uses, particularly as post-exposure prophylaxis against infection with Omicron variants. This would likely have highest applicability among immunocompromised people who cannot mount a vaccine response, indicating a need to study performance in immunocompromised populations.

Perhaps we can sum this all up by harboring high hopes, but moderate to low expectations — suggested by some to be the recipe for great happiness in a world where Happiness=Reality Minus Expectations. However, some others have countered that a higher-utility and more effective formula may be Happiness=Finding the Opportunity for Learning and Growth | Below-Expectations Event. And in precisely this moment in COVID-19’s trajectory, when viral evolution prompts first human disappointment and then human innovation, real though modest advances deserve our (happy) salute.

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