A striking new study examines how far antibodies elicited by vaccines against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), or by natural infection, can neutralize the closely related bat coronavirus (CoV) RaTG13.
The study, available as a preprint on the bioRxiv* server, shows that the bat CoV is, unexpectedly, neutralized more efficiently by antisera raised by SARS-CoV-2 than the latter virus itself.
*Important notice: bioRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.
Background
Several pathogenic coronaviruses have caused outbreaks of infection in humans over the last two decades. The latest of these, SARS-CoV-2, is responsible for the ongoing coronavirus disease 2019 (COVID-19) pandemic that has taken over 4.39 million lives so far.
Intensive epidemiological and ecological studies have revealed the existence of hundreds of other coronaviruses, especially in bats. Several of these use the same receptor for host cell infection, including SARS-CoV-2, that is, the angiotensin-converting enzyme 2 (ACE2).
RaTG13 is the closest relative of SARS-CoV-2, with over 96% genome identity. The researchers, therefore, focused on comparing the neutralization of these two viruses by antisera raised against the latter alone.
The repeated emergence of more infectious or neutralization-resistant variants of the virus, called variants of concern (VOCs), has focused much attention on the nature of mutations in the viral spike glycoprotein that mediates its attachment to and entry into the host cell. Especially important are mutations in the receptor-binding domain (RBD) as these may impact antibody recognition and binding.
These variants include the Alpha (B.1.1.7), Beta (B.1.351) and Delta (B.1.617.2). The Beta variant, in particular, shows a significant reduction in neutralization, thus allowing immune escape. The E484K mutation in the Beta spike RBD is key to its evasion of neutralization.
Other SARS-CoV-2 RBD escape mutations include N439, Y449, E484, F486, Q493, N501 and Y505. These sites show substituted residues in RaTG13 RBD, however.
What did the study show?
The scientists first used five sets of sera, including one negative control sample, with gradually increasing amounts of antibodies that specifically neutralize SARS-CoV-2, comprising the WHO (World Health Organization) International Reference Panel for anti-SARS-CoV-2 immunoglobulin. They found that with this set, RaTG13 was neutralized more efficiently than SARS-CoV-2 in three of four positive sera.
This was replicated with convalescent sera samples from 25 individuals with prior SARS-CoV-2 infection, acquired during the first wave. Conversely, the Beta VOC was > six-fold less efficiently neutralized than SARS-CoV-2.
When exposed to sera from healthcare workers who had got one dose of either the messenger ribonucleic acid (mRNA) vaccine BNT162b2 from Pfizer/BioNTech or the adenovirus vectored vaccine AZD1222 from Oxford-AstraZeneca, the same findings were found, with RaTG13 being neutralized twice as efficiently as SARS-CoV-2, irrespective of a history of prior infection.
The researchers write that:
Together these data provide compelling evidence that vaccination or natural infection provides cross-protective immunity to RaTG13, at least at the level of neutralising antibodies.”
Chimeras are composed of bits and pieces from different species. In this experiment, the scientists went on to use SARS-CoV-2 and RaTG13 chimeric spike proteins that contain substituted amino acids in the RBD that interacts with the ACE2 receptor. Many of these residues are implicated in escape mutations, though in some cases, the evading mutations are different in the two viruses.
When tested against the same sets of convalescent and vaccinated patient sera, the SARS-CoV-2 chimera was neutralized more efficiently than the wildtype SARS-CoV-2 spike, but the RaTG13 was a little more resistant to neutralization. These slight differences may be due to the substitutions of different residues in the chimeras.
Individual mutations showed little effect on neutralization of RaTG13, but the opposite was true for SARS-CoV-2, where N501D showed threefold higher neutralization potency, among other mutations. These residues are therefore key in determining how these pseudoviruses compare with each other in terms of neutralization by convalescent sera.
E484K mutation
The scientists also looked at the effect of the mutation E484K on immune escape in RaTG13. While the sera from fully vaccinated individuals suffered a loss of neutralization potency against SARS-CoV-2 E484K, by 1.5-fold, the RaTG13 was neutralized twice as efficiently.
Thus, E484K is a mutation with varying effects on virus neutralization depending on the spike sequence. It seems that such immune evasion mutations are driven by antibody pressures.
Reasons for increased efficiency of neutralization of RaTG13
The binding affinity of the RBD for the ACE2 receptor may be lower for RaTG13 than SARS-CoV-2, which allows for easier or more rapid dissociation from the receptor when there is a competition by high-affinity antibodies. This could explain why the N501D mutation in SARS-CoV-2 that reduces receptor usage is also associated with higher neutralization.
The RaTG13 chimera is designed to increase ACE2 binding, and, as expected, it thereby reduces neutralization. The T484K mutation does not, however, behave as predicted, increasing neutralization despite higher receptor usage. This could be explained by seeing the activity of each mutation within the overall RBD structure.
Earlier research suggests that spillover events are linked to increased human ACE2 usage. In the light of the above pattern of increased cross-neutralization when receptor binding affinity is lower, vaccination against COVID-19 could prevent such spillover of other CoVs, since most Sarbecoviruses have lower binding affinity in their natural host.
What are the implications?
The study helps understand the immune response to betacoronavirus infections and the possible course of events if similar agents emerge in the future in a world with a high level of population immunity to SARS-CoV-2.
Secondly, the emerging VOCs seem to be handled efficiently by the immune response to the parental variant, despite the many mutations in the RBD. This could be because there are few mutations that significantly alter neutralization.
Thirdly, E484K and similar escape mutations appeared because of strong antibody responses.
Our data shows that RaTG13 is potently neutralised by antibodies in convalescent sera from SARS-CoV-2 previously infected and/or vaccinated patients, suggesting that future potential spillover of RaTG13 or a closely related virus may be mitigated by pre-existing immunity to SARS-CoV-2 within the human population,” conclude the team.
*Important notice: bioRxiv 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.
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