The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) – the causative pathogen of coronavirus disease 2019 (COVID-19) – is only one of the seven pathogenic coronaviruses (CoVs) to have emerged among humans over less than 20 years. The massive scale of the ongoing COVID-19 pandemic has led to intensive research on the creation of pan-coronavirus vaccines that will protect against related but divergent viruses from this group of viruses.

A new study provides encouraging proof of the feasibility of this project, showing that both natural infection with and vaccination against SARS-CoV-2 are associated with an increase in cross-reactive antibodies against other CoVs.

Study: Cross-reactive antibodies after SARS-CoV-2 infection and vaccination. Image Credit: ktsdesign / Shutterstock

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

Background

The SARS-CoV-2 vaccine is based on the viral spike protein, a trimeric glycoprotein composed of three spike protomers. Each has an S1 and S2 subunit, the first containing the receptor-binding domain (RBD) and the second the fusion peptide. Both are essential for viral engagement with and entry into the host cell.

The spike protein sequence of SARS-CoV-2 is 75% identical with that of the earlier SARS-CoV, and 50% identical to the Middle East respiratory syndrome CoV (MERS-CoV) spike sequence. It has 25% to 30% identity with the spike proteins of various less pathogenic human CoVs (hCoVs) that cause seasonal colds.

Despite this relatively low identify, cross-reactive antibodies against the hCoVs have been observed in the serum samples of many COVID-19 patients.

SARS-CoV-2 infection boosts cross-reactivity

In the current experiment, serum samples from SARS-CoV-2-infected patients over a spectrum of severity, collected 4-6 weeks after symptom onset, contained antibodies to the viral spike protein at approximately 1000-fold higher titers than found in healthy donor serum collected before the pandemic.

Antibody levels were strongly correlated with disease severity, being four-fold higher in hospitalized patients compared to others and eight-fold in the oldest age group compared to the youngest, as expected, since age is associated with increased risk of severe disease.

Antibody levels were also strongly linked to neutralizing capacity.

Convalescent COVID-19 serum also contained higher titers of binding antibodies against all human coronavirus proteins, SARS-CoV, MERS-CoV, hCoV-OC43, hCoV-HKU1, hCoV-229E and hCoV-NL63, than pre-pandemic healthy donor serum. However, the degree of cross-reactivity was variable, with a 123-fold increase in SARS-CoV reactivity vs. 11-fold for MERS-CoV, but only 2-4-fold for the seasonal hCoVs.

S2 domain is the prime target

The greatest binding affinity was for the SARS-CoV-2 spike protein. When 92% of these antibodies were removed, there was a 61% reduction in SARS-CoV binding antibodies vs. 25% for MERS-CoV. For the seasonal hCoVs, insignificant reductions were observed, albeit, individually, some patients did show a loss of binding antibodies by 34% to 70%.

This reduction was absent for antibodies to the spike proteins of other hCoVs found in pre-pandemic sera, indicating that SARS-CoV-2 induces cross-reactive specific antibodies. As expected, the greater the identity, the greater the cross-reactivity.

However, neutralizing activity was not associated with the cross-reactive antibodies, neither did these contribute to disease severity.

The use of separate S1 and S2 domains to deplete the antibodies to these subunits separately showed that the S2 was the main target of the cross-reactive SARS-CoV-2 antibodies. Once S2-reactive antibodies were depleted, cross-reactivity was reduced by 50% and 20% for SARS-CoV and MERS-CoV/hCoV-OC43, respectively.

On an individual basis, cross-reactivity declined by up to 80% for these viruses, and by 60% to 70% for hCoV-HKU1 and hCoV-229E. S1 depletion consistently caused little change.

Again, as expected, S2 sequence identity was closely associated with loss of cross-reactivity.

Vaccination elicits cross-reactivity

A macaque vaccination experiment was used to distinguish cross-reactive antibodies elicited de novo to SARS-CoV-2 by natural infection from a cross-boost given to pre-existing memory B cells from prior hCoV infection. Interestingly, all animals developed antibodies to all hCoV spike proteins.

The titers to SARS-CoV, MERS-CoV and hCoV-OC43 spike proteins increased by approximately 3,300-, 170- and 100-fold, respectively, from the baseline levels, beginning from just two weeks after the first vaccine dose. Antibodies to hCoV-HKU1 and hCoV-229E increased by 16- to 40-fold, and hCoV-NL63 by six-fold only.

Here again, the S2 subunit was the primary target, with S2 antibodies accounting for 75% to 99% of cross-reactive antibodies to the other human CoVs.

The team writes:

Together, these results demonstrate that the SARS-CoV-2 S protein is capable of inducing cross-reactive antibodies to both alpha and beta hCoVs, in macaques that we assume have no pre-existing hCoV immunity.”

What are the implications?

The vaccine used in this experiment was based on a pre-fusion stabilized SARS-CoV-2 spike protein, indicating that the currently used vaccines may be inducing an increase in cross-reactive antibodies. Nonetheless, the loss of correlation with neutralization is a red flag since it could cause Antibody Dependent Enhancement (ADE) of infection.

Newer vaccines should target the S2 subunit, considering its potential for cross-reactive antibodies. Already, the presence of neutralizing antibodies to S2, with protective activity against SARS-CoV-2, has been noted. It is possible that S2 antibodies may trigger antibody effector functions, accounting in part for this protection.

With the use of other novel vaccine designs, such cross-reactivity may be amplified and broadened.

The results from this study on the presence and specificity of cross-reactive antibodies to other hCoVs after SARS-CoV-2 infection and vaccination, emphasize the feasibility of broad coronavirus vaccines and may guide future vaccine designs.”

*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.

Written by

Dr. Liji Thomas

Dr. Liji Thomas is an OB-GYN, who graduated from the Government Medical College, University of Calicut, Kerala, in 2001. Liji practiced as a full-time consultant in obstetrics/gynecology in a private hospital for a few years following her graduation. She has counseled hundreds of patients facing issues from pregnancy-related problems and infertility, and has been in charge of over 2,000 deliveries, striving always to achieve a normal delivery rather than operative.