Receptor-binding domain-associated serotypes of SARS-CoV-2

With the global circulation of SARS-CoV-2, numerous variants have continuously emerged during the past 4 years. Following the emergence of the initial Omicron BA.1 variant, many licensed COVID-19 vaccines and therapeutic antibodies, originally developed on the basis of the ancestral SARS-CoV-2 strain, have shown a decline in efficacy with time [1]. Meanwhile, various Omicron subvariants, including the XBB sublineages, have sprung up. These subvariants have demonstrated a remarkable ability to evade nearly all approved therapeutic antibodies and vaccines [2], despite updates designed to keep pace. The SARS-CoV-2 variant XBB is more immune evasive than SARS-CoV when tested against neutralizing antibodies generated to ancestral SARS-CoV-2. This prompts the question of whether SARS-CoV-2 Omicron should be considered as a unique serotype that is distinguishable from other strains serologically clustered with the ancestral SARS-CoV-2 [3].

Early in the pandemic of SARS-CoV, we pioneered the studies on receptor-binding domain (RBD)-based vaccines and nAbs against SARS-CoV. We reported, for the first time, that the RBD in SARS-CoV spike protein S1 subunit harboured six conformational nAb epitopes and that human IgG Fc-conjugated RBD (RBD-Fc) dimer could elicit extremely potent nAb responses, suggesting that RBD could serve as an important target for the development of SARS-CoV vaccines and nAb drugs (Figure 1(a)) [4–6]. These foundational investigations played a pivotal role in shaping the development of the current COVID-19 vaccines and nAb drugs.

Figure 1. Classification of SARS-CoV-2 RBD-associated serotypes. a. The capacity to induce neutralizing antibodies among S2, S, S1 and RBD of SARS-CoV-2 is revealed in the following order: RBD>S1>S >S2, which justifies why RBD was selected for serotype classification. b. Five serotypes of SARS-CoV-2. Blue, red, yellow, green, purple and grey circles represent the coverage of neutralizing antibodies for serotypes Ia, Ib, II, III, IV and V, respectively.

Early in the pandemic of SARS-CoV-2, Gao and colleagues developed a tandem-repeat fusion RBD dimer vaccine [7], eventually becoming the first world-approved protein-based COVID-19 vaccine. Furthermore, because approximately 90% of neutralizing antibodies in the plasma of convalescent individuals target RBD, mutations predominantly manifest in this region under immune pressure. Therefore, the RBD is the most crucial antigen in developing SARS-CoV-2 vaccines, and classifying SARS-CoV-2 variants based on the RBD is thus justified.

Recently, Wang and colleagues reached a milestone in the coronavirus field by systematically classifying the serotypes of SARS-CoV-2 variants [8]. Their approach involved immunizing mice with an mRNA vaccine expressing the RBD from one of the 23 representative SARS-CoV-2 variants. Through a comprehensive assessment of cross-neutralizing activities against these variants, they successfully categorized SARS-CoV-2 into five distinct serotypes (Figure 1(b)). Serotype I encompasses both Ia (WT, Alpha, Lambda, Epsilon, Delta) and Ib (Beta, Theta, Gamma, Zeta, Eta, Mu, Kappa). The Omicron subvariants were further delineated into four serotypes, including serotype II (BA.1.1, BA.1), serotype III (BA.2/BA.2.12.1/BA.275), serotype IV (BA.5/BF.7/BQ.1/BQ.1.1) and serotype V (XBB) (Figure 1(b)). Immunization with RBD from Ia proved effective in eliciting potent nAb against SARS-CoV-2 variants within both Ia and Ib. Immunization with RBD from Ib demonstrated a broader spectrum of cross-nAbs against variants spanning serotypes Ia, Ib, II, and III. The RBD of BA.1 and BA.1.1 (serotype II) exclusively induced nAbs against themselves. serotype III RBD-elicited nAb could cross-neutralize Omicron subvariants in serotypes II and III. Mouse antisera against RBD in serotype IV neutralize themselves well, with limited cross-neutralization activities against Omicron subvariants in serotype III. Additionally, the RBD of XBB in serotype V could elicit cross-nAb against Omicron subvariants from serotypes V, IV, and III. Thus, the reported neutralization spectra of these five serotypes appear to form the basis for the development of pan-SARS-CoV-2 vaccines. Moreover, considering the antigenic distance of RBD, the strategic selection of three RBDs from serotypes Ib, IV, and V could sufficiently induce broad nAb against all 23 SARS-CoV-2 variants. This, in turn, means that multivalent vaccines developed by utilizing current vaccine platforms, such as trivalent vaccines or nanoparticles co-displaying these three RBDs [9], might be effective in combating most of the circulating Omicron subvariants. However, the recently emerged BA.2.86 and JN.1 variants may exhibit antigenic properties that are significantly different from those observed previously. Therefore, further classification of these newly emerged variants is necessary.

Gao and colleagues [10] along with our team [11] have revealed that booster immunization and extended intervals between vaccine doses can enhance the potency and breadth of nAbs. Given that the mice in this study received only two doses of mRNA vaccines, it would be intriguing to investigate whether additional booster immunizations or altered boosting intervals could yield different neutralization spectra. Additionally, exploring the consistency of the five serotypes with other vaccine platforms, such as subunit vaccines, would be a crucial avenue for further investigation. Our previous study further demonstrated that the addition of a strong adjuvant (CF501) could significantly elicit broadly neutralizing antibodies (BnAbs) targeting the conserved epitope on RBD to cross-neutralize most Omicron subvariants [11,12]. Neutralizing antibodies recognizing quaternary epitopes derived from the Spike trimer have also been reported [13]. Therefore, further classification of SARS-CoV-2 sera should take into account the factors associated with these quaternary epitopes. It should be noted that the immune imprinting induced by current COVID-19 vaccines based on wild-type SARS-CoV-2 raises concerns about compromised nAb responses against Omicron subvariants, presenting a substantial challenge for updating boosters. However, Wang and colleagues’ research focused solely on idealized conditions and verification within animal models, without addressing the present concern of immune imprinting. It would be constructive to identify a serotype suitable for an updated vaccine, employing rational design for booster vaccinations based on antigenic distance. Finally, it is worth noting that vaccine-induced nAbs may differ between mice and humans. Accordingly, non-human primates could serve as a valuable model for further confirmation of these serotypes.

Apart from SARS-CoV-2 variants, sarbecoviruses also contain SARS-CoV and multiple SARS-related coronaviruses (SARSr-CoVs), such as WIV1, Rs3367 and RsSHC014 from bats, and GX/P2 V/2017 from pangolin coronaviruses. Notably, multiple SARSr-CoVs can bind to human ACE2, posing an ongoing threat of cross-species transmission that warrants attention. This underscores the urgent need for the additional development of pan-sarbecovirus vaccines and antibodies to address the continuous risk these viruses pose to human health. This means that the serotyping of sarbecoviruses, encompassing SARS-CoV-2 variants and other SARSr-CoVs, is crucial for facilitating the development of broad-spectrum vaccines and nAbs against sarbecoviruses. It is noteworthy that Gao and colleagues also demonstrated that mice immunized with the tandem-repeat RBD of wild-type SARS-CoV-2 (ZF2001) generated cross-nAbs against pangolin coronavirus GX/P2 V/2017, thereby alleviating pathological damage in the lungs [14]. This suggests the potential classification of pangolin coronavirus into serotype Ia or Ib. Another limitation of this serotype classification system is the lack of considering the antigenicity and immunogenicity of neutralizing epitopes in the conserved regions in S2 subunit of spike protein [15], which may be important components in some broad-spectrum pan-sarbecovirus or pan-betacoronavirus vaccines. Therefore, more comprehensive and systematic studies are essential for the detailed classification of serotypes within the sarbecovirus family.

In summary, the five serotypes of SARS-CoV-2 systematically classified by Wang and colleagues are of great significance in enhancing the understanding the antigenicity and immunogenicity of RBD in spikes of SARS-CoV-2 and for updating vaccine antigens against the newly emerged variants. Conducting additional research on serotyping sarbecoviruses, considering variations in doses, booster intervals, immunoenhancing agents or strategies, and employing diverse animal models, is imperative for crafting effective responses to the evolving landscape of these viruses.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Additional information

Funding

Z.L. is supported by the National Key Research and Development Program of China (2022YFC2305800). S.J., L.L. and Z.L. are supported by grants from the National Natural Science Foundation of China [92169112, 82041036 and 82202490].