ABSTRACT The naturally occurring mutation E484D in the spike (S) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can render viral entry ACE2 independent and imdevimab resistant. Here, we investigated whether the cellular proteins ASGR1, DC-SIGN, and TMEM106B, which interact with the viral S protein, can contribute to these processes. Employing S protein-pseudotyped particles, we found that expression of ASGR1 or DC-SIGN jointly with TMEM106B allowed for robust entry of mutant E484D into otherwise non-susceptible cells, while this effect was not observed upon separate expression of the single proteins and upon infection with SARS-CoV-2 wild type (WT). Furthermore, expression of ASGR1 or DC-SIGN conferred ACE2 independence and imdevimab resistance to entry of mutant E484D but not WT, and entry under those conditions was dependent on endogenous TMEM106B. These results suggest that engagement of certain cellular lectins can direct SARS-CoV-2 mutant E484D to an ACE2-independent, TMEM106B-dependent entry pathway that is not inhibited by imdevimab. IMPORTANCE The interaction of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein with the ACE2 receptor determines the viral cell tropism and is the key target of the neutralizing antibody response. Here, we show that SARS-CoV-2 with a single, naturally occurring mutation in the spike protein, E484D, can use the cellular lectins ASGR1 and DC-SIGN in conjunction with TMEM106B for ACE2-independent entry and evasion of therapeutic antibodies. These results suggest that engagement of cellular lectins might modulate target cell choice of SARS-CoV-2 and might allow evasion of certain neutralizing antibodies.

The interaction of the SARS-CoV-2 spike protein (S) with the cellular receptor ACE2 is considered essential for infection and constitutes the key target for antibodies induced upon infection and vaccination. Here, using a surrogate system for viral entry, we provide evidence that a naturally occurring mutation can liberate SARS-CoV-2 from ACE2-dependence and that ACE2-independent entry may protect the virus from neutralization by an antibody used for COVID-19 therapy.

The SARS-CoV-2 spike (S) protein engages ACE2 for cell entry, and the S protein/ACE2 interface is an important target for neutralizing antibodies.In the course of the COVID-19 pandemic, SARS-CoV-2 variants have emerged that harbor mutations in the S protein, which confer neutralization resistance and allow viral spread in immunologically nonnaive populations.The most prominent example is the highly mutated Omicron variant, which infects convalescent or vaccinated individuals with unprecedented efficiency [1, 2], highlighting the threat that emerging SARS-CoV-2 variants pose to efforts to control the pandemic.Recently, a novel SARS-CoV-2 variant, B.1.640.2, which harbors an unusually high number of mutations in the S protein, was detected in southern France [3].Here, we analyzed the impact of these mutations on viral cell tropism, ACE2 interactions, and antibodymediated neutralization.The B.1.640.2 variant was detected in November 2021 in a vaccinated adult patient who had returned from Cameroon and exhibited mild respiratory symptoms [3].B.1.640.2 infection was also detected in 12 other individuals living in the same area [3].The B.1.640.2 S protein analyzed in the present study harbors 13 amino acid substitutions and two deletions (Fig. 1a,b).Three amino acid substitutions and two deletions are located in the N-terminal domain of the S protein (Fig. 1a,b), while six amino acid substitutions are found in the receptor-binding domain (RBD), the portion of the S protein that binds to ACE2 (Fig. 1a,b).While some of these mutations likely alter epitopes for neutralizing antibodies, the Y449N substitution in the RBD is known to impair ACE2 binding [4].For analysis of the B.1.640.2 S protein, we employed rhabdoviral pseudotypes, which faithfully mimic SARS-CoV-2 entry and antibody-mediated neutralization [5].We first asked whether particles pseudotyped with B.1.640.2 S protein (B.1.640.2 pp ) can enter cell lines commonly used for SARS-CoV-2 research.The S proteins of variant B.1, which circulated early in the pandemic, and the Omicron variant (sublineage BA.1) served as controls.All particles entered Huh-7 (human liver) and Vero cells (African green monkey kidney) robustly and at comparable rates, and entry efficiency was not increased by the expression of TMPRSS2, an S protein-activating host cell protease (Fig. 1c).Furthermore,

The Omicron variant of SARS-CoV-2 evades antibody-mediated neutralization with unprecedented efficiency. At least three Omicron sublineages have been identified-BA.1, BA.2, and BA.3-and BA.2 exhibits increased transmissibility. However, it is currently unknown whether BA.2 differs from the other sublineages regarding cell entry and antibody-mediated inhibition. Here, we show that BA.1, BA.2, and BA.3 enter and fuse target cells with similar efficiency and in an ACE2-dependent manner. However, BA.2 was not efficiently neutralized by seven of eight antibodies used for COVID-19 therapy, including Sotrovimab, which robustly neutralized BA.1. In contrast, BA.2 and BA.3 (but not BA.1) were appreciably neutralized by Cilgavimab, which could constitute a treatment option. Finally, all sublineages were comparably and efficiently neutralized by antibodies induced by BNT162b2 booster vaccination after previous two-dose homologous or heterologous vaccination. Collectively, the Omicron sublineages show comparable cell entry and neutralization by vaccine-induced antibodies but differ in susceptibility to therapeutic antibodies.

SARS-CoV-2 continues to evolve into variants of concern (VOC), with greatest variability in the multidomain, entry-facilitating spike proteins. To recognize the significance of adaptive spike protein changes, we compare variant SARS-CoV-2 virus particles in several assays reflecting authentic virus-cell entry. Virus particles with adaptive changes in spike amino-terminal domains (NTDs) are hypersensitive to proteolytic activation of membrane fusion, an essential step in virus-cell entry. Proteolysis is within fusion domains (FDs), at sites over 10 nm from the VOC-specific NTD changes, indicating allosteric inter-domain control of fusion activation. In addition, NTD-specific antibodies block FD cleavage, membrane fusion, and virus-cell entry, suggesting restriction of inter-domain communication as a neutralization mechanism. Finally, using structure-guided mutagenesis, we identify an inter-monomer β sheet structure that facilitates NTD-to-FD transmissions and subsequent fusion activation. This NTD-to-FD axis that sensitizes viruses to infection and to NTD-specific antibody neutralization provides new context for understanding selective forces driving SARS-CoV-2 evolution.

Since the beginning of the COVID-19 pandemic, multiple SARS-CoV-2 variants have emerged. While some variants spread only locally, others, referred to as variants of concern, disseminated globally and became drivers of the pandemic. All SARS-CoV-2 variants harbor mutations relative to the virus circulating early in the pandemic, and mutations in the viral spike (S) protein are considered of particular relevance since the S protein mediates host cell entry and constitutes the key target of the neutralizing antibody response. As a consequence, mutations in the S protein may increase SARS-CoV-2 infectivity and enable its evasion of neutralizing antibodies. Furthermore, mutations in the S protein can modulate viral transmissibility and pathogenicity.

The SARS-CoV-2 omicron (B.1.1.529) variant has rapidly become globally dominant, displacing the previously dominant delta (B1.617.2) variant. The viral spike (S) protein is the key target of the neutralising antibody response, and the omicron variant harbours more than 35 mutations in the S protein, which allow highly efficient evasion from neutralising antibodies.1Hoffmann M Krüger N Schulz S et al.The omicron variant is highly resistant against antibody-mediated neutralization: implications for control of the COVID-19 pandemic.Cell. 2022; 185: 447-456Summary Full Text Full Text PDF PubMed Scopus (271) Google Scholar In keeping with these findings, the omicron variant efficiently spreads in populations with a high percentage of convalescent or vaccinated individuals.2Altarawneh HN Chemaitelly H Hasan MR et al.Protection against the omicron variant from previous SARS-CoV-2 infection.N Engl J Med. 2022; (published online Feb 9.)https://doi.org/10.1056/NEJMc2200133Crossref PubMed Scopus (87) Google Scholar, 3Collie S Champion J Moultrie H Bekker LG Gray G Effectiveness of BNT162b2 vaccine against omicron variant in South Africa.N Engl J Med. 2022; 386: 494-496Crossref PubMed Scopus (233) Google ScholarThe three main subvariants of the omicron variant are BA.1, BA.2, and BA.3. Initial data suggest that BA.2 might have a growth advantage over BA.1,4Mahase E COVID-19: what do we know about omicron sublineages?.BMJ. 2022; 376: o358Crossref PubMed Scopus (16) Google Scholar posing a rapidly increasing threat to health systems. The omicron subvariants display remarkable differences regarding S protein mutations, particularly with respect to the N-terminal domain and the receptor-binding domain (appendix pp 2–3), which are known to harbour key epitopes of neutralising antibodies.5McCallum M De Marco A Lempp FA et al.N-terminal domain antigenic mapping reveals a site of vulnerability for SARS-CoV-2.Cell. 2021; 184: 2332-2347Summary Full Text Full Text PDF PubMed Scopus (330) Google Scholar, 6Piccoli L Park YJ Tortorici MA et al.Mapping neutralizing and immunodominant sites on the SARS-CoV-2 spike receptor-binding domain by structure-guided high-resolution serology.Cell. 2020; 183: 1024-1042Summary Full Text Full Text PDF PubMed Scopus (570) Google Scholar Here, we compared BA.1, BA.2, and BA.3 for sensitivity to neutralisation by antibodies induced by infection and vaccination, using pseudoviruses as a model system, which adequately mirrors SARS-CoV-2 neutralisation by antibodies.7Schmidt F Weisblum Y Muecksch F et al.Measuring SARS-CoV-2 neutralizing antibody activity using pseudotyped and chimeric viruses.J Exp Med. 2020; 217e20201181 Crossref Google ScholarWe analysed particles harbouring the S protein of B.1—which is identical to the wildtype strain apart from the D614G mutation—and S proteins of BA.1, BA.2, and BA.3. We first examined neutralisation by antibodies from convalescent patients, who were infected during the first (February to May, 2020) and second (December, 2020, to February, 2021) waves of COVID-19 in Germany (appendix pp 2–3, 4–6). Neutralisation of particles bearing the B.1 S protein (B.1pp) was robust, whereas neutralisation of BA.1pp and BA.3pp was at least 32-times less than B.1pp (BA.1 p=0·0020; BA.3 p=0·0020). Neutralisation of BA.2pp was also diminished, but the reduction was less pronounced than that measured for the other omicron subvariants (9·2-times less than B.1pp; p=0·0020).Analysis of neutralisation by antibodies induced by double vaccination with BNT162b2 (BNT) yielded similar results as neutralisation with antibodies from convalescent patients (appendix pp 2–3). Particles harbouring the S proteins of BA.1 and BA.3 showed 17-times lower neutralisation than B.1pp (BA.1 p=0·0020; BA.3 p=0·0020), whereas neutralisation of BA.2pp was 9-times reduced (p=0·0020). Triple BNT vaccination induced a more potent antibody response, and only modest evasion of neutralisation was seen for particles bearing omicron S proteins (BA.1 2·5-times, p=0·0039; BA.2 1·9-times, p=0·012; BA.3 2·4-times, p=0·0039; appendix pp 2–3). Finally, neutralisation by antibodies induced in fully vaccinated (three vaccine doses) individuals with breakthrough infection during the fourth wave in Germany (October, 2021, to January, 2022, dominated by the delta variant) was most potent and neutralisation of particles bearing omicron S protein was 9–12-times less efficient than B.1pp (BA.1 p=0·0020; BA.2 p=0·0039; BA.3 p=0·0039; appendix pp 2–3). However, no significant differences were observed between BA.1pp, BA.2pp, and BA.3pp (appendix pp 2–3).Our results show that all presently circulating omicron subvariants evade neutralisation by vaccine-induced antibodies with comparably high efficiency, suggesting that increased antibody evasion is not the reason for the current expansion of BA.2 in several countries.4Mahase E COVID-19: what do we know about omicron sublineages?.BMJ. 2022; 376: o358Crossref PubMed Scopus (16) Google Scholar, 8Lyngse FP Kirkeby CT Denwood M et al.Transmission of SARS-CoV-2 omicron VOC subvariants BA.1 and BA.2: evidence from Danish households.medRxiv. 2022; (published online Jan 30.) (preprint).https://doi.org/10.1101/2022.01.28.22270044Google Scholar Since currently available vaccines provided robust protection against early omicron isolates circulating in South Africa from Nov 15 to Dec 7, 2021,3Collie S Champion J Moultrie H Bekker LG Gray G Effectiveness of BNT162b2 vaccine against omicron variant in South Africa.N Engl J Med. 2022; 386: 494-496Crossref PubMed Scopus (233) Google Scholar which was likely to be BA.1, our results suggest that this protection should extend to all omicron subvariants. The SARS-CoV-2 omicron (B.1.1.529) variant has rapidly become globally dominant, displacing the previously dominant delta (B1.617.2) variant. The viral spike (S) protein is the key target of the neutralising antibody response, and the omicron variant harbours more than 35 mutations in the S protein, which allow highly efficient evasion from neutralising antibodies.1Hoffmann M Krüger N Schulz S et al.The omicron variant is highly resistant against antibody-mediated neutralization: implications for control of the COVID-19 pandemic.Cell. 2022; 185: 447-456Summary Full Text Full Text PDF PubMed Scopus (271) Google Scholar In keeping with these findings, the omicron variant efficiently spreads in populations with a high percentage of convalescent or vaccinated individuals.2Altarawneh HN Chemaitelly H Hasan MR et al.Protection against the omicron variant from previous SARS-CoV-2 infection.N Engl J Med. 2022; (published online Feb 9.)https://doi.org/10.1056/NEJMc2200133Crossref PubMed Scopus (87) Google Scholar, 3Collie S Champion J Moultrie H Bekker LG Gray G Effectiveness of BNT162b2 vaccine against omicron variant in South Africa.N Engl J Med. 2022; 386: 494-496Crossref PubMed Scopus (233) Google Scholar The three main subvariants of the omicron variant are BA.1, BA.2, and BA.3. Initial data suggest that BA.2 might have a growth advantage over BA.1,4Mahase E COVID-19: what do we know about omicron sublineages?.BMJ. 2022; 376: o358Crossref PubMed Scopus (16) Google Scholar posing a rapidly increasing threat to health systems. The omicron subvariants display remarkable differences regarding S protein mutations, particularly with respect to the N-terminal domain and the receptor-binding domain (appendix pp 2–3), which are known to harbour key epitopes of neutralising antibodies.5McCallum M De Marco A Lempp FA et al.N-terminal domain antigenic mapping reveals a site of vulnerability for SARS-CoV-2.Cell. 2021; 184: 2332-2347Summary Full Text Full Text PDF PubMed Scopus (330) Google Scholar, 6Piccoli L Park YJ Tortorici MA et al.Mapping neutralizing and immunodominant sites on the SARS-CoV-2 spike receptor-binding domain by structure-guided high-resolution serology.Cell. 2020; 183: 1024-1042Summary Full Text Full Text PDF PubMed Scopus (570) Google Scholar Here, we compared BA.1, BA.2, and BA.3 for sensitivity to neutralisation by antibodies induced by infection and vaccination, using pseudoviruses as a model system, which adequately mirrors SARS-CoV-2 neutralisation by antibodies.7Schmidt F Weisblum Y Muecksch F et al.Measuring SARS-CoV-2 neutralizing antibody activity using pseudotyped and chimeric viruses.J Exp Med. 2020; 217e20201181 Crossref Google Scholar We analysed particles harbouring the S protein of B.1—which is identical to the wildtype strain apart from the D614G mutation—and S proteins of BA.1, BA.2, and BA.3. We first examined neutralisation by antibodies from convalescent patients, who were infected during the first (February to May, 2020) and second (December, 2020, to February, 2021) waves of COVID-19 in Germany (appendix pp 2–3, 4–6). Neutralisation of particles bearing the B.1 S protein (B.1pp) was robust, whereas neutralisation of BA.1pp and BA.3pp was at least 32-times less than B.1pp (BA.1 p=0·0020; BA.3 p=0·0020). Neutralisation of BA.2pp was also diminished, but the reduction was less pronounced than that measured for the other omicron subvariants (9·2-times less than B.1pp; p=0·0020). Analysis of neutralisation by antibodies induced by double vaccination with BNT162b2 (BNT) yielded similar results as neutralisation with antibodies from convalescent patients (appendix pp 2–3). Particles harbouring the S proteins of BA.1 and BA.3 showed 17-times lower neutralisation than B.1pp (BA.1 p=0·0020; BA.3 p=0·0020), whereas neutralisation of BA.2pp was 9-times reduced (p=0·0020). Triple BNT vaccination induced a more potent antibody response, and only modest evasion of neutralisation was seen for particles bearing omicron S proteins (BA.1 2·5-times, p=0·0039; BA.2 1·9-times, p=0·012; BA.3 2·4-times, p=0·0039; appendix pp 2–3). Finally, neutralisation by antibodies induced in fully vaccinated (three vaccine doses) individuals with breakthrough infection during the fourth wave in Germany (October, 2021, to January, 2022, dominated by the delta variant) was most potent and neutralisation of particles bearing omicron S protein was 9–12-times less efficient than B.1pp (BA.1 p=0·0020; BA.2 p=0·0039; BA.3 p=0·0039; appendix pp 2–3). However, no significant differences were observed between BA.1pp, BA.2pp, and BA.3pp (appendix pp 2–3). Our results show that all presently circulating omicron subvariants evade neutralisation by vaccine-induced antibodies with comparably high efficiency, suggesting that increased antibody evasion is not the reason for the current expansion of BA.2 in several countries.4Mahase E COVID-19: what do we know about omicron sublineages?.BMJ. 2022; 376: o358Crossref PubMed Scopus (16) Google Scholar, 8Lyngse FP Kirkeby CT Denwood M et al.Transmission of SARS-CoV-2 omicron VOC subvariants BA.1 and BA.2: evidence from Danish households.medRxiv. 2022; (published online Jan 30.) (preprint).https://doi.org/10.1101/2022.01.28.22270044Google Scholar Since currently available vaccines provided robust protection against early omicron isolates circulating in South Africa from Nov 15 to Dec 7, 2021,3Collie S Champion J Moultrie H Bekker LG Gray G Effectiveness of BNT162b2 vaccine against omicron variant in South Africa.N Engl J Med. 2022; 386: 494-496Crossref PubMed Scopus (233) Google Scholar which was likely to be BA.1, our results suggest that this protection should extend to all omicron subvariants. SP acknowledges funding from Bundesministerium für Bildung und Forschung (BMBF; grant numbers 01KI2006D, 01KI20328A, 01KX2021), the Ministry for Science and Culture of Lower Saxony (grant numbers 14-76103-184, MWK HZI COVID-19), and the German Research Foundation (DFG; grant numbers PO 716/11-1, PO 716/14-1). MSW received unrestricted funding from Sartorius, Lung research. H-MJ received funding from BMBF (grant numbers 01KI2043, NaFoUniMedCovid19-COVIM 01KX2021), Bavarian State Ministry for Science and the Arts, and DFG through the research training groups RTG1660 and TRR130, the Bayerische Forschungsstiftung (Project CORAd), and the Kastner Foundation. GMNB acknowledges funding from the German Center for Infection Research (grant number 80018019238) and a European Regional Development Fund (Defeat Corona, grant number ZW7-8515131, together with AD-J). All other authors declare no competing interests. Supplementary Material Download .pdf (1.78 MB) Help with pdf files Supplementary appendix Download .pdf (1.78 MB) Help with pdf files Supplementary appendix

Rapid spread of SARS-CoV-2 variants C.1.2 and B.1.621 (Mu variant) in Africa and the Americas, respectively, as well as a high number of mutations in the viral spike proteins raised concerns that these variants might pose an elevated threat to human health. Here, we show that C.1.2 and B.1.621 spike proteins mediate increased entry into certain cell lines but do not exhibit increased ACE2 binding. Further, we demonstrate that C.1.2 and B.1.621 are resistant to neutralization by bamlanivimab but remain sensitive to inhibition by antibody cocktails used for COVID-19 therapy. Finally, we show that C.1.2 and B.1.621 partially escape neutralization by antibodies induced upon infection and vaccination, with escape of vaccine-induced antibodies being as potent as that measured for B.1.351 (Beta variant), which is known to be highly neutralization resistant. Collectively, C.1.2 and B.1.621 partially evade control by vaccine-induced antibodies, suggesting that close monitoring of these variants is warranted.

SUMMARYThe global spread of SARS-CoV-2/COVID-19 is devastating health systems and economies worldwide. Recombinant or vaccine-induced neutralizing antibodies are used to combat the COVID-19 pandemic. However, recently emerged SARS-CoV-2 variants B.1.1.7 (UK), B.1.351 (South Africa) and B.1.1.248 (Brazil) harbor mutations in the viral spike (S) protein that may alter virus-host cell interactions and confer resistance to inhibitors and antibodies. Here, using pseudoparticles, we show that entry of UK, South Africa and Brazil variant into human cells is susceptible to blockade by entry inhibitors. In contrast, entry of the South Africa and Brazil variant was partially (Casirivimab) or fully (Bamlanivimab) resistant to antibodies used for COVID-19 treatment and was less efficiently inhibited by serum/plasma from convalescent or BNT162b2 vaccinated individuals. These results suggest that SARS-CoV-2 may escape antibody responses, which has important implications for efforts to contain the pandemic.

Transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from humans to farmed mink has been observed in Europe and the US. In the infected animals, viral variants arose that harbored mutations in the spike (S) protein, the target of neutralizing antibodies, and these variants were transmitted back to humans. This raised concerns that mink might become a constant source of human infection with SARS-CoV-2 variants associated with an increased threat to human health and resulted in mass culling of mink. Here, we report that mutations frequently found in the S proteins of SARS-CoV-2 from mink are mostly compatible with efficient entry into human cells and its inhibition by soluble angiotensin-converting enzyme 2 (ACE2). In contrast, mutation Y453F reduces neutralization by an antibody with emergency use authorization for coronavirus disease 2019 (COVID-19) therapy and sera/plasma from COVID-19 patients. These results suggest that antibody responses induced upon infection or certain antibodies used for treatment might offer insufficient protection against SARS-CoV-2 variants from mink.

SUMMARYThe delta variant of SARS-CoV-2, B.1.617.2, emerged in India and has subsequently spread to over 80 countries. B.1.617.2 rapidly replaced B.1.1.7 as the dominant virus in the United Kingdom, resulting in a steep increase in new infections, and a similar development is expected for other countries. Effective countermeasures require information on susceptibility of B.1.617.2 to control by antibodies elicited by vaccines and used for COVID-19 therapy. We show, using pseudotyping, that B.1.617.2 evades control by antibodies induced upon infection and BNT162b2 vaccination, although with lower efficiency as compared to B.1.351. Further, we found that B.1.617.2 is resistant against Bamlanivimab, a monoclonal antibody with emergency use authorization for COVID-19 therapy. Finally, we show increased Calu-3-lung cell entry and enhanced cell-to-cell fusion of B.1.617.2, which may contribute to augmented transmissibility and pathogenicity of this variant. These results identify B.1.617.2 as an immune evasion variant with increased capacity to enter and fuse lung cells.

The SARS-CoV-2 pandemic has spread to all parts of the world and can cause life-threatening pneumonia and other severe disease manifestations known as COVID-19. This health crisis has resulted in a significant effort to stop the spread of this new coronavirus. However, while propagating itself in the human population, the virus accumulates mutations and generates new variants with increased fitness and the ability to escape the human immune response. Here we describe a color-based barcoded spike flow cytometric assay (BSFA) that is particularly useful to evaluate and directly compare the humoral immune response directed against either wild type (WT) or mutant spike (S) proteins or the receptor-binding domains (RBD) of SARS-CoV-2. This assay employs the human B lymphoma cell line Ramos, transfected for stable expression of WT or mutant S proteins or a chimeric RBD-CD8 fusion protein. We find that the alpha and beta mutants are more stably expressed than the WT S protein on the Ramos B cell surface and/or bind with higher affinity to the viral entry receptor ACE2. However, we find a reduce expression of the chimeric RBD-CD8 carrying the point mutation N501Y and E484K characteristic for the alpha and beta variant, respectively. The comparison of the humoral immune response of 12 vaccinated probands with 12 COVID-19 patients shows that after the boost, the S-specific IgG class immune response in the vaccinated group is similar to that of the patient group. However, in comparison to WT the specific IgG serum antibodies bind less well to the alpha variant and only poorly to the beta variant S protein. This is in line with the notion that the beta variant is an immune escape variant of SARS-CoV-2. The IgA class immune response was more variable than the IgG response and higher in the COVID-19 patients than in the vaccinated group. In summary, we think that our BSFA represents a useful tool to evaluate the humoral immunity against emerging variants of SARS-CoV-2 and to analyze new vaccination protocols against these variants.

The rapid spread of the SARS-CoV-2 Omicron variant suggests that the virus might become globally dominant. Further, the high number of mutations in the viral spike protein raised concerns that the virus might evade antibodies induced by infection or vaccination. Here, we report that the Omicron spike was resistant against most therapeutic antibodies but remained susceptible to inhibition by sotrovimab. Similarly, the Omicron spike evaded neutralization by antibodies from convalescent patients or individuals vaccinated with the BioNTech-Pfizer vaccine (BNT162b2) with 12- to 44-fold higher efficiency than the spike of the Delta variant. Neutralization of the Omicron spike by antibodies induced upon heterologous ChAdOx1 (Astra Zeneca-Oxford)/BNT162b2 vaccination or vaccination with three doses of BNT162b2 was more efficient, but the Omicron spike still evaded neutralization more efficiently than the Delta spike. These findings indicate that most therapeutic antibodies will be ineffective against the Omicron variant and that double immunization with BNT162b2 might not adequately protect against severe disease induced by this variant.

The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants threatens efforts to contain the coronavirus disease 2019 (COVID-19) pandemic. The number of COVID-19 cases and deaths in India has risen steeply, and a SARS-CoV-2 variant, B.1.617, is believed to be responsible for many of these cases. The spike protein of B.1.617 harbors two mutations in the receptor binding domain, which interacts with the angiotensin converting enzyme 2 (ACE2) receptor and constitutes the main target of neutralizing antibodies. Therefore, we analyze whether B.1.617 is more adept in entering cells and/or evades antibody responses. B.1.617 enters two of eight cell lines tested with roughly 50% increased efficiency and is equally inhibited by two entry inhibitors. In contrast, B.1.617 is resistant against bamlanivimab, an antibody used for COVID-19 treatment. B.1.617 evades antibodies induced by infection or vaccination, although less so than the B.1.351 variant. Collectively, our study reveals that antibody evasion of B.1.617 may contribute to the rapid spread of this variant.

The global spread of SARS-CoV-2/COVID-19 is devastating health systems and economies worldwide. Recombinant or vaccine-induced neutralizing antibodies are used to combat the COVID-19 pandemic. However, the recently emerged SARS-CoV-2 variants B.1.1.7 (UK), B.1.351 (South Africa), and P.1 (Brazil) harbor mutations in the viral spike (S) protein that may alter virus-host cell interactions and confer resistance to inhibitors and antibodies. Here, using pseudoparticles, we show that entry of all variants into human cells is susceptible to blockade by the entry inhibitors soluble ACE2, Camostat, EK-1, and EK-1-C4. In contrast, entry of the B.1.351 and P.1 variant was partially (Casirivimab) or fully (Bamlanivimab) resistant to antibodies used for COVID-19 treatment. Moreover, entry of these variants was less efficiently inhibited by plasma from convalescent COVID-19 patients and sera from BNT162b2-vaccinated individuals. These results suggest that SARS-CoV-2 may escape neutralizing antibody responses, which has important implications for efforts to contain the pandemic.