The effect of cilgavimab and neutralization by vaccine-induced antibodies in emerging SARS-CoV-2 sublines BA.4 and BA.5

Since the first detection of the omicron variant of SARS-CoV-2 (B.1.1.529 and sublines) in November 2021 in South Africa, Botswana and Hong Kong, several omicron sublines have evolved. Some of these sublines including BA.2.75, BA.4, and BA.5, showed increased resistance against antibody-mediated neutralization.
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  • Arora P
  • Kempf A
  • Nehlmeier I
  • et al.
Increased resistance to neutralization of emerging omicron subvariants BA.2.12.1, BA.4, and BA.5.

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Evasion of neutralizing antibodies by the omicron BA.2.75 sub-line.

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  • Wang Q
  • Guo Y
  • Iketani S
  • et al.
Antibody evasion by SARS-CoV-2 Omicron subvariants BA.2.12.1, BA.4 and BA.5.

Thus, these sublines outperform earlier Omicron sublines in populations with pre-existing immune responses due to either infection, vaccination, or both.
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Emergence of SARS-CoV-2 Omicron BA.4 and BA.5 lines in South Africa.

In recent months, viruses belonging to different BA.4 and BA.5 sublines with mutations at the R346 residue (R346T, R346S or R346S) in the spike S protein receptor binding domain virus were detected with an increase in the frequency

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CoV-Spectrum: analysis of globally shared SARS-CoV-2 data to identify and characterize new variants.

(Appendix p 1) This increased frequency was detected for the BA.4.6 (R346T or N658S), BA.5.9 (R346I) and BF.7 (R346T) sublines. Since protein S mediates viral entry into cells and is the key target for neutralizing antibodies, we investigated whether a mutation at R346T, R346S, or R346S could increase infectivity or resistance to neutralization, or both. For this, we used pseudovirus particles (dp), which have been shown to faithfully model SARS-CoV-2 host cell entry and neutralization.

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Measurement of SARS-CoV-2 neutralizing antibody activity using pseudotyped and chimeric viruses.

Cell entry by BA.4/5 (R346T, R346S or R346S))dp was reduced from entry by BA.4/5dp (reduced by about 1.6 times [Vero, Caco-2] 2 0 times [293T, Calu-3]) (appendix p 1). In contrast, particles carrying the BA.4.6 S protein (BA.4.6dp), which contains the R346T mutation together with the N658S mutation, entered cells with the same efficiency as BA.4–5dp. This result suggests that the N658S mutation compensates for the negative effect of the R346T mutation on host cell entry. We further investigated protein S-induced cell-cell fusion, which is believed to contribute to pathogenesis.
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Persistence of viral RNA, pneumocyte syncytia, and thrombosis are hallmarks of advanced COVID-19 pathology.

No difference between the BA.4/5, BA.4/5 (R346T, R346S or R346S) and BA.4.6 proteins was observed (appendix p 1).

Next, we analyzed neutralization by monoclonal antibodies for COVID-19 treatment. In line with previous studies,
1
  • Arora P
  • Kempf A
  • Nehlmeier I
  • et al.
Increased resistance to neutralization of emerging omicron subvariants BA.2.12.1, BA.4, and BA.5.

,

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  • Yamasoba D
  • Kosugi Y
  • Kimura I
  • et al.
Sensitivity to neutralization of SARS-CoV-2 omicron subvariants to therapeutic monoclonal antibodies.

five of ten antibodies (casirivimab, bamlanivimab, etesevimab, tixagevimab, and regdanvimab) failed to neutralize BA.4/5dp. Additionally, two antibodies (imdevimab and sotrovimab) showed more than ten-fold reduced efficacy against BA.4/5dp compared to B.1dp, which harbors the S protein of a virus that was circulating at the start of the pandemic. Three antibodies (cilgavimab, bebtelovimab, and S2H97), two of which are in clinical use (cilgavimab and bebtelovimab), retained appreciable neutralization efficacy against BA.4/5dp. However, BA.4/5 (R346T, R346S or R346S)dp, and BA.4.6dp sensitivity largely lost against cilgavimab, being effectively neutralized only by bebtelovimab (appendix p 3).

Finally, we assessed the neutralization of protein S-mediated cell entry by antibodies elicited during triple vaccination with different combinations of BNT162b2 mRNA and AZD1222 adenovirus vaccines, and a early omicron wave infection (i.e., February-May 2022, in Germany) in triply vaccinated people (Appendix, table). According to previous studies,
1
  • Arora P
  • Kempf A
  • Nehlmeier I
  • et al.
Increased resistance to neutralization of emerging omicron subvariants BA.2.12.1, BA.4, and BA.5.

,

3
  • Wang Q
  • Guo Y
  • Iketani S
  • et al.
Antibody evasion by SARS-CoV-2 Omicron subvariants BA.2.12.1, BA.4 and BA.5.

neutralization of BA.4/5dp has been reduced compared to B.1dp (by between 3.5 times and 11.5 times). Neutralization of BA.4/5 (R346T, R346S or R346S) S)dp and BA.4.6dp has been further reduced from BA.4/5dp (by about twice), suggesting that the mutations (R346T, R346S or R346S) further extend the already high neutralization escape potential of the BA.4 and BA.5 sublines (appendix p 3).

Our data indicate that the emerging BA.4 and BA.5 sublines harboring protein S mutations (R346T, R346S, or R346S) further extended their ability to escape neutralization. As a result, the availability of therapeutic antibodies for the treatment of individuals infected with such viruses is further reduced, and infections in triply vaccinated individuals may become increasingly frequent.

AK, IN, SP and MH are conducting contract research (testing vaccinated sera to neutralize activity against SARS-CoV-2) for Valneva, unrelated to this work. GMNB served as an advisor for Moderna and acknowledges funding from the German Center for Infection Research (Grant No. 80018019238) and a European Regional Development Fund (Defeat Corona, ZW78–515131). SP served as an advisor to BioNTech, unrelated to this work. SP acknowledges funding from the Bundesministerium fur Bildung und Forshung (Bundesministerium fur Bildung und Forshung; 01KI2006D, 01KI20328A, 01KX2021), EU hunam genetic and immunological determinants of clinical manifestations of SARS-Cov-2 infection: vers a personalized medicine project (grant agreement number 101057100), the Lower Saxony Ministry of Science and Culture (147–61031–84, MWK HZI COVID-19), and the German Research Foundation (DFG; PO716/111–, PO716/141–). H-MJ has received funding from the BMBF (01KI2043, NaFoUniMedCovid19-COVIM: 01KX2021), the Bavarian Ministry of Science and Arts and the DFG through the research training groups RTG1660 and TRR130, the Bayerische Forschungsstiftung ( CORAd project), and the Kastner Foundation. All other authors declare no competing interests.

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