Neutralization Escape by SARS-CoV-2 Omicron Subvariants BA.2.12.1, BA.4 and BA.5

To the editors:

Figure 1. Figure 1. Omicron subvariant mutations and neutralizing antibody responses.

Panel A shows the lineage of mutations identified in the omicron BA.1, BA.2, BA.2.12.1 and BA.4 or BA.5 subvariants of SARS-CoV-2, compared to the reference WA1/2020 isolate. BA.4 and BA.5 have identical sequences of the spike protein and thus are grouped together. FP stands for fusion peptide, HR1 heptad repeat 1, HR2 heptad repeat 2, NTD N-terminal domain, RBD receptor binding domain, RBM receptor binding motif, SD1 subdomain 1 and SD2 subdomain 2. Panel B shows neutralizing antibody titers as determined by pressing luciferase-based pseudovirus neutralization assays in samples obtained from 27 participants 6 months after receiving the two-dose BNT162b2 messenger RNA vaccine series and 2 weeks after the third (booster) dose. Panel C shows neutralizing antibody titers in subjects infected with the BA.1 or BA.2 subvariant. All infected participants were vaccinated except 1 participant who had a negative neutralizing antibody titer. In 9 participants, two or three time points after infection are shown. Neutralizing antibody titers were measured against the SARS-CoV-2 reference isolate WA1/2020 and the omicron subvariants BA.1, BA.2, BA.2.12.1 and BA.4 or BA.5. In Panels B and C, medians (black bars) are represented numerically and factor differences with other sub-variants are indicated; the dashed horizontal line indicates the lower limit of detection for the test.

In recent months, several lines of the omicron (B.1.1.529) variant of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have emerged,¹ with subvariants BA.1 and BA.2 showing significant escape from neutralizing antibodies.^2-5 Subvariant BA.2.12.1 is now the dominant strain in the United States and BA.4 and BA.5 are dominant in South Africa (Figure 1A† Subvariants BA.4 and BA.5 have identical sequences of the spike protein.

We evaluated neutralizing antibody titers against the reference WA1/2020 isolate of SARS-CoV-2 along with omicron subvariants BA.1, BA.2, BA.2.12.1 and BA.4 or BA.5 in 27 participants who were vaccinated and boosted with messenger RNA vaccine BNT162b2 (Pfizer-BioNTech) and in 27 participants infected with the BA.1 or BA.2 subvariant a median of 29 days earlier (range, 2 to 113) (Tables S1 and S2 in the Supplementary Appendix, available with the full text of this letter at NEJM.org). In the vaccine cohort, participants were excluded if they had a history of SARS-CoV-2 infection or a positive result on nucleocapsid serological analysis or if they had received another vaccine against coronavirus disease 2019 (Covid-19) or an immunosuppressive drug.

Six months after the first two BNT162b2 immunizations, the median neutralizing antibody pseudovirus titer was 124 against WA1/2020, but less than 20 against all omicron subvariants tested (Figure 1B† Two weeks after the booster dose, the median neutralizing antibody titer increased significantly to 5783 against the WA1/2020 isolate, 900 against the BA.1 subvariant, 829 against the BA.2 subvariant, 410 against the BA.2.12. 1. subvariant, and 275 against the BA.4 or BA.5 subvariant. These data show that compared to the response against the WA1/2020 isolate, the neutralizing antibody titer was 6.4-fold lower against BA.1, 7.0-fold against BA.2, 14.1-fold against BA . 2.12.1, and by a factor of 21.0 against BA.4 or BA.5. In addition, compared to the median neutralizing antibody titer against the BA.1 subvariant, the median titer was 2.2-fold lower against the BA.2.12.1 subvariant and 3.3-fold against the BA.4 or BA. 5 sub variant.

Of the participants infected with the BA.1 or BA.2 subvariant of omicron, all but one had been vaccinated against Covid-19. Due to the variation in sampling after infection onset, some samples may not reflect peak neutralizing antibody titers (Table S2). Among participants with a history of Covid-19, the median neutralizing antibody titer was 11,050 against the WA1/2020 isolate, 1740 against the BA.1 subvariant, 1910 against the BA.2 subvariant, 1150 against the BA.2.12.1 subvariant , and 590 against the BA.4 or BA.5 subvariant (Figure 1C† These data show that compared to the WA1/2020 isolate, the median neutralizing antibody titer was 6.4-fold lower against BA.1, 5.8-fold against BA.2, 9.6-fold against BA.2.12. 1, and by a factor of 18.7 against BA.4 or BA.5. In addition, compared to the median titers against the BA.1 subvariant, the median titer was 1.5-fold lower against the BA.2.12.1 subvariant and 2.9-fold against the BA.4 or BA.5 -sub variant .

These data show that the BA.2.12.1, BA.4 and BA.5 subvariants substantially escape neutralizing antibodies induced by both vaccination and infection. In addition, neutralizing antibody titers against the BA.4 or BA.5 subvariant and (to a lesser extent) against the BA.2.12.1 subvariant were lower than against the BA.1 and BA.2 subvariants, suggesting that the SARS-CoV-2 ommicron variant has continued to evolve with increasing neutralization escape. These findings provide an immunological context for the current peaks caused by the subvariants BA.2.12.1, BA.4 and BA.5 in populations with high vaccination frequencies and BA.1 or BA.2 infection.

Nicole P. Hachmann, BS
Jessica Miller, BS
Ai-ris Y. Collier, MD
John D. Ventura, Ph.D.
Jingyou Yu, Ph.D.
Marjorie Rowe, BS
Esther A. Bondzie, MSN
Olivia Powers, BS
Nehalee Surve, MS
Kevin Hall, BS
Dan H. Barouch, MD, Ph.D.
Beth Israel Deaconess Medical Center, Boston, MA
[email protected]

This letter was published on NEJM.org on June 22, 2022.