SARS-CoV-2 Omicron Variant Infection of Individuals with High Titer Neutralizing Antibodies Post-3rd mRNA Vaccine Dose

Background: Vaccination with COVID-19 mRNA vaccines prevent hospitalization and severe disease caused by wildtype SARS-CoV-2 and several variants, and likely prevented infection when serum neutralizing antibody (NAb) titers were >1:160. Preventing infection limits viral replication resulting in mutation, which can lead to the emergence of additional variants.

During a longitudinal study to evaluate durability of a three-dose mRNA vaccine regimen (2 primary doses and a booster) using a rapid test that semi-quantitatively measures NAbs, the Omicron variant emerged and quickly spread globally. We evaluated NAb levels measured prior to symptomatic breakthrough infection, in groups infected prior to and after the emergence of Omicron.

During the SARS-CoV-2 Delta variant wave, 93% of breakthrough infections in our study occurred when serum NAb titers were <1:80. In contrast, after the emergence of Omicron, study participants with high NAb titers that had received booster vaccine doses became symptomatically infected. NAb titers prior to infection were ≥1:640 in 64% of the Omicron- infected population, ≥1:320 (14%), and ≥1:160 (21%).

These results indicate that high titers of NAbs elicited by currently available mRNA vaccines do not protect against infection with the Omicron variant, and that mild to moderate symptomatic infections did occur in a vaccinated and boosted population, although did not require hospitalization. All rights reserved. No reuse allowed without permission. (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprintthis version posted March 6, 2022. ; https://doi.org/10.1101/2022.03.03.22270812doi: medRxiv preprint SARS-CoV-2 (B.1.1.529) Omicron variant is highly mutated in the receptor-binding domain (RBD) of spike protein and consequently, prone to immune evasion.1 Previous reports indicate evasion of vaccine-induced immunity is due in part to a higher degree of neutralizing antibody (NAb) escape compared to NAb escape of previous variants of concern.2 While a NAb threshold sufficient to prevent infection and disease remains undefined, particularly regarding the most recent surge in Omicron cases, our findings demonstrate that NAb titers ≥1:640, observed in a majority of our Omicron-infected population, were inadequate for protection from infection and mild to moderate symptomatic disease. Here we report SARS-CoV-2 Omicron variant caused symptomatic infection of 14 individuals who had high titers of neutralizing antibodies after receiving 3rd doses of BNT162b2 or mRNA-1273 vaccines. All individuals were tested on a semi-quantitative rapid test that measures neutralizing antibodies.3 Results in Figure 1 are shown as percent neutralization prior to infection, comparing pre- and post-December 2021 breakthrough infections. Prior to December of 2021 and the Omicron surge in the USA, we observed only 14 PCR- confirmed breakthrough infections in our study population of 269 mRNA vaccine recipients. Thirteen of those breakthrough infections occurred when NAb levels had declined to titers 1:80 (Supplementary Figure S1). Conversely, 14 individuals that had high NAb titers (≥1:640 [n=9], ≥1:320 [n=2] and ≥1:160 [n=3], average 90% neutralization) after receiving a 3rd mRNA vaccine dose became symptomatically infected after Omicron became the dominant variant in circulation,4 (range 67- 99% neutralization, median 97%) (Figure 1). Population demographics, vaccination data, and time between NAb and PCR testing are shown in the Supplementary Appendix (Table S1). All rights reserved. No reuse allowed without permission. (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprintthis version posted March 6, 2022. ; https://doi.org/10.1101/2022.03.03.22270812doi: medRxiv preprint Figure 1. Peripheral NAb prior to breakthrough infection pre- and post-December 2021. NAb data prior to infection are shown as percent neutralization violin plots where solid black lines represent median, and dotted black lines indicate upper and lower quartiles. Significance was assessed using a non-parametric Mann-Whitney test to evaluate mean rank between groups with a two-tailed p<0.0001 and 95% confidence interval. A single outlier in the pre-December 2021 group had 84% neutralization prior to infection, however, was on the 2nd week of a 40 mg/day prednisone taper at the time of infection. Demographic information pertaining to individuals in both groups are detailed in Supplementary Table S1. Although one limitation of this study is small sample size, our results are the first to show that high neutralizing antibody titers induced by a 3rd dose of currently available mRNA vaccines do not protect against symptomatic breakthrough infections with the SARS-CoV-2 Omicron variant. However, other reports have also observed symptomatic breakthrough infection in individuals with mRNA vaccine booster doses.5 It is important to note that all Omicron infections described in this study self-reported symptoms as mild to moderate, such as upper respiratory congestion, All rights reserved. No reuse allowed without permission. (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprintthis version posted March 6, 2022. ; https://doi.org/10.1101/2022.03.03.22270812doi: medRxiv preprint sore throat, cough, headache, myalgia, lymphadenopathy, and fever (<39.4°C). Although a higher NAb titer is seemingly less protective against Omicron (B.1.1.529) than with previous variants of concern, our data support other reports that current vaccines remain highly effective at preventing severe disease.6,7 Most notably, our data demonstrate that even those at the highest NAb titers detected by our rapid test (≥1:640) remain susceptible to symptomatic Omicron infection and are presumably capable of transmitting virus. All rights reserved. No reuse allowed without permission. (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprintthis version posted March 6, 2022. ; https://doi.org/10.1101/2022.03.03.22270812doi: medRxiv preprint

1. Wu L, Zhou L, Mo M, Liu T, Wu C, Gong C, et al. SARS-CoV-2 Omicron RBD shows weaker binding affinity than the currently dominant Delta variant to human ACE2. Sig Transduct Target Ther. 2022 Dec;7(1):8. 2. Cao Y, Wang J, Jian F, Xiao T, Song W, Yisimayi A, et al. Omicron escapes the majority of existing SARS-CoV-2 neutralizing antibodies. Nature. 2021 Dec 23; https://www.nature.com/articles/s41586- 021-04385-3 3. Lake DF, Roeder AJ, Kaleta E, Jasbi P, Pfeffer K, Koelbela C, et al. Development of a rapid point-of- care test that measures neutralizing antibodies to SARS-CoV-2. Journal of Clinical Virology. 2021 Dec;145:105024. 4. TGen Arizona COVID-19 Sequencing Dashboard. Available from: https://pathogen.tgen.org/covidseq-tracker/ [accessed 2022 Jan 24] 5. Kuhlmann C, Mayer CK, Claassen M, Maponga T, Burgers WA, Keeton R, et al. Breakthrough infections with SARS-CoV-2 omicron despite mRNA vaccine booster dose. The Lancet. 2022 Jan 18; https://doi.org/10.1016/ S0140-6736(22)00090-3 6. Collie S, Champion J, Moultrie H, Bekker L-G, Gray G. Effectiveness of BNT162b2 Vaccine against Omicron Variant in South Africa. N Engl J Med. 2021 Dec 29;NEJMc2119270. 7. Thompson MG, Natarajan K, Irving SA, Rowley EA, Griggs EP, Gaglani M, et al. Effectiveness of a Third Dose of mRNA Vaccines Against COVID-19–Associated Emergency Department and Urgent Care Encounters and Hospitalizations Among Adults During Periods of Delta and Omicron Variant Predominance — VISION Network, 10 States, August 2021–January 2022. MMWR Morb Mortal Wkly Rep. 2022 Jan 21 [cited 2022 Jan 24];71(4): 139-145. http://www.cdc.gov/mmwr/volumes/71/wr/mm7104e3.htm?s_cid=mm7104e3_w All rights reserved. No reuse allowed without permission. (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprintthis version posted March 6, 2022. ; https://doi.org/10.1101/2022.03.03.22270812doi: medRxiv preprint