Preliminary Research: Pfizer-Biontech Vaccine is 22-fold less Effective Against SARS-CoV-2 Omicron Variant

Alex Sigal Lab which is a part of African Health Research Institute (AHRI) published a pre-print (not peer reviewed research article) in Medrxiv (pre-print server) of their final findings on the efficiency of Pfizer-Biontech vaccine against Omicron variant on 15th of December. On 23rd of December, Nature (a peer-reviewed prestigious journal) accepted this research article for publishing named “Omicron extensively but incompletely escapes Pfizer BNT162b2 neutralization”.

Alex Sigal’s remarks on the paper:

Experiments converged on a 22-fold decline in neutralization of Omicron by the Pfizer-BNT vaccine

Prediction of vaccine efficacy against symptomatic infection with Omicron was 35% for the vaccinated only and 72% for infected+vaccinated.

Prediction of protection against severe disease was high for both groups.

Details About the Paper and the Omicron Variant

A new Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) variant emerged from South Africa on 9th of November 2021 and reported to World Health Organization (WHO) on 24th of November 2021 . WHO classified this variant as Variant of Concern (VOC) and named it as “Omicron”. (1) The main reason this new variant is classified as VOC is it’s different epidemiological profile and it’s potential to reinfect humans. The non-typical profile of Omicron variant is associated with the high amount of mutations in it’s spike protein. Omicron has 32 mutations which affect the spike protein (Fig.1), whereas the VOC before Omicron, Delta , had only 9 mutations on it’s spike protein. (2) As SARS-CoV-2 enters the cells via the attachment of spike proteins to ACE-2 receptors, these mutations on spike protein caused questions about a potential change in entry mechanism for the Omicron variant. However, S. Cele et al. showed that the entry mechanism of Omicron variant stayed the same but the efficiency of Pfizer BNT162b2 vaccine is notably reduced. (3) Focus Reduction Neutralization Test with %50 neutralization cutoff (FRNT50) showed that the vaccine efficiency dropped 22-fold when infected with the Omicron variant in comparison to the native D614G SARS-CoV-2. (3) (Fig.2)

Polymerase Chain Reaction (PCR) tests can still detect Omicron variant and Spike (S) gene target failure (SGTF) occurs because of del69/70 mutation in S gene. This can be used as a market to detect Omicron cases as PCR tests can’t detect the S gene when SGTF occurs. (1)

Overall, early research shows that Omicron variant can reinfect people, is likely to be contagious than other variants and it’s part of the genome which encodes the spike protein is highly mutated. Also, Pfizer BNT162b2 vaccine efficacy is decreased against the Omicron variant.

Figure 1. Mutations on SARS-CoV-2 Omicron Variant genome. (2)

Figure 2. Vaccine efficiency of Pfizer BNT162b2 vaccine. The native D614G mutation containing SARS-CoV-2 variant is used as a reference to analyze the vaccine efficiency of Pfizer BNT162b2 vaccine against Omicron. Green lines represent patients who had 2 doses of BNT16b2 vaccine end were previously infected by SARS-CoV-2. Red lines represent patients who were not infected before and received 2 doses of BNT162b2 vaccine. Blue lines represent all of the data. C) Neutralization comparison of Omicron versus D614G mutated native SARS-CoV-2. D) Fold change of neutralization in different participant groups. E) Predicted vaccine efficacy against the Omicron variant.

Original Research Article:

Omicron extensively but incompletely escapes Pfizer BNT162b2 neutralization

References

1. “Classification of Omicron (B.1.1.529): SARS-CoV-2 Variant of Concern”. World Health Organization. 26 November 2021.
2. BA.1 Lineage Report. Alaa Abdel Latif, Julia L. Mullen, Manar Alkuzweny, Ginger Tsueng, Marco Cano, Emily Haag, Jerry Zhou, Mark Zeller, Emory Hufbauer, Nate Matteson, Chunlei Wu, Kristian G. Andersen, Andrew I. Su, Karthik Gangavarapu, Laura D. Hughes, and the Center for Viral Systems Biology. outbreak.info, (available at https://outbreak.info/situation-reports?pango=BA.1). Accessed 21 December 2021.
3. - Cele, S. et al. SARS-CoV-2 Omicron has extensive but incomplete escape of Pfizer BNT162b2 elicited neutralization and requires ACE2 for infection. medRxiv 2021.12.08.21267417 (2021) doi:10.1101/2021.12.08.21267417.
4. https://sigallab.net/
5. https://twitter.com/sigallab
6. Omicron extensively but incompletely escapes Pfizer BNT162b2 neutralization https://www.nature.com/articles/d41586-021-03824-5