Escape from vaccine-induced immunity likely contributed to rapid rise of SARS-CoV-2 Omicron

In a recent study published on the medRxiv* preprint server, researchers investigate whether the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant of concern (VOC) was more likely to infect vaccinated individuals than the SARS-CoV-2 Delta VOC.  

Study: Rapid emergence of SARS-CoV-2 Omicron variant is associated with an infection advantage over Delta in vaccinated persons. Image Credit: DOERS / Shutterstock.com

The emergence of new SARS-CoV-2 VOCs necessitates studies that analyze the impact of these new variants on current coronavirus disease 2019 (COVID-19) vaccines and their efficiency in protecting individuals against infection and severe disease. With the increasing number of breakthrough infections, the Omicron VOC was found to be less effectively neutralized by sera collected from vaccinated individuals as compared to the neutralization of Delta VOC.

About the study

In the present study, the researchers analyzed nasal swab reverse-transcriptase polymerase chain reaction (PCR) tests and calculated SARS-CoV-2 positivity rates for Omicron and Delta VOCs by the vaccination status of the patients.

A surveillance program conducted in Southern Connecticut in the United States detected the presence of the Omicron variant using sequencing and spike-gene target failure (SGTF) RT-PCR signatures. A total of 37,877 PCR tests performed using nasal swabs were collected. Along with each PCR test, the date and manufacturer of the COVID-19 vaccine administered, as well as the cycle threshold (Ct) values of less than 30 were noted.

The researchers then measured the test positivity rate for Omicron and Delta VOCs according to the vaccination status of the individuals. Test positivity results were confirmed by a logistic generalized estimating equation model that calculated the chances of Omicron detection as compared to Delta detection.

A surveillance program was also conducted at Yale University to study the local emergence of Omicron. A review of medical records was performed on the collected RT-PCR tests samples between December 12, 2021, to December 26, 2021. For each case, information like gender and

age of the patient, test date, test outcome, as well as the manufacturer and date of each COVID-19 vaccine administration were collected. The number of positive rates for each variant, positivity rate doubling time for each variant, and Ct value of each nasal swab sample were the primary outcomes of the study.

Study findings

The results of the current study showed that twice the number of Omicron VOC cases were detected every 3.2 days, which was 3.7 times shorter than the doubling time of the Delta VOC. Furthermore, between 71% to 74% of the population tested were fully vaccinated.

Among unvaccinated individuals, the test positivity rate for Delta was 5.2% as compared to 4.5% for Omicron, while a similar trend was observed for individuals who had received only one vaccine dose. In contrast, Omicron and Delta VOCs had a positivity rate of 4.7% and 2.6%, respectively, for individuals who had received two vaccine doses in five months.

The positivity rates for Omicron and Delta were 4.2% and 2.9%, respectively, for individuals who had received two vaccine doses more than five months ago, while the rates were 2.2% and 0.9%, respectively, for individuals vaccinated with three doses. At the time of RT-PCR testing, 91.2% of the Omicron-infected partially vaccinated individuals were eligible for one or more vaccine doses.

The positivity rates for Omicron in individuals vaccinated with one or two doses did not significantly differ from that of unvaccinated individuals, while a reduction in positivity of 49.7% was observed in the case of individuals who had received three vaccine doses. However, a 45.6%, 49.6%, and 83.2% reduction in Delta VOC positivity rates was observed in the unvaccinated, two-dose vaccinated, and three-dose vaccinated groups, respectively.    

Variant case counts, test positivity, and odds of infection by vaccination status.

Conclusions

The findings of the current study demonstrate that vaccinated individuals with COVID-19 are more likely to have Omicron infection than Delta infection. These odds consistently increased as the number of vaccine doses administered increased.

In individuals who were unvaccinated and were partially vaccinated with only one vaccine dose, higher test positivity rates were observed for the Delta VOC than for the Omicron VOC. Individuals who were received two vaccine doses had a higher positivity rate for Omicron as compared to Delta. Age, gender, or manufacturer of the vaccine had no impact on the odds of infection.

The researchers believe that the waning of vaccine efficacy was responsible for the rapid spread of Omicron. Despite the higher number of Omicron infections in vaccinated individuals, the study reported sufficient vaccine efficacy against severe disease.

*Important notice

medRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.

Written by

Susha Cheriyedath

Susha has a Bachelor of Science (B.Sc.) degree in Chemistry and Master of Science (M.Sc) degree in Biochemistry from the University of Calicut, India. She always had a keen interest in medical and health science. As part of her masters degree, she specialized in Biochemistry, with an emphasis on Microbiology, Physiology, Biotechnology, and Nutrition. In her spare time, she loves to cook up a storm in the kitchen with her super-messy baking experiments.