Investigating high rate of Omicron sublineage breakthrough infections in triple vaccinated healthcare workers

In a recent study posted to the medRxiv* pre-print server, researchers identified breakthrough infections (BTI) by Omicron sublineages BA.1, BA.1.1, and BA.2 in triple-vaccinated healthcare workers (HCW) of Sweden.

The researchers also analyzed the serological responses to a messenger ribonucleic acid (mRNA)-1273 (MOD) booster dose, disease symptoms, and viral characteristics during the study period.

Background

Vaccine-induced serological responses to the ancestral severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strain and pre-Omicron SARS-CoV-2 variants of concern (VOCs) have been extensively studied. However, studies elucidating the serological responses against the new SARS-CoV-2 VOC Omicron are sparse.

In addition, studies have not fully characterized Omicron characteristics and clearance between the Omicron sublineages. Notably, all three Omicron sublineages, BA.1, BA.1.1, and BA.2, were co-circulating and caused the recent BTIs in Sweden.

About the study

In the present study, researchers enrolled 2,149 HCW from Danderyd Hospital, Stockholm, Sweden, between April and May 2020. They were vaccinated with either BNT162b2 (BNT) or ChAdOx1 nCoV-19 (ChAd) vaccines starting January 2021.

The researchers stratified 300 participants into groups depending on the primary vaccination series and the occurrence of SARS-CoV-2 infection before primary vaccination. These individuals were immunized with a MOD booster dose between December 13 and  23, 2021, after primary SARS-CoV-2 vaccination with two doses of BNT, ChAd, or one dose of ChAd followed by one dose of BNT.

The team collected blood samples 13 weeks after the second vaccine dose and five weeks after the booster dose. They measured SARS-CoV-2 anti-wild-type (wt) immunoglobulin G (IgG), cross-reactive IgG, and IgGs blocking wt and Omicron spike (S)-angiotensin-converting enzyme 2 (ACE2) binding in sera samples collected at the beginning of the screening but post-vaccination.

After boosting, they performed a twice-weekly quantitative reverse transcription-polymerase chain reaction (RT-qPCR) screening on 375 participants for four weeks. The RT-qPCR screening continued after 15 days of follow-up sampling till the end of the study period. Additionally, the researchers performed whole-genome sequencing (WGS) and virus isolation.

The researchers also performed a micro-neutralization assay on sera from 86 participants to evaluate neutralizing antibody titers against wt and Omicron, whereas 100% cytopathic effect (CPE) inhibition (IC₁₀₀) represented serum neutralizing activity. Using survival analysis by the logistic regression model, they evaluated the overall risk of BTIs over four weeks of screening.

Study findings

The researchers observed a high rate (22% over four weeks) of BTIs in an HCW cohort that recently received a booster immunization. In these cases, SARS-CoV-2 RNA loads were present consistently for up to nine days after the first RT-qPCR-positive sample, even after symptom resolution. This finding suggests that Omicron-infected individuals transmitted SARS-CoV-2 for more than five days.

Notably, the current guidelines recommend five days of quarantine for Omicron cases, but for vulnerable environments such as the healthcare settings, this time was inadequate.

Further, after the booster dose, participants with and without subsequent BTIs had similar antibody titers, indicating the limitations of vaccine-induced antibody titers as a marker of protection against Omicron re-infections.

The study findings did not show any significant differences in the viral load between the cases of three Omicron sublineages. However, there was a trend toward higher initial viral load and prolonged viral shedding in BA.2 infections. This finding pointed to higher transmissibility of BA.2 rather than enhanced immunologic escape compared to BA.1.

Less than 10% of Omicron BTIs had an entirely asymptomatic course of infection, which contradicted previous reports. The majority of the asymptomatic cases in the triple-vaccinated study cohort had low cycle threshold (C_t) values. This finding elucidated the role of asymptomatic transmission in highly vaccinated populations.

Although the differences were not statistically significant (p=0.06), the median C_t values of the initial positive samples from BA.1 vs. BA.2 infections were 29.4 and 25, respectively, demonstrating an approximately 100-fold higher SARS-CoV-2 RNA level in the BA.2-infected individuals.

There were no asymptomatic cases among the BA.2-infected individuals, although symptom duration was significantly longer in the BA.2 than in the BA.1 cases, with an average symptom duration of eight vs. six days, respectively (p<0.01).

Conclusions

Overall, the incidence of Omicron BTIs was high with a high viral load in the triple vaccinated HCW cohort of the present study, which likely contributed to the global surge in Omicron cases. The study findings also highlighted that vaccine-induced neutralizing antibody titers were largely ineffective in combating Omicron BTIs.

*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

Neha Mathur

Neha is a digital marketing professional based in Gurugram, India. She has a Master’s degree from the University of Rajasthan with a specialization in Biotechnology in 2008. She has experience in pre-clinical research as part of her research project in The Department of Toxicology at the prestigious Central Drug Research Institute (CDRI), Lucknow, India. She also holds a certification in C++ programming.