Abstract

Study background: The SARS CoV2 pandemic has led to many severe infections and deaths. With the development of vaccines, we are now seeing declining numbers of infections. However, individuals that get fully vaccinated may still experience a breakthrough infection. Are these infections clinically significant?

Methods: This study was performed as part of a surveillance program for SARS-CoV-2 on a university campus with 49,700 students and employees. Surveillance testing was random and included approximately 10% of the population each week. Additionally, individuals self-identified with COVID-19 related symptoms or those that had close contact with SARS-CoV-2 positive individuals were also tested. Anterior nasal swabs were collected from individuals for a Nucleic Acid Amplification Test (NAAT) for detection of SARS-CoV-2. A subset of NAAT positive samples was sequenced to determine variants associated with infections. Included in the testing and sequencing protocol were individuals that were fully vaccinated. We paired random and passive surveillance nucleic acid testing with analysis of viral whole genomic sequences to detect and describe breakthrough infections, focusing on a university community.

Conclusion: In this retrospective analysis, we identified breakthrough infections in 14 individuals out of 2,551 nucleic acid amplification tests performed from samples of fully vaccinated individuals from February to early May 2021. Cases were associated with all three of the currently EUA approved vaccines and were associated with 5 variants, including variants of concern/variants of interest. Our data support the need to continue surveillance and mitigation strategies, including active surveillance testing and viral genomic sequencing for variant characterization of asymptomatic infections, particularly but not limited to university settings.

Keywords: SARS CoV-2; Genetic sequencing; Variants of concern; Vaccines