Clinical and Genomic Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS CoV-2) Infections in mRNA Vaccinated Health Care Personnel in New York City

Elizabeth V Robilotti; Karissa Whiting; Anabella Lucca; Chester Poon; Rebecca Guest; Tracy McMillen; Krupa Jani; Alexander Solovyov; Suzanne Kelson; Kevin Browne; Scott Freeswick; Tobias M Hohl; Deborah Korenstein; Denis Ruchnewitz; Michael Lässig; Marta Łuksza; Benjamin Greenbaum; Venkatraman E Seshan; N Esther Babady; Mini Kamboj

doi:10.1093/cid/ciab886

Clinical and Genomic Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS CoV-2) Infections in mRNA Vaccinated Health Care Personnel in New York City

Clin Infect Dis. 2022 Aug 24;75(1):e774-e782. doi: 10.1093/cid/ciab886.

Authors

Elizabeth V Robilotti^{1

2

3}, Karissa Whiting⁴, Anabella Lucca^{1

5

3}, Chester Poon⁶, Rebecca Guest⁵, Tracy McMillen⁷, Krupa Jani⁷, Alexander Solovyov⁴, Suzanne Kelson⁸, Kevin Browne⁹, Scott Freeswick¹⁰, Tobias M Hohl^{1

3}, Deborah Korenstein^{3

11}, Denis Ruchnewitz¹², Michael Lässig¹², Marta Łuksza^{13

14}, Benjamin Greenbaum^{4

15}, Venkatraman E Seshan⁴, N Esther Babady^{1

7}, Mini Kamboj^{1

2

3

16}

Affiliations

¹ Infectious Diseases, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA.
² Infection Control, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA.
³ Department of Medicine, Joan and Sanford Weill Medical College of Cornell University, New York, New York, USA.
⁴ Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York, USA.
⁵ Employee Health Service, Memorial Sloan Kettering Cancer Center, New York, New York, USA.
⁶ Division of Digital Informatics and Technology Solutions, Memorial Sloan Kettering Cancer Center, New York, New York, USA.
⁷ Clinical Microbiology Service, Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA.
⁸ Division of Digital Products and Informatics, Memorial Sloan Kettering Cancer Center, New York, New York, USA.
⁹ Department of Nursing, Memorial Sloan Kettering Cancer Center, New York, New York, USA.
¹⁰ Division of Pharmacy, Memorial Sloan Kettering Cancer Center, New York, New York, USA.
¹¹ Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA.
¹² Institute for Biological Physics, University of Cologne, Cologne, Germany.
¹³ Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.
¹⁴ Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.
¹⁵ Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, New York, USAand.
¹⁶ Division of Quality and Safety, Memorial Sloan Kettering Cancer Center, New York, New York, USA.

Abstract

Background: Vaccine-induced clinical protection against severe acute respiratory syndrome coronavirus 2 (SARS CoV-2) variants is an evolving target. There are limited genomic level data on SARS CoV-2 breakthrough infections and vaccine effectiveness (VE) since the global spread of the B.1.617.2 (Delta) variant.

Methods: In a retrospective study from 1 November 2020 to 31 August 2021, divided as pre-Delta and Delta-dominant periods, laboratory-confirmed SARS CoV-2 infections among healthcare personnel (HCP) at a large tertiary cancer center in New York City were examined to compare the weekly infection rate-ratio in vaccinated, partially vaccinated, and unvaccinated HCP. We describe the clinical and genomic epidemiologic features of post-vaccine infections to assess for selection of variants of concern (VOC)/variants of interest (VOI) in the early post-vaccine period and impact of B.1.617.2 (Delta) variant domination on VE.

Results: Among 13658 HCP in our cohort, 12379 received at least 1 dose of a messenger RNA (mRNA) vaccine. In the pre-Delta period overall VE was 94.5%. Whole genome sequencing (WGS) of 369 isolates in the pre-Delta period did not reveal a clade bias for VOC/VOI specific to post-vaccine infections. VE in the Delta dominant phase was 75.6%. No hospitalizations occurred among vaccinated HCP in the entire study period, compared to 17 hospitalizations and 1 death among unvaccinated HCP.

Conclusions: Findings show high VE among HCP in New York City in the pre-Delta phase, with moderate decline in VE post-Delta emergence. SARS CoV-2 clades were similarly distributed among vaccinated and unvaccinated infected HCP without apparent clustering during the pre-Delta period of diverse clade circulation. Strong vaccine protection against hospitalization was maintained through the entire study period.

Keywords: SARS-CoV-2; breakthrough infections; vaccine effectiveness.

Publication types

Research Support, Non-U.S. Gov't
Research Support, N.I.H., Extramural

MeSH terms

COVID-19* / epidemiology
COVID-19* / prevention & control
Delivery of Health Care
Genomics
Humans
New York City / epidemiology
RNA, Messenger
Retrospective Studies
SARS-CoV-2* / genetics

Substances

RNA, Messenger

Supplementary concepts

SARS-CoV-2 variants

Grants and funding

P30 CA008748/CA/NCI NIH HHS/United States