Clinical and Genomic Characterization of SARS CoV-2 infections in mRNA Vaccinated Health Care Personnel in New York City.

Background Vaccine-induced clinical protection against SARS CoV-2 variants is an evolving target. There is 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 November 1st, 2020 - August 31st , 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 (NYC) 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 VOC/VOI in the early post-vaccine period and impact of B.1.617.2 (Delta) variant domination on VE. Results Among 13,658 HCP in our cohort, 12,379 received at least one dose of an mRNA vaccine. In the pre-Delta period overall VE was 94.5%. 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 one death among unvaccinated HCP. Conclusions Findings show high VE among HCP in NYC 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.