NYU Dataset

Clinical and genomic signatures of rising SARS-CoV-2 Delta breakthrough infections in New York

UID: 10497
* Corresponding Author

Investigators obtained high quality SARS-CoV-2 sequences from 132 vaccinated and 283 unvaccinated individuals who were seen at NYU Langone Health facilities between May 1, 2021 and August 3, 2021. Fully vaccinated individuals received either two doses of the BNT162b2 (Pfizer/BioNTech) or mRNA-1273 (Moderna) vaccines, or a single-dose of the COVID-19 Janssen vaccine. Breakthrough infections were defined as positive real-time PCR tests for SARS-CoV-2 RNA regardless of threshold (Ct) values at least 14 days after the second dose. The unvaccinated control group consisted of all positive cases who had not received a dose of any vaccine at the time of positivity, which were collected and sequenced in the same period as the breakthrough infections.

The median ages and age distribution were 37 versus 42 years old and 33.5% versus 29.5% male among vaccinated and unvaccinated groups, respectively. 63% of recorded breakthrough infections occurred over 120 days after full vaccination with any vaccine. SARS-CoV-2 variants identified during the study period included alpha, gamma, delta, iota, and omicron.

Geographic Coverage
New York (State) - New York City
Subject of Study
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Genomic data has been shared through the NCBI BioProject Sequence Read Archive (SRA) repository under accession ID PRJNA769411.

Genetic sequences may also be found in the GISAID repository by searching for "NYUMC" in the nCov project. The associated publication includes a list of all GISAID reference numbers for sequences in this dataset in Supplemental Table 1. A GISAID account is required to access the genetic sequences in the GISAID repository. Users must complete a Database Access Agreement and Registration Form to obtain credentials.

Access via NCBI BioProject

Links to raw sequence reads
Accession #: PRJNA769411

Access via GISAID

Genetic sequences
Accession #: NYUMC

Associated Publications
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