Breakthrough SARS-CoV-2 outcomes in immune-disordered people during the Omicron era: A prospective cohort study

Introduction: Immune-deficient/disordered people (IDP) elicit a less robust immune response to COVID-19 vaccination than the general US population. Despite millions of IDP at presumed elevated risk, few population-level studies of IDP have been conducted in the Omicron era to evaluate breakthrough infection-related outcomes.
Methods: We followed a prospective cohort of 219 IDP and 63 healthy volunteers (HV) in the US from April 2021 (Alpha variant peak) to July 2023 (Omicron XBB variant peak). IDP had a primary or secondary immune disorder. All participants were ≥3 years old and received COVID-19 vaccines external to this study. We quantified anti-spike IgG titer levels by ELISA, measured breakthroughs via participant reports and laboratory tests on saliva samples, compared breakthrough incidence among HV and IDP, assessed infection complications [persistent infections, reinfections, and post-acute sequelae of COVID-19 (PASC)], and used surveys to capture COVID-19 symptoms and preventiv..., All methods for the collection and processing of these data are published in the associated manuscript at BMJ Public Health (https://doi.org/10.1136/bmjph-2024-002436) and the associated manuscript https://doi.org/10.1126/sciadv.adh3150. Code and survey instruments are available at https://github.com/ericotta/PERSIST_Study/.
, , # Breakthrough SARS-CoV-2 outcomes in immune-disordered people during the Omicron era: A prospective cohort study

[https://doi.org/10.5061/dryad.9p8cz8wsr](https://doi.org/10.5061/dryad.9p8cz8wsr)

This data was collected as part of the PERSIST cohort study (NCT04852276), which aimed to assess the immune response to COVID-19 vaccines in people with immune disorders and healthy volunteers. We collected and analyzed data from April 2021 through July 2023 for this study. Laboratory methods that describe the assay specifics can be found in the associated publication, “Characterization of the anti-spike IgG immune response to COVID-19 vaccines in people with a wide variety of immunodeficiencies” in *Science Advances* and our publication in *BMJ Public Health*, \"Breakthrough SARS-CoV-2 Outcomes in Immune-Disordered People During the Omicron Era: A Prospective Cohort Study \".

### Data and file information

Nine unique datasets were used in our study, all of which are provided in a .csv forma..., This study (NCT04852276) was approved by the Institutional Review Board of the National Institutes of Health (NIH000384-I) and was conducted in accordance with the Declaration of Helsinki and Good Clinical Practice guidelines. Adult participants and parents or legal guardians of pediatric participants provided written, informed consent for the study and for unrestricted use of deidentified data. Pediatric participants six years and older gave verbal assent.

To limit the possibility of our participants being identified by means of our data, the datasets we include do not report on participants’ age, sex, race, ethnicity, specific immunological conditions, and the collection date of the samples. There were a variety of date variables (e.g., the date of vaccine receipt) that were critical to our analyses. These variables have been retained. However, each date variables’ values were shifted and jittered by different amounts in the datasets we publicly present. Moreover, a different random...