DOI: 10.5061/dryad.4xgxd25m0
title: The omicron variant of SARS-CoV-2 drove broadly increased seroprevalence in a public university setting

description: Omicron is the comparatively most transmissible and contagious variant of
 severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). We conducted
 a seroprevalence study spring 2022, to investigate the seroprevalence of
 SARS-CoV-2 antibodies among individuals aged 18 years and older after the
 Omicron outbreak. The seroprevalence of anti-receptor binding domain (RBD)
 antibodies was found to be 96.3% (95% CI 95.2-97.2%) compared to 88.2%
 (95% CI 86.1-90%) in our previous serosurvey. For anti-nucleocapsid (NC)
 antibodies, the seroprevalence was 39.1% (95% CI 36.6-41.7%) compared to
 19.7% (95% CI 17.5-22.2%) earlier. Individuals that experienced
 breakthrough infections exhibited the highest levels of anti-RBD
 antibodies. Additionally, saliva samples showed promise as a potential
 diagnostic biofluid for measuring antibody levels, as they exhibited a
 strong agreement with the data obtained from serum samples. The near
 doubling of anti-NC reactivity, a proxy for history of infection, reflects
 the contagiousness of the omicron variant, but may also have been
 influenced by a more relaxed approach to precautions in the spring of
 2022. Serosurveys repeated at regular intervals monitor the trend of
 infections in the community, delineate the geographical spread of the
 infection, and may guide containment measures in communities, and prompt
 response to future outbreaks.
description: Recruitment for this study was conducted through invitations,
 email announcements to the university community, and social media
 advertising, and potential participants were required to complete an
 electronic consent and a survey before giving biological specimens. The
 sample collection was extended for three days, in spring 2022.
 Participants were initially invited via emails and social media channels.
 Individuals were eligible for inclusion if they were 18 years of age or
 older and were able to provide informed consent. All
 demographic information and assay results were provided via Excel files.
 Any participant under the age of 18, those who did not provide a
 biological sample, or those with non-unique sample IDs were removed from
 the study. Assay information was first merged together by a sample ID and
 those in common were kept in the study (inner join). The combined assay
 data was then merged to the demographic information. Those who provided
 biological samples but no demographic information were removed from the
 study (left join). Finally, we performed data cleaning in order to fix
 input mistakes (e.g. spelling, wrong dates, etc.) and group responses in
 the appropriate categories. We corrected input mistakes
 by participants (e.g. wrong spelling of vaccine source). We also checked
 whether the vaccination dates were sequential. For example, if the second
 vaccination date was reported before the first vaccination date, then the
 second vaccination date was recorded as missing (NA). 
description: # The omicron variant of SARS-CoV-2 drove broadly increased seroprevalence
 in a public university setting
 [https://doi.org/10.5061/dryad.4xgxd25m0](https://doi.org/10.5061/dryad.4xgxd25m0) ## Description of the data and file structure ## Description of methods used for collection/generation of data: Recruitment for this study was conducted through invitations, email announcements to the university community, and social media advertising, and potential participants were required to complete an electronic consent and a survey before giving biological specimens. The sample collection was extended for three days, in spring 2022. Participants were initially invited via emails and social media channels. Individuals were eligible for inclusion if they were 18 years of age or older and were able to provide informed consent. ## Methods for processing the data: All demographic information and assay results were provided via Excel files. Any participant under the age of 18, those who did not provide a biological sample, or those with non-unique sample IDs were removed from the study. Assay information was first merged together by a sample ID and those in common were kept in the study (inner join). The combined assay data was then merged to the demographic information. Those who provided biological samples but no demographic information were removed from the study (left join). Finally, we performed data cleaning in order to fix input mistakes (e.g. spelling, wrong dates, etc.) and group responses in the appropriate categories. ## Missing and Incomplete Data: Certain cells are empty when the data is not available, not collected or assays are not performed. For example, column L-O Servey 2 data are missing because lateral flow assays were not performed during survey 2. In some instances values are recorded as *NaN means "not a number*" due to value could not be calculated due to fitting range (too low). ### Files and variables #### File: Hou\_et\_al\_SSI.SSII\_RawData.xlsx | **Variable** | **Type** | **Description** | **Additional Descriptions** | | :-------------------------------------- | :-------------------- | :----------------------------------------------------------- | :----------------------------------------------------------------------------------------------------------------------------------------------------------- | | surv.type | Character | Indicator of survey the participant took part in | ·       sero1- Serosurvey I | | pseudoid | Numeric | Deidentified patient ID | ·       Samples with the same pseudoid correspond to the same participant | | survey.date | Date (year-month-day) | Date of sample collection |   | | age.gr2 | Character | Age group |   | | gender | Character | Gender | ·       Others include non-binary, third gender & prefer not to say | | status | Character | Employment status: |   | | howheard1 | Character | How they heard about the study | ·       Ad: Advertisement | | covid19 | Character | Have you ever been diagnosed with covid? |   | | vaccine | Character | Have you been vaccinated for COVID-19? |   | | vaccine.source | Character | Vaccine Source: | ·        Sinopharm included “BBIBP” and “VEROCELL” was replaced with Sinopharm | | vaccine.source.gr | Character | Vaccine Source group: | ·       A- Spike protein-based COVID-19 vaccines: AstraZeneca, Pfizer, Moderna, Janssen | | NC.LFA.IgG | Character | Nucleocapsid IgG results: |  Lateral flow assays were not performed for survey 2 | | NC.LFA.IgM | Character | Nucleocapsid IgM results: |   Lateral flow assays were not performed for survey 2 | | Spike.LFA.IgG | Character | Spike IgG results: |   Lateral flow assays were not performed for survey 2 | | Spike.LFA.IgM | Character | Spike IgM results: |   Lateral flow assays were not performed for survey 2 | | Spike.Dxi.IgG.value2 | Numeric | Value for Spike Dxi IgG results, after dilution | ·       Anything &gt; 10 was considered as positive. Otherwise, negative. | | Spike.Dxi.IgG | Character | Spike Dxi IgG results: |   | | Spike Dxi.IgM.value | Numeric | Value for Spike Dxi IgM results. | ·       Anything &gt; 1 was considered positive. Otherwise, negative. | | Spike Dxi.IgM | Character | Spike Dxi IgM results: |   | | NC.ELISA.value | Numeric | Value for NC ELISA results |   | | NC.ELISA | Character | ELISA results: |   | | qPCR\_result | Character | Saliva qPCR results: |   | | SARS.CoV.2.S1.RBD.value.MSD\_serum | Numeric | SARS-CoV-2 RBD values (serum sample) | ·      Anything &gt; 538 was considered positive. Otherwise, negative. | | SARS.CoV.2.S1.RBD.MSD\_serum | Character | SARS-CoV-2 RBD serum sample results: |   | | SARS.CoV.2Nucleocapsid.value.MSD\_serum | Numeric | SARS-CoV-2 NC values (serum sample) | ·      Anything &gt; 5000 was considered positive. Otherwise, negative. | | SARS.CoV.2Nucleocapsid.MSD\_serum | Character | SARS-CoV-2 NC serum sample results: |   | | SARS.CoV.2.RBD.value.MSD\_saliva | Numeric | SARS-CoV-2 RBD values (saliva sample) | ·       Anything &gt; 3.308 was considered positive. Otherwise, negative. | | SARS.CoV.2.RBD.MSD\_saliva | Character | SARS-CoV-2 RBD saliva sample results: |   | | SARS.CoV.2.RBD\_BA.2.MSD\_saliva | Numeric | SARS-CoV-2 RBD values, BA.2 variant (saliva sample) |   | | SARS.CoV.2.RBD\_BA.2.12.1.MSD\_saliva | Numeric | SARS-CoV-2 RBD values, BA.2.12.1 variant (saliva sample) |   | | SARS.CoV.2.RBD\_BA.2+L452M.MSD\_saliva | Numeric | SARS-CoV-2 RBD values, BA.2+L452M variant (saliva sample) |   | | SARS.CoV.2.RBD\_BA.2+L452R.MSD\_saliva | Numeric | SARS-CoV-2 RBD values, BA.2+L452R variant (saliva sample) |   | | SARS.CoV.2.RBD\_BA.3.MSD\_saliva | Numeric | SARS-CoV-2 RBD values, BA.3 variant (saliva sample) |   | | SARS.CoV.2.RBD\_BA.4;BA.5.MSD\_saliva | Numeric | SARS-CoV-2 RBD values, BA.4 and BA.5 variant (saliva sample) |   | | SARS.CoV.2.RBD\_Alpha.MSD\_saliva | Numeric | SARS-CoV-2 RBD values, Alpha variant (saliva sample) |   | | SARS.CoV.2.RBD\_Beta.MSD\_saliva | Numeric | SARS-CoV-2 RBD values, Beta variant (saliva sample) |   | | SARS.CoV.2.RBD\_Delta.MSD\_saliva | Numeric | SARS-CoV-2 RBD values, Delta variant (saliva sample) |   | | Fig2A\_sel | Character | Samples selected for analysis of Figure 2A: | Participants selected received vaccinations, but no infections. They were subdivided based on their participation in Serosurvey I or II | | Fig2A\_time\_monts | Character | Months post-vaccination (grouped): | Spike.Dxi.IgG.value2 compared between grouped time frames | | Fig2B\_sel | Character | Samples selected for analysis of Figure 2B: | Participants selected did not have an infection and were subdivided based on whether they received a booster dose | | Fig2B\_time\_monts | Character | Months post-vaccination (grouped): | Spike.Dxi.IgG.value2 compared between grouped time frames | | Fig2C\_sel | Character | Samples selected for analysis of Figure 2C: | Participants selected had previous infections vaccinations, or both. | | Fig2C\_time\_monts | Character | Months post-vaccination or infection (grouped): | Spike.Dxi.IgG.value2 compared between grouped time frames | | Fig2D\_sel | Character | Samples selected for analysis of Figure 2D: | Participants selected had both previous vaccinations and infections. They were subdivided by the order in which they received vaccinations or were infected. | | Fig2D\_time\_monts | Character | Months post-vaccination or infection (grouped): | Spike.Dxi.IgG.value2 compared between grouped time frames | ## Code/software None ## Access information Other publicly accessible locations of the data: * n/a Data was derived from the following sources: * n/a