Eberhardt et al. Preceding anti-spike IgG levels predicted risk and severity of COVID-19 during the Omicron-dominant wave in Santa Fe city, Argentina
Description
The matrices are the full datasets used to construct the models presented in the work "Preceding anti-spike IgG levels predicted risk and severity of COVID-19 during the Omicron-dominant wave in Santa Fe city, Argentina" (Epidemiology & Infection). The first dataset (named "Prewave survey ") was used for the cross-sectional pre-wave survey which enabled the characterisation of the acquired humoral defences prior to the Omicron-dominant wave. The outputs of models 1 and 2 to study antibody levels according to vaccine doses and schemes used this dataset and are shown in Table 1, 2 and 3. The second dataset (named "Longitudinal study omicron wave") is data from a longitudinal study in which 514 individuals were followed during the wave to see how the previous immunological status was associated with Omicron risk and severity. These data were used for models 3, 4 and 5 and their outputs are shown in Table 4, 5, 6 and 7.
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During November and December of 2021, we conducted a survey collecting relevant information on COVID-19 by a first questionnaire, and measuring anti-spike IgG antibodies in people from randomly selected households of Santa Fe city, Argentina, and from citizens that volunteered to participate in the study. This provided the opportunity of characterising the acquired humoral defences of the population of Santa Fe city immediately prior to the arrival of Omicron. Omicron began around 18th December 2022 in Santa Fe city, and the number of daily cases started to decline by mid-January 2022. In March 2022, after the wave was over, a subset of the study participants was asked to complete a second questionnaire. The first questionnaire included queries on sex, age, having been diagnosed with COVID-19 (with dates and diagnosis details), COVID-19 severity and duration, vaccine shots received (with type and dates), close contacts with COVID-19 cases, co-morbidities, among other information. Those that were sampled after 15th November 2021, were asked to complete the second questionnaire in March 2022. This allowed us to follow the participants from whom there was an antibody measurement within a month prior to the Omicron-dominant wave, which gave us confidence that the antibody levels recorded reflected the humoral defences with which each participant faced the wave. The second questionnaire inquired for the period that went from the date of the blood sample collection to 28th February 2022, and included information on close contact with cases during that period, COVID-19 diagnosis (with dates and diagnosis details), vaccine shots (with type and dates), and disease severity and duration. Using the information obtained from the questionnaires, we established a COVID-19 case when the participant indicated that she/he was given positive by the government after an official PCR test, or given positive by the government due to having symptoms while cohabitating with a case, or had a PCR positive test by a private laboratory, or had a positive rapid antigen test while having symptoms or after having had a close contact with a case. Levels of anti-SARS-CoV-2 spike protein IgG were quantified by COVID AR IgG immunoassay developed by Instituto Leloir in Argentina (Ojeda et al. 2021), following the manufacturer's instructions. This IgG immunoassay kit consists of a solid phase ELISA that utilizes as antigens the trimer of native protein S and a domain of that SPIKE protein that contains the receptor binding domain, obtained by recombinant DNA techniques produced in human cells.