Viral load dynamics of SARS-CoV-2 Delta and Omicron variants after multiple doses of vaccine and previous infection
The study was approved by the Institutional Review Board (IRB) of Sheba Medical Center. Helsinki approval number: SMC-8228-21. Individuals included in this study were tested free of charge as part of the Israeli Testing and Surveillance Program. Patient consent was not given as this is a retrospective analysis using data collected as part of a national testing and surveillance programme. The investigators did not have access to deanonymized information.
Data set construction
We used the national database of Ct values of positive cases. Samples were collected between June 15, 2021 and January 29, 2022. SAS and Python were used for data retrieval, and R (version 4.0.3) and R Studio (version 1.4.1103) were used for analysis. The dataset contained more than four million records of positive PCR tests with Ct-values. Records contained Ct measurements for N, E, Orf1ab or S genes. Results are presented for N and E and four different laboratories, two of which are the main laboratories of the Israel Health Maintenance Organization, which together represent ~40% of the Israeli population, and the other two are laboratories authorized to perform tests for the Israeli Ministry of Health. Ct values < 10 ili >40 units were removed from the data set, as such values were likely the result of reading errors. A small number of such samples were identified and removed from four laboratories, N & E final data set (9 records).
Multiple Ct measurements for the same individual and gene may belong to the same or different infection events. Sequences of Ct measurements within a single 90-day interval were defined as belonging to the same infection events. For each such series, only the first (earliest) Ct value was taken. Multiple infection events for a single individual were included if the time difference between the last measurement of the first sequence and the first measurement of the second sequence was at least 90 days. For the second infection, the patient’s status was defined as ‘Recovered’.
PCR and Ct values of over 460,000 were initially collected. Using coded identification numbers, we merged Ct data with demographic and vaccination data to determine the patient’s age, sex, and vaccination status. The merged data contained both Ct date and PCR sampling date. For the Ct measurements included in this study, the number of days between these two dates was at most one day. Since the PCR date is the actual sampling date, these dates were used for analyses. Overall, our analyses, performed on samples from four laboratories, and for the vaccination statuses listed below, contained 327,659 individuals, 315,111 Ct measurements for the N gene, and 228,125 measurements for the E gene.
Vaccination statuses were determined for each patient and case of infection, based on the PCR laboratory date. Individuals who had an infection between the first and second doses were excluded from the analysis.
Unvaccinated: until the first dose.
2-doses 10–39: From 10 days after the second dose to 39 days after the second dose.
2-doses 40–69: From 40 days after the second dose to 69 days after the second dose.
2 doses 70+: from 70 days onwards after the second dose, until the third dose
3 doses 10–39: From 10 days after the third dose to 39 days after the third dose.
3 doses 40–69: From 40 days after the third dose to 69 days after the third dose.
3 doses 70+: from 70 days onwards after the third dose, until the fourth dose
4 doses 10+: From 10 days onwards after the fourth dose.
Recovered: Individuals who had a previous case of infection with a positive PCR test at least 90 days before the current infection and who did not receive a dose of vaccine between the two events.
Recovered+vaccine: People who had a previous infection with a positive PCR test at least 90 days before the current infection, who received one dose after the first infection and no later than 10 days before the second infection. The results for this group are shown only in Additional information.
We divided the follow-up study into two separate periods, each dominated by a different variant:
Delta time period: June 15 – December 1, 2021 (>90% of cases identified as Delta, see ref. 21).
Omicron time period: December 28, 2021 – January 29, 2022 (>90% of cases identified as Omicron, see ref. 21).
These periods are also consistent with the first documented case of Omicron infection in Israel (see Supplementary Fig. 1).
To account for time effects in our regression analyses, we divided the Delta and Omicron time periods into 7-day time intervals (bins), using PCR dates to classify Ct measurements. Age groups are defined as 0-11, 12-15, 16-39, 40-59 and 60 or older. Due to national policy, individuals aged 0 to 11 years were vaccinated relatively late, and were therefore excluded from the main analysis. Nevertheless, ages 5 to 11 years are included in the parts of the sensitivity analysis presented in the Supplementary Note 1 (see additional table 5).
For the analysis of the decline in ‘Recovered’ (fig. 3), we divided the time elapsed between the first and second infection into intervals of 60 days (2 months). Intervals for which the number of samples was <50 were merged with the adjacent interval.
The main tools in assessing the effect of various factors on Ct-values are linear and quantile regression. When examining different cohorts, we used cohort, age category, gender and categorized calendar date as explanatory variables. Daily Ct values can be sampled from those infected at different stages of infection (ie, time since infection). Therefore, we also examined the median and lower quartile of Ct values, controlling for variability by age of infection (see Supplementary Tables 2 and 3). To calculate the error bars in Fig. 1–3as well as supplementary images. 2–4we used the estimated coefficients of the cohort, while we set all other coefficients to their mean values (as in the diagrams of predictor effects22). We then calculated the (0.025,0.975)-percentiles to obtain confidence intervals through the multivariate normal distribution.
Summary of the report
Additional information about the research design is available at Nature Research Report Summary linked to this article.