Population Immunity and Covid-19 Severity with Omicron Variant in South Africa6 min read
This survey (conducted from October 22 to December 9, 2021) included the same households that were sampled during our previous survey (conducted from November 4, 2020, to January 22, 2021).9 To account for possible nonparticipation, out-migration, and death since the previous survey, there was a 10% increase in the households that were sampled; the additional households were sampled in the same clusters used previously.
We obtained samples that were adequate for serostatus evaluation from 7010 of 7498 participants from 3047 households (Figure 1); 83% of the samples had been obtained by November 25, 2021, when the omicron variant was first identified (Fig. S1). Demographic and household characteristics, known underlying medical conditions and participant-reported human immunodeficiency virus status, and vaccination status of the survey participants are shown in Table 1. The degree to which the survey population was representative of the general population of Gauteng and of South Africa is described in Table S2. Vaccination in Gauteng according to district, age, and vaccine is summarized in Table S3. As of November 25, 2021, of the total population of 12,191,569 persons 12 years of age or older (who were eligible for vaccination), 4,386,646 (36.0%) had received at least one dose of BNT162b2 or Ad26.COV2.S, and 2,452,017 (20.1%) had received two doses. Of the 2,416,045 persons older than 50 years of age, 1,074,303 (44.5%) had received two doses of BNT162b2.
Among unvaccinated participants, the overall prevalence of anti-spike or anti-nucleocapsid IgG seropositivity was 68.4% (95% confidence interval [CI], 67.2 to 69.6), whereas the prevalence of anti-nucleocapsid IgG seropositivity was 39.7% (95% CI, 38.4 to 41.0), a finding that indicates a lack of sensitivity of anti-nucleocapsid IgG for the detection of previous infection. We thus focused on the overall prevalence of anti-spike or anti-nucleocapsid IgG seropositivity.
Among all participants, the overall seroprevalence was 73.1% (95% CI, 72.0 to 74.1) (Table 1). The seroprevalence was heterogeneous across provincial districts, ranging from 66.7% (95% CI, 54.2 to 69.0) in Tshwane, where the omicron variant was first identified, to 76.2% (95% CI, 74.5 to 77.8) in Johannesburg (Fig. S2). In addition, the seroprevalence was heterogeneous across subdistricts, ranging from 72.7% to 85.8% within Johannesburg and from 58.9% to 77.4% within Tshwane (Table S4).
Female participants were more likely to be seropositive than male participants (76.9% vs. 67.9%; risk ratio, 1.13; 95% CI, 1.10 to 1.17). The seroprevalence varied according to age group; it was lowest among children younger than 12 years of age (56.2%) and highest among adults older than 50 years of age (79.7%). Children 12 to 17 years of age were more likely to be seropositive than children younger than 12 years of age (73.8% vs. 56.2%; risk ratio, 1.31; 95% CI, 1.21 to 1.42). Participants who had received a Covid-19 vaccine were more likely to be seropositive than unvaccinated participants (93.1% vs. 68.4%; risk ratio, 1.36; 95% CI, 1.33 to 1.39). Among vaccinated participants, the seroprevalence was consistently high across age groups; among adults 18 to 50 years of age, those who were vaccinated had a higher seroprevalence than those who were unvaccinated.
Participants who had previously tested positive for SARS-CoV-2 infection were more likely to be seropositive than participants who had never been tested (88.2% vs. 71.7%; risk ratio, 1.23; 95% CI, 1.17 to 1.30). Participants living in an informal settlement had a lower seroprevalence than participants living in a standalone house (66.3% vs. 74.2%; risk ratio, 0.89; 95% CI, 0.86 to 0.93). Daily smoking was associated with a lower seroprevalence than was not smoking (66.5% vs. 77.6%; risk ratio, 0.86; 95% CI, 0.82 to 0.90).
Shown are incidences of daily cases, weekly hospitalizations, daily recorded deaths, and weekly excess deaths attributable to coronavirus disease 2019 (Covid-19). The inset shows the incidence of daily recorded deaths on an enlarged y axis. The horizontal dashed line indicates an incidence of zero. The data were sourced from the National Institute for Communicable Diseases daily databases through January 12, 2022, except for the data regarding weekly excess deaths attributable to Covid-19, which were defined by and sourced from the South African Medical Research Council through January 8, 2022.16 The B.1.1.529 (omicron) variant was first identified on November 25, 2021. Cases included asymptomatic and symptomatic infections with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) confirmed by either a nucleic acid amplification assay or a rapid antigen test. Changes in the frequency of testing limit direct comparisons of case numbers; in particular, the lower frequency of testing during the first wave, which was due to constraints in laboratory capacity and prioritization of testing for hospitalized persons, prevents the direct comparison of cases from the first wave with those from subsequent waves. Hospitalizations included admissions for SARS-CoV-2 infection, as well as admissions for other illnesses in which SARS-CoV-2 infection was incidentally identified on routine screening at the time of admission. The DATCOV system was developed during the first wave, with gradual onboarding of facilities; thus, hospitalizations from the first wave may be underestimated. Definitions of recorded death and excess death attributable to Covid-19 are provided in the Supplementary Appendix.
Shown are 7-day moving averages of the incidences of daily cases, hospitalizations, and recorded deaths among participants 4 years of age or younger (Panel A), 5 to 17 years of age (Panel B), 18 to 44 years of age (Panel C), 45 to 59 years of age (Panel D), and 60 years of age or older (Panel E). The horizontal dashed line indicates an incidence of zero. Because the incidences differ across age groups, different y-axis scales are used for each age group to provide clarity and aid in the visual interpretation of the trends in each group.
Daily cases, weekly hospitalizations, daily recorded deaths, and weekly excess deaths attributable to Covid-19 in Gauteng are shown in Figure 2. Daily cases, hospitalizations, and recorded deaths are also shown with stratification according to age group (Figure 3) and according to sex (Fig. S3).
During the fourth wave of Covid-19, in which the omicron variant was dominant, the daily case incidence increased more rapidly and also appeared to be decreasing more quickly than it had during the three previous waves (Figure 2). The time from the onset to the peak of the wave was 1 month in the fourth wave, as compared with 2 months in the third wave. As of January 12, 2022, the case incidence had not yet fully returned to the level before the onset of the fourth wave, but the wave was nearing its end, on the basis of the trajectory shown in Figure 2. At that time, there were almost no recorded or excess deaths attributable to Covid-19 per 100,000 population.
The number of documented Covid-19 cases in the fourth wave (226,932) was higher than that in the second wave (182,564) and lower than that in the third wave (511,638), whereas the incidences of hospitalization, recorded death, and excess death attributable to Covid-19 in the fourth wave were consistently lower than the incidences in earlier waves (Table 2). In addition, the peak incidences of hospitalization, recorded death, and excess death in the fourth wave were lower than the peak incidences in previous waves. The fourth wave contributed 11.2%, 3.9%, and 3.3% of overall hospitalizations, recorded deaths, and excess deaths due to Covid-19, respectively, whereas the third wave, in which the delta variant was dominant, contributed 43.6%, 49.3%, and 52.7%. Similar trends were observed across all districts (Fig. S4). Although there is a lag in the reporting of weekly excess deaths, the incidence in the fourth wave as of January 8, 2022 (12 per 100,000 population), was lower than the incidence in the third wave (197 per 100,000 population). As of January 12, 2022, incidences were on an ongoing downward trajectory, with a 7-day moving average of 7.28 cases, 0.96 hospitalizations, and 0.11 recorded deaths per 100,000 population — a decrease by a factor of 9.3, 3.3, and 2.4 from the peak incidence of 67.56 cases, 3.18 hospitalizations, and 0.26 recorded deaths per 100,000 population, respectively. The incidences were nearing prewave levels (as of October 25, 2021) of 0.46 cases, 0.15 hospitalizations, and 0.04 recorded deaths per 100,000 population.
During the fourth wave, decreased incidences of hospitalization and recorded death were evident across all age groups older than 17 years and among both men and women. The incidences of hospitalization and recorded death among children 17 years of age or younger, which have consistently been markedly lower than the incidences in older age groups, were similar to the incidences during earlier waves, except for a lower mortality among children 5 to 17 years of age during the fourth wave than during the third (delta-dominant) wave (Figure 3 and Tables S5, S6, and S7).