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Rapidly shifting immunologic landscape and severity of SARS-CoV-2 in the Omicron era in South AfricaSun, Kaiyuan; Tempia, Stefano; Kleynhans, Jackie; von Gottberg, Anne; McMorrow, Meredith L; Wolter, Nicole; Bhiman, Jinal N; Moyes, Jocelyn; Carrim, Maimuna; Martinson, Neil A; Kahn, Kathleen; Lebina, Limakatso; du Toit, Jacques D; Mkhencele, Thulisa; Viboud, Cécile; Cohen, Cheryl
Nature communications, 01/2023, Letnik: 14, Številka: 1Journal Article
South Africa was among the first countries to detect the SARS-CoV-2 Omicron variant. However, the size of its Omicron BA.1 and BA.2 subvariants (BA.1/2) wave remains poorly understood. We analyzed sequential serum samples collected through a prospective cohort study before, during, and after the Omicron BA.1/2 wave to infer infection rates and monitor changes in the immune histories of participants over time. We found that the Omicron BA.1/2 wave infected more than half of the cohort population, with reinfections and vaccine breakthroughs accounting for > 60% of all infections in both rural and urban sites. After the Omicron BA.1/2 wave, we found few (< 6%) remained naïve to SARS-CoV-2 and the population immunologic landscape is fragmented with diverse infection/immunization histories. Prior infection with the ancestral strain, Beta, and Delta variants provided 13%, 34%, and 51% protection against Omicron BA.1/2 infection, respectively. Hybrid immunity and repeated prior infections reduced the risks of Omicron BA.1/2 infection by 60% and 85% respectively. Our study sheds light on a rapidly shifting landscape of population immunity in the Omicron era and provides context for anticipating the long-term circulation of SARS-CoV-2 in populations no longer naïve to the virus.
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