Rapidly shifting immunologic landscape and severity of SARS-CoV-2 in the Omicron era in South Africa
Kaiyuan Sun, Stefano Tempia, Jackie Kleynhans, Anne von Gottberg, Meredith McMorrow, Nicole Wolter, Jinal N. Bhiman, Jocelyn Moyes, Maimuna Carrim, Neil Martinson, Kathleen Kahn, Limakatso Lebina, Jacques du Toit, Thulisa Mkhencele, Cécile Viboud, Cheryl Cohen, the PHIRST-C group, Amelia Buys, Linda de Gouveia, Mignon du Plessis, F. Xavier Gómez‐Olivé, Kgaugelo Patricia Kgasago, Retshidisitswe Kotane, Tumelo Moloantoa, Stephen Tollman, Floidy Wafawanaka
Abstract
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.