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Characteristics of infections with ancestral, Beta and Delta variants of SARS-CoV-2 in the PHIRST- C community cohort study, South Africa, 2020-2021

Article scientifique 2023 Anglais

Résumé

Abstract Background Data on the characteristics of individuals with mild and asymptomatic infections with different SARS-CoV-2 variants are limited. We therefore compared the characteristics of individuals infected with ancestral, Beta and Delta SARS-CoV-2 variants in South Africa. Methods We conducted a prospective cohort study in a rural and an urban site during July 2020-August 2021. Mid-turbinate nasal swabs were collected twice-weekly from household members irrespective of symptoms and tested for SARS-CoV-2 using real-time reverse transcription polymerase chain reaction (rRT-PCR). Differences by variant were evaluated using multinomial regression. Results We included 1200 individuals from 222 households and 648 rRT-PCR-confirmed infection episodes (66, 10%ancestral, 260, 40% Beta, 322, 50%Delta). Symptomatic proportion was similar for ancestral (7, 11%), Beta (44, 17%), and Delta (46, 14%) infections (p=0.4). After accounting for previous infection, peak incidence shifted to younger age groups in successive waves (40-59 years ancestral, 19-39 years Beta, 13-18 years Delta). On multivariable analysis, compared to ancestral, Beta infection was more common in individuals aged 5-12 years (vs 19-39)(adjusted odds ratio (aOR) 2.6, 95% confidence interval (CI)1.1-6.6) and PCR cycle threshold (Ct) value <30 (vs >35)(aOR 3.2, 95%CI 1.3-7.9), while Delta was more common in individuals aged <5 (aOR 6.7, 95%CI1.4-31.2) and 5-12 years (aOR 6.6 95%CI2.6-16.7)(vs 19-39) and Ct value <30 (aOR 4.5, 95%CI 1.3-15.5) and 30-35 (aOR 6.0, 95%CI 2.3-15.7)(vs >35). Conclusions Consecutive SARS-CoV-2 waves with Beta and Delta variants were associated with a shift to younger individuals. Beta and Delta infections were associated with higher viral loads potentially increasing infectiousness.

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Cohen, C., Kleynhans, J., Gottberg, A., McMorrow, M., Wolter, N., Bhiman, J., Moyes, J., Plessis, M., Carrim, M., Buys, A., Kahn, K., Tollman, S., Lebina, L., Wafawanaka, F., Toit, J., Gómez‐Olivé, F., Dawood, F., Mkhencele, T., Martinson, N., Tempia, S. (2023). Characteristics of infections with ancestral, Beta and Delta variants of SARS-CoV-2 in the PHIRST- C community cohort study, South Africa, 2020-2021. https://doi.org/10.21203/rs.3.rs-3452480/v1

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Auteur(s)

Cheryl Cohen Jackie Kleynhans Anne von Gottberg Meredith McMorrow Nicole Wolter Jinal N. Bhiman Jocelyn Moyes Mignon du Plessis Maimuna Carrim Amelia Buys Kathleen Kahn Stephen Tollman Limakatso Lebina Floidy Wafawanaka Jacques du Toit F. Xavier Gómez‐Olivé Fatimah S. Dawood Thulisa Mkhencele Neil Martinson Stefano Tempia

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