BMC Infectious Diseases (Mar 2024)

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

  • Cheryl Cohen,
  • Jackie Kleynhans,
  • Anne von Gottberg,
  • Meredith L. McMorrow,
  • Nicole Wolter,
  • Jinal N. Bhiman,
  • Jocelyn Moyes,
  • Mignon du Plessis,
  • Maimuna Carrim,
  • Amelia Buys,
  • Neil A. Martinson,
  • Kathleen Kahn,
  • Stephen Tollman,
  • Limakatso Lebina,
  • Floidy Wafawanaka,
  • Jacques du Toit,
  • Francesc Xavier Gómez-Olivé,
  • Fatimah S. Dawood,
  • Thulisa Mkhencele,
  • for the PHIRST group,
  • Stefano Tempia

DOI
https://doi.org/10.1186/s12879-024-09209-z
Journal volume & issue
Vol. 24, no. 1
pp. 1 – 11

Abstract

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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 in demographic and clinical characteristics, shedding and cycle threshold (Ct) value of infection episodes by variant were evaluated using multinomial regression. Overall and age-specific incidence rates of infection were compared by variant. 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 35)(aOR 3.2, 95%CI 1.3-7.9), while Delta was more common in individuals aged 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 peak viral loads, potentially increasing infectiousness.

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