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

• Published in: BMC infectious diseases Vol. 24; no. 1; p. 336
• Main Authors: Cohen, Cheryl, Kleynhans, Jackie, von Gottberg, Anne, McMorrow, Meredith L, Wolter, Nicole, Bhiman, Jinal N, Moyes, Jocelyn, du Plessis, Mignon, Carrim, Maimuna, Buys, Amelia, Martinson, Neil A, Kahn, Kathleen, Tollman, Stephen, Lebina, Limakatso, Wafawanaka, Floidy, du Toit, Jacques, Gómez-Olivé, Francesc Xavier, Dawood, Fatimah S, Mkhencele, Thulisa, Tempia, Stefano
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 21.03.2024; BioMed Central; BMC
• Subjects: Cohort analysis; Cohort study; Comparative analysis; Confidence intervals; COVID-19; Data collection; Epidemiology; Genomes; Global positioning systems; GPS; Health aspects; Households; Infection; Infections; Mutation; Nose; Polymerase chain reaction; Public health; Reverse transcription; SARS-CoV-2; Severe acute respiratory syndrome coronavirus 2; South Africa; Statistical analysis; Urban areas; Viral diseases; South Africa; South Korea; Seoul South Korea; United States > US; South Africa; SARS-CoV-2; Epidemiology; Cohort study
• ISSN: 1471-2334; 1471-2334
• DOI: 10.1186/s12879-024-09209-z

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. 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. 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). 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.