Evidence map›Paper›PMID 38515050›Full record

ArticleBMC infectious diseases2024

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 and 11 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC infectious diseases, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.

0numbers the graph read from it
0cells of the map it votes in
5citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

5 citing papers in PubMed.

  1. Article
  2. Article
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  4. Review
  5. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

21 authors.

Cheryl CohenCentre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa. cherylc@nicd.ac.za.
Jackie KleynhansCentre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.
Anne von GottbergCentre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.
Meredith L McMorrowCenters for Disease Control and Prevention (CDC) COVID-19 Response, Atlanta, Georgia, United States of America.
Nicole WolterCentre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.
Jinal N BhimanCentre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.
Jocelyn MoyesCentre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.
Mignon du PlessisCentre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.
Maimuna CarrimCentre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.
Amelia BuysCentre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.
Neil A MartinsonPerinatal HIV Research Unit, University of the Witwatersrand, Johannesburg, South Africa.
Kathleen KahnMRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), Faculty of Health Sciences, School of Public Health, University of the Witwatersrand, Johannesburg, South Africa.
Stephen TollmanMRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), Faculty of Health Sciences, School of Public Health, University of the Witwatersrand, Johannesburg, South Africa.
Limakatso LebinaPerinatal HIV Research Unit, University of the Witwatersrand, Johannesburg, South Africa.
Floidy WafawanakaMRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), Faculty of Health Sciences, School of Public Health, University of the Witwatersrand, Johannesburg, South Africa.
Jacques du ToitMRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), Faculty of Health Sciences, School of Public Health, University of the Witwatersrand, Johannesburg, South Africa.
Francesc Xavier Gómez-OlivéMRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), Faculty of Health Sciences, School of Public Health, University of the Witwatersrand, Johannesburg, South Africa.
Fatimah S DawoodCenters for Disease Control and Prevention (CDC) COVID-19 Response, Atlanta, Georgia, United States of America.
Thulisa MkhenceleCentre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.
PHIRST group
Stefano TempiaCentre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.

Funding

NCIRD CDC HHS U01 IP001048Wellcome TrustWellcome Trust 221003/Z/20/Z
6 · The paper itself

Abstract

backgroundData 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.

methodsWe 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.

resultsWe 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).

conclusionsConsecutive 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.

Indexed as

COVID-19Cohort StudiesHumansProspective StudiesSARS-CoV-2South AfricaCohort studyEpidemiologySARS-CoV-2South Africa

Identifiers

PMID38515050
PMCPMC10956206

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.