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Published on in Vol 13 (2024)

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SARS-CoV-2 Infections in a Triad of Primary School Learners (Grades 1-7), Their Parents, and Teachers in KwaZulu-Natal, South Africa: Protocol for a Cross-Sectional and Nested Case-Cohort Study

SARS-CoV-2 Infections in a Triad of Primary School Learners (Grades 1-7), Their Parents, and Teachers in KwaZulu-Natal, South Africa: Protocol for a Cross-Sectional and Nested Case-Cohort Study

SARS-CoV-2 Infections in a Triad of Primary School Learners (Grades 1-7), Their Parents, and Teachers in KwaZulu-Natal, South Africa: Protocol for a Cross-Sectional and Nested Case-Cohort Study

Authors of this article:

Reshmi Dassaye1 Author Orcid Image ;   Terusha Chetty1, 2 Author Orcid Image ;   Brodie Daniels1 Author Orcid Image ;   Zakir Gaffoor1 Author Orcid Image ;   Elizabeth Spooner1 Author Orcid Image ;   Trisha Ramraj1 Author Orcid Image ;   Ncengani Mthethwa1 Author Orcid Image ;   Duduzile Faith Nsibande1 Author Orcid Image ;   Saresha Pillay1 Author Orcid Image ;   Arvin Bhana3, 4 Author Orcid Image ;   Vuyolwethu Magasana1 Author Orcid Image ;   Tarylee Reddy5 Author Orcid Image ;   Khanya Mohlabi1 Author Orcid Image ;   Penelope Linda Moore6, 7, 8 Author Orcid Image ;   Wendy A Burgers9, 10, 11 Author Orcid Image ;   Tulio de Oliveira11, 12, 13, 14 Author Orcid Image ;   Nokukhanya Msomi15, 16 Author Orcid Image ;   Ameena Goga1, 17 Author Orcid Image
Article Authors Cited by Tweetations Metrics

    Protocol

    1HIV and Other Infectious Diseases Research Unit, South African Medical Research Council, Cape Town, South Africa

    2Discipline of Public Health Medicine, University of KwaZulu-Natal, Durban, South Africa

    3Center for Rural Health, School of Nursing and Public Health, University of KwaZulu-Natal, Durban, South Africa

    4Health Systems Research Unit, South African Medical Research Council, Durban, South Africa

    5Biostatistics Research Unit, South African Medical Research Council, Durban, South Africa

    6Centre for the AIDS Programme of Research in South Africa, Durban, South Africa

    7National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa

    8South African Medical Research Council Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa

    9Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Cape Town, South Africa

    10Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, South Africa

    11Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa

    12Centre for Epidemic Response and Innovation, School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa

    13KwaZulu-Natal Research Innovation and Sequencing Platform, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa

    14Department of Global Health, University of Washington, Seattle, WA, United States

    15Discipline of Virology, School of Laboratory Medicine and Medical Sciences, University of KwaZulu Natal, Durban, South Africa

    16National Health Laboratory Service, Durban, South Africa

    17Department of Paediatrics and Child Health, University of Pretoria, Pretoria, South Africa

    Corresponding Author:

    Reshmi Dassaye, MMedSci, PhD

    HIV and Other Infectious Diseases Research Unit

    South African Medical Research Council

    Francie van Zijl Drive

    Parowvallei

    Cape Town, 7505

    South Africa

    Phone: 27 312604486

    Email: Reshmi.Dassaye@mrc.ac.za


    Background: In low- and middle-income countries (LMICs) such as South Africa, there is paucity of data on SARS-CoV-2 infections among children attending school, including seroprevalence and transmission dynamics.

    Objective: This pilot study aims to assess (1) the prevalence of self-reported or confirmed SARS-CoV-2 prior infections, COVID-19 symptoms (including long COVID), seroprevalence of SARS-CoV-2 antibodies, and general/mental health, (2) longitudinal changes in SARS-CoV-2 seroprevalence, and (3) SARS-CoV-2 acute infections, immune responses, transmission dynamics, and symptomatic versus asymptomatic contacts in a unique cohort of unvaccinated primary school learners, their parents, teachers, and close contacts in semirural primary school settings.

    Methods: Learners (grades 1-7) from primary schools in KwaZulu-Natal, South Africa, their parents, and teachers will be invited to enroll into the COVID kids school study (CoKiDSS). CoKiDSS comprises 3 parts: a cross-sectional survey (N=640), a follow-up survey (n=300), and a nested case-cohort substudy. Finger-prick blood and saliva samples will be collected for serological and future testing, respectively, in the cross-sectional (451 learners:147 parents:42 teachers) and follow-up (210 learners:70 parents:20 teachers) surveys. The nested case-cohort substudy will include cases from the cross-sectional survey with confirmed current SARS-CoV-2 infection (n=30) and their close contacts (n=up to 10 per infected participant). Finger-prick blood (from all substudy participants), venous blood (from cases), and nasal swabs (from cases and contacts) will be collected for serological testing, immunological testing, and viral genome sequencing, respectively. Questionnaires covering sociodemographic and general and mental health information, prior and current SARS-CoV-2 symptoms and testing information, vaccination status, preventative behavior, and lifestyle will be administered. Statistical methods will include generalized linear mixed models, intracluster correlation, descriptive analysis, and graphical techniques.

    Results: A total of 645 participants were enrolled into the cross-sectional survey between May and August 2023. A subset of 300 participants were followed up in the follow-up survey in October 2023. Screening of the participants into the nested case-cohort substudy is planned between November 2023 and September 2024. Data cleanup and analysis for the cross-sectional survey is complete, while those for the follow-up survey and nested case substudy will be completed by the third quarter of 2024. The dissemination and publication of results is anticipated for the fourth quarter of 2024.

    Conclusions: This study provides data from an LMIC setting on the impact of SARS-CoV-2 on school-attending learners, their parents, and teachers 3 years after the SARS-CoV-2 pandemic was declared and 21-24 months after resumption of normal school attendance. In particular, this study will provide data on the prevalence of self-reported or confirmed SARS-CoV-2 prior infection, prior and current symptoms, seroprevalence, changes in seroprevalence, SARS-CoV-2 transmission, SARS-CoV-2 adaptive immune responses, and symptoms of long COVID and mental health among a triad of learners, their parents, and teachers.

    International Registered Report Identifier (IRRID): DERR1-10.2196/52713

    JMIR Res Protoc 2024;13:e52713

    doi:10.2196/52713

    Keywords

    COVID-19; SARS-CoV-2; learners; seroprevalence; long COVID; transmission dynamics 


    Since the onset of the COVID-19 pandemic, an estimated 75.3 million (21%) children and adolescents <20 years of age have tested positive globally [1]. In South Africa, like many low- and middle-income countries (LMICs), there is a significant population youth bulge: children aged <20 years and children attending primary school make up almost 37% and 28% of the populations, respectively [2]. In their last publicly available report, the National Institute of Communicable Diseases, South Africa, reported that as of December 4, 2021, individuals aged ≤19 years comprised 14.8% of the SARS-CoV-2 tests, 12.5% of laboratory-confirmed COVID-19 cases, 5% of all COVID-19–associated admissions, and 0.7% of COVID-19–associated in-hospital deaths [3]. In most LMICs, children aged <12 years were not offered SARS-CoV-2 vaccines and not prioritized for SARS-CoV-2 testing. In this context, the long-term impact of the COVID-19 pandemic on children requires investigation.

    SARS-CoV-2 seroprevalence studies provide an estimate of SARS-CoV-2 antibodies and thus better insight into overall infections, given that access to viral diagnostic testing and testing among mild and asymptomatic cases may be low [4]. In South Africa, during the COVID-19 pandemic, 3 cardinal community studies have reported SARS-CoV-2 seroprevalence among adults and children (Table 1), with an overall increase in the seroprevalence with each successive wave [5-7]. Further, all studies reported that the seroprevalence in adolescents is analogous to that reported in adults, while young children had lower seroprevalence compared to adolescents and adults. Noteworthily, children constituted only a fraction of the sample size in all 3 seroprevalence community surveys (ie, ~55%, 10%, and 20%, respectively) [5-7]. To our knowledge, there is paucity of data reporting the seroprevalence of SARS-CoV-2 among primary school-age children in school settings in South Africa.

    Table 1. Summary of SARS-CoV-2 seroprevalence studies in South Africa.
    StudyPeriodVariant of concernStudy settingParticipants (n)Children and adolescents (n)Age groupsSARS-CoV-2 infection/seroprevalence among childrenSARS-CoV-2 infection/seroprevalence among adults
    Cohen et al [5], 2022July 2020 to August 2021Beta and Delta variantsMpumalanga and North West (2 provinces)12006645 years of age (n=154, 12.8%) 5-12 years of age (n=340, 28.3%) 13-18 years of age (n=170, 14.2%) 19-39 years of age (n=265, 22.1%) 40-59 years of age (n=168, 14%) ≥50 years of age (n=103, 8.6%)49% (75/154) in 5 years of agea 60% (205/340) in 5-12 years of agea 78% (132/170) in 13-18 years of agea62.3% (165/265) among 19-39 years of ageb 68.5% (115/168) among 40-59 years of ageb 55.3% (57/103) among ≥50 years of ageb
    National household-based population seroprevalence survey of SARS-CoV-2 antibodies report [6]November 2020 to February 2021 and April 2021 to June 2021Beta and Delta variantsWestern Cape, Eastern Cape, Northern Cape, Free State, Kwazulu-Natal, Northwest, Gauteng, Mpumalanga, and Limpopo (9 provinces in South Africa)13,2121363Children12 years not included 12-17 years of age (n=1363, 10.3%) 18-35 years of age (n=4494, 34%) 36-49 years of age (n=3060, 23.2%) >50 years of age (n=4294, 32.5%)23.2%, (95% CI 19.2-27.8), 12-17 years of agec17.3% (95% CI 15.0-19.9) among 18-35 years of aged 20.1% (95% CI 17.6-22.8) among 36-49 years of aged 21.3% (95% CI 19.1-23.7) among 50 years of aged
    Madhi et al [7], 2022October 2021 to December 9, 2021OmicronGauteng (1 province)7010137512 years of age (n=753, 10.7%) 12-17 years of age (n=622, 8.9%) 18-50 years of age (n=4047, 57.7%) >50 years of age (n=1588, 22.7%)56.2% (95% CI 52.5-59.7) among 12 years of agec 73.8% (95% CI 70.2-77.1) among 12-17 years of agec73.6% (95% CI 72.2-74.9) among 18-50 years of aged 79.7% (95% CI 77.6-81.5) among 50 years of aged

    aSARS-CoV-2 infection among children.

    bSARS-CoV-2 infection among adults.

    cSARS-CoV-2 seroprevalence among children.

    dSARS-CoV-2 seroprevalence among adults.

    Initial evidence suggested that children and adolescents are susceptible to infections with ancestral SARS-CoV-2 but at a reduced risk of severe illness or death relative to adults [8]. However, the subsequent Delta and Omicron variants have been more infectious in children than previous variants [9]. A retrospective study in China (n=2135) demonstrated that up to 90% of the pediatric cases were asymptomatic, mild, or moderate [10]. The majority of children hospitalized with severe COVID-19 were unvaccinated or had additional comorbidities such as type 2 diabetes or obesity [11]. A study in the United Kingdom reported that children with underlying neurodisabilities or multiple comorbidities are vulnerable to hospital admission or death [12]. Similar to adults, children and adolescents can also experience long COVID, the frequency and characteristics of which are still under investigation [13].

    Studies have focused on differentiating the SARS-CoV-2 immune response between adults and children. In response to SARS-CoV-2 exposure or infection, children elicit a stronger mucosal innate immune response, which facilitates viral clearance [14-22], a lower level of neutrophilia that has previously been associated with microangiopathy and thrombosis [18,20], and a difference in cytokine profiling with a reduced tendency to trigger a cytokine storm [18,19,21-24]. With reference to adaptive immunity, higher lymphocyte counts with a higher proportion of naïve T cells, T regulatory cells, and T follicular helper cells have been reported [24-27]. Additionally, there are conflicting data on mucosal and serum antibody levels reported in children [18-20,24,28-32], and there are discordant reports on the durability and sustainability of the nucleocapsid antibody response in children after infection [33-35]. The Texas Coronavirus Antibody Response ongoing survey reported that 95% of the previously infected children of 5-19 years of age tested positive for nucleocapsid antibodies at the onset of the study and continued to have nucleocapsid antibodies up to 6 months later [36]. SARS-CoV-2 variants have evolving mechanisms to evade host immune defenses; intermittent testing to understand immune response in children exposed to or infected with SARS-CoV-2 infection may contribute to providing key insights into the pathogenesis of severe COVID-19.

    During the COVID-19 pandemic, decisions on school closures varied widely between and within countries [37]. Children play a critical role in the transmission of respiratory viruses such as influenza, and school closures were partly guided by such evidence [38,39]. However, the epidemiological benefits of school closures on the transmission of SARS-CoV-2 remain elusive. There are conflicting data on the transmission of SARS-CoV-2 from children to children and from children to adults [40-45], with a lower prevalence of infection reported in younger children [46-48], with studies focusing primarily on household transmissions, while the role of schools remains unclear [47,49]. Young children infected with SARS-CoV-2 have viral loads in their respiratory tract similar to those of adolescents and adults [50,51]. School infection control measures played a role in decreasing outbreaks in some countries [52-54], but cluster outbreaks were reported among children in several provinces of South Africa when schools fully opened in 2022. Hence, further evaluation is needed to determine whether children (and the school setting) play a more substantive role in the community spread of SARS-CoV-2, especially in LMICs.

    The overall aim of the COVID kids school study (CoKiDSS) is to assess SARS-CoV-2 prior infection, prior and current COVID-19 symptoms, seroprevalence, acute infection, transmission, immune responses, and symptoms of long COVID among a unique cohort of learners in grades 1-7, their parents/guardians, and teachers in the KwaZulu-Natal province of South Africa. The objectives of this study are shown in Table 2. Here, we describe the research study, its implementation processes, methodology, and expected results.

    Table 2. COVID kids school study objectives.
    ObjectiveDescription
    Primary objective
    • Objective 1: To assess the prevalence of self-reported confirmed SARS-CoV-2 prior infections, prior and current COVID-19 symptoms, and seroprevalence of SARS-CoV-2 antibodies in the overall triad of learners (grades 1-7), their parents/guardians, and teachers.
    Secondary objectives
    • Objective 2: To determine the prevalence of long COVID-19 symptoms, general health and mental health in participants overall, and by SARS-CoV-2 antibody status.
    • Objective 3: To determine the longitudinal changes in SARS-CoV-2 seroprevalence and symptoms in a subset of participants who are followed up.
    Exploratory objectives
    • Objective 4: To conduct viral genome sequencing and describe transmission dynamics in a subgroup of 30 consenting SARS-CoV-2–positive individuals from the learner-parent-teacher triad and up to 10 of their close contacts.
    • Objective 5: To determine the proportion of previously asymptomatic contacts who test SARS-CoV-2–positive above.
    • Objective 6: To investigate B-cell and T-cell responses in the subgroup of 30 SARS-CoV-2–positive individuals enrolled and correlate these with symptoms.

    Study Setting

    This study will be conducted within the catchment areas of the South African Medical Research Council (SAMRC)’s Verulam Clinical Research Site (CRS) based in the Verulam suburb of the eThekwini district in KwaZulu-Natal. The KwaZulu-Natal province has the second largest population in South Africa, with an estimated 11.3 million people; 43% of the population are younger than 18 years [2]. The province is divided into 1 metropolitan municipality (eThekwini Metropolitan Municipality; Durban) and 11 district municipalities. Verulam is an urban area in the northern part of eThekwini Municipality in close proximity to the iLembe district municipality. Approximately 94% of the school-age children between 5 and 17 years are in school in this municipality [3]. The catchment areas of the Verulam CRS comprise urban, periurban, and rural localities. In South Africa, the COVID-19 pandemic evolved against a backdrop of longstanding tuberculosis and HIV epidemics. KwaZulu-Natal has the largest burden of HIV and tuberculosis infections [55], and of the 9 provinces in South Africa, KwaZulu-Natal had the third highest cumulative number of COVID-19 cases recorded as of June 29, 2022 [56].

    Study Design

    This pilot study will implement a cross-sectional survey, follow up a subsample of survey participants, and conduct a nested case-cohort substudy in a preselect number of primary schools within the catchment area of the Verulam CRS in KwaZulu-Natal. Participating learners from primary schools (grades 1-7), their parents/guardians, and teachers will be invited to enroll in the CoKiDSS cross-sectional survey from May to August 2023 (primary objective 1; Figure 1). The cross-sectional survey will be conducted over 6 consecutive school weeks (window ±3 weeks; Figure 1). A subset of participants from the cross-sectional survey will be invited to participate in the follow-up survey (secondary objectives 2 and 3), with repeat SARS-CoV-2 antibody testing (3-4 months later from October 2023) until the desired sample is achieved (Figure 1). Saliva samples will be collected and stored from the first 10% (65/645 and 30/300, respectively) of the participants enrolled across the cross-sectional survey and in the follow-up survey for future testing. The nested case-cohort substudy (exploratory objectives 4-6) aims to enroll 30 cross-sectional survey participants with confirmed current SARS-CoV-2 infection—preferably all or at least 20 children (Figure 1) from November 2023 to September 2024. The follow-up survey will allow us to monitor the dynamics of SARS-CoV-2 seroprevalence. Long COVID will also be assessed in the cross-sectional and follow-up surveys as well as in the nested case-cohort substudy. Participants in the cross-sectional survey will have 1 study visit, while participants in the follow-up survey will have 2 study visits (Figure 1). During the follow-up survey, participants lost to follow-up will not be replaced.

    ‎
    Figure 1. Study design, objectives, and data collection. CRF: case report form; DBS: dried blood spot; PCR: polymerase chain reaction.

    For objectives 4-6, the first 30 participants in the cross-sectional surveys (learner/parent/teacher) who test SARS-CoV-2 polymerase chain reaction (PCR)–positive (30 children or at least 20 children) identified through the school or existing linkages with the National Institute of Communicable Diseases/National Health Laboratory Services will be invited to enroll into the exploratory substudy (nested case-cohort substudy; Figure 1). These participants are referred to as the primary positives. To assess transmission dynamics (objective 4) and proportion of asymptomatic cases (objective 5), all close contacts of the 30 primary positives (30 SARS-CoV-2 PCR-positive participants) up to a maximum of 10 contacts will be tested with a South African Health Products Regulatory Authority–approved SARS-CoV-2 point-of-care antigen test, and a swab will be sent to the National Health Laboratory Services for a SARS-CoV-2 PCR test. Only 1 swab will be collected from children who are primary positives or close contacts. For the primary positives and their PCR-positive contacts, remnant swabs will be sent for viral genome sequencing (objective 4; Figure 1). To assess B-cell and T-cell immune responses (objective 6), the primary positives (30 SARS-CoV-2 PCR-positive participants) will also provide venous blood at baseline (ie, within 10 days of a positive SARS-CoV-2 test), 30 days, 3 months, and 6 months post diagnosis (nested case-cohort substudy; Figure 1). Dried blood spot samples will be collected from all participants enrolled in the cross-sectional and follow-up surveys as well as the nested case-cohort substudy for future antibody testing.

    Study Populations

    The inclusion and exclusion criteria for the school, school-age learners, their parents or guardians, and teachers are summarized in Table 3.

    Table 3. Inclusion and exclusion criteria for the school, learners in grades 1-7, their parents/guardians, and teachers.
    Participant and part of the studyInclusion criteriaExclusion criteria
    School

    		Cross-sectional and follow-up surveys and nested case-cohort substudy
    • Primary schools within the catchment areas of the Verulam South African Medical Research Council clinical research site in eThekwini, KwaZulu-Natal, South Africa.
    • Special schools, learner referral units, and education colleges.
    • Schools where other school-based COVID-19 studies are already being conducted.
    • Small school size with 40 learners per grade in grades 1-7.
    Learners, parents/guardians, and teachers

    		Cross-sectional survey
    • Learner must be attending school in person.
    • A parent/guardian is only eligible if his/her child is eligible and participating in the study.
    • A teacher is only eligible if the teacher teaches at a participating school.
    • For learners 18 years of age, a parent/guardian is able to provide consent.
    • For learners 8 to 18 years of age, the learner can provide assent.
    • For learners 7 years of age, only parental/guardian consent is required.
    • Willing for study staff to obtain routine SARS-CoV-2 results from National Institute of Communicable Diseases/National Health Laboratory Services.
    • Learners 8 to 18 years of age who are unable to provide appropriate informed assent.
    • Parent excluded if learner already has 1 parent enrolled in the study.
    • Learner does not anticipate completing the school year in the selected school.
    • Learners with physical or intellectual challenges.
    • Learners who, in the opinion of the principal investigators or designees, will be at risk if they participate in this study.

    		Follow-up survey
    • Same criteria as for cross-sectional survey
    • Learner must be attending school in person during the 2023 academic year.
    • Willing to be followed up once and to give blood during follow-up.
    • Same criteria as for cross-sectional survey.

    Ethics Approval

    This study has been approved by the SAMRC Human Research Ethics Committee (EC018-9/2022) and the South African Department of Basic Education (national and provincial) and the South African Department of Health (provincial). Written informed consent will be obtained from parents or guardians of participating learners and from all participating parents/guardians and teachers. Additionally, assent will be obtained from children aged 8 to 18 years. All participants will be reimbursed with a voucher valued at R 300 (US $16), in accordance with local ethics guidance to cover the cost of time, inconvenience, and expenses.

    Schools: Sampling and Sample Size

    For objectives 1-6, a convenience sample of schools will be selected. In the first stage, a sampling frame of all public primary schools within the Verulam CRS catchment areas will be developed. Attempts will be made to obtain the head counts in these schools and number of classes. Only large schools (≥40 learners per grade in grades 1-7) able to contribute to the sample size will be shortlisted (short list 1) and their principals approached to ascertain interest. From short list 1, schools whose principals are agreeable to study participation will be identified (short list 2), and a sample of 2 primary schools will be selected from short list 2. We will expand to additional selected primary schools if needed, until the enrolment target is reached.

    Madhi et al [7] demonstrated a seroprevalence of 56.2% (95% CI 52.6%-59.7%) among children younger than 12 years in a seroepidemiological study conducted from October to December 2021 [7]. We opted to be more conservative due to the waning immunity anticipated in unvaccinated children or those who did not receive the booster dose almost 2 years after the pandemic. The sample size calculations for this study were based on estimating seroprevalence rates with a specific degree of precision. Specifically, the was used, where DE refers to the design effect, p refers to the estimated prevalence, and d to the margin of error. A sample size of 640 will allow us to estimate seroprevalence rates in the combined group of 40% and greater with a margin of error of 6%, accounting for a design effect of 2.5 and assuming a 5% α. The survey is designed to be stratified by school, with class defining the cluster. We expect a minimum of 40 clusters in total across the 2 schools with an average cluster size of 16. In Figure 2, we have illustrated the margin of error for estimation under various sample sizes assuming all the other aforementioned parameters are fixed. As depicted in Figure 2, a reduction in the sample size below 600 will result in a greater margin of error (lower precision) larger than 7%.

    A review of 14 studies indicated that long COVID symptoms varied from 4% to 66% among children and adolescents [57]. A cohort of 300 individuals will enable us to estimate the prevalence rates of long COVID at follow-up, 45% or greater with a 7% margin of error, accounting for a 20% loss to follow-up rate, and a maximum design effect of 1.2. Tables 4-5 summarize the sample size allocation for the respective surveys. The nested case-cohort substudy sample size is described in Table 6.

    ‎
    Figure 2. Margin of error for various sample sizes assuming a fixed prevalence of 40% and design effect of 2.5. MOE: margin of error.
    Table 4. Sample size allocation of primary school learners, parents, and teachers for the cross-sectional survey (N=640).a
    SampleGrade

    		1 (n=91)2 (n=91)3 (n=91)4 (n=91)5 (n=92)6 (n=92)7 (n=92)
    Learners (n=451)64646464656565
    Parents (learner: parent, 3:1) (n=147)21212121212121
    Teachers (learner: teacher, 11:1) (n=42)6666666

    aThe sample size might vary by ±10 people per group (learner, parent, teacher).

    Table 5. Sample size allocation of primary school learners, parents, and teachers for the follow-up survey (n=300).a
    SampleGrade

    		1 (n=43)2 (n=43)3 (n=43)4 (n=43)5 (n=43)6 (n=43)7 (n=43)
    Learners (% of cross-sectional survey ~50%) (n=210)30303030303030
    Parents (% of cross-sectional survey ~50%) (n=70)10101010101010
    Teachers (% of cross-sectional survey ~50%) (n=20)3333332

    aThe sample size might vary by ±5 people per group (learner, parent, teacher).

    Table 6. Sample size allocation for the nested case-cohort substudy.
    ParticipantsValue, n
    SARS-CoV-2–positive learners across grades 1-720-30
    SARS-CoV-2–positive parents/teachers0-10
    Close contacts10 per positive participant

    Study Procedures

    Stakeholder Engagement

    A strong community engagement program is underway to assist with buy-in and recruitment for the study among the Department of Basic Education, school principals, school governing boards, teachers, and parents/guardians of learners in grades 1-7. Schools that agree to participate will be asked to register and complete a short questionnaire.

    Participant Recruitment and Follow-Up

    Informed consent will be sought from teachers and from parents/guardians for their own/their children’s participation. Simplified informed consent forms were piloted to evaluate their understanding of the study and implications of the study. Assent will also be obtained from children aged 8 to 18 years, and participation will be contingent on obtaining both assent and parental consent. Only parental consent will be required for 7-year-old children. Flexible systems will be used to engage with parents, including weekend meetings and interviewer-administered or self-administered parental questionnaires. Multiple learners from one family can participate, but separate consent will be sought for each learner. Recruitment for the cross-sectional survey commenced on May 9, 2023, and was completed before the end of August 2023. The follow-up survey will follow up the first 210 learners, 70 parents, and 20 teachers who consent to follow-up at least 6 weeks after the first interview and after a school holiday. SARS-CoV-2–positive participants enrolled in the immunological substudy will be followed up for 6 months.

    Data Collection

    Questionnaire data will be gathered from school principals or a substitute member of the school senior leadership team, teachers, and parents/guardians of the primary school learners (in grades 1-7) (Table 7 and Multimedia Appendices 1-7).

    Information will be collected on sociodemographic and basic health information; use of nonpharmacological measures; COVID-19 vaccination status of learner, parent/guardian, and teacher; household structure and COVID-19 history; symptoms of long COVID; household exposures; lifestyle; and preventive behavior related to the pandemic since January 2020 (see Multimedia Appendices 1-6). Parents/guardians will complete all the study case report forms on the children’s behalf (Multimedia Appendices 3 and 4).

    Additionally, information will be collected on the learner’s lifestyle, mental health, and well-being. The Revised Children’ Anxiety and Depression Scale will be used to determine the internalizing symptoms of anxiety and depression among children and young adolescents enrolled in this study (see Multimedia Appendix 7) [58]. If the tool triggers negative memories in participants, these participants will be referred to a counsellor at the nearest health care facility. Samples will be collected from participants as outlined in Table 7 and described in Multimedia Appendix 8.

    Table 7. Summary of data collection.
    ParticipantCross-sectional and follow-up surveyNested case-cohort substudy


    		ImmunologyTransmission dynamics
    School principal or senior school leadershipQuestionnaire about number of learners, number of staff, and nonpharmaceutical interventionsN/AaN/A
    Learner/parent/teacher triadQuestionnaire at baseline and follow-up (if applicable) about contacts/nonpharmaceutical interventions/symptoms of long COVID. Blood draw to determine seroprevalence (rapid antibody test), dried blood spot for anti-S IgA/IgG, anti-N IgG, neutralizing antibody and antibody titers. Saliva samples will be collected in 10% of participants and stored if applicable.N/AN/A
    Primary positives identification and follow-up within 10 days, 30 days, 3 months, and 6 months of a positive SARS-CoV-2–positive testN/AQuestionnaire at baseline and follow-up (if applicable) about contacts/nonpharmaceutical interventions/symptoms of long COVID. Blood draw to determine seroprevalence (rapid antibody test), dried blood spot for anti-S IgA/IgG, anti-N IgG, neutralizing antibody and antibody titers. Saliva samples will be collected in 10% of participants and stored if applicable.Telephonic questionnaire to identify contacts. Initial swab sent for viral genome sequencing.
    Contacts of the primary positivesMay or may not be included in the cross-sectional and follow-up surveys.N/AQuestionnaire + rapid antigen test + polymerase chain reaction + dried blood spot

    aN/A: not applicable.

    Data Management

    Data will be collected in research electronic data capture, a secure web-based application hosted by the SAMRC. More information on this platform can be found elsewhere [59,60]. Research electronic data capture access will be restricted to CoKiDSS personnel. A lookup function will be created in research electronic data capture to link/track participants enrolled in the cross-sectional survey, follow-up survey, and nested case-cohort substudy. This will be useful if the close contact is already a participant in the study.

    Biospecimen Management

    Samples will be stored at the HIV and other Infectious Diseases Research Unit, SAMRC, biorepository. The Laboratory Data Management System program developed by Frontier Science is used by the HIV and other Infectious Diseases Research Unit biorepository and is a storage module that conforms to US Food and Drug Administration, 21 Code of Federal Regulations part 58 and 11 [61]. The program is utilized to manage specimen tracking, inventory storage, and specimen shipment.

    Data Analysis

    We will perform descriptive analysis of participant sociodemographic, lifestyle, and behavior information. Total seroprevalence and cumulative incidence (ie, total number of reverse transcription-PCR–confirmed infections in official statistics per population) will be calculated and compared as well as age-specific and time-specific estimates. The total numbers of learners in the respective grades per school will be used for poststratification so that the estimates are representative of the demographics in KwaZulu-Natal, which will be incorporated via weights. The prevalence prior and current COVID-19 symptoms and seroprevalence will be presented with 95% CIs, where standard errors will be computed via jackknife methods. Within the cohort, changes in seroprevalence, symptoms, mental health, and physical health will be assessed using generalized linear mixed models, considering the within-individual correlation of responses as well as the hierarchical structure of the data. The clustering of seropositivity within classes and school will be quantified using the intracluster correlation. To analyze the exploratory objectives, the following statistical methods will be employed: (1) means with standard deviations or medians with interquartile ranges (as appropriate depending on the distribution) will be presented for continuous data, (2) the graphical presentation of continuous outcomes will be undertaken using box plots, (3) bar charts will be used to represent categorical data across groups of interest, and (4) the correlation between variables will be addressed using 2-way scatterplots with the presentation of Spearman correlation coefficient.

    Patient and Public Involvement

    Several school principals were consulted during the development of the protocol to ensure the feasibility of the planned study procedures. Early feedback was collected from learners and parents invited to participate to adapt the communication strategies and channels. Further feedback will also be collected from enrolled learners and school principals during the cross-sectional survey to adapt the follow-up survey. Results of individual tests will be communicated to the participants, and overall study results disseminated to participating schools. Findings will be disseminated to the South African Department of Basic Education and Department of Health.


    Recruitment for the cross-sectional survey occurred between May and August 2023, and a total of 645 participants were enrolled. Three hundred participants were followed up in the follow-up survey implemented in October 2023. Screening of the participants into the nested case-cohort substudy is planned between November 2023 and September 2024. Data cleanup and analysis for the cross-sectional survey is complete. Data cleanup and analysis for the follow-up survey and nested case substudy will be completed in the third quarter of 2024. The dissemination and publication of study findings is anticipated for the fourth quarter of 2024. The abovementioned activities and timelines are outlined in Multimedia Appendix 9.


    Anticipated Main Findings of This Study

    We anticipate that this study will find high SARS-CoV-2 seroprevalence, especially among teachers and parents, despite low reported SARS-CoV-2 infections and low prevalence of long COVID-19 and that transmission dynamics will favor parent-child transmission.

    Contextualization of the Anticipated Results

    The direct impact of COVID-19 on child and adolescent mortality is limited, with these age groups accounting for a meagre 0.4% (over 17,400) of COVID-19 deaths worldwide as of March 2023 [1]. However, according to UNICEF (United Nations Children’s Fund), children and adolescents bear the brunt of the indirect effects of the COVID-19 pandemic, including more households plummeting into multidimensional poverty, exacerbating the hardships of children living in the poorest countries, augmenting the learning crisis, threatening child survival and death, increasing child malnutrition, and deprivation and disruptions in health services [62]. Hence, the harms associated with school closures were profound. CoKiDSS is centered around the school rather than community settings, as schools play a critical role in a child’s learning and development, and in many countries, schools also provide access to immunizations, health care, and nutritional services.

    In LMICs, among children aged 5-13 years, there is a paucity of data on SARS-CoV-2 infections, including seroprevalence and transmission dynamics. In South Africa, 3 cardinal community studies have been published to date, reporting SARS-CoV-2 seroprevalence among adults and children [5-7]. However, the last serosurvey was conducted in December 2021 during the Omicron wave, and children constituted a small proportion of the study population [7].

    CoKiDSS will provide data on the impact of COVID-19 on school-attending children ~36 months after the pandemic was declared and 21-24 months after the resumption of normal school attendance. In particular, data will be provided on the prevalence of confirmed prior SARS-CoV-2 infections, prior and current COVID-19 symptoms, seroprevalence of SARS-CoV-2 antibodies, prevalence of long COVID symptoms, and general and mental health in a triad of learners, their parents/guardians, and teachers in the current COVID-19 endemic. The longitudinal design will allow a description of the temporal trends of immunity to SARS-CoV-2. Presently, in South Africa, children aged 5-11 years are only eligible to receive SARS-CoV-2 vaccination if they are at risk of developing severe COVID-19. The CoKiDSS data will provide a better understanding on the natural protection within this population and could potentially guide local vaccination strategies.

    Strengths and Limitations

    This study is the first study of SARS-CoV-2 infections in a school setting within a high HIV/tuberculosis prevalence LMIC. Thus, it will provide information on the impact of COVID-19 on schools, learners, teachers, and parents in these settings, and could guide future responses to pandemics within these settings. However, this study is not without challenges and limitations. Given the limited geographic area and number of schools, the findings may not be representative of all South African schools. In order to recruit a triad of learners in grades 1-7, their parents, and teachers, several rounds of engagement may be needed, resulting in oversampling or undersampling at schools. This study will assess SARS-CoV-2 seroprevalence by using a qualitative SARS-CoV-2 point-of-care antibody test. It is possible that the qualitative antibody assessment is below the threshold of conferring immunity. We would, however, prefer to use a minimally invasive test in this vulnerable population. Notwithstanding these, this study will contribute to the limited body of knowledge on the effect of the COVID-19 pandemic on school-attending children 21-24 months after resumption of normal school attendance.

    Dissemination Plan

    The study objectives and outcomes will be disseminated to participants, community, and other stakeholders, including the South African Department of Health and South African Department of Basic Education (district, provincial, and national levels), regulatory bodies, research organizations, community members, and participants. Additionally, the information linked to this study will be shared by the community staff with the participating school principals and members of the school governing board as well as the community advisory board/community working group members. The results of this study will be disseminated via virtual methods and face-to-face meetings. Communication methods will include the use of SMS text messaging to mobiles, monthly telephone calls with community advisory board members, hand delivery of relevant written material, email, Microsoft Teams, and social media platforms (WhatsApp). These methods will contribute to ongoing community acceptance of the study and trust in the research team and the program.

    Acknowledgments

    We are grateful to the South African Medical Research Council (grant SAMRC-RFA-GIPD-03-2021) and the European Union Horizon Europe program under the project “EU-Africa Concerted Action on SARS-CoV-2 Virus Variant and Immunological Surveillance” (grant 101046041) for funding this pilot study. Views and opinions expressed are, however, those of the author(s) only and do not necessarily reflect those of the European Union or the Health and Digital Executive Agency. Neither the European Union nor the granting authority can be held responsible for them. Additionally, we would like to extend a huge thank you to the study participants and the communities that participated.

    Data Availability

    Data availability will need to be requested from the corresponding author. The request will be considered a concept note, and the reason for data access will be required. Data will only be shared after the minimum papers have been written by the authors. Data will be made publicly available on the South African Medical Research Council website after all the main papers have been published.

    Authors' Contributions

    RD and AG conceived, designed, and wrote the manuscript. TC, BD, ZG, ES, TR, NM, DFN, SP, AB, VM, PLM, WAB, TdO, and NM contributed to reviewing and critiquing the manuscript. TR and KM were responsible for the statistical design and data management plan for the study, respectively. All authors read and approved the final manuscript. There were no conflicts of interest. No artificial intelligence was used in developing this manuscript.

    Conflicts of Interest

    None declared.

    Multimedia Appendix 1

    Principal enrollment and follow-up case report form.

    PDF File (Adobe PDF File), 168 KB
    Multimedia Appendix 2

    Teacher enrollment and follow-up case report form.

    PDF File (Adobe PDF File), 401 KB
    Multimedia Appendix 3

    Parent of learner enrollment and follow-up e-case report form.

    PDF File (Adobe PDF File), 745 KB
    Multimedia Appendix 4

    Parent of learner enrollment and follow-up case report form.

    PDF File (Adobe PDF File), 460 KB
    Multimedia Appendix 5

    Close contact case report form.

    PDF File (Adobe PDF File), 149 KB
    Multimedia Appendix 6

    Nested case-cohort substudy case report form.

    PDF File (Adobe PDF File), 253 KB
    Multimedia Appendix 7

    Learner mental health case report form.

    PDF File (Adobe PDF File), 439 KB
    Multimedia Appendix 8

    Detailed data collection.

    DOCX File , 20 KB
    Multimedia Appendix 9

    Study timeline.

    DOCX File , 16 KB
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    ‎
    CoKiDSS: COVID kids school study
    CRS: clinical research site
    LMIC: low- and middle-income country
    PCR: polymerase chain reaction
    SAMRC: South African Medical Research Council
    UNICEF: United Nations Children’s Fund

    Edited by T Leung; submitted 13.09.23; peer-reviewed by D Gornyk; comments to author 21.07.24; revised version received 29.07.24; accepted 16.09.24; published 19.12.24.

    Copyright

    ©Reshmi Dassaye, Terusha Chetty, Brodie Daniels, Zakir Gaffoor, Elizabeth Spooner, Trisha Ramraj, Ncengani Mthethwa, Duduzile Faith Nsibande, Saresha Pillay, Arvin Bhana, Vuyolwethu Magasana, Tarylee Reddy, Khanya Mohlabi, Penelope Linda Moore, Wendy A Burgers, Tulio de Oliveira, Nokukhanya Msomi, Ameena Goga. Originally published in JMIR Research Protocols (https://www.researchprotocols.org), 19.12.2024.

    This is an open-access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work, first published in JMIR Research Protocols, is properly cited. The complete bibliographic information, a link to the original publication on https://www.researchprotocols.org, as well as this copyright and license information must be included.