Investigating SARS-CoV-2 immune responses in children
| dc.contributor.advisor | Keeton, Roanne | |
| dc.contributor.advisor | Burgers Wendy | |
| dc.contributor.author | Benede, Ntombi | |
| dc.date.accessioned | 2025-07-02T10:50:29Z | |
| dc.date.available | 2025-07-02T10:50:29Z | |
| dc.date.issued | 2025 | |
| dc.date.updated | 2025-07-02T10:48:18Z | |
| dc.description.abstract | Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infec<on causes a highly transmissible respiratory disease, coronavirus disease 2019 (COVID-19), with variable disease outcomes. Children infected with SARS-CoV-2 are more likely to exhibit asymptoma<c or mild illness compared to severe clinical outcome, oSen observed in adults. A severe manifesta<on of SARS-CoV-2 infec<on in children is mul<system inflammatory syndrome (MIS-C), a delayed hyperinflammatory disease that occurs aSer exposure to SARS-CoV-2 and shares clinical features with Kawasaki disease (KD). MIS-C develops in a small propor<on of children who have been previously exposed to SARS-CoV-2. Poten<al contributors to the reduced COVID-19 clinical outcome in children compared to adults, includes less comorbidi<es, differences in the expression of viral entry factors, robust innate immunity, age-associated differences in humoral and cellular immunity, and pre-exis<ng immunity against endemic human coronaviruses (HCoVs). Notably, a cri<cal role for T cells in controlling COVID-19 severity, has been well documented. The immune mechanisms for the differences in disease progression between children and adults remain to be fully understood and studies evalua<ng SARS-CoV2 immune responses of paediatric popula<ons in Africa are s<ll rare. This thesis aims to inves<gate why children were ini<ally spared from severe COVID-19 outcomes, whether T cell responses are maintained in children as seen in adults, and why a small frac<on of children develop MIS-C aSer SARS-CoV-2 infec<on. Overall, this thesis focused on characterizing SARS-CoV-2-specific immune responses in pediatric cohorts, determining the durability of T cell responses over a 16-month period, and finally assessing cross-reac<ve immunity to SARS-CoV-2 variants of concern (VOC) in children. In Chapter 3, we aimed to inves<gate the SARS-CoV-2-specific T cell responses in unvaccinated asymptoma<c children (median age: 7 years) who were seroposi<ve (n=41) or seronega<ve (n=30) for SARS-CoV-2. Our results showed that the magnitude of SARS-CoV-2-specific CD4+ and CD8+ T cell responses was comparable between SARS-CoV-2 seroposi<ve and seronega<ve children. However, the func<onal profiles of SARS-CoV-2-specific CD4+ T cells were dis<nct, with seroposi<ve children displaying a higher propor<on of polyfunc<onal T cells, whereas seronega<ve children had predominantly monofunc<onal T cells. Addi<onally, the frequency of SARS-CoV-2-specific CD4+ T cells in seronega<ve children was moderately associated with endemic HCoV-HKU1 an<body responses. Sugges<ng that SARS-CoV-2- reac<ve T cells in seronega<ve children may be due to pre-exis<ng immunity from prior infec<on with endemic HCoVs. We also demonstrated that seroposi<ve children had lower frequency of SARS-CoV-2-specific CD4+ and CD8+ T cell responses, in comparison to COVID19 convalescent (n=30, median age: 38 years) adults. A limita<on of this cohort was that the children did not have an exact <me of SARS-CoV-2 infec<on by PCR confirma<on, whereas the adults had PCR-confirmed SARS-CoV-2 infec<on. Therefore, the lower magnitude of responses in children might be due to more distant infec<on compared to the adults. Taken together, these findings provide insight into SARS-CoV-2 immunity in children. In Chapter 4, we aimed to extend previous findings with another larger cohort of 73 matched household mother (median age: 33 years)-child (median age: 7 years) pairs, to address the limita<on of the poten<al differing <me of SARS-CoV-2 infec<on between children and adults in the previous cohort in Chapter 3. A small propor<on (36%) of children living in the same household as their SARS-CoV-2 seroposi<ve mother, were seronega<ve for SARS-CoV-2, despite the likelihood of shared SARS-CoV-2 exposure. The apparent resistance of infec<on in these children may be due to three reasons, namely 1) cross-reac<ve immunity to endemic HCoVs, 2) early aborted SARS-CoV-2 infec<on in children and/or 3) possibly early rapid viral clearance by innate immunity. Despite the serostatus, children in comparison to matched mothers displayed lower frequency of SARS-CoV-2-specific T cell responses. The overall func<onal profile of SARS-CoV-2-specific T cells were comparable between children and mothers, sugges<ng although lower, the quality of the T cell response is equivalent during SARS-CoV-2 infec<on. When comparing the memory differen<a<on profile of SARS-CoV-2- specific T cells, we found that children and mothers had early differen<ated (ED) memory profile as the dominant memory subset of SARS-CoV-2-specific T cells, which is associated with long-term immunity. The reduced SARS-CoV-2-specific T cell responses found in children compared to adults raised the ques<on of whether these responses would be durable and cross reac<ve to SARS-CoV-2 VOCs. We therefore evaluated of the maintenance of SARS-CoV2-specific T cell responses over 16-month period since the ini<al visit. This analysis was somewhat confounded by possible repeated exposures to SARS-CoV-2 during the Delta and/or Omicron BA.1/2, BA.4/5 waves preceding the second sampling visit. Nonetheless, the predominant ED memory subsets at the 16-month sampling does suggest poten<al durability albeit in the context of an ongoing pandemic. Lastly, we reported that, T cell responses were cross-reac<ve to SARS-CoV-2 Delta and BA.1 VOC, demonstra<ng T cells are preserved across variants of concern in South African unvaccinated children. Finally, in Chapter 5, we inves<gated the underlying immune pathology of MIS-C, by quan<fying SARS-CoV-2-specific T cell responses in children with MIS-C compared to SARSCoV-2 seroposi<ve children with clinically similar paediatric febrile diseases (non-MIS-C) and healthy SARS-CoV-2 seroposi<ve children (HC). The magnitude of SARS-CoV-2-specific T cell responses was comparable in children with MIS-C, non-MIS-C and HC. However, healthy SARSCoV-2 seroposi<ve children had a higher propor<on of polyfunc<onal SARS-CoV-2-specific CD4+ T cells compared to children with MIS-C and those with other inflammatory or infec<ous diagnoses, who both presented a largely monofunc<onal SARS-CoV-2-specific CD4+ T cell profile. Addi<onally, children with MIS-C displayed a higher frequency of TCR V21.3+ SARSCoV-2-specific CD4+ T cells compared to HC but similar to non-MIS-C controls. The skewed T cell profile in children with MIS-C and non-MIS-C controls could be due to sustained systemic inflamma<on inducing T cell exhaus<on and/or superan<gen-like responses inducing polyclonal expansion of V21.3+ T cells to SARS-CoV-2 spike protein. Overall, this thesis provides important relevant data for understanding the adap<ve immunity of SARS-CoV-2 in children compared to adults and provides insights into the cross-reac<ve immunity that may provide protec<on against re-infec<ons in children. Despite the end of the COVID-19 pandemic as a global health emergency and decrease in MIS-C incidence rates over the last 3 years, SARS-CoV-2 con<nues to circulate and may possibly evolve into endemi seasonal waves of infec<on. This exposes children, the vulnerable and least vaccinated popula<on to increasing respiratory viral coinfec<ons. Future work includes inves<ga<ng systemic and local immune responses against respiratory syncy<al virus (RSV) in the context of recent or concurrent SARS-CoV-2 infec<on in children to beher understand the immunological mechanisms contribu<ng to the increased RSV disease severity observed aSer the COVID-19 pandemic | |
| dc.identifier.apacitation | Benede, N. (2025). <i>Investigating SARS-CoV-2 immune responses in children</i>. (). University of Cape town ,Faculty of Health Sciences ,Department of Pathology. Retrieved from http://hdl.handle.net/11427/41503 | en_ZA |
| dc.identifier.chicagocitation | Benede, Ntombi. <i>"Investigating SARS-CoV-2 immune responses in children."</i> ., University of Cape town ,Faculty of Health Sciences ,Department of Pathology, 2025. http://hdl.handle.net/11427/41503 | en_ZA |
| dc.identifier.citation | Benede, N. 2025. Investigating SARS-CoV-2 immune responses in children. . University of Cape town ,Faculty of Health Sciences ,Department of Pathology. http://hdl.handle.net/11427/41503 | en_ZA |
| dc.identifier.ris | TY - Thesis / Dissertation AU - Benede, Ntombi AB - Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infec<on causes a highly transmissible respiratory disease, coronavirus disease 2019 (COVID-19), with variable disease outcomes. Children infected with SARS-CoV-2 are more likely to exhibit asymptoma<c or mild illness compared to severe clinical outcome, oSen observed in adults. A severe manifesta<on of SARS-CoV-2 infec<on in children is mul<system inflammatory syndrome (MIS-C), a delayed hyperinflammatory disease that occurs aSer exposure to SARS-CoV-2 and shares clinical features with Kawasaki disease (KD). MIS-C develops in a small propor<on of children who have been previously exposed to SARS-CoV-2. Poten<al contributors to the reduced COVID-19 clinical outcome in children compared to adults, includes less comorbidi<es, differences in the expression of viral entry factors, robust innate immunity, age-associated differences in humoral and cellular immunity, and pre-exis<ng immunity against endemic human coronaviruses (HCoVs). Notably, a cri<cal role for T cells in controlling COVID-19 severity, has been well documented. The immune mechanisms for the differences in disease progression between children and adults remain to be fully understood and studies evalua<ng SARS-CoV2 immune responses of paediatric popula<ons in Africa are s<ll rare. This thesis aims to inves<gate why children were ini<ally spared from severe COVID-19 outcomes, whether T cell responses are maintained in children as seen in adults, and why a small frac<on of children develop MIS-C aSer SARS-CoV-2 infec<on. Overall, this thesis focused on characterizing SARS-CoV-2-specific immune responses in pediatric cohorts, determining the durability of T cell responses over a 16-month period, and finally assessing cross-reac<ve immunity to SARS-CoV-2 variants of concern (VOC) in children. In Chapter 3, we aimed to inves<gate the SARS-CoV-2-specific T cell responses in unvaccinated asymptoma<c children (median age: 7 years) who were seroposi<ve (n=41) or seronega<ve (n=30) for SARS-CoV-2. Our results showed that the magnitude of SARS-CoV-2-specific CD4+ and CD8+ T cell responses was comparable between SARS-CoV-2 seroposi<ve and seronega<ve children. However, the func<onal profiles of SARS-CoV-2-specific CD4+ T cells were dis<nct, with seroposi<ve children displaying a higher propor<on of polyfunc<onal T cells, whereas seronega<ve children had predominantly monofunc<onal T cells. Addi<onally, the frequency of SARS-CoV-2-specific CD4+ T cells in seronega<ve children was moderately associated with endemic HCoV-HKU1 an<body responses. Sugges<ng that SARS-CoV-2- reac<ve T cells in seronega<ve children may be due to pre-exis<ng immunity from prior infec<on with endemic HCoVs. We also demonstrated that seroposi<ve children had lower frequency of SARS-CoV-2-specific CD4+ and CD8+ T cell responses, in comparison to COVID19 convalescent (n=30, median age: 38 years) adults. A limita<on of this cohort was that the children did not have an exact <me of SARS-CoV-2 infec<on by PCR confirma<on, whereas the adults had PCR-confirmed SARS-CoV-2 infec<on. Therefore, the lower magnitude of responses in children might be due to more distant infec<on compared to the adults. Taken together, these findings provide insight into SARS-CoV-2 immunity in children. In Chapter 4, we aimed to extend previous findings with another larger cohort of 73 matched household mother (median age: 33 years)-child (median age: 7 years) pairs, to address the limita<on of the poten<al differing <me of SARS-CoV-2 infec<on between children and adults in the previous cohort in Chapter 3. A small propor<on (36%) of children living in the same household as their SARS-CoV-2 seroposi<ve mother, were seronega<ve for SARS-CoV-2, despite the likelihood of shared SARS-CoV-2 exposure. The apparent resistance of infec<on in these children may be due to three reasons, namely 1) cross-reac<ve immunity to endemic HCoVs, 2) early aborted SARS-CoV-2 infec<on in children and/or 3) possibly early rapid viral clearance by innate immunity. Despite the serostatus, children in comparison to matched mothers displayed lower frequency of SARS-CoV-2-specific T cell responses. The overall func<onal profile of SARS-CoV-2-specific T cells were comparable between children and mothers, sugges<ng although lower, the quality of the T cell response is equivalent during SARS-CoV-2 infec<on. When comparing the memory differen<a<on profile of SARS-CoV-2- specific T cells, we found that children and mothers had early differen<ated (ED) memory profile as the dominant memory subset of SARS-CoV-2-specific T cells, which is associated with long-term immunity. The reduced SARS-CoV-2-specific T cell responses found in children compared to adults raised the ques<on of whether these responses would be durable and cross reac<ve to SARS-CoV-2 VOCs. We therefore evaluated of the maintenance of SARS-CoV2-specific T cell responses over 16-month period since the ini<al visit. This analysis was somewhat confounded by possible repeated exposures to SARS-CoV-2 during the Delta and/or Omicron BA.1/2, BA.4/5 waves preceding the second sampling visit. Nonetheless, the predominant ED memory subsets at the 16-month sampling does suggest poten<al durability albeit in the context of an ongoing pandemic. Lastly, we reported that, T cell responses were cross-reac<ve to SARS-CoV-2 Delta and BA.1 VOC, demonstra<ng T cells are preserved across variants of concern in South African unvaccinated children. Finally, in Chapter 5, we inves<gated the underlying immune pathology of MIS-C, by quan<fying SARS-CoV-2-specific T cell responses in children with MIS-C compared to SARSCoV-2 seroposi<ve children with clinically similar paediatric febrile diseases (non-MIS-C) and healthy SARS-CoV-2 seroposi<ve children (HC). The magnitude of SARS-CoV-2-specific T cell responses was comparable in children with MIS-C, non-MIS-C and HC. However, healthy SARSCoV-2 seroposi<ve children had a higher propor<on of polyfunc<onal SARS-CoV-2-specific CD4+ T cells compared to children with MIS-C and those with other inflammatory or infec<ous diagnoses, who both presented a largely monofunc<onal SARS-CoV-2-specific CD4+ T cell profile. Addi<onally, children with MIS-C displayed a higher frequency of TCR V21.3+ SARSCoV-2-specific CD4+ T cells compared to HC but similar to non-MIS-C controls. The skewed T cell profile in children with MIS-C and non-MIS-C controls could be due to sustained systemic inflamma<on inducing T cell exhaus<on and/or superan<gen-like responses inducing polyclonal expansion of V21.3+ T cells to SARS-CoV-2 spike protein. Overall, this thesis provides important relevant data for understanding the adap<ve immunity of SARS-CoV-2 in children compared to adults and provides insights into the cross-reac<ve immunity that may provide protec<on against re-infec<ons in children. Despite the end of the COVID-19 pandemic as a global health emergency and decrease in MIS-C incidence rates over the last 3 years, SARS-CoV-2 con<nues to circulate and may possibly evolve into endemi seasonal waves of infec<on. This exposes children, the vulnerable and least vaccinated popula<on to increasing respiratory viral coinfec<ons. Future work includes inves<ga<ng systemic and local immune responses against respiratory syncy<al virus (RSV) in the context of recent or concurrent SARS-CoV-2 infec<on in children to beher understand the immunological mechanisms contribu<ng to the increased RSV disease severity observed aSer the COVID-19 pandemic DA - 2025 DB - OpenUCT DP - University of Cape Town KW - Pathology LK - https://open.uct.ac.za PB - University of Cape town PY - 2025 T1 - Investigating SARS-CoV-2 immune responses in children TI - Investigating SARS-CoV-2 immune responses in children UR - http://hdl.handle.net/11427/41503 ER - | en_ZA |
| dc.identifier.uri | http://hdl.handle.net/11427/41503 | |
| dc.identifier.vancouvercitation | Benede N. Investigating SARS-CoV-2 immune responses in children. []. University of Cape town ,Faculty of Health Sciences ,Department of Pathology, 2025 [cited yyyy month dd]. Available from: http://hdl.handle.net/11427/41503 | en_ZA |
| dc.language.rfc3066 | Eng | |
| dc.publisher.department | Department of Pathology | |
| dc.publisher.faculty | Faculty of Health Sciences | |
| dc.publisher.institution | University of Cape town | |
| dc.subject | Pathology | |
| dc.title | Investigating SARS-CoV-2 immune responses in children | |
| dc.type | Thesis / Dissertation | |
| dc.type.qualificationlevel | Doctoral | |
| dc.type.qualificationlevel | PhD |