{"id":{"repo_id":"cape-town","oai_identifier":"oai:open.uct.ac.za:11427/41503"},"canonical_url":"https://search.dev.ndltd.org/etd/cape-town/oai:open.uct.ac.za:11427/41503","repository":{"repo_id":"cape-town","name":"University of Cape Town","base_url":"https://open.uct.ac.za/oai/request"},"display":{"title":"Investigating SARS-CoV-2 immune responses in children","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","abstract_html":"Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infec&lt;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&lt;c or mild illness compared to severe clinical outcome, oSen observed in adults. A severe manifesta&lt;on of SARS-CoV-2 infec&lt;on in children is mul&lt;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&lt;on of children who have been previously exposed to SARS-CoV-2. Poten&lt;al contributors to the reduced COVID-19 clinical outcome in children compared to adults, includes less comorbidi&lt;es, differences in the expression of viral entry factors, robust innate immunity, age-associated differences in humoral and cellular immunity, and pre-exis&lt;ng immunity against endemic human coronaviruses (HCoVs). Notably, a cri&lt;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&lt;ng SARS-CoV2 immune responses of paediatric popula&lt;ons in Africa are s&lt;ll rare. This thesis aims to inves&lt;gate why children were ini&lt;ally spared from severe COVID-19 outcomes, whether T cell responses are maintained in children as seen in adults, and why a small frac&lt;on of children develop MIS-C aSer SARS-CoV-2 infec&lt;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&lt;ve immunity to SARS-CoV-2 variants of concern (VOC) in children. In Chapter 3, we aimed to inves&lt;gate the SARS-CoV-2-specific T cell responses in unvaccinated asymptoma&lt;c children (median age: 7 years) who were seroposi&lt;ve (n=41) or seronega&lt;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&lt;ve and seronega&lt;ve children. However, the func&lt;onal profiles of SARS-CoV-2-specific CD4+ T cells were dis&lt;nct, with seroposi&lt;ve children displaying a higher propor&lt;on of polyfunc&lt;onal T cells, whereas seronega&lt;ve children had predominantly monofunc&lt;onal T cells. Addi&lt;onally, the frequency of SARS-CoV-2-specific CD4+ T cells in seronega&lt;ve children was moderately associated with endemic HCoV-HKU1 an&lt;body responses. Sugges&lt;ng that SARS-CoV-2- reac&lt;ve T cells in seronega&lt;ve children may be due to pre-exis&lt;ng immunity from prior infec&lt;on with endemic HCoVs. We also demonstrated that seroposi&lt;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&lt;on of this cohort was that the children did not have an exact &lt;me of SARS-CoV-2 infec&lt;on by PCR confirma&lt;on, whereas the adults had PCR-confirmed SARS-CoV-2 infec&lt;on. Therefore, the lower magnitude of responses in children might be due to more distant infec&lt;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&lt;on of the poten&lt;al differing &lt;me of SARS-CoV-2 infec&lt;on between children and adults in the previous cohort in Chapter 3. A small propor&lt;on (36%) of children living in the same household as their SARS-CoV-2 seroposi&lt;ve mother, were seronega&lt;ve for SARS-CoV-2, despite the likelihood of shared SARS-CoV-2 exposure. The apparent resistance of infec&lt;on in these children may be due to three reasons, namely 1) cross-reac&lt;ve immunity to endemic HCoVs, 2) early aborted SARS-CoV-2 infec&lt;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&lt;onal profile of SARS-CoV-2-specific T cells were comparable between children and mothers, sugges&lt;ng although lower, the quality of the T cell response is equivalent during SARS-CoV-2 infec&lt;on. When comparing the memory differen&lt;a&lt;on profile of SARS-CoV-2- specific T cells, we found that children and mothers had early differen&lt;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&lt;on of whether these responses would be durable and cross reac&lt;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&lt;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&lt;al durability albeit in the context of an ongoing pandemic. Lastly, we reported that, T cell responses were cross-reac&lt;ve to SARS-CoV-2 Delta and BA.1 VOC, demonstra&lt;ng T cells are preserved across variants of concern in South African unvaccinated children. Finally, in Chapter 5, we inves&lt;gated the underlying immune pathology of MIS-C, by quan&lt;fying SARS-CoV-2-specific T cell responses in children with MIS-C compared to SARSCoV-2 seroposi&lt;ve children with clinically similar paediatric febrile diseases (non-MIS-C) and healthy SARS-CoV-2 seroposi&lt;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&lt;ve children had a higher propor&lt;on of polyfunc&lt;onal SARS-CoV-2-specific CD4+ T cells compared to children with MIS-C and those with other inflammatory or infec&lt;ous diagnoses, who both presented a largely monofunc&lt;onal SARS-CoV-2-specific CD4+ T cell profile. Addi&lt;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&lt;on inducing T cell exhaus&lt;on and/or superan&lt;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&lt;ve immunity of SARS-CoV-2 in children compared to adults and provides insights into the cross-reac&lt;ve immunity that may provide protec&lt;on against re-infec&lt;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&lt;nues to circulate and may possibly evolve into endemi seasonal waves of infec&lt;on. This exposes children, the vulnerable and least vaccinated popula&lt;on to increasing respiratory viral coinfec&lt;ons. Future work includes inves&lt;ga&lt;ng systemic and local immune responses against respiratory syncy&lt;al virus (RSV) in the context of recent or concurrent SARS-CoV-2 infec&lt;on in children to beher understand the immunological mechanisms contribu&lt;ng to the increased RSV disease severity observed aSer the COVID-19 pandemic","abstract_has_math":false,"creators":["Benede, Ntombi"],"institution":"Department of Pathology","degree_name":null,"degree_level":null,"degree_discipline":null,"degree_department":null,"school":null,"contributors":[],"advisors":["Keeton, Roanne","Burgers Wendy"],"committee_chairs":[],"committee_members":[],"year":2025,"date_issued":"2025","date_published":"2025","updated_at":"2026-07-22T22:22:39Z","subjects":["Pathology"],"languages":[],"rights":[],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"http://hdl.handle.net/11427/41503","outbound_label":"Handle","outbound_source":"dc:identifier.uri"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor.advisor","label":"Advisor","values":["Keeton, Roanne","Burgers Wendy"]},{"key":"dc:creator","label":"Author","values":["Benede, Ntombi"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date.accessioned","label":"Dc Date Accessioned","values":["2025-07-02T10:50:29Z"]},{"key":"dc:date.available","label":"Dc Date Available","values":["2025-07-02T10:50:29Z"]},{"key":"dc:date.issued","label":"Date","values":["2025"]},{"key":"dc:publisher.department","label":"Dc Publisher Department","values":["Department of Pathology"]},{"key":"dc:publisher.institution","label":"Dc Publisher Institution","values":["University of Cape town"]},{"key":"dc:type","label":"Dc Type","values":["Thesis / Dissertation"]},{"key":"dc:type.qualificationlevel","label":"Dc Type Qualificationlevel","values":["Doctoral","PhD"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["Pathology"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier.uri","label":"Identifier URI","values":["http://hdl.handle.net/11427/41503"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description.abstract","label":"Abstract","values":["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"]},{"key":"dc:title","label":"Title","values":["Investigating SARS-CoV-2 immune responses in children"]}]}],"canonical_facts":{"dc:contributor.advisor":["Keeton, Roanne","Burgers Wendy"],"dc:creator":["Benede, Ntombi"],"dc:date.accessioned":["2025-07-02T10:50:29Z"],"dc:date.available":["2025-07-02T10:50:29Z"],"dc:date.issued":["2025"],"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.uri":["http://hdl.handle.net/11427/41503"],"dc:publisher.department":["Department of Pathology"],"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","PhD"]},"updated_at":"2026-07-22T22:22:39Z"}