Adaptive immune response in COVID-19 patients and innate immune modulation of SARS-CoV-2
| dc.contributor.advisor | Burt, Felicity | en_ZA |
| dc.contributor.author | Litabe, Matefo Millicent | en_ZA |
| dc.date.accessioned | 2024-06-11T09:08:43Z | |
| dc.date.available | 2024-06-11T09:08:43Z | |
| dc.date.issued | 2023 | en_ZA |
| dc.description | Thesis (Ph.D.(Medical Virology))--University of the Free State, 2023 | en_ZA |
| dc.description.abstract | In December 2019, a cluster of cases of atypical pneumonia were reported in Wuhan, China. All patients had a history of attending a large seafood market. Surveillance and detection methods established during the 2003 severe acute respiratory syndrome coronavirus (SARS-CoV)-1 outbreak contributed towards the identification of the virus as a novel coronavirus (CoV). The virus was later named SARS-CoV-2 and identified as the causative agent of Coronavirus Disease 2019 (COVID-19). Despite massive attempts to contain the virus in China, the cases rapidly increased and spread globally, and the World Health Organization (WHO) declared COVID-19 a Public Health Emergency of International Concern on 30 January 2020 and characterized the outbreak as a pandemic on 11 March 2020. Assessing immunoglobulin (Ig)-G and neutralizing antibodies is essential to comprehensively evaluate the efficacy and duration of immunity conferred by natural infection and the COVID-19 vaccines. Effectively determining SARS-CoV-2 seroprevalence within a population is important as it helps to improve our understanding of virus circulation dynamics, identify individuals at risk of infection, and the extent of virus exposure in the community. Therefore, this study investigated the duration and kinetics of adaptive immunity, particularly the persistence of IgG and neutralizing antibodies, in patients who recovered from SARS-CoV-2 in the Free State, South Africa. Commercial assays are expensive, and hence two anti-spike (S) inhouse assays, enzyme-linked immunosorbent assay (ELISA) and immunofluorescence assay (IFA), were developed and validated for detection of anti-S IgG. A total of 89 serum samples were collected from COVID-19 PCR-confirmed patients between 2-94 days post-symptom onset to validate the assay. A 100 prepandemic samples were used as a negative control panel to determine the cutoff of the assay. A cutoff value of 30% was considered accurate to differentiate between negative and positive samples using a two-graph receiver operating characteristic (TG-ROC). The assays exhibited a sensitivity of 100% for ELISA and 98.8% for IFA when testing samples collected more than one week after the onset of illness. The positive predictive values (ppv) were 92.1% for ELISA and 91.0% for IFA on PCR-confirmed positive samples. The assays were also compared to a commercially available SAPRHA-approved assay, where the ELISA showed a higher ppv of 95.8 %, while the Roche assay was 89.6 %, and the commercial lateral flow was 93.9 %. The two in-house assays also detected IgG antibodies in samples collected from waves in which new variants were circulating, showing that despite mutations of the SARS-CoV-2 S protein, the assay was still sensitive to detect IgG antibodies in circulating variants. This indicates that these assays could be used for surveillance of the South African population. To investigate the duration of anti-S IgG and neutralizing antibodies against SARS-CoV-2, 100 individuals with previously confirmed COVID-19 infection were recruited for the study. The cohort included 64/100 vaccinated and 36/100 unvaccinated individuals. Initial samples were collected between March 2021 and January 2022, with confirmed infection between June 2020 and December 2021. Follow-up samples were collected from 82/100 in 2022 and 62/100 in 2023 of the initial cohort. Samples were tested for anti-S IgG antibodies and neutralizing antibodies against Ancestral strain, Delta, and Omicron variants. A total of 95/100 baseline samples tested positive for anti-S IgG and 79/82 and 53/62 for follow-up samples. A total of 99/100, 78/100, and 72/100 baseline samples tested positive for neutralizing antibodies against the Ancestral strain, Delta, and Omicron variants. A total of 80/82, 63/82, 77/82 in 2022 and 53/62, 50/62, 56/62 in 2023 tested positive for neutralizing antibodies against the Ancestral, Delta, and Omicron variants, respectively. Samples were grouped based on the time (days) the samples were collected post-onset of illness. Results showed that IgG antibodies were significantly higher directly after infection, between 1-180 days, then gradually declined significantly with time. Neutralizing antibody titers against the Ancestral strain and Delta variant were significantly higher early after infection, between 1-180 days, remained relatively stable for an extended period, and then waned gradually before declining significantly. In contrast, although not significant, neutralizing antibodies against the Omicron variant increased with time, but this may be because samples were collected when the Omicron variant was still prevalent. Results also showed that vaccinated individuals had significantly higher antibody titers than unvaccinated, highlighting the importance of continued vaccination. The study shows the longevity of antibodies against SARS-CoV-2, as most individuals still had detectable titers at least 24 months post-acute infection, possibly boosted by vaccination or reinfection. The study also shows that the dynamics of antibodies vary among individuals; most individuals display declining antibody titers with time, and a smaller proportion maintain stable antibodies or a fluctuation of antibodies over time. Traditional medicinal plants have been proposed as promising, cost-effective treatments for SARS-CoV-2, with studies showing the potential to induce protection against different viral infections. The study also investigated the potential of Phela, a traditional medicine prepared from the extracts of four South African plants, and the individual components to modulate the release of cytokines in SARS-CoV-2 Omicron-infected mammalian cells and to investigate the influence of the plant extracts on viral replication. Cells were treated with the plant extracts before or after infection with SARS-CoV-2. Subsequently, cell culture media was collected at 12, 24, 48, and 72 hours post-infection and tested for virus replication and levels of Interleukin (IL)-1β, IL-2Rα, IL-6, IL-10, tumour necrosis factor (TNF)-α, and interferon (IFN)-γ cytokines. There was no statistically significant difference in viral load between infected cells treated with plant extracts compared to infected and untreated cells, showing that the plant extracts may have little to no effect on virus replication. Treatment with plant extracts resulted in significantly lower release of IL-1β, IL-2Rα, and TNF-α, with better response post-treatment than pretreatment, showing that the plant extracts may have the potential to manage cytokine storms and be a potential source of treatment for SARS-CoV-2. | en_ZA |
| dc.identifier.uri | http://hdl.handle.net/11660/12555 | |
| dc.language.iso | en | |
| dc.publisher | University of the Free State | en_ZA |
| dc.rights.holder | University of the Free State | en_ZA |
| dc.title | Adaptive immune response in COVID-19 patients and innate immune modulation of SARS-CoV-2 | en_ZA |
| dc.type | Thesis |