Epidemiology and genotypes of Enteroviruses in patients with respiratory illness in South Africa

Hellferscee, Orienka
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Globally, lower respiratory tract infections (LRTI) are the leading cause of death in children aged less than 5 years. This study focuses on enteroviruses, which are a known cause of respiratory illness but whose epidemiology and molecular characterization have not been well described in South Africa. The first aim of this study was to describe enterovirus genotypes circulating among South African patients hospitalized with severe respiratory illness (SRI). Upper respiratory samples were tested for the presence of enteroviruses using polymerase chain reaction (PCR) and characterized using a partial VP1 gene segment through Sanger sequencing. Enteroviruses were identified in 8.2% of patients with SRI. We demonstrated a high diversity, 17 genotypes, from all four enterovirus species circulating in South Africa. The second aim was to use Sanger sequencing to characterize the enterovirus genotypes circulating among South African patients with influenza-like illness (ILI), SRI, and asymptomatic individuals. We found high genetic diversity (33 genotypes) but no association of enterovirus species with disease severity; however, some genotypes (echovirus 30 (E30), coxsackie virus B5, and EV-D68) were more prevalent in symptomatic cases. The E30 strains formed a new cluster proposed to be named genotype k. The third aim described a novel approach for next generation sequencing of E30, based on sequence-independent single primer amplification (SISPA). Complete full genome phylogenetic analysis supports the designation of genotype k, and distinct grouping was confirmed that could be a result of the diversity of different subgenomic regions in E30 driven by different evolutionary paths. Five E30 whole genomes were submitted to GenBank, contributing to global data. The fourth aim was to determine the fraction of rhinovirus (the most commonly identified species of Enterovirus) detection associated with mild or severe respiratory illness. Rhinovirus was detected in 17.4% (368/2120), 26.8% (979/3654) and 23.0% (1003/4360) of controls, ILI and SRI, respectively. The overall RV-AF (ILI: 54.6%; severe acute respiratory illness (SARI): 54.3%) were similar to those reported in a previous study conducted in South Africa (ILI: 52.0%; SARI: 46.9%), but was lower compared to those of other important respiratory pathogens such as influenza viruses (ILI: 93.3%; SARI: 86.3%) and respiratory syncytial virus (ILI: 63.1%; SARI: 83.7%) (21). Even though the attributable fraction was lower than influenza and RSV, the attributable burden of rhinoviruses (RV-AF) was equivalent to influenza and RSV, because of the high rhinovirus detection rate. In conclusion, we found (i) no difference in enterovirus genotypes detected in mild versus severe disease; (ii) that outbreak-associated EV strains like EV-D68 are circulating in South Africa; (iii) that E30 strains from respiratory illness cases in South Africa belong to a newly proposed genotype k; and (iv) that rhinovirus species contribute to mild and severe respiratory illness
A thesis submitted to the Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, in fulfilment of the requirement for the degree of Doctor of Philosophy