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Genotypic and phenotypic assays to improve strain coverage assessments of sub-capsular meningococcal vaccines

Clark, Stephen Andrew (2018) Genotypic and phenotypic assays to improve strain coverage assessments of sub-capsular meningococcal vaccines. Doctoral thesis (PhD), Manchester Metropolitan University.

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Abstract

The licensure of recombinant protein-based meningococcal vaccines has increased the complexity of strain coverage assessments. In 2015, the 4CMenB vaccine was introduced into the UK national infant immunisation schedule and an Enhanced Surveillance programme was launched by Public Health England’s Meningococcal Reference Unit. Meningococcal isolates, representing ~50% of laboratory-confirmed cases, are comprehensively characterised using whole genome sequencing and 4CMenB strain coverage is assessed phenotypically using the Meningococcal Antigen Typing System. For the remaining cases, which are confirmed using PCR only, strain characterisation was until recently restricted to geno-grouping and geno-subtyping. The purpose of this research was to establish new genotypic assays to improve strain coverage assessment among non-culture cases, as well as introduce the MEASURE assay to predict coverage of a second sub-capsular vaccine, rLP2086, among isolates. A PCR sequencing assay targeting the Factor H-Binding Protein antigen gene (fHbp) was developed and had an estimated analytical sensitivity limit of between 600ag/μL and 6fg/μL. Using this assay, fHbp was successfully sequenced from 1510 of the 1661 PCR-positive clinical samples tested (91%). The distributions of fHbp peptide variants among culture and non-culture strains were compared and, whilst differences were observed for a small number of predominant variants, the distribution was very similar within each capsular group. The prospect of performing WGS directly from non-culture specimens was investigated using the Agilent SureSelectXT system. Eight of ten clinical specimens yielded genomes of acceptable quality. It was estimated that up to 54% of non-culture cases could be sequenced using this technique, however, the financial cost is currently prohibitive. Finally, the MEASURE assay was risk assessed and overnight formaldehyde incubation was introduced to ensure cells were fully fixed. The assay results were similar to those generated in a collaborating laboratory, however, further standardisation may be required. These assays will help to increase the accuracy of strain coverage predictions of the currently-licenced and future sub-capsular meningococcal vaccines.

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