Genomics and Molecular Epidemiology of Adenovirus in Paediatric Immunocompromised Patients

Abstract

Very little is known about the origins, evolution and resistance dynamics of human mastadenovirus (HAdV) infection. Despite an association with significant morbidity and mortality amongst the immunocompromised population, current treatment strategies have a weak evidence base. Existing diagnostic tools are inadequate for influencing management decisions or infection control strategies. Furthermore, a recent surge in HAdV cases, amongst a haematopoietic transplant population, including five deaths, led this study to use whole genome sequencing (WGS) to investigate. To gain a complete transmission picture for the first epidemiology chapter, outbreak and non-outbreak HAdV sequences (54 sequences from 37 patients) were compared with GenBank sequences and a database of previously sequenced HAdVs. An improved bait set for WGS was used. Maximum likelihood trees and pairwise differences were used to evaluate genotypic relationships paired with epidemiological data from routine Infection, Prevention and Control (IPC) activity. During this time period two formal outbreaks had been identified by IPC, while WGS detected nine monophyletic clusters, seven were corroborated by epidemiological evidence and by comparison of single nucleotide polymorphisms. One of the formal IPC outbreaks was confirmed, one was not. Of the five HAdV-associated deaths, three were unlinked, the remaining two considered the source of transmission events. Existing antivirals used to treat HAdV infections target the DNA polymerase of the virus. Immunosuppressed patients, particularly children, are susceptible to overwhelming HAdV infection. The subsequent chapter of this thesis interrogates variants identified within the DNA polymerase. Linking sequence data with patient data and published mutations, the association between antiviral therapy response/failure and mutations is described. None of the previously reported confirmed or putative resistance mutations were identified in this patient cohort. The clinical consequences of unmitigated HAdV transmission events are high. Focusing on two high risk wards using WGS, this study identified six transmission events that, over prolonged periods, would have gone unnoticed using traditional polymerase chain reaction and epidemiology. Mixed infection is frequent (10% of patients), providing a sentinel source of recombination and superinfection. Prolonged HAdV viraemia is associated with poor outcomes; two of the ten patients failing to respond to therapy in this study did not survive. A few HAdV-C5 and for the first time HAdV-A31 mutations warrant further investigation to confirm or refute their association with antiviral resistance. Resistance is likely to be multifactorial but existing diagnostic methods fail to provide the reassurance that toxic antivirals should be withdrawn or continued. Immunosuppressed patients harbouring a high rate of HAdV positivity require comprehensive surveillance. As a consequence of this study, HAdV WGS is being incorporated routinely into a clinical algorithm to monitor antiviral resistance, prevent transmission and influence IPC policy in real-time.

Date of Award	1 Aug 2021
Original language	English
Awarding Institution	The University of Manchester
Supervisor	Pamela Vallely (Supervisor)