The evolutionary dynamics of norovirus

Abstract

Norovirus (NoV) is the leading cause of both outbreak and sporadic community acquired acute gastroenteritis. The overall incidence of NoV infection has grown dramatically since the emergence of epidemic NoV strains of the GII.4 lineage in the mid-1990s that have been associated with five pandemics and account for 80% of NoV infections. This thesis aimed to describe the mechanisms of evolution that facilitate the emergence of epidemic GII.4 variants and to elucidate factors that contribute to their higher epidemiological fitness. Two molecular epidemiological studies were performed to characterise the NoV strains linked to epidemics in New South Wales, Australia and those in circulation globally between 2007 and 2010. The pandemic GII.4 variant 2006b was identified as the cause of the 2007 and 2008 epidemics and the GII.4 variant New Orleans 2010 was the aetiological agent of the epidemics of 2009 and 2010. Each variant demonstrated antigenic drift in the capsid P2 domain that likely contributed to their epidemic potential. These studies also highlighted the role that recombination played in the emergence of New Orleans 2010. A number of factors were identified that may have contributed to the higher epidemiological fitness of the pandemic NoV GII.4 variants. Firstly, by comparing the enzymatic properties of different NoV polymerases, including replication efficiency and fidelity, it was shown that GII.4 variants have higher replication and mutation rates. It was also shown that polymerases from more prevalent genotypes, such as GII.4 and GII.b, are phosphorylated by an important cellular kinase, Akt, at a residue (Thr33) that decreases the de novo polymerase activity. Using next-generation sequencing technology, patterns of intra-host evolution were compared between acute and chronic NoV infections. Extensive heterogeneity and toggling at antigenic sites of the viral capsid was observed in the chronic patient, which suggests that immune-compromised individuals with chronic NoV infections could be a source for novel antigenic variants. In the same study, a transmission cluster was also examined and a strong genetic bottleneck was identified at the point of transmission. Overall, this thesis suggests that a complex pattern of mutation, recombination and adaptation drive NoV evolution in response to herd immunity.