Norovirus GII.4 and GII.7 capsid sequences undergo positive selection in chronically infected patients

Norovirus has become an important cause for infectious gastroenteritis. Particularly genotype II.4 (GII.4) has been shown to spread rapidly and causes worldwide pandemics. Emerging new strains evade population immunity and lead to high norovirus prevalence. Chronic infections have been described recently and will become more prevalent with increasing numbers of immunocompromized patients. Here, we studied norovirus evolution in three chronically infected patients, two genotypes II.4 and one II.7.A 719 and 757 nt region was analyzed for GII.4 and GII.7, respectively. This covers the entire hypervariable P2 domain of the VP1 capsid gene. Genetic variability at given and between different time points was assessed. Evolutionary adaptation was analyzed by Bayesian sampling of genealogies. This analysis clearly demonstrated positive selection rather than incidental drift for all three strains. The GII.7 and one GII.4 strain accumulated on average 5-9 mutations per 100 days, most of them non-synonymous. This is a much higher evolutionary rate than observed for noroviruses on a global level.Our data demonstrate that norovirus quasispecies are positively selected in chronically infected patients. The numbers of intraindividual amino acid mutations acquired in the capsid gene are similar to those separating consecutive GII.4 epidemic strains. Evolution in a given, chronically infected individual may thus generate novel genotypes at risk to expedite global evolution particularly for slowly evolving genotypes, as GII.7.

► We study the evolution of norovirus genotypes II.4 and II.7 in chronic infection. ► Eight to ten clones of capsid sequences are analyzed per longitudinal sample. ► We apply coalescent-based computations with Bayesian sampling of genealogies. ► We infer positive selection in all three analyzed isolates.