Within-host evolution of virus variants during chronic infection with novel GII.P26-GII.26 norovirus.

Highlights • Novel norovirus GII.P26 and GII.26 genotypes are confirmed. • The first near complete GII.P26-GII.26 norovirus genome is provided. • New viral phenotypes occurred predominantly under negative selection. • Within-host evolution of p22 and of the N-terminal arm of VP1 was enhanced. Abstract Background Noroviruses are a leading cause of acute gastroenteritis in all age groups. They generally cause a rapidly self-limiting illness. However, chronic norovirus diarrheal disease occurs in immunocompromised individuals, and is accompanied by persistent shedding of infectious norovirus in stool. Objectives The study aims to characterize a novel GII.P26-GII.26 norovirus strain. Furthermore, it analyses viral mutations arising during chronic infection of an immunocompromised host. Study design Over the course of more than three years, stool samples were obtained from an immunocompromised patient and screened for the presence of norovirus RNA by real-time PCR and norovirus antigen by immunoassay. Viral population kinetics was analyzed by conventional and high-throughput-sequencing. Results Real-time PCR yielded high amounts of norovirus RNA in the stool, but antigen immunoassays failed to detect the virus. The near complete norovirus genome was assigned as novel GII.P26-GII.26 genotype. Conventional as well as high-throughput sequencing pointed to a heterogeneous viral population with low rates of non-synonymous substitutions. Within-host evolution was enhanced in non-structural protein p22 and the N-terminal arm of the capsid protein VP1 but reduced in the viral polymerase RdRp. Intermittent non-synonymous substitutions in the protruding domain of the VP1 reverted fully over time. Conclusions Confirmation of novel GII.P26-GII.26 norovirus genotypes provides insight into norovirus genetic diversity. The study further illustrates norovirus infection as an important differential diagnosis of recurrent persistent diarrhea in immunocompromised patients. The provided data on within-host evolution contribute to the insight of the mechanisms of viral persistence and pathogenesis in chronic norovirus infections. [ABSTRACT FROM AUTHOR]