Taking gastro-surveillance into the 21st century

Enteric viruses, particularly rotaviruses and noroviruses, are leading causes of gastroenteritis worldwide. Human rotaviruses are ubiquitous and globally almost every child has been infected by 3-5 years of age. Noroviruses affect people of all ages and is the leading cause of foodborne outbreaks. Rota- and noroviruses account for ˜40% and ˜17% of diarrhea-associated hospitalizations, and ˜200,000 deaths annually respectively, with most deaths occurring in developing countries. Two rotavirus vaccines have currently been implemented in ˜95 countries and several norovirus vaccine candidates are currently in development and/or clinical testing. Surveillance of enteric viruses is an important part of outbreak investigations as well as pre- and post-vaccine impact studies but is even in developed countries often limited to investigation of sporadic cases or comprehensive outbreaks. Conventional methods for enteric virus detection and subtyping relies on standard RT-PCR methods, supplemented with Sanger-sequencing. However, for viruses with even moderate mutationrates, PCR-based-typing of only limited parts of the virus genome is challenging and requires regular update of primers. Full-genomecharacterization technologies based on sequence independent methods based on next generation sequencing (NGS), have demonstrated great potential for enteric virus detection and/or typing in both clinical and environmental samples. However, cost-benefits must balance for such methods to be widely accepted for public health purposes. In Europe as also globally, routine use of NGS-methods for surveillance of enteric viruses is currently limited to few national public health laboratories. What important lessons can be learned from these and what is the future of NGS-based surveillance?