Viruses change constantly during replication, leading to high intra-species diversity.
Although many changes are neutral or deleterious, some can confer on the virus different …

Background Strain-level RNA virus characterization is essential for developing prevention
and treatment strategies. Viral metagenomic data, which can contain sequences of both …

Without relying on cultivation, metagenomic sequencing greatly accelerated the novel RNA
virus detection. However, it is not trivial to accurately identify RNA viral contigs from a …

Background Viruses are a significant player in many biosphere and human ecosystems, but
most signals remain “hidden” in metagenomic/metatranscriptomic sequence datasets due to …

Despite a rapid expansion in the number of documented viruses following the advent of
metagenomic sequencing, the identification and annotation of highly divergent RNA viruses …

Background RNA viruses such as HCV and HIV mutate at extremely high rates, and as a
result, they exist in infected hosts as populations of genetically related variants. Recent …

Motivation: The study of RNA virus populations is a challenging task. Each population of
RNA virus is composed of a collection of different, yet related genomes often referred to as …

The development of rapid, economical genome sequencing has shed new light on the
classification of viruses. As of October 2016, the National Center for Biotechnology …

Next generation sequencing (NGS)-based studies have vastly increased our understanding
of viral diversity. Viral sequence data obtained from NGS experiments are a rich source of …

RNA viruses within infected individuals exist as a population of evolutionary-related variants.
Owing to evolutionary change affecting the constitution of this population, the frequency …