Dynamic interactions between RNA viruses and human hosts unravelled by a decade of next generation sequencing

Next generation sequencing (NGS) methods have significantly contributed to a paradigm shift in genomic research for nearly a decade now. These methods have been useful in studying the dynamic interactions between RNA viruses and human hosts.

In this review, we summarise and discuss key applications of NGS in studying the host - pathogen interactions in RNA viral infections of humans with examples.

Use of NGS to study globally relevant RNA viral infections have revolutionized our understanding of the within host and between host evolution of these viruses. These methods have also been useful in clinical decision-making and in guiding biomedical research on vaccine design.

NGS has been instrumental in viral genomic studies in resolving within-host viral genomic variants and the distribution of nucleotide polymorphisms along the full-length of viral genomes in a high throughput, cost effective manner. In the future, novel advances such as long read, single molecule sequencing of viral genomes and simultaneous sequencing of host and pathogens may become the standard of practice in research and clinical settings. This will also bring on new challenges in big data analysis.