Population Genomics of Human Viruses

Viruses, and a few RNA viruses in particular, represent one of the greatest threats for human health. High mutation rates, large population sizes, and short generation times contribute to their typically fast evolutionary rates. However, many additional processes operate on their genomes, often in opposite directions, driving their evolution and allowing them to adapt to diverse host populations and antiviral drugs. Until recently, the high levels of genetic variation of most viruses have been explored only at a few genes or genome regions. The recent advent and increasing affordability of next-generation sequencing techniques have allowed obtaining complete genome sequences of large numbers of viruses, mainly HIV, HCV, influenza A, and others associated with emerging infections, such as Zika, chikungunya, or dengue virus. This opens the possibility to explore the effects of the different processes affecting viral diversity and evolution at the genome level. Consequently, population genomics provides the conceptual and empirical tools necessary to interpret genetic variation in viruses and its dynamics and drivers and to transform these results into information that may complement the epidemiological surveillance of the virus and its disease. This chapter provides an overview of human viruses from a population genomics perspective, with a special emphasis on RNA viruses, and the potential benefits of “genomic surveillance” to establish public health policies that improve the control and monitoring of the diseases caused by these viruses.