RNA virus genomics: a world of possibilities

Abstract

The increasing availability of complete genome sequences of RNA viruses has the potential to shed new light on fundamental aspects of their biology. Here, I use case studies of 3 RNA viruses to explore the impact of genomic sequence data, with particular emphasis on influenza A virus. Notably, the studies of RNA virus genomics undertaken to date largely focused on issues of evolution and epidemiology, and they have given these disciplines new impetus. However, genomic data have so far made fewer inroads into areas of more direct importance for disease, prevention, and control; thus, harnessing their full potential remains an important goal.

Figure 1. Process of reassortment in influenza A virus.

Reassortment occurs when 2 viruses (denoted here as A and B) coinfect a single host cell. Each virus contains 8 gene segments, shown as open and closed bars. Reassortment among these 2 viruses then produces viruses with a variety of segment combinations.

Figure 2. Genetic diversity of human influenza A/H1N1 virus in the United States during the 2006–2007 influenza season.

The phylogenetic tree depicts the diversity of the gene encoding NA in 284 isolates sampled across the United States. Isolates from different geographical locations are color coded according to the inset map. Note that there is remarkable genetic diversity, manifest as the circulation of multiple lineages likely to be independently imported, and that there is no clear spatial patterning, as reflected in the mix of colors. Figure adapted with permission from PLoS Pathogens (14).

Figure 3. Global migration of influenza A virus.

Seasonal epidemics of human influenza A/H3N2 virus are thought to begin in a circulation network located in East and Southeast Asia before being exported to other geographical localities (arrows denote direction of migration). The virus is thought to be exported directly from the circulation network in East and Southeast Asia to Australia, Europe, and North America. It is then exported to South America from both Europe and North America. Figure adapted with permission from Science (20).

Figure 4. Global distribution of DENV.

The broad-scale geographic locations of the different serotypes and genotypes of DENV are indicated: (I)–(IV), genotypes I–IV; (Am), American; (Am/As), American/Asian; (As I), (As II); Asian I and II; (Cos), cosmopolitan. Note the abundance of viral genetic diversity in Southeast Asia and the relative lack of information about DENV in Africa. Figure adapted with permission from The evolution and emergence of RNA viruses (90).