Can genomics replace electron microscopy?
This might be suggested by the rise of rapid sequencing and the ensuing increased availability of wholly sequenced virus genomes. It is indeed advocated in discussions by unconditional partisans of genomics. The answer is round ‘‘no.’’ Genomics gives us the genome and genes, thus the elementary building blocks of a virus. It also provides gene order and direction of transcription. It identifies genes coding for proteins with homology to known enzymes or virion components, restriction-modification enzymes, capsid protein size, or the length of tape measure proteins. Further, genomics indicates horizontal gene transfer or gene swapping, may reveal relationships between virus groups and individual viruses, and allow quantifying connections and constructing phylogenetic trees. This provides unprecedented insights into virus evolution and is a precious help in phage classification.