Elusive preferred hosts or nucleic acid level selection? A commentary   on: Evolutionary interpretations of mycobacteriophage biodiversity and   host-range through the analysis of codon usage bias (Esposito et al. 2016)
  While confirming the long held view that viruses do not closely imitate the use of their host's codon catalogue, Esposito and coworkers nevertheless consider it surprising that, despite having the ability to infect the same host, many mycobacteriophages share little or no genetic similarity (i.e. similarity in their GC contents and codon utilization patterns). Arguing correctly that efficient translation of a phage's proteins within a host is likely to be optimized by the phage's ability to match the host's codon usage pattern, it is concluded that the preferred host of many mycobacteriophages is not Mycobacterium smegmatis, despite their having been isolated on that organism. Thus, a virus and its elusive preferred hosts would have had similar GC percentages and codon usages, but the same virus could still infect a less-preferred host (Mycobacterium smegmatis), where the virus-host similarity would be less evident. However, there is another evolutionary interpretation. 
Donald R. Forsdyke
q-bio.PE