First crAss-Like Phage Genome Encoding the Diversity-Generating Retroelement (DGR)

Viruses. 2020 May 22;12(5):573. doi: 10.3390/v12050573.


A new crAss-like genome encoding diversity-generating retroelement (DGR) was found in the fecal virome of a healthy volunteer. The genome of the phage referred to as the crAssphage LMMB, belonged to the candidate genus I of the AlphacrAssvirinae subfamily. The DGR-cassette of the crAssphage LMMB contained all the essential elements: the gene encoding reverse transcriptase (RT), the target gene (TG) encoding the tail-collar fiber protein, and variable and template repeats (VR and TR) with IMH (initiation of mutagenic homing) and IMH* sequences at the 3'-end of the VR and TR, respectively. Architecture of the DGR-cassette was TG-VR(IMH)-TR(IMH*)-RT and an accessory variable determinant (avd) was absent from the cassette. Analysis of 91 genomes and genome fragments from genus I of the AlphacrAssvirinae showed that 15 (16%) of the genomes had DGRs with the same architecture as the crAssphage LMMB, while 66 of the genomes contained incomplete DGR-cassettes or some elements of the DGR.

Keywords: crAssphage; diversity-generating retroelement (DGR); genome; initiation of mutagenic homing; template repeat; variable repeat.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacteriophages / classification
  • Bacteriophages / genetics*
  • Chromosome Mapping
  • DNA, Viral / isolation & purification
  • Feces / virology
  • Genome*
  • Humans
  • Mutagenesis
  • Phylogeny
  • RNA-Directed DNA Polymerase / classification
  • RNA-Directed DNA Polymerase / genetics
  • Retroelements / genetics*


  • DNA, Viral
  • Retroelements
  • RNA-Directed DNA Polymerase