CRISPR analysis suggests that small circular single-stranded DNA smacoviruses infect Archaea instead of humans

Nat Commun. 2019 Jan 17;10(1):294. doi: 10.1038/s41467-018-08167-w.


Smacoviridae is a family of small (~2.5 Kb) CRESS-DNA (Circular Rep Encoding Single-Stranded (ss) DNA) viruses. These viruses have been found in faeces, were thought to infect eukaryotes and are suspected to cause gastrointestinal disease in humans. CRISPR-Cas systems are adaptive immune systems in prokaryotes, wherein snippets of genomes from invaders are stored as spacers that are interspersed between a repeated CRISPR sequence. Here we report several spacer sequences in the faecal archaeon Candidatus Methanomassiliicoccus intestinalis matching smacoviruses, implicating the archaeon as a firm candidate for a host. This finding may be relevant to understanding the potential origin of smacovirus-associated human diseases. Our results support that CRESS-DNA viruses can infect non-eukaryotes, which would mean that smacoviruses are the viruses with the smallest genomes to infect prokaryotes known to date. A probable target strand bias suggests that, in addition to double-stranded DNA, the CRISPR-Cas system can target ssDNA.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Archaea / genetics*
  • Archaea / virology
  • CRISPR-Cas Systems / genetics
  • Clustered Regularly Interspaced Short Palindromic Repeats / genetics
  • DNA Viruses / genetics
  • DNA Viruses / isolation & purification
  • DNA Viruses / pathogenicity*
  • DNA, Single-Stranded / genetics*
  • Feces / microbiology
  • Gastrointestinal Microbiome / genetics*
  • Host-Pathogen Interactions / genetics*
  • Humans
  • Phylogeny


  • DNA, Single-Stranded