A ~40-kb flavi-like virus does not encode a known error-correcting mechanism.

Area of Science:

• Virology
• Genomics
• Evolutionary Biology

Background:

• A fundamental relationship exists between RNA virus genome size and error rate, known as the error threshold.
• High mutation rates in RNA viruses typically limit genome size to prevent extinction from deleterious mutations.
• Exceptions like Nidovirales possess error-correcting exonucleases, enabling larger genomes.

Purpose of the Study:

• To investigate the evolutionary mechanisms allowing large RNA virus genomes.
• To explore alternative strategies beyond exonucleases for overcoming the error threshold.
• To characterize a novel large-genome flavi-like virus found in a sponge.

Main Methods:

• Metatranscriptomic sequencing to identify novel viruses.
• Bioinformatic analysis to determine genome size and identify viral proteins.
• Structural analysis to investigate potential nucleic acid metabolism domains.
• Phylogenetic inference to determine evolutionary relationships.

Main Results:

• Discovery of a ~40 kb flavi-like virus in a Haliclona sponge metatranscriptome.
• The identified virus lacks known viral exonuclease domains.
• Structural analysis suggests the virus may have acquired cellular nucleic acid metabolism domains.
• Phylogenetic analysis places the virus as a divergent pesti-like lineage, named 'Maximus pesti-like virus'.

Conclusions:

• This flavi-like virus achieves a genome size comparable to Nidovirales without relying on known viral exonucleases.
• RNA viruses have evolved multiple, diverse solutions to overcome the genome size error threshold.
• The findings expand our understanding of RNA virus genome evolution and adaptation.