In a study published in the journal Journal of Virology, Prof. CUI Jie’s group at the Institut Pasteur of Shanghai of the Chinese Academy of Sciences reported hundreds of amphibian foamy viruses (FVs) by integrating and analyzing transcriptomic and genomic data.

Foamy viruses are complex retroviruses that can infect humans and other animals. Incidentally, foamy viruses infect germ line of the host and integrate into host’s genome, becoming the endogenous foamy viruses (EFVs) which could be passed from the parents to the offspring.  

Foamy viruses represent, more so than other viruses, the best model of co-evolution between viruses and hosts, because of low substitution rates and relatively stable genomes. 

Prof. CUI’s group discovered 412 FVs from six lineages from three major orders of amphibians, which significantly increased the known set of FVs in amphibians. Among these lineages, salamander FVs maintained a co-evolutionary pattern with their hosts that could be dated back to the Paleozoic era, while, on the contrary, frog FVs were much more likely acquired from cross-species (class level) transmission in the Cenozoic era. 

In addition, the researchers found that three distinct FV lineages had integrated into the genome of a salamander. 

Unexpectedly, they identified a lineage of endogenous FV in caecilian expressed all complete major genes, demonstrating the potential existence of exogenous form of FV outside of mammals and suggesting that active FVs could be underestimated in nature. 

The discovery of rare phenomena in amphibian FVs has significantly increased the understanding of the macroevolution of the complex retrovirus from the Paleozoic era.