In the study published in the journal Journal of Virology on April 28, entitled Multiple infiltration and cross-species transmission of foamy viruses across Paleozoic to Cenozoic era, 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.

Unrooted phylogeny of retroviruses and foamy-like elements (Image by IPS). The tree was inferred from reverse transcriptase (RT) protein alignment. The host information of FVs, EFVs and exFVs is indicated using shaded box. The newly identified viral elements are labeled in red. The scale bar indicates the number of amino acid changes per site. Bootstrap values <70 percent are not shown.

Here, CUI Jie’s team discovered 412 FVs from 6 lineages from 3 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 team found 3 distinct FV lineages had integrated into the genome of a salamander. Unexpectedly, the team 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 active FVs could be underestimated in nature. Their discovery of rare phenomena in amphibian FVs has significantly increased the understanding of the macroevolution of the complex retrovirus from the Paleozoic era.

Link of Article: https://jvi.asm.org/content/early/2021/04/22/JVI.00484-21