Discovery of two novel foamy viruses in sea lions and dolphins provides insight into their evolutionary history

The prevalence and evolution of foamy viruses (FVs) have become the focus of research because of the risk of new zoonotic diseases. FVs have been isolated from various mammals and exhibit long-term co-speciation with their hosts. They also appear to be mild and nonpathogenic to their hosts. However, they may increase the risk of infection by other pathogens or exacerbate the symptoms of other diseases. Based on the data obtained using next-generation sequencing (NGS), we amplified and obtained the complete genomes of the two new FVs discovered in the bottlenose dolphin (Tursiops truncatus) and the South American sea lion (Otaria byronia) at the Qingdao Polar Haichang Ocean Park. Analysis and prediction of the novel FV's genomic structure revealed that it was consistent with that of the known mammalian FVs. The polmerase (pol) genes of the novel OFVoby_1 and DFVttr_1 showed less than 61.87 % and 61.83 % amino acid identity, respectively, with other known FVs belonging to the Retroviridae family. The host was likely to carry the FV for a considerable amount of time, as evidenced by the different times DFVttr_1 was discovered. The phylogenetic analysis revealed that the pol of OFVoby_1 and DFVttr_1 closely clustered with the FVs of Simiispumavirus and Felispumavirus, respectively. However, they both displayed distinct branches. According to the international committee on taxonomy of viruses (ICTV) FV classification criteria, FVs carried by dolphins and sea lions belong to two new genera within the Spumaretrovirinae subfamily. Using Bayesian analysis to simultaneously determine divergence dates and phylogenetic relationships revealed unique FVs with a divergence date of approximately 60 million years. This study helps us understand the FVs evolution and provides a scientific basis for future investigations into animal-borne infectious diseases.