Abstract
Influenza viruses (family Orthomyxoviridae) infect a variety of vertebrates, including birds, humans, and other mammals. Recent metatranscriptomic studies have uncovered divergent influenza viruses in amphibians, fish and jawless vertebrates, suggesting that these viruses may be widely distributed. We sought to identify additional vertebrate influenza-like viruses through the analysis of publicly available RNA sequencing data. Accordingly, by data mining, we identified the complete coding segments of five divergent vertebrate influenza-like viruses. Three fell as sister lineages to influenza B virus: salamander influenza-like virus in Mexican walking fish (Ambystoma mexicanum) and plateau tiger salamander (Ambystoma velasci), Siamese algae-eater influenza-like virus in Siamese algae-eater fish (Gyrinocheilus aymonieri) and chum salmon influenza-like virus in chum salmon (Oncorhynchus keta). Similarly, we identified two influenza-like viruses of amphibians that fell as sister lineages to influenza D virus: cane toad influenza-like virus and the ornate chorus frog influenza-like virus, in the cane toad (Rhinella marina) and ornate chorus frog (Microhyla fissipes), respectively. Despite their divergent phylogenetic positions, these viruses retained segment conservation and splicing consistent with transcriptional regulation in influenza B and influenza D viruses, and were detected in respiratory tissues. These data suggest that influenza viruses have been associated with vertebrates for their entire evolutionary history.
Highlights
Influenza viruses are segmented, negative-sense RNA viruses of the family Orthomyxoviridae, which includes the genera Quaranjavirus, Isavirus and Thogotovirus, as well as a wide diversity of orthomyxo-like viruses found in invertebrates [1,2,3]
We initially screened 776 vertebrate de novo assembled transcriptomes deposited in the Transcriptome Shotgun Assembly Sequence Database (TSA) and a further 158 transcriptomes available on the Fish-T1K Project
We detected influenza-like viruses in 0.6% of the bony fish libraries (n = 2) and in 7% (n = 4) of the amphibian libraries
Summary
Negative-sense RNA viruses of the family Orthomyxoviridae, which includes the genera Quaranjavirus, Isavirus and Thogotovirus, as well as a wide diversity of orthomyxo-like viruses found in invertebrates [1,2,3]. Viruses 2020, 12, 1042 encompassing eight or seven segments for IAV/IBV and ICV, IDV, respectively. All influenza viruses contain segments polymerase basic protein 1 (PB1), polymerase basic protein 2 (PB2), and polymerase acidic protein (PA) (or P3 for ICV/IDV) encoding for the polymerase complex, NP (nucleoprotein),. This difference in segment number between IAV/IBV and ICV/IDV is due to differences in the glycoproteins. ICV and IDV have a single glycoprotein, hemagglutinin esterase fusion (HEF) which facilitates both virus entry and release, and as such have a genome comprising seven segments. More divergent orthomyxoviruses and orthomyxo-like viruses have other genomic modifications, such as Salmon isavirus (Isavirus), a pathogen of fish that encodes fusion (F) and a hemagglutinin esterase (HE), rather than HA, NA or HEF proteins [5]. Wuhan spiny eel influenza virus phylogenetically groups to a sister clade to IBV and all eight segments have been recovered [3]
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