Metagenomes of a Freshwater Charavirus from British Columbia Provide a Window into Ancient Lineages of Viruses

• Main Authors: Marli Vlok, Adrian J. Gibbs, Curtis A. Suttle
• Format: Article
• Language: English
• Published: MDPI AG 2019-03-01
• Series: Viruses
• Subjects: Charavirus; RNA viruses; capsid proteins; metagenomes; virome; phylogenetics
• Online Access: https://www.mdpi.com/1999-4915/11/3/299

Charophyte algae, not chlorophyte algae, are the ancestors of &#8216;higher plants&#8217;; hence, viruses infecting charophytes may be related to those that first infected higher plants. Streamwaters from British Columbia, Canada, yielded single-stranded RNA metagenomes of Charavirus canadensis (CV-Can), that are similar in genomic architecture, length (9593 nt), nucleotide identity (63.4%), and encoded amino-acid sequence identity (53.0%) to those of Charavirus australis (CV-Aus). The sequences of their RNA-dependent RNA-polymerases (RdRp) resemble those found in benyviruses, their helicases those of hepaciviruses and hepegiviruses, and their coat-proteins (CP) those of tobamoviruses; all from the alphavirus/flavivirus branch of the &#8216;global RNA virome&#8217;. The 5&#8217;-terminus of the CV-Can genome, but not that of CV-Aus, is complete and encodes a methyltransferase domain. Comparisons of CP sequences suggests that Canadian and Australian charaviruses diverged 29&#8211;46 million years ago (mya); whereas, the CPs of charaviruses and tobamoviruses last shared a common ancestor 212 mya, and the RdRps of charaviruses and benyviruses 396 mya. CV-Can is sporadically abundant in low-nutrient freshwater rivers in British Columbia, where <i>Chara</i><i> </i><i>braunii</i>, a close relative of <i>C. </i><i>australis</i>, occurs, and which may be its natural host. Charaviruses, like their hosts, are ancient and widely distributed, and thus provide a window to the viromes of early eukaryotes and, even, Archaea.