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

1,†, 2,* and 1,3,4,5,*
1
Department of Botany, University of British Columbia, Vancouver, BCV6T 1Z4, Canada
2
Emeritus Faculty, Australian National University, Canberra, ACT 2601, Australia
3
Institute for the Oceans and Fisheries, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
4
Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
5
Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
*
Authors to whom correspondence should be addressed.
Current address: Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BCV6T 1Z3, Canada.
Viruses 2019, 11(3), 299; https://doi.org/10.3390/v11030299
Received: 3 March 2019 / Revised: 19 March 2019 / Accepted: 21 March 2019 / Published: 25 March 2019
(This article belongs to the Special Issue Plant Virus Ecology and Biodiversity)
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Abstract

Charophyte algae, not chlorophyte algae, are the ancestors of ‘higher plants’; 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 ‘global RNA virome’. The 5’-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 29–46 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 Chara braunii, a close relative of C. australis, 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. View Full-Text
Keywords: Charavirus; RNA viruses; capsid proteins; metagenomes; virome; phylogenetics Charavirus; RNA viruses; capsid proteins; metagenomes; virome; phylogenetics
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Vlok, M.; Gibbs, A.J.; Suttle, C.A. Metagenomes of a Freshwater Charavirus from British Columbia Provide a Window into Ancient Lineages of Viruses. Viruses 2019, 11, 299.

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