Marine RNA Virus Quasispecies Are Distributed throughout the Oceans

ABSTRACT RNA viruses, particularly genetically diverse members of the Picornavirales, are widespread and abundant in the ocean. Gene surveys suggest that there are spatial and temporal patterns in the composition of RNA virus assemblages, but data on their diversity and genetic variability in differ...

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Autores principales:	Marli Vlok, Andrew S. Lang, Curtis A. Suttle
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2019
Materias:	Picornavirales biogeography marine RNA virus purifying selection quasispecies Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/bae6b29bf2d749d68bc6ee78d9e3c92c
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spelling	oai:doaj.org-article:bae6b29bf2d749d68bc6ee78d9e3c92c2021-11-15T15:22:22ZMarine RNA Virus Quasispecies Are Distributed throughout the Oceans10.1128/mSphereDirect.00157-192379-5042https://doaj.org/article/bae6b29bf2d749d68bc6ee78d9e3c92c2019-04-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSphereDirect.00157-19https://doaj.org/toc/2379-5042ABSTRACT RNA viruses, particularly genetically diverse members of the Picornavirales, are widespread and abundant in the ocean. Gene surveys suggest that there are spatial and temporal patterns in the composition of RNA virus assemblages, but data on their diversity and genetic variability in different oceanographic settings are limited. Here, we show that specific RNA virus genomes have widespread geographic distributions and that the dominant genotypes are under purifying selection. Genomes from three previously unknown picorna-like viruses (BC-1, -2, and -3) assembled from a coastal site in British Columbia, Canada, as well as marine RNA viruses JP-A, JP-B, and Heterosigma akashiwo RNA virus exhibited different biogeographical patterns. Thus, biotic factors such as host specificity and viral life cycle, and not just abiotic processes such as dispersal, affect marine RNA virus distribution. Sequence differences relative to reference genomes imply that virus quasispecies are under purifying selection, with synonymous single-nucleotide variations dominating in genomes from geographically distinct regions resulting in conservation of amino acid sequences. Conversely, sequences from coastal South Africa that mapped to marine RNA virus JP-A exhibited more nonsynonymous mutations, probably representing amino acid changes that accumulated over a longer separation. This biogeographical analysis of marine RNA viruses demonstrates that purifying selection is occurring across oceanographic provinces. These data add to the spectrum of known marine RNA virus genomes, show the importance of dispersal and purifying selection for these viruses, and indicate that closely related RNA viruses are pathogens of eukaryotic microbes across oceans. IMPORTANCE Very little is known about aquatic RNA virus populations and genome evolution. This is the first study that analyzes marine environmental RNA viral assemblages in an evolutionary and broad geographical context. This study contributes the largest marine RNA virus metagenomic data set to date, substantially increasing the sequencing space for RNA viruses and also providing a baseline for comparisons of marine RNA virus diversity. The new viruses discovered in this study are representative of the most abundant family of marine RNA viruses, the Marnaviridae, and expand our view of the diversity of this important group. Overall, our data and analyses provide a foundation for interpreting marine RNA virus diversity and evolution.Marli VlokAndrew S. LangCurtis A. SuttleAmerican Society for MicrobiologyarticlePicornaviralesbiogeographymarine RNA viruspurifying selectionquasispeciesMicrobiologyQR1-502ENmSphere, Vol 4, Iss 2 (2019)
institution	DOAJ
collection	DOAJ
language	EN
topic	Picornavirales biogeography marine RNA virus purifying selection quasispecies Microbiology QR1-502
spellingShingle	Picornavirales biogeography marine RNA virus purifying selection quasispecies Microbiology QR1-502 Marli Vlok Andrew S. Lang Curtis A. Suttle Marine RNA Virus Quasispecies Are Distributed throughout the Oceans
description	ABSTRACT RNA viruses, particularly genetically diverse members of the Picornavirales, are widespread and abundant in the ocean. Gene surveys suggest that there are spatial and temporal patterns in the composition of RNA virus assemblages, but data on their diversity and genetic variability in different oceanographic settings are limited. Here, we show that specific RNA virus genomes have widespread geographic distributions and that the dominant genotypes are under purifying selection. Genomes from three previously unknown picorna-like viruses (BC-1, -2, and -3) assembled from a coastal site in British Columbia, Canada, as well as marine RNA viruses JP-A, JP-B, and Heterosigma akashiwo RNA virus exhibited different biogeographical patterns. Thus, biotic factors such as host specificity and viral life cycle, and not just abiotic processes such as dispersal, affect marine RNA virus distribution. Sequence differences relative to reference genomes imply that virus quasispecies are under purifying selection, with synonymous single-nucleotide variations dominating in genomes from geographically distinct regions resulting in conservation of amino acid sequences. Conversely, sequences from coastal South Africa that mapped to marine RNA virus JP-A exhibited more nonsynonymous mutations, probably representing amino acid changes that accumulated over a longer separation. This biogeographical analysis of marine RNA viruses demonstrates that purifying selection is occurring across oceanographic provinces. These data add to the spectrum of known marine RNA virus genomes, show the importance of dispersal and purifying selection for these viruses, and indicate that closely related RNA viruses are pathogens of eukaryotic microbes across oceans. IMPORTANCE Very little is known about aquatic RNA virus populations and genome evolution. This is the first study that analyzes marine environmental RNA viral assemblages in an evolutionary and broad geographical context. This study contributes the largest marine RNA virus metagenomic data set to date, substantially increasing the sequencing space for RNA viruses and also providing a baseline for comparisons of marine RNA virus diversity. The new viruses discovered in this study are representative of the most abundant family of marine RNA viruses, the Marnaviridae, and expand our view of the diversity of this important group. Overall, our data and analyses provide a foundation for interpreting marine RNA virus diversity and evolution.
format	article
author	Marli Vlok Andrew S. Lang Curtis A. Suttle
author_facet	Marli Vlok Andrew S. Lang Curtis A. Suttle
author_sort	Marli Vlok
title	Marine RNA Virus Quasispecies Are Distributed throughout the Oceans
title_short	Marine RNA Virus Quasispecies Are Distributed throughout the Oceans
title_full	Marine RNA Virus Quasispecies Are Distributed throughout the Oceans
title_fullStr	Marine RNA Virus Quasispecies Are Distributed throughout the Oceans
title_full_unstemmed	Marine RNA Virus Quasispecies Are Distributed throughout the Oceans
title_sort	marine rna virus quasispecies are distributed throughout the oceans
publisher	American Society for Microbiology
publishDate	2019
url	https://doaj.org/article/bae6b29bf2d749d68bc6ee78d9e3c92c
work_keys_str_mv	AT marlivlok marinernavirusquasispeciesaredistributedthroughouttheoceans AT andrewslang marinernavirusquasispeciesaredistributedthroughouttheoceans AT curtisasuttle marinernavirusquasispeciesaredistributedthroughouttheoceans
_version_	1718428029508648960

Marine RNA Virus Quasispecies Are Distributed throughout the Oceans

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