Fifteen Marseilleviruses Newly Isolated From Three Water Samples in Japan Reveal Local Diversity of Marseilleviridae

Keita Aoki,Motohiro Akashi,Kenta Sasaki,Masaharu Takemura,Hiroyuki Ogata,Kazuyoshi Murata,Reika Hagiwara

doi:10.3389/fmicb.2019.01152

Abstract

The family Marseilleviridae, defined as a group of icosahedral double-stranded DNA viruses with particle size of approximately 250 nm and genome size of 350–380 kbp, belongs to the nucleo-cytoplasmic family of large DNA viruses. The family Marseilleviridae is currently classified into lineages A–E. In this study, we isolated 12 or 15 new members of the family Marseilleviridae from three sampling locations in Japan. Molecular phylogenetic analysis of the MCP genes showed that the new viruses could be further classified into three groups, hokutoviruses, kashiwazakiviruses, and kyotoviruses. Hokutoviruses were closely related to lineage B, kyotoviruses were related to lineage A, and kashiwazakiviruses were also classified into lineage B but a new putative subgroup of lineage B, revealing the diversity of this lineage. Interestingly, more than two viruses with slightly different MCP genes were isolated from a single water sample from a single location, i.e., two hokutoviruses and one kashiwazakivirus were isolated from a small reservoir, five kashiwazakiviruses from the mouth of a river, and five kyotoviruses from fresh water of a river, suggesting that several milliliters of water samples contain several types of giant viruses. Amoeba cells infected with hokutoviruses or kashiwazakiviruses exhibited a “bunch” formation consisting of normal and infected cells similarly to a tupanvirus, whereas cells infected with kyotoviruses or tokyovirus did not. These results suggest the previously unrecognized local diversity of the family Marseilleviridae in aquatic environments.

Highlights

During the past two decades, nucleo-cytoplasmic large DNA viruses (NCLDVs) have been found to form diverse groups and families of viruses
The family Marselleviridae is currently classified into several lineages (Chatterjee and Kondabagil, 2017; Fabre et al, 2017): Marseillevirus marseillevirus (Boyer et al, 2009), melbournvirus (Doutre et al, 2014), Cannes 8 virus (Aherfi et al, 2013), senegalvirus (Lagier et al, 2012), tokyovirus (Takemura, 2016), and Marseillevirus shanghai are classified in lineage A; lausannevirus (Thomas et al, 2011), Port-miou virus (Doutre et al, 2015), noumeavirus (Fabre et al, 2017), and kurlavirus (Chatterjee and Kondabagil, 2017) are classified in lineage B; tunisvirus (Aherfi et al, 2014) and insectomime virus (Boughalmi et al, 2013) are classified in lineage C; Brazilian marseillevirus (Dornas et al, 2016) are classified in lineage D; and golden marseillevirus (Dos Santos et al, 2016) are classified in lineage E
Full-length major capsid protein (MCP) genes including part of the intergenic regions flanking MCP were amplified by PCR using extracted genomic DNA as a template, F1 as a forward primer, and R5 as a reverse primer

Summary

Introduction

During the past two decades, nucleo-cytoplasmic large DNA viruses (NCLDVs) have been found to form diverse groups and families of viruses. Several groups of giant viruses, such as the family Mimiviridae, family Marseilleviridae, pandoraviruses, pithoviruses, mollivirus, and. Local Diversity of Marseilleviridae medusavirus, have been isolated from various environments worldwide (La Scola et al, 2003; Boyer et al, 2009; Legendre et al, 2013, 2014, 2015; Philippe et al, 2013; Yoshikawa et al, 2019). Many members of the family Marseilleviridae have been discovered in a variety of aquatic environments, and in the human intestines and insect bodies (Lagier et al, 2012; Boughalmi et al, 2013). The family Marselleviridae is currently classified into several lineages (Chatterjee and Kondabagil, 2017; Fabre et al, 2017): Marseillevirus marseillevirus (Boyer et al, 2009), melbournvirus (Doutre et al, 2014), Cannes 8 virus (Aherfi et al, 2013), senegalvirus (Lagier et al, 2012), tokyovirus (Takemura, 2016), and Marseillevirus shanghai are classified in lineage A; lausannevirus (Thomas et al, 2011), Port-miou virus (Doutre et al, 2015), noumeavirus (Fabre et al, 2017), and kurlavirus (Chatterjee and Kondabagil, 2017) are classified in lineage B; tunisvirus (Aherfi et al, 2014) and insectomime virus (Boughalmi et al, 2013) are classified in lineage C; Brazilian marseillevirus (Dornas et al, 2016) are classified in lineage D; and golden marseillevirus (Dos Santos et al, 2016) are classified in lineage E

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Conclusion