title: Discovery of the first insect nidovirus, a missing evolutionary link in the emergence of the largest RNA virus genomes.
abstract: Nidoviruses with large genomes (26.3-31.7 kb; 'large nidoviruses'), including Coronaviridae and Roniviridae, are the most complex positive-sense single-stranded RNA (ssRNA+) viruses. Based on genome size, they are far separated from all other ssRNA+ viruses (below 19.6 kb), including the distantly related Arteriviridae (12.7-15.7 kb; 'small nidoviruses'). Exceptionally for ssRNA+ viruses, large nidoviruses encode a 3'-5'exoribonuclease (ExoN) that was implicated in controlling RNA replication fidelity. Its acquisition may have given rise to the ancestor of large nidoviruses, a hypothesis for which we here provide evolutionary support using comparative genomics involving the newly discovered first insect-borne nidovirus. This Nam Dinh virus (NDiV), named after a Vietnamese province, was isolated from mosquitoes and is yet to be linked to any pathology. The genome of this enveloped 60-80 nm virus is 20,192 nt and has a nidovirus-like polycistronic organization including two large, partially overlapping open reading frames (ORF) 1a and 1b followed by several smaller 3'-proximal ORFs. Peptide sequencing assigned three virion proteins to ORFs 2a, 2b, and 3, which are expressed from two 3'-coterminal subgenomic RNAs. The NDiV ORF1a/ORF1b frameshifting signal and various replicative proteins were tentatively mapped to canonical positions in the nidovirus genome. They include six nidovirus-wide conserved replicase domains, as well as the ExoN and 2'-O-methyltransferase that are specific to large nidoviruses. NDiV ORF1b also encodes a putative N7-methyltransferase, identified in a subset of large nidoviruses, but not the uridylate-specific endonuclease that - in deviation from the current paradigm - is present exclusively in the currently known vertebrate nidoviruses. Rooted phylogenetic inference by Bayesian and Maximum Likelihood methods indicates that NDiV clusters with roniviruses and that its branch diverged from large nidoviruses early after they split from small nidoviruses. Together these characteristics identify NDiV as the prototype of a new nidovirus family and a missing link in the transition from small to large nidoviruses.
authors.affiliation: Department of Virology, National Institute of Hygiene and Epidemiology, Hanoi, Vietnam.
authors.forename: Phan Thi
authors.initials: PT
authors.lastname: Nga
authors.forename: Maria del Carmen
authors.initials: Mdel C
authors.lastname: Parquet
authors.forename: Chris
authors.initials: C
authors.lastname: Lauber
authors.forename: Manmohan
authors.initials: M
authors.lastname: Parida
authors.forename: Takeshi
authors.initials: T
authors.lastname: Nabeshima
authors.forename: Fuxun
authors.initials: F
authors.lastname: Yu
authors.forename: Nguyen Thanh
authors.initials: NT
authors.lastname: Thuy
authors.forename: Shingo
authors.initials: S
authors.lastname: Inoue
authors.forename: Takashi
authors.initials: T
authors.lastname: Ito
authors.forename: Kenta
authors.initials: K
authors.lastname: Okamoto
authors.forename: Akitoyo
authors.initials: A
authors.lastname: Ichinose
authors.forename: Eric J
authors.initials: EJ
authors.lastname: Snijder
authors.forename: Kouichi
authors.initials: K
authors.lastname: Morita
authors.forename: Alexander E
authors.initials: AE
authors.lastname: Gorbalenya
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001483:Base Sequence; D005075:Biological Evolution; D002460:Cell Line; D003001:Cloning, Molecular; D019295:Computational Biology; D003465:Culex / Q000821:virology*; D005091:Exons; D005095:Exoribonucleases / Q000235:genetics; D015967:Gene Expression Regulation, Viral; D005814:Genes, Viral; D059646:Genome Size; D008969:Molecular Sequence Data; D028381:Nidovirales / Q000145:classification* / Q000235:genetics* / Q000502:physiology; D009690:Nucleic Acid Conformation; D016366:Open Reading Frames / Q000235:genetics; D010802:Phylogeny; D012367:RNA, Viral / Q000235:genetics*; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D014744:Vietnam; D014779:Virus Replication
chemical_list: D012367:RNA, Viral; D005095:Exoribonucleases