Mesoniviridae: a proposed new family in the order Nidovirales formed by a single species of mosquito-borne viruses

Abstract

Recently, two independent surveillance studies in Côte d'Ivoire and Vietnam, respectively, led to the discovery of two mosquito-borne viruses, Cavally virus and Nam Dinh virus, with genome and proteome properties typical for viruses of the order Nidovirales. Using a state-of-the-art approach, we show that the two insect nidoviruses are (i) sufficiently different from other nidoviruses to represent a new virus family, and (ii) related to each other closely enough to be placed in the same virus species. We propose to name this new family Mesoniviridae. Meso is derived from the Greek word "mesos" (in English "in the middle") and refers to the distinctive genome size of these insect nidoviruses, which is intermediate between that of the families Arteriviridae and Coronaviridae, while ni is an abbreviation for "nido". A taxonomic proposal to establish the new family Mesoniviridae, genus Alphamesonivirus, and species Alphamesonivirus 1 has been approved for consideration by the Executive Committee of the ICTV.

Fig. 1

Genome organization of mesoniviruses. The coding and 5′- and 3′-untranslated regions of the genome are represented, respectively, by the outer rectangle and horizontal lines. ORFs are shown as open rectangles and are arranged in three reading frames (−1, 0, +1) relative to that of ORF1a. ORF1a- and ORF1b-encoded protein domains identified by bioinformatics analysis (see ref. [6]) are highlighted in grey. The predicted location of −1 ribosomal frameshift signals are indicated by a black dot. The genome organization is shown for NDiV but is virtually identical to that of CAVV except for the reading frame of some ORFs (see Table 1)

Fig. 2

Phylogenetic position of CAVV and NDiV. To infer phylogenetic relationships of Nam Dinh virus isolate 02VN178 (NDiV), Cavally virus isolate C79 (CAVV) (arrow) and other nidoviruses, a partially constrained tree was calculated using a concatenated alignment of the three nidovirus-wide conserved domains and a set of viruses representing currently recognized species. The alignment was produced with Muscle version 3.52 [17] in the Viralis platform [18], and the phylogenetic analysis was performed using BEAST version 1.4.7 [19]. For further details, see ref. [6]. Numbers indicate posterior probability support values (on a scale from 0 to 1); all internal nodes for which no support value is provided have been fixed in the analysis based on prior analyses of nidovirus subsets (data not shown). The scale bars represent the average number of substitutions per amino acid position. The tree was rooted on the arterivirus branch. Virus names and GenBank/Refseq accession numbers: lactate dehydrogenase-elevating virus (LDV; U15146), porcine respiratory and reproductive syndrome virus European type (PRRSV-LV; M96262), porcine respiratory and reproductive syndrome virus North American type (PRRSV-NA; AF176348), simian hemorrhagic fever virus (SHFV; NC_003092), equine arteritis virus (EAV; AY349167), Nam Dinh virus (NDiV; DQ458789), Cavally virus (CAVV; HM746600), gill-associated virus (GAV; AF227196), yellow head virus (YHV; EU487200), human coronavirus HKU1 (HCoV-HKU1; AY884001), human coronavirus OC43 (HCoV-OC43; AY585228), mouse hepatitis virus (MHV; AY700211), Pipistrellus bat coronavirus HKU5 (Pi-BatCoV-HKU5; EF065509), Tylonycteris bat coronavirus HKU4 (Ty-BatCoV-HKU4; EF065505), Rousettus bat coronavirus HKU9 (Ro-BatCoV-HKU9; EF065513), SARS coronavirus (SARS-HCoV; AY345988), feline coronavirus (FCoV; NC_007025), Miniopterus bat coronavirus 1A (Mi-BatCoV-1A; NC_010437), Miniopterus bat coronavirus HKU8 (Mi-BatCoV-HKU8; NC_010438), porcine epidemic diarrhoea virus (PEDV; NC_003436), Scotophilus bat coronavirus 512 (Sc-BatCoV-512; DQ648858), human coronavirus NL63 (HCoV-NL63; DQ445911), human coronavirus 229E (HCoV-229E; NC_002645), Rhinolophus bat coronavirus HKU2 (Rh-BatCoV-HKU2; NC_009988), beluga whale coronavirus SW1 (BWCoV; EU111742), avian infectious bronchitis virus (IBV; NC_001451), equine torovirus (EToV; X52374), bovine torovirus (BToV; NC_007447), white bream virus (WBV; NC_008516)

Fig. 3

Evolutionary distance between CAVV and NDiV in relation to intra-species genetic divergence in large-sized nidoviruses. Multiple amino acid alignments for 154 nidoviruses with large genomes (all major nidovirus lineages except arteriviruses) comprising three nidovirus-wide conserved protein domains (a, c) or five domains conserved in all large-sized nidoviruses (b, d) were used to compile pairwise evolutionary distances (PEDs) between all virus pairs. These distances are shown as frequency distributions (a, b), and zoom-ins on small distances are provided (c, d). The PED between CAVV and NDiV (indicated by the arrow) is well within the intra-species distance range of other nidoviruses. Several currently recognized nidovirus species show a maximum genetic divergence larger than that of the CAVV-NDiV pair (see text)