Epidemiology and genetic characteristics of murine kobuvirus from faecal samples of Rattus losea, Rattus tanezumi and Rattus norvegicus in southern China

Figures

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  Fig. 1.. Phylogenetic analysis of the MuKVs based on the nucleotide sequences of partial 3D regions. The tree was generated by the maximum-likelihood method based on the Kimura 2-parameter model (gamma distributed and partial deletion) with 1000 bootstrap replicates. Statistics values >70% are displayed above the tree branches. Lateral blank triangles indicate the MuKVs identified in this study, and YY101 (MW292457) is the other MuKV identified in this study. The sequences YY12 (MW292465), YY91 (MW292464), YY93 (MW292463), YY95 (MW292461), YY96 (MW292460), YY98 (MW292459), YY100 (MW292458), YY101, YY103 (MW292456), YY104 (MW292455), YY106 (MW292453), YY108 (MW292451), YN21 (MW292469), YN25 (MW292468), YN45 (MW292467) and YN52 (MW292466) were isolated from Rattus norvegicus. The sequences YY94 (MW292462), YY105 (MW292454), YY107 (MW292452) and XM105 (MW292470) were isolated from Rattus tanezumi. The sequences XM97 (MW292472) and XM102 (MW292471) were isolated from Rattus losea. BKV, bovine kobuvirus; BatKV, bat kobuvirus; CaKV, canine kobuvirus; CapKV, caprine kobuvirus; FKV, ferret kobuvirus; FeKV, feline kobuvirus; PKV, porcine kobuvirus; RKV, rabbit kobuvirus. (For a better view of the…

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  Fig. 2.. Phylogenetic tree of the MuKVs based on the complete nucleotide sequences of VP1. The tree was generated by the maximum-likelihood method based on the general time Reversible (GTR) model (gamma distributed and partial deletion) with 1000 bootstrap replicates. Black diamonds indicate the MuKV sequences identified in this study.

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  Fig. 3.. Genome organization and genetic characterization of the MuKV sequences identified in this study. (a) Genome organization of MuKV/XM34/CHN, with initial nucleotide positions labelled for each functional region. The partial 5’UTR is located at positions 1–372 and the partial 3′UTR is located at positions 7666–7714. P1 represents the structural proteins, and P2 and P3 represent the nonstructural proteins. (b) Similarity plot analysis of the complete polyprotein sequences of MuKV/XM34/CHN (red line), MuKV/XM86/CHN (blue line) and MuKV/YN27/CHN (green line), with feline kobuvirus sequence WHJ-1/MF598159.1 (orange line) as the out-group sequence and MuKV sequence GZ85/MN648601.1 as the query sequence, using the Kimura 2-parameter model in Simplot v3.5.1.

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  Fig. 4.. Phylogenetic relationships between kobuviruses and other picornaviruses based on complete polyprotein nucleotide sequences. The tree was generated by the maximum-likelihood method based on the GTR model (gamma distributed with Invariant sites [G+I]) and partial deletion) with 1000 bootstrap replicates. Representative members of the family Picornaviridae are marked with letters and some are marked with blue circles. Black diamonds indicate the MuKV sequences identified in this study.