貉源阿留申病毒全基因组测序及末端序列分子特征分析

貉源阿留申病毒(Raccoon dog and arctic fox amdoparvovirus,RFAV)是自然感染貉和蓝狐的新种阿留申病毒(Amdoparvovirus),为测序RFAV全基因组序列,预测分析RFAV末端发夹结构序列分子特征。本研究采用分段克隆成功获得3株长4832nt、4827nt、4830nt的RFAV全基因组序列,分别命名为RFAV-Y9J、RFAV-RD15、RFAV-HS-R,利用在线软件预测RFAV末端序列二级结构,并与水貂阿留申病毒(AMDV)末端序列进行同源性比对。结果显示阿留申病毒种间、种内3’末端基因组序列保守性强,均存在116nt的Y型发夹结构;RFAV-Y9J与RFAV-RD15毒株5′末端分别存在310nt、305nt的U型发夹结构,RFAV和AMDV种内5′末端基因组序列保守性强,而种间5′末端基因组序列有较大变异。本研究首次完整测序了RFAV的3′和5′末端序列,为其他种阿留申病毒的末端序列扩增提供一种有效方法,为构建RFAV的全基因组序列感染性克隆奠定了基础。

Complete Genome Sequencing and Terminal Sequences Molecular Characteristics Analysis of Raccoon Dog and Arctic Fox Amdoparvovirus

Raccoon dog and arctic fox amdoparvovirus(RFAV)is a new species of Amdoparvovirus that naturally infects raccoon dog and arctic fox.This study aimed to sequence the complete genome of RFAV,predict and analyze the molecular characteristics of the RFAV terminal hairpin sequence.Here,the complete genome of two RFAV strains with a length of 4832nt and 4827nt were obtained,and named as RFAV-Y9J and RFAV-RD15,respectively.The mfold Web Server was used to predict the secondary structure of the RFAV terminal sequences.Besides,the homology comparison was conducted with the AMDV terminal sequences.The results showed that the 3′end genome sequence with a 116nt Y-shaped hairpin structure,which is highly conserved between and within strains of RFAV or AMDV;the 5′end genomic sequence of RFAV-Y9J and RFAV-RD15 have 310nt and 305nt U-shaped hairpin structures,respectively.The 5′end genomic sequence is highly conserved,within strains of RFAV or AMDV,while the inter-species 5′end genomic sequence has a greater variation.This study sequenced the 3′-and 5′-terminal sequences of RFAV for the first time and provides an effective method for the amplification of the 3′-and 5′-terminal sequences of other amdoparvoviruses,and also provides fundamental basis for the construction of infectious clones of the whole genome sequence of RFAV.