Characterisation of a rare, reassortant human G10P[14] rotavirus strain detected in Honduras

BACKGROUND Although first detected in animals, the rare rotavirus strain G10P[14] has been sporadically detected in humans in Slovenia, Thailand, United Kingdom and Australia among other countries. Earlier studies suggest that the strains found in humans resulted from interspecies transmission and reassortment between human and bovine rotavirus strains. OBJECTIVES In this study, a G10P[14] rotavirus genotype detected in a human stool sample in Honduras during the 2010-2011 rotavirus season, from an unvaccinated 30-month old boy who reported at the hospital with severe diarrhea and vomiting, was characterised to determine the possible evolutionary origin of the rare strain. METHODS For the sample detected as G10P[14], 10% suspension was prepared and used for RNA extraction and sequence independent amplification. The amplicons were sequenced by next-generation sequencing using the Illumina MiSeq 150 paired end method. The sequence reads were analysed using CLC Genomics Workbench 6.0 and phylogenetic trees were constructed using PhyML version 3.0. FINDINGS The next generation sequencing and phylogenetic analyses of the 11-segmented genome of the G10P[14] strain allowed classification as G10-P[14]-I2-R2-C2-M2-A3-N2-T6-E2-H3. Six of the genes (VP1, VP2, VP3, VP6, NSP2 and NSP4) were DS-1-like. NSP1 and NSP5 were AU-1-like and NSP3 was T6, which suggests that multiple reassortment events occurred in the evolution of the strain. The phylogenetic analyses and genetic distance calculations showed that the VP7, VP4, VP6, VP1, VP3, NSP1, NSP3 and NSP4 genes clustered predominantly with bovine strains. NSP2 and VP2 genes were most closely related to simian and human strains, respectively, and NSP5 was most closely related to a rhesus strain. MAIN CONCLUSIONS The genetic characterisation of the G10P[14] strain from Honduras suggests that its genome resulted from multiple reassortment events which were possibly mediated through interspecies transmissions.

背景 尽管罕见的G10P[14]型轮状病毒（rotavirus）株最初在动物体内被检出，但目前已在斯洛文尼亚、泰国、英国、澳大利亚等多个国家的人类病例中零星发现。既往研究表明，在人类体内检出的该类毒株，源自人类与牛轮状病毒毒株之间的跨物种传播与基因重配事件。

目的 本研究对2010-2011年轮状病毒流行季，在洪都拉斯一名未接种疫苗的30月龄男性患儿粪便样本中检出的G10P[14]型轮状病毒基因型毒株进行特征分析——该患儿因严重腹泻与呕吐前往医院就诊，旨在明确这一罕见毒株的潜在进化起源。

方法 针对检测为G10P[14]的样本，制备10%悬液用于RNA提取及序列非依赖性扩增。采用Illumina MiSeq 150 bp双端测序法进行下一代测序，对扩增产物进行测序。使用CLC Genomics Workbench 6.0分析序列读段，并通过PhyML 3.0版本构建系统发育树。

结果 对该G10P[14]毒株的11节段基因组进行下一代测序与系统发育分析后，将其归类为G10-P[14]-I2-R2-C2-M2-A3-N2-T6-E2-H3。其中6个基因（VP1、VP2、VP3、VP6、NSP2及NSP4）属于DS-1样毒株；NSP1与NSP5为AU-1样毒株，NSP3为T6型，提示该毒株进化过程中发生了多次基因重配事件。系统发育分析与遗传距离计算结果显示，VP7、VP4、VP6、VP1、VP3、NSP1、NSP3及NSP4基因主要与牛源性毒株聚类；NSP2基因与猿类毒株亲缘关系最近，VP2基因则与人类毒株最为相近，而NSP5基因与恒河猴毒株亲缘关系最近。

主要结论 对洪都拉斯分离的G10P[14]毒株进行的基因特征分析表明，其基因组源自多次基因重配事件，且该过程可能通过跨物种传播介导。