柯萨奇病毒B组(Coxsackievirus B，CVB)感染细胞时其基因组RNA存在不稳定现象，但产生机制尚不清楚。本研究将柯萨奇病毒B组3型(CVB3)感染细胞后，利用5′ cDNA末端快速扩增技术(5′ rapid amplification of cDNA ends，5′ RACE)扩增并克隆细胞内CVB3基因组片段，并对每条序列及其5′端的二级结构进行分析。结果获得的20条CVB3基因组片段，长度为 2 067～5 547 bp，片段断端主要分布于2Apro和2C编码区。RNAfold分析显示，这些片段多数在5′断点端形成二级茎-环结构。本研究显示，CVB在宿主细胞感染时可形成大量不完整基因组RNA片段，这些片段可在5′断点端形成局部双链结构，提示片段不是随机产生，可能是RNA酶剪切产物。此发现有助于理解CVB基因组不稳定的机制。

The genomic RNA instability of Coxsackievirus B (CVB) occurs in the infected cells. The sequence characteristics and generating mechanism of these viral RNA fragments remain unknown. In this study, the genomic segments of CVB group B type 3 (CVB3) in infected cells were amplified, cloned with 5′ rapid amplification of cDNA ends (5′ RACE) assay and sequenced. The secondary structures of their 5′ ends were analyzed. The results showed that twenty fragments derived from CVB3 genome were obtained with lengths ranging from 2 067 to 5 547 bp. The 5′ ends of these fragments mainly located in the 2Apro- and 2C-coding regions. RNA folding analysis showed that the majority of these fragments could form secondary stem-loop structure in their 5′ ends. This study indicates that incomplete RNA fragments derived from CVB genome were abundant in the infected cells. These fragments could form a partial dsRNA in their 5′ ends. Our data suggests that these fragments are not generated randomly but more likely by the cleavage of RNA endonuclease. This observation is helpful to understand the mechanism for the genome instability of CVB.