Department of Food and Nutrition, College of Biotechnology and Natural Resources, Chung-Ang University, Anseong, Republic of Korea.
Department of Life Science, College of Natural Sciences, Chung-Ang University, Seoul, Republic of Korea.
J Med Virol. 2024 Sep;96(9):e29902. doi: 10.1002/jmv.29902.
The whole-genome sequence (WGS) analysis of Aichivirus (AiV) identified in Korea was performed in this study. Using Sanger and Nanopore sequencing, the 8228-nucleotide-long genomic sequence of AiV (OQ121963) was determined and confirmed to belong to genotype A. The full-length genome of OQ121963 consisted of a 7296 nt open reading frame (ORF) that encodes a single polyprotein, and 5' UTR (676 nt) and 3' UTR (256 nt) at 5' and 3' ends, respectively. The ORF consisted of leader protein (L), structural protein P1 (VP0, VP1, and VP3), and nonstructural protein P2 (2A, 2B, and 2C) and P3 (3A, 3B, 3C, and 3D). The secondary structure analysis of the 5' UTR identified only stem-loop C (SL-C) and not SL-A and SL-B. The variable region of the AiV genome was analyzed by MegAlign Pro and reconfirmed by SimPlot analysis using 16 AiV whole genomes known to date. Among the entire regions, structural protein region P1 showed the lowest amino acid identity (96.07%) with reference sequence AB040749 (originated in Japan; genotype A), while the highest amino acid identity (98.26%) was confirmed in the 3D region among nonstructural protein region P2 and P3. Moreover, phylogenetic analysis of the WGS of OQ121963 showed the highest homology (96.96%) with JX564249 (originated in Taiwan; genotype A) and lowest homology (90.14%) with DQ028632 (originated in Brazil; genotype B). Therefore, the complete genome characterization of OQ121963 and phylogenetic analysis of the AiV conducted in this study provide useful information allowing to improve diagnostic tools and epidemiological studies of AiVs.
本研究对韩国分离的 Aichivirus（AiV）进行了全基因组序列（WGS）分析。通过 Sanger 和 Nanopore 测序，确定了 AiV（OQ121963）的 8228 个核苷酸长的基因组序列，并证实其属于基因型 A。OQ121963 的全长基因组由 7296 个核苷酸的开放阅读框（ORF）组成，该 ORF 编码单一的多聚蛋白，以及 5'UTR（676 个核苷酸）和 3'UTR（256 个核苷酸）分别位于 5'和 3'末端。ORF 由前导蛋白（L）、结构蛋白 P1（VP0、VP1 和 VP3）和非结构蛋白 P2（2A、2B 和 2C）和 P3（3A、3B、3C 和 3D）组成。5'UTR 的二级结构分析仅鉴定出茎环 C（SL-C），而未鉴定出 SL-A 和 SL-B。通过 MegAlign Pro 对 AiV 基因组的可变区进行分析，并使用迄今为止已知的 16 个 AiV 全基因组通过 SimPlot 分析进行重新确认。在整个区域中，结构蛋白区 P1 与参考序列 AB040749（起源于日本；基因型 A）的氨基酸同一性最低（96.07%），而在非结构蛋白区 P2 和 P3 中 3D 区域则确认了最高的氨基酸同一性（98.26%）。此外，OQ121963 的 WGS 系统发育分析显示与 JX564249（起源于中国台湾；基因型 A）的同源性最高（96.96%），与 DQ028632（起源于巴西；基因型 B）的同源性最低（90.14%）。因此，本研究对 OQ121963 进行了全基因组特征描述和 AiV 的系统发育分析，为改进 AiV 的诊断工具和流行病学研究提供了有用的信息。
