Lee Su-Kyung, Choi Seoheui, Kim Jae-Seok, Lee Eun Jin, Hyun Jungwon, Kim Hyun Soo
1Department of Laboratory Medicine, Hallym University Dongtan Sacred Heart Hospital, College of Medicine, Hallym University, 7, Keunjaebong-gil, Hwaseong-si, Gyeonggi-Do, 18450 South Korea.
2Department of Pediatrics, Hallym University Dongtan Sacred Heart Hospital, College of Medicine, Hallym University, 7, Keunjaebong-gil, Hwaseong-si, Gyeonggi-Do, 18450 South Korea.
Gut Pathog. 2019 Jul 10;11:37. doi: 10.1186/s13099-019-0318-5. eCollection 2019.
Group A rotaviruses are the major causative agents of pediatric gastroenteritis worldwide. Several studies have reported the predominance of G4P[6] rotavirus genotypes in Korean neonates, which is uncommon in other countries. Therefore, the purposes of this study were to determine the genotype constellations of complete genomes of G4P[6] rotavirus strains isolated from Korean neonates using next-generation sequencing, to compare these sequences with other G4P[6] strains in other countries, and to determine the reason for the predominance of G4P[6] genotypes in Korean neonates.
Twenty rotavirus G4P[6] strains, isolated from January 2013 to January 2016, were selected for whole-genome sequencing. Eleven rotavirus genes were amplified using specific primer sets, and sequencing was carried out using an Ion S5 XL next-generation sequencing platform. Genotypes of each gene were determined, and phylogenetic analyses were performed to investigate genetic distances between genes of rotaviruses in this study and those of other rotavirus G4P[6] strains whose whole-genome sequences were previously published. All 20 rotavirus strains in this study had the same genotype: G4-P[6]-I1-R1-C1-M1-A1-N1-T1-E1-H1, representing the Wa-like genotype constellation. BLAST searches of 20 G4P[6] rotavirus strains revealed that all G4 sequences in this study showed the highest nucleotide identity to G4 sequences of G4P[6] rotavirus strains isolated in Korea in 2008 (GenBank accession number: FJ603447). Additionally, P[6] gene sequences in this study showed the highest nucleotide identity to P[6] sequences of G4P[6] strains detected in Korea in 2002 (AY158093). Phylogenetic and nucleotide sequence analyses showed that G4P[6] strains in this study and previously reported G4P[6] strains in Korea were mostly detected in neonates and had similar G4 and P[6] sequences compared with other G4P[6] strains detected in other countries.
This study showed that the whole-genome constellation of rotavirus G4P[6] strains from Korean neonates resembled a Wa-like genotype constellation. Additionally, rotavirus genotypes detected in Korean neonates had unique P[6] sequences, which may be the cause of Korean neonatal rotavirus infection.
A组轮状病毒是全球小儿胃肠炎的主要病原体。多项研究报告称，G4P[6]轮状病毒基因型在韩国新生儿中占主导地位，这在其他国家并不常见。因此，本研究的目的是使用下一代测序技术确定从韩国新生儿中分离出的G4P[6]轮状病毒株完整基因组的基因型组合，将这些序列与其他国家的其他G4P[6]株进行比较，并确定G4P[6]基因型在韩国新生儿中占主导地位的原因。
选择2013年1月至2016年1月分离的20株轮状病毒G4P[6]株进行全基因组测序。使用特异性引物对扩增11个轮状病毒基因，并使用Ion S5 XL下一代测序平台进行测序。确定每个基因的基因型，并进行系统发育分析，以研究本研究中轮状病毒基因与先前已发表全基因组序列的其他轮状病毒G4P[6]株基因之间的遗传距离。本研究中的所有20株轮状病毒株具有相同的基因型：G4-P[6]-I1-R1-C1-M1-A1-N1-T1-E1-H1，代表Wa样基因型组合。对20株G4P[6]轮状病毒株进行BLAST搜索发现，本研究中的所有G4序列与2008年在韩国分离的G4P[6]轮状病毒株的G4序列具有最高的核苷酸同一性（GenBank登录号：FJ603447）。此外，本研究中的P[6]基因序列与2002年在韩国检测到的G4P[6]株的P[6]序列具有最高的核苷酸同一性（AY158093）。系统发育和核苷酸序列分析表明，本研究中的G4P[6]株和韩国先前报道的G4P[6]株大多在新生儿中检测到，与在其他国家检测到的其他G4P[6]株相比，具有相似的G4和P[6]序列。
本研究表明，来自韩国新生儿的轮状病毒G4P[6]株的全基因组组合类似于Wa样基因型组合。此外，在韩国新生儿中检测到的轮状病毒基因型具有独特的P[6]序列，这可能是韩国新生儿轮状病毒感染的原因。
