Whole-genome analysis of rotavirus G4P[6] strains isolated from Korean neonates: association of Korean neonates and rotavirus P[6] genotypes
Whole-genome analysis of rotavirus G4P[6] strains isolated from Korean neonates: association of Korean neonates and rotavirus P[6] genotypes
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DOI：
10.1186/s13099-019-0318-5
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发表时间：
2019-07-10
期刊：
影响因子：
4.2
通讯作者：
Kim, Hyun Soo
中科院分区：
文献类型：
--
作者：
Lee, Su-Kyung;Choi, Seoheui;Kim, Hyun Soo
研究背景A组轮状病毒是全球小儿胃肠炎的主要病原。几项研究报告了G4 P [6]轮状病毒基因型在韩国新生儿中的优势，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确定从韩国新生儿分离的G4 P [6]轮状病毒株的完整基因组的基因型星座，将这些序列与其他国家的其他G4 P [6]株进行比较，并确定韩国新生儿中G4 P [6]基因型占优势的原因。从2013年1月至2016年1月分离，选择用于全基因组测序。使用特异性引物组扩增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，以调查本研究中的轮状病毒基因与先前发表的全基因组序列的其他轮状病毒G4 P [6]株基因之间的遗传距离。本研究中的所有20株轮状病毒具有相同的基因型：G4-P[6]-I1-R1-C1-M1-A1-N1-T1-E1-H1，代表Wa样基因型星座。对20株G4 P [6]轮状病毒株进行BLAST检索，结果显示本研究中所有G4序列与2008年韩国分离的G4 P [6]轮状病毒株G4序列（GenBank登录号：FJ 603447）的核苷酸同源性最高。此外，本研究中的P[6]基因序列与2002年在韩国检测到的G4 P [6]菌株的P[6]序列（AY 158093）具有最高的核苷酸同一性。系统发育和核苷酸序列分析表明，本研究中的G4 P [6]株和先前报道的韩国G4 P [6]株主要在新生儿中检测到，并且与其他国家检测到的G4 P [6]株相比具有相似的G4和P[6]序列。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。
BackgroundGroup 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.ResultsTwenty 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.ConclusionsThis 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.