中国肠病毒 9 型的起源、进化分析及其遗传特征。

Origin and evolution analysis and genetic characteristics of echovirus 9 in China.

机构信息

WHO WPRO Regional Polio Reference Laboratory and NHC Key Laboratory for Biosafety, NHC Key Laboratory for Medical Virology, Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, Beijing, 102206, People's Republic of China.

Beijing Fengtai District Center for Disease Control and Prevention, Beijing, 10071, People's Republic of China.

出版信息

Virol J. 2022 Jun 3;19(1):98. doi: 10.1186/s12985-022-01820-3.

DOI:10.1186/s12985-022-01820-3

PMID:35659318

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC9166342/

Abstract

BACKGROUND

Echovirus 9 (E9) is associated with a wide variety of diseases and medical conditions, and the clinical symptoms of sporadic cases caused by E9 often are severe. With a high global prevalence, E9 has caused multiple outbreaks worldwide. However, little is known about the genetic and geographic population dynamics of E9.

METHOD

A total of 131 VP1 gene sequences, including15 generated in this study and 116 obtained from GenBank, were used to coestimate time-resolved phylogenies to infer viral evolution and transmission in worldwide. Overlapping fragments representing whole genomes were amplified by reverse transcription polymerase chain reaction (RT-PCR) using specific primers. Then, we reported the genetic characteristics of fifteen E9 strains in the Chinese Mainland. Similarity plots and bootscanning analysis were used to determine recombination patterns of E9.

RESULTS

The estimated mean evolutionary rate of global E9 VP1 gene was 4.278 × 10 substitutions per site per year (95% confidence interval [CI], 3.822 × 10/site/year to 4.710 × 10/site/year), and the common ancestor of E9 likely emerged around 1868 (95% CI, 1840 to 1892). The full-length genomic sequences of the fifteen E9 strains showed 76.9-79.6% nucleotide identity and 95.3-95.9% amino acid identity with E9 Barty strain. 11 of 15 E9 whole genome sequence present four recombination patterns, and E9 recombinants have extensive genetic exchanges in the 2C and P3 regions with other Enterovirus B (EV-B) circulated in China. Four of six E9 strains were temperature sensitive, and two were temperature resistant, and a comparative genomics analysis suggested that 411, 865 and 867 amino acid substitution in the P1 region was related to temperature sensitivity.

CONCLUSION

This study highlights a persistent transmission network of E9 in worldwide, provides valuable information regarding the molecular epidemiology of E9.

摘要

背景

肠病毒 9（E9）与多种疾病和医疗状况有关，由 E9 引起的散发性病例的临床症状通常较为严重。E9 在全球的流行率很高，已在全球范围内引发了多次暴发。然而，人们对 E9 的遗传和地理种群动态知之甚少。

方法

共使用了 131 个 VP1 基因序列，包括本研究中生成的 15 个序列和从 GenBank 获得的 116 个序列，以共同估计时间分辨系统发育树，以推断全球范围内病毒的进化和传播。使用特异性引物通过逆转录聚合酶链反应（RT-PCR）扩增代表全基因组的重叠片段。然后，我们报告了中国大陆 15 株 E9 株的遗传特征。相似性图和引导扫描分析用于确定 E9 的重组模式。

结果

全球 E9 VP1 基因的估计平均进化率为 4.278×10 个取代/位点/年（95%置信区间[CI]，3.822×10/位点/年至 4.710×10/位点/年），E9 的共同祖先可能出现在 1868 年左右（95%CI，1840 年至 1892 年）。15 株 E9 的全长基因组序列与 E9 Barty 株的核苷酸同一性为 76.9-79.6%，氨基酸同一性为 95.3-95.9%。15 个 E9 全基因组序列中的 11 个呈现出 4 种重组模式，E9 重组体与在中国流行的其他肠道病毒 B（EV-B）在 2C 和 P3 区有广泛的遗传交换。6 株 E9 中有 4 株为温度敏感株，2 株为温度抗性株，比较基因组学分析表明，P1 区的 411、865 和 867 位氨基酸取代与温度敏感性有关。