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Complete genome of a novel recombinant human astrovirus and its quasispecies in patients following hematopoietic stem cell transplantation.
Virus Research ( IF 5 ) Pub Date : 2020-08-19 , DOI: 10.1016/j.virusres.2020.198138
Jie-Mei Yu 1 , Zhen-Hua Wang 2 , Na Liu 3 , Qing Zhang 3 , Yu-Jun Dong 4 , Zhao-Jun Duan 3
Affiliation  

Human astroviruses (HAstVs) were first identified in 1975 and can be classified into three clades: classic HAstVs (HAstV 1–8), MLB (MLB1−3) and VA (VA1−5), with MLB and VA were newly identified. Recombination and a high mutation rate make HAstV as one of the rapidly evolving infectious agents. This study reported a novel identified recombinant human astrovirus (Y/1−CHN) and its long existence in two immunocompromised patients with diarrhea following allogeneic hematopoietic stem cell transplantation (allo-HSCT). The identified Yu/1−CHN genome contains 6801 base pairs encoding three open reading frames, with ORF1a best hit to the HAstV1 (Pune strain, 97 % nucleotide identity), while ORF1b and ORF2 best hit to HAstV-5 (DL30 strain, 99 % nucleotide identity). Possible recombination breakpoint was predicted to be located in the boundary of ORF1a and ORF1b. Different quasispecies were found in the host, and the dN/dS ratios of the S and P domains were determined to be 1.189 and 1.444, respectively, suggesting a positive selection existed. Fecal samples collected in different clinical phases from the two patients were all positive for Yu/1−CHN, suggesting a long existence of the virus in the host. It was indicated that immunocompromised patients may a reservoir for astrovirus, their excreta should be monitored even after discharge from hospital.



中文翻译:

造血干细胞移植后新型重组人星状病毒及其准种的完整基因组。

人类星状病毒 (HAstVs) 于 1975 年首次被发现,可分为三个进化枝:经典 HAstVs (HAstV 1-8)、MLB (MLB1-3) 和 VA (VA1-5),其中 MLB 和 VA 是新发现的。重组和高突变率使 HAstV 成为快速发展的传染源之一。该研究报告了一种新型鉴定的重组人星状病毒 (Y/1-CHN) 及其在两名同种异体造血干细胞移植 (allo-HSCT) 后出现腹泻的免疫功能低下患者中的长期存在。鉴定的 Yu/1-CHN 基因组包含 6801 个碱基对,编码三个开放阅读框,ORF1a 对 HAstV1(浦那菌株,97% 核苷酸同一性)的命中率最高,而 ORF1b 和 ORF2 对 HAstV-5(DL30 菌株,99 % 核苷酸同一性)。预测可能的重组断点位于 ORF1a 和 ORF1b 的边界。在宿主中发现了不同的准种,S 域和 P 域的 dN/dS 比分别确定为 1.189 和 1.444,表明存在正选择。从两名患者的不同临床阶段收集的粪便样本均呈 Yu/1-CHN 阳性,表明该病毒在宿主中长期存在。有人指出,免疫功能低下的患者可能是星状病毒的宿主,即使出院后也应监测其排泄物。从两名患者的不同临床阶段收集的粪便样本均呈 Yu/1-CHN 阳性,表明该病毒在宿主中长期存在。有人指出,免疫功能低下的患者可能是星状病毒的宿主,即使出院后也应监测其排泄物。从两名患者的不同临床阶段收集的粪便样本均呈 Yu/1-CHN 阳性,表明该病毒在宿主中长期存在。有人指出,免疫功能低下的患者可能是星状病毒的宿主,即使出院后也应监测其排泄物。

更新日期:2020-08-27
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