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The establishment of reference sequence for SARS-CoV-2 and variation analysis.

SARS-CoV-2 参考序列的建立及变异分析.

  • 影响因子:1.94
  • DOI:10.1002/jmv.25762
  • 作者列表:"Wang C","Liu Z","Chen Z","Huang X","Xu M","He T","Zhang Z
  • 发表时间:2020-06-01
Abstract

:Starting around December 2019, an epidemic of pneumonia, which was named COVID-19 by the World Health Organization, broke out in Wuhan, China, and is spreading throughout the world. A new coronavirus, named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by the Coronavirus Study Group of the International Committee on Taxonomy of Viruses was soon found to be the cause. At present, the sensitivity of clinical nucleic acid detection is limited, and it is still unclear whether it is related to genetic variation. In this study, we retrieved 95 full-length genomic sequences of SARAS-CoV-2 strains from the National Center for Biotechnology Information and GISAID databases, established the reference sequence by conducting multiple sequence alignment and phylogenetic analyses, and analyzed sequence variations along the SARS-CoV-2 genome. The homology among all viral strains was generally high, among them, 99.99% (99.91%-100%) at the nucleotide level and 99.99% (99.79%-100%) at the amino acid level. Although overall variation in open-reading frame (ORF) regions is low, 13 variation sites in 1a, 1b, S, 3a, M, 8, and N regions were identified, among which positions nt28144 in ORF 8 and nt8782 in ORF 1a showed mutation rate of 30.53% (29/95) and 29.47% (28/95), respectively. These findings suggested that there may be selective mutations in SARS-COV-2, and it is necessary to avoid certain regions when designing primers and probes. Establishment of the reference sequence for SARS-CoV-2 could benefit not only biological study of this virus but also diagnosis, clinical monitoring and intervention of SARS-CoV-2 infection in the future.

摘要

: 从 2019 年 12 月左右开始,中国武汉爆发了被世界卫生组织命名为新型冠状病毒肺炎的肺炎疫情,并正在全球蔓延。一种新的冠状病毒,由国际病毒分类委员会的冠状病毒研究组命名新型冠状病毒冠状病毒 2 (SARS-CoV-2),很快就被发现是原因。目前,临床核酸检测的灵敏度有限,是否与遗传变异有关还不清楚。在本研究中,我们从国家生物技术信息中心和GISAID数据库中检索了 95 株SARAS-CoV-2 的全长基因组序列,通过多序列比对和系统发育分析建立了参考序列,并分析了沿SARS-CoV-2 基因组的序列变异。所有病毒株之间的同源性普遍较高,其中,核苷酸水平上的同源性为 99.99% (99.91%-100%),氨基酸水平上的同源性为 99.99% (99.79%-100%)。虽然开放阅读框 (ORF) 区域的总体变异s i s低,但在 1a、 1b、s、 3a、M、 8 中 13 个变异s ite S,和N区s进行了鉴定,其中po s ition s nt28144 在ORF 8 和nt8782 在ORF 1a s how的突变率为 30.53% (29/95) 和 29.47% (28/95),分别。这些发现提示SARS-COV-2 可能存在选择性突变,在设计引物和探针时需要避开某些区域。建立SARS-CoV-2 的参考序列,不仅有利于该病毒的生物学研究,而且有利于今后对SARS-CoV-2 感染的诊断、临床监测和干预。

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DOI:10.3346/jkms.2020.35.e79
作者列表:["Lim J","Jeon S","Shin HY","Kim MJ","Seong YM","Lee WJ","Choe KW","Kang YM","Lee B","Park SJ"]

METHODS::Since mid-December of 2019, coronavirus disease 2019 (COVID-19) infection has been spreading from Wuhan, China. The confirmed COVID-19 patients in South Korea are those who came from or visited China. As secondary transmissions have occurred and the speed of transmission is accelerating, there are rising concerns about community infections. The 54-year old male is the third patient diagnosed with COVID-19 infection in Korea. He is a worker for a clothing business and had mild respiratory symptoms and intermittent fever in the beginning of hospitalization, and pneumonia symptoms on chest computerized tomography scan on day 6 of admission. This patient caused one case of secondary transmission and three cases of tertiary transmission. Hereby, we report the clinical findings of the index patient who was the first to cause tertiary transmission outside China. Interestingly, after lopinavir/ritonavir (Kaletra, AbbVie) was administered, β-coronavirus viral loads significantly decreased and no or little coronavirus titers were observed.

影响因子:4.36
发表时间:2020-02-17
DOI:10.1080/22221751.2020.1729071
作者列表:["Zhang W","Du RH","Li B","Zheng XS","Yang XL","Hu B","Wang YY","Xiao GF","Yan B","Shi ZL","Zhou P"]

METHODS::In December 2019, a novel coronavirus (2019-nCoV) caused an outbreak in Wuhan, China, and soon spread to other parts of the world. It was believed that 2019-nCoV was transmitted through respiratory tract and then induced pneumonia, thus molecular diagnosis based on oral swabs was used for confirmation of this disease. Likewise, patient will be released upon two times of negative detection from oral swabs. However, many coronaviruses can also be transmitted through oral-fecal route by infecting intestines. Whether 2019-nCoV infected patients also carry virus in other organs like intestine need to be tested. We conducted investigation on patients in a local hospital who were infected with this virus. We found the presence of 2019-nCoV in anal swabs and blood as well, and more anal swab positives than oral swab positives in a later stage of infection, suggesting shedding and thereby transmitted through oral-fecal route. We also showed serology test can improve detection positive rate thus should be used in future epidemiology. Our report provides a cautionary warning that 2019-nCoV may be shed through multiple routes.

翻译标题与摘要 下载文献
影响因子:2.48
发表时间:2020-04-01
来源期刊:Infection
DOI:10.1007/s15010-020-01401-y
作者列表:["Cheng ZJ","Shan J"]

METHODS::There is a current worldwide outbreak of a new type of coronavirus (2019-nCoV), which originated from Wuhan in China and has now spread to 17 other countries. Governments are under increased pressure to stop the outbreak spiraling into a global health emergency. At this stage, preparedness, transparency, and sharing of information are crucial to risk assessments and beginning outbreak control activities. This information should include reports from outbreak sites and from laboratories supporting the investigation. This paper aggregates and consolidates the virology, epidemiology, clinical management strategies from both English and Chinese literature, official news channels, and other official government documents. In addition, by fitting the number of infections with a single-term exponential model, we report that the infection is spreading at an exponential rate, with a doubling period of 1.8 days.

呼吸道感染方向

呼吸道感染分为上呼吸道感染与下呼吸道感染。上呼吸道感染是指自鼻腔至喉部之间的急性炎症的总称,是最常见的感染性疾病。下呼吸道感染是最常见的感染性疾患,治疗时必须明确引起感染的病原体以选择有效的抗生素。

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