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Genetic cluster analysis of SARS-CoV-2 and the identification of those responsible for the major outbreaks in various countries.

SARS-CoV-2 的遗传聚类分析和确定各国主要疫情的责任人。

  • 影响因子:4.36
  • DOI:10.1080/22221751.2020.1773745
  • 作者列表:"Yang X","Dong N","Chan EW","Chen S
  • 发表时间:2020-12-01
Abstract

:A newly emerged coronavirus, SARS-CoV-2, caused severe pneumonia outbreaks in China in December 2019 and has since spread to various countries around the world. To trace the evolution route and probe the transmission dynamics of this virus, we performed phylodynamic analysis of 247 high quality genomic sequences available in the GISAID platform as of 5 March 2020. Among them, four genetic clusters, defined as super-spreaders (SSs), could be identified and were found to be responsible for the major outbreaks that subsequently occurred in various countries. SS1 was widely disseminated in Asia and the US, and mainly responsible for outbreaks in the states of Washington and California as well as South Korea, whereas SS4 contributed to the pandemic in Europe. Using the signature mutations of each SS as markers, we further analysed 1539 genome sequences reported after 29 February 2020 and found that 90% of these genomes belonged to SSs, with SS4 being the most dominant. The relative degree of contribution of each SS to the pandemic in different continents was also depicted. Identification of these super-spreaders greatly facilitates development of new strategies to control the transmission of SARS-CoV-2.

摘要

: 一种新出现的冠状病毒,SARS-CoV-2,于 2019 年 12 月在中国引发重症肺炎疫情,此后已蔓延到世界各国。为了追踪该病毒的进化路线和探测其传播动力学,我们对截至 2020 年 3 月 5 日GISAID平台上可用的 247 个高质量基因组序列进行了系统发育分析。其中,可以确定 4 个遗传集群,定义为超级传播者 (SSs),并被发现对随后在各国发生的重大疫情负责。SS1 在亚洲和美国广泛传播,主要是在华盛顿州和加利福尼亚州以及韩国的暴发,而SS4 则导致了欧洲的大流行。以每个SS的签名突变为标记,我们进一步分析了 2020 年 2 月 29 日后报告的 1539 个基因组序列,发现这些基因组中有 90% 属于SSs,其中SS4 占主导地位。还描述了每个SS对不同大陆大流行的相对贡献程度。这些超级传播者的识别极大地促进了控制SARS-CoV-2 传播的新策略的开发。

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影响因子:1.60
发表时间:2020-02-17
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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