Phylogeographic reconstruction using air transportation data and its application to the 2009 H1N1 influenza A pandemic.

利用航空运输数据进行系统地理重建及其在 2009 H1N1 甲型流感大流行中的应用。

  • 影响因子:4.35
  • DOI:10.1371/journal.pcbi.1007101
  • 作者列表:"Reimering S","Muñoz S","McHardy AC
  • 发表时间:2020-02-07

:Influenza A viruses cause seasonal epidemics and occasional pandemics in the human population. While the worldwide circulation of seasonal influenza is at least partly understood, the exact migration patterns between countries, states or cities are not well studied. Here, we use the Sankoff algorithm for parsimonious phylogeographic reconstruction together with effective distances based on a worldwide air transportation network. By first simulating geographic spread and then phylogenetic trees and genetic sequences, we confirmed that reconstructions with effective distances inferred phylogeographic spread more accurately than reconstructions with geographic distances and Bayesian reconstructions with BEAST that do not use any distance information, and led to comparable results to the Bayesian reconstruction using distance information via a generalized linear model. Our method extends Bayesian methods that estimate rates from the data by using fine-grained locations like airports and inferring intermediate locations not observed among sampled isolates. When applied to sequence data of the pandemic H1N1 influenza A virus in 2009, our approach correctly inferred the origin and proposed airports mainly involved in the spread of the virus. In case of a novel outbreak, this approach allows to rapidly analyze sequence data and infer origin and spread routes to improve disease surveillance and control.


: 甲型流感病毒在人群中引起季节性流行和偶尔的大流行。虽然季节性流感的全球流行至少部分被理解,但国家、州或城市之间的确切迁移模式没有得到很好的研究。在这里,我们使用Sankoff算法与基于全球航空运输网络的有效距离一起进行简约的系统地理重建。通过首先模拟地理传播,然后是系统发育树和遗传序列,我们证实,与使用不使用任何距离信息的地理距离重建和使用BEAST的贝叶斯重建相比,使用有效距离推断的系统地理学重建传播更准确,并通过广义线性模型导致与使用距离信息的贝叶斯重建具有可比性的结果。我们的方法扩展了贝叶斯方法,通过使用机场等细粒度位置和推断抽样分离株中未观察到的中间位置,从数据中估计速率。当应用于 2009 年大流行H1N1 甲型流感病毒的序列数据时,我们的方法正确地推断了起源,并提出了主要参与病毒传播的机场。在新爆发的情况下,这种方法可以快速分析序列数据,推断起源和传播途径,以改善疾病监测和控制。



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.

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
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.