新泽西州的市长证实自己"去年11月就已感染新冠"

[lindamy]

1 hr 35 min ago
French hospital reports evidence patient had coronavirus in December
From CNN’s Maggie Fox and Edward Upright

A French first aid worker disinfects an ambulance after it was used to transport a suspected coronavirus patient in Paris on April 3. Lucas Barioulet/AFP/Getty Images

Doctors at a Paris hospital claim to have found evidence a patient who got sick in December was infected with the novel coronavirus.

If verified, it may show the virus was circulating in Europe as early as December. The first reports of Covid-19 in France were reported on January 24, in two people who had a history of travel to Wuhan, China.

“Covid-19 was already spreading in France in late December 2019, a month before the official first cases in the country,” the team at Groupe Hospitalier Paris Seine in Saint-Denis wrote.

Yves Cohen and colleagues at the Paris hospital decided to check the records of patients who got sick before the January 24 cases to see if the virus may have been spreading undetected earlier than first thought.

The French team looked at people admitted to the hospital with flu-like illnesses between December 2 and January 16 who were not subsequently diagnosed with influenza. The doctors re-tested samples stored in a freezer for coronavirus.

“One sample was positive, taken from a 42-year-old man born in Algeria, who lived in France for many years and worked as a fishmonger,” the team wrote in the International Journal of Antimicrobial Agents.
“His last trip was in Algeria during August 2019,” they wrote. The man had not been to China, and one of his children had also been sick, the team reported.
“Identifying the first infected patient is of great epidemiological interest as it changes dramatically our knowledge regarding SARS-COV-2 and its spreading in the country. Moreover, the absence of a link with China and the lack of recent travel suggest that the disease was already spreading among the French population at the end of December 2019,” they wrote.

Remember: This claim has not yet been independently verified.

Europe did not start reporting cases of coronavirus until January. In Italy, the European country hit hardest by the virus, the first two cases were reported on January 31, in two Chinese tourists in Rome. The first known community transmission was recorded in February in Codogno, in northern Italy.

 

[lindamy]

CNN上文的google 译文：


法国医院报告称患者在12月患有冠状病毒

来自CNN的Maggie Fox和Edward Edward

巴黎一家医院的医生声称已发现证据，表明一名12月生病的患者感染了新型冠状病毒。

如果得到验证，则表明该病毒最早于12月在欧洲传播。 1月24日，法国发生了Covid-19的首次报道，当时有两个人曾到中国武汉旅行。

“ Covid-19已于2019年12月下旬在法国传播，比该国正式的首例病例早一个月，”圣丹尼斯巴黎塞纳集团医院团队写道。

巴黎医院的伊夫·科恩（Yves Cohen）和他的同事决定检查1月24日病例之前生病的患者的记录，以查看该病毒是否在未曾想到的情况下传播而未被发现。

法国小组调查了12月2日至1月16日之间因流感样疾病入院的人，这些人随后均未被诊断出流感。医生重新测试了保存在冰箱中的冠状病毒样品。
该小组在《国际抗菌剂杂志》上写道：“一个样本是阳性的，取自42岁的阿尔及利亚人，他在法国生活了多年并担任鱼贩。”

他们写道：“他的最后一次旅行是在2019年8月在阿尔及利亚。”该小组报告说，这名男子没有去过中国，他的一个孩子也有病。

“确定第一位感染患者具有极大的流行病学意义，因为它极大地改变了我们对SARS-COV-2及其在全国的传播的了解。此外，与中国的联系缺乏以及近期旅行的缺乏表明该疾病已在2019年12月末在法国人群中传播，”他们写道。

切记：此声明尚未经过独立验证。

欧洲直到一月份才开始报告冠状病毒病例。在这个受到该病毒打击最严重的欧洲国家，意大利，1月31日报道了前两起病例，该病例是在罗马的两名中国游客中发生的。最早的已知社区传播是2月在意大利北部的科多诺录制的。

 

[joe_xj]

quote:
切记：此声明尚未经过独立验证。quote

医学工作者努力找出源头当然正确。为什么就不能安静地工作，总是查了个大概就跟媒体掺和上了，这有助于工作的进展，还是政治的需要?

 

[superlover]

quote:
切记：此声明尚未经过独立验证。quote

医学工作者努力找出源头当然正确。为什么就不能安静地工作，总是查了个大概就跟媒体掺和上了，这有助于工作的进展，还是政治的需要?

人家医院自己发布自己独立检测结果，它有自己的事实与结论了，就可以马上发布
第三方机构验不验证，与医院无关，难道医院还能拒绝媒体采访与报导
真是迂腐可笑

 

[joe_xj]

人家医院自己发布自己独立检测结果，它有自己的事实与结论了，就可以马上发布
第三方机构验不验证，与医院无关，难道医院还能拒绝媒体采访与报导
真是迂腐可笑

科学家可能只是在学术刊物上发表了一篇文章，媒体呢？来看看同一个CASE，两家媒体报道的不同之处：

重定向声明

法国十二月份这病例 不是 antibody 测试，测的是保存的样本。

Coronavirus21 hours ago (May 04, 2020 11:40AM ET)

Neither Cohen nor his team were immediately available for comment on Monday.
France, which has seen almost 25,000 people die from the virus since March 1, confirmed its first three COVID-19 cases on Jan. 24, including two patients in Paris and another in the southwestern city of Bordeaux.
Cohen said it was too early to know if the patient whose Dec. 27 test was COVID-19 positive is France's "patient zero".
Cohen said the patient had survived and that a first investigation to trace the first contamination has been carried out.
"He was sick for 15 days and infected his two children, but not his wife, who works in a supermarket.
"He was amazed, he didn't understand how he had been infected. We put the puzzle together and he had not made any trips. The only contact that he had was with his wife."
The man's wife worked alongside a Sushi stand, close to colleagues of Chinese origin, Cohen said. It was not clear whether those colleagues had travelled to China, and the local health authority should investigate, he said.
"We're wondering whether she was asymptomatic," he said.
"He may be the 'patient zero', but perhaps there are others in other regions. All the negative PCRs for pneumonia must be tested again. The virus was probably circulating (then)," he said.

1 hr 35 min ago From CNN’s Maggie Fox and Edward Upright

The first reports of Covid-19 in France were reported on January 24, in two people who had a history of travel to Wuhan, China.

“Covid-19 was already spreading in France in late December 2019, a month before the official first cases in the country,” the team at Groupe Hospitalier Paris Seine in Saint-Denis wrote.

“One sample was positive, taken from a 42-year-old man born in Algeria, who lived in France for many years and worked as a fishmonger,” the team wrote in the International Journal of Antimicrobial Agents.
“His last trip was in Algeria during August 2019,” they wrote. The man had not been to China, and one of his children had also been sick, the team reported.
“Identifying the first infected patient is of great epidemiological interest as it changes dramatically our knowledge regarding SARS-COV-2 and its spreading in the country. Moreover, the absence of a link with China and the lack of recent travel suggest that the disease was already spreading among the French population at the end of December 2019,” they wrote.

我没有去查 International Journal of Antimicrobial Agents，我不能从这两份报道中得出什么确定的结论

 

[lindamy]

1 hr 54 min ago
Many early Covid-19 cases in the UK came from Europe, not China, says chief scientific adviser
From CNN's Niamh Kennedy in Dublin

Britain's Chief Scientific Adviser Patrick Vallance arrives at 10 Downing street in London on April 9, to take part in the daily government coronavirus briefing. Tolga Akmen/AFP/Getty Images

Many of the early Covid-19 cases imported into the UK came from European countries, rather than China, the UK government’s chief scientific adviser Patrick Vallance said Tuesday.

Early in March the UK got many, many different imports of virus from many different places, and those places were particularly from European countries with outbreaks," Vallance told the UK Parliament’s committee on health and social care.

"So we see a big influx – probably from Italy and Spain, looking at the genomics of the virus, in early March – seeded right across the country.

Whether that was people returning from half term or business travelers we don’t know, but a lot of the cases in the UK didn’t come from China and didn’t come from places you might have expected."

"They actually came from European imports and the high level of travel into the UK around that time,” he explained -- despite the UK’s initial focus on contact tracing which concentrated on arrivals from China.

The first two cases of coronavirus in the UK were confirmed by England’s chief medical officer, Chris Witty, on January 31.

When asked whether the UK should have imposed a lockdown earlier than March 23, Vallance said: “when you look at everything that happened and the speed at which it happened, maybe days either way would have made a difference.”

Vallance said that the UK has not yet managed to get the reproduction rate of the virus -- known as the R-rate -- down to a manageable number, whereby the virus could be controlled using contact tracing and isolation.

He said the country's lockdown should not be lifted until this outcome is achieved.

The UK must review its lockdown measures by Thursday, but is not expected to announce major changes yet.

 

[lindamy]

42 min ago
Coronavirus quickly spread around the world starting late last year, new genetic analysis shows
From CNN's Maggie Fox


A new genetic analysis of the virus that causes Covid-19 taken from more than 7,600 patients around the world shows the virus has been circulating in people since late last year, and must have spread extremely quickly after the first infection.

Researchers in Britain looked at mutations in the virus and found evidence of quick spread, but not evidence the virus is becoming more easily transmitted or more likely to cause serious disease.

“The virus is changing, but this in itself does not mean it’s getting worse,” genetics researcher Francois Balloux of the University College London Genetics Institute told CNN.

Balloux and colleagues pulled viral sequences from a giant global database that scientists around the world are using to share data. They looked at samples taken at different times and from different places, and said they indicate that the virus first started infecting people at the end of last year.

“This rules out any scenario that assumes SARSCoV-2 may have been in circulation long before it was identified, and hence have already infected large proportions of the population,” Balloux’s team wrote in their report, published in the journal Infection, Genetics and Evolution.

“Our results are in line with previous estimates and point to all sequences sharing a common ancestor towards the end of 2019, supporting this as the period when SARS-CoV-2 jumped into its human host,” the team wrote in the report, published Tuesday.

“It’s very recent,” Balloux said. “We are really, really, really confident that the host jump happened late last year.”

They also found genetic evidence that supports suspicions the virus was infecting people in Europe, the US and elsewhere weeks or even months before the first official cases were reported in January and February.

Balloux’s team had their findings reviewed by other experts, a process called peer review, before they were published in the journal. He said some reports by other teams, published online in on what are called pre-print websites, may have drawn incorrect conclusions.

“All viruses naturally mutate. Mutations in themselves are not a bad thing and there is nothing to suggest SARS-CoV-2 is mutating faster or slower than expected. So far we cannot say whether SARS-CoV-2 is becoming more or less lethal and contagious,” Balloux said.

 

[lindamy]

Prof Francois Balloux

 

[lindamy]

Emergence of genomic diversity and recurrent mutations in SARS-CoV-2

Highlights

•
Phylogenetic estimates support that the COVID-2 pandemic started sometimes around 6 October 2019–11 December 2019, which corresponds to the time of the host-jump into humans.
•
The diversity of SARS-CoV-2 strains in many countries recapitulates its full global diversity, consistent with multiple introductions of the virus to regions throughout the world seeding local transmission events.
•
198 sites in the SARS-CoV-2 genome appear to have already undergone recurrent, independent mutations based on a large-scale analysis of public genome assemblies.
•
Detected recurrent mutations may indicate ongoing adaptation of SARS-CoV-2 to its novel human host.
•
Monitoring the build-up and patterns of genetic diversity in SARS-CoV-2 has potential to inform targets for drug and vaccine development.

Abstract
SARS-CoV-2 is a SARS-like coronavirus of likely zoonotic origin first identified in December 2019 in Wuhan, the capital of China's Hubei province. The virus has since spread globally, resulting in the currently ongoing COVID-19 pandemic. The first whole genome sequence was published on January 52,020, and thousands of genomes have been sequenced since this date. This resource allows unprecedented insights into the past demography of SARS-CoV-2 but also monitoring of how the virus is adapting to its novel human host, providing information to direct drug and vaccine design. We curated a dataset of 7666 public genome assemblies and analysed the emergence of genomic diversity over time. Our results are in line with previous estimates and point to all sequences sharing a common ancestor towards the end of 2019, supporting this as the period when SARS-CoV-2 jumped into its human host. Due to extensive transmission, the genetic diversity of the virus in several countries recapitulates a large fraction of its worldwide genetic diversity. We identify regions of the SARS-CoV-2 genome that have remained largely invariant to date, and others that have already accumulated diversity. By focusing on mutations which have emerged independently multiple times (homoplasies), we identify 198 filtered recurrent mutations in the SARS-CoV-2 genome. Nearly 80% of the recurrent mutations produced non-synonymous changes at the protein level, suggesting possible ongoing adaptation of SARS-CoV-2. Three sites in Orf1ab in the regions encoding Nsp6, Nsp11, Nsp13, and one in the Spike protein are characterised by a particularly large number of recurrent mutations (>15 events) which may signpost convergent evolution and are of particular interest in the context of adaptation of SARS-CoV-2 to the human host. We additionally provide an interactive user-friendly web-application to query the alignment of the 7666 SARS-CoV-2 genomes.

Keywords
Betacoronaviridae
Homoplasies
Mutation
Phylogenetics

1. Introduction
On December 31 2019, China notified the World Health Organisation (WHO) about a cluster of pneumonia cases of unknown aetiology in Wuhan, the capital of the Hubei Province. The initial evidence was suggestive of the outbreak being associated with a seafood market in Wuhan, which was closed on January 1 2020. The aetiological agent was characterised as a SARS-like betacoronavirus, later named SARS-CoV-2, and the first whole genome sequence (Wuhan-HU-1) was deposited on NCBI Genbank on January 5 2020 (Wu et al., 2020). Human-to-human transmission was confirmed on January 14 2020, by which time SARS-CoV-2 had already spread to many countries throughout the world. Further extensive global transmission led to the WHO declaring COVID-19 as a pandemic on March 11 2020.

Betacoronaviridae comprise a large number of lineages that are found in a wide range of mammals and birds (Shaw et al., 2020), including the other human zoonotic pathogens SARS-CoV-1 and MERS-COV. The propensity of Betacoronaviridiae to undergo frequent host jumps supports SARS-CoV-2 also being of zoonotic origin. To date, the genetically closest-known lineage is found in horseshoe bats (BatCoV RaTG13) (Zhou et al., 2020). However, this lineage shares 96% identity with SARS-CoV-2, which is not sufficiently high to implicate it as the immediate ancestor of SARS-CoV-2 (Shaw et al., 2020). The zoonotic source of the virus remains unidentified at the date of writing (April 23 2020).

The analysis of genetic sequence data from pathogens is increasingly recognised as an important tool in infectious disease epidemiology (Rambaut et al., 2008; Grenfell et al., 2004). Genetic sequence data sheds light on key epidemiological parameters such as doubling time of an outbreak/epidemic, reconstruction of transmission routes and the identification of possible sources and animal reservoirs. Additionally, whole-genome sequence data can inform drug and vaccine design. Indeed, genomic data can be used to identify pathogen genes interacting with the host and allows characterization of the more evolutionary constrained regions of a pathogen genome, which should be preferentially targeted to avoid rapid drug and vaccine escape mutants.

There are thousands of global SARS-CoV-2 whole-genome sequences available on the rapid data sharing service hosted by the Global Initiative on Sharing All Influenza Data (GISAID; https://www.epicov.org) (Elbe and Buckland-Merrett, 2017; Shu and McCauley, 2017). The extraordinary availability of genomic data during the COVID-19 pandemic has been made possible thanks to a tremendous effort by hundreds of researchers globally depositing SARS-CoV-2 assemblies (Table S1) and the proliferation of close to real time data visualisation and analysis tools including NextStrain (https://nextstrain.org) and CoV-GLUE (http://cov-glue.cvr.gla.ac.uk).

In this work we use this data to analyse the genomic diversity that has emerged in the global population of SARS-CoV-2 since the beginning of the COVID-19 pandemic, based on a download of 7710 assemblies. We focus in particular on mutations that have emerged independently multiple times (homoplasies) as these are likely candidates for ongoing adaptation of SARS-CoV-2 to its novel human host. After filtering, we characterise homoplasies at 198 sites in the SARS-CoV-2 genome. We identify a strong signal of recurrent mutation at nucleotide position 11,083 (Codon 3606 Orf1a), together with two further sites in Orf1ab encoding the non-structural proteins Nsp11 and Nsp13. These, together with a mutation in the Spike protein (21,575, Codon 5), comprise the strongest putative regions under selection in our dataset.

The current distribution of genomic diversity as well as ongoing allele frequency changes both between isolates and along the SARS-CoV-2 genome are publicly available as an open access and interactive web-resource available here:

SARS-CoV-2 Alignment Screen.

Emergence of genomic diversity and recurrent mutations in SARS-CoV-2

SARS-CoV-2 is a SARS-like coronavirus of likely zoonotic origin first identified in December 2019 in Wuhan, the capital of China's Hubei province. The…

www.sciencedirect.com

如果感兴趣可以从Link查看PDF版的全文，共25页。因为看不懂，就不贴出来了。

 

[cfhk]

 

[cfhk]