COVID-19: Genetic network analysis provides 'snapshot' of pandemic origins
Summary: The first use of phylogenetic techniques shows the 'ancestral' virus genome closest to those in bats was not Wuhan's predominant virus type. The study charts the 'incipient supernova' of COVID-19 through genetic mutations as it spread from China and Asia to Australia, Europe and North America. Researchers say their methods could be used to help identify undocumented infection sources.
Researchers from Cambridge, UK, and Germany have reconstructed the early " evolutionary paths" of COVID-19 in humans -- as infection spread from Wuhan out to Europe and North America -- using genetic network techniques.
By analysing the first 160 complete virus genomes to be sequenced from human patients, the scientists have mapped some of the original spread of the new coronavirus through its mutations, which creates different viral lineages.
"There are too many rapid mutations to neatly trace a COVID-19 family tree. We used a mathematical network algorithm to visualise all the plausible trees simultaneously," said geneticist Dr Peter Forster, lead author from the University of Cambridge.
"These techniques are mostly known for mapping the movements of prehistoric human populations through DNA. We think this is the first time they have been used to trace the infection routes of a coronavirus like COVID-19."
The team used data from virus genomes sampled from across the world between 24 December 2019 and 4 March 2020. The research revealed three distinct " variants" of COVID-19, consisting of clusters of closely related lineages, which they label 'A', 'B' and 'C'.
Forster and colleagues found that the closest type of COVID-19 to the one discovered in bats -- type 'A', the "original human virus genome" -- was present in Wuhan, but surprisingly was not the city's predominant virus type.
Mutated versions of 'A' were seen in Americans reported to have lived in Wuhan, and a large number of A-type viruses were found in patients from the US and Australia.
Wuhan's major virus type, 'B', was prevalent in patients from across East Asia. However, the variant didn't travel much beyond the region without further mutations -- implying a "founder event" in Wuhan, or "resistance" against this type of COVID-19 outside East Asia, say researchers.
The 'C' variant is the major European type, found in early patients from France, Italy, Sweden and England. It is absent from the study's Chinese mainland sample, but seen in Singapore, Hong Kong and South Korea.
The new analysis also suggests that one of the earliest introductions of the virus into Italy came via the first documented German infection on January 27, and that another early Italian infection route was related to a " Singapore cluster."
Importantly, the researchers say that their genetic networking techniques accurately traced established infection routes: the mutations and viral lineages joined the dots between known cases.
As such, the scientists argue that these "phylogenetic" methods could be applied to the very latest coronavirus genome sequencing to help predict future global hot spots of disease transmission and surge.
"Phylogenetic network analysis has the potential to help identify undocumented COVID-19 infection sources, which can then be quarantined to contain further spread of the disease worldwide," said Forster, a fellow of the McDonald Institute of Archaeological Research at Cambridge, as well as the University's Institute of Continuing Education.
The findings are published today in the journal Proceedings of the National Academy of Sciences (PNAS). The software used in the study, as well as classifications for over 1,000 coronavirus genomes and counting, is available free at http://www.fluxus-technology.com.
Variant 'A', most closely related to the virus found in both bats and pangolins, is described as "the root of the outbreak" by researchers. Type 'B' is derived from 'A', separated by two mutations, then 'C' is in turn a " daughter" of 'B'.
Researchers say the localisation of the 'B' variant to East Asia could result from a "founder effect": a genetic bottleneck that occurs when, in the case of a virus, a new type is established from a small, isolated group of infections.
Forster argues that there is another explanation worth considering. "The Wuhan B-type virus could be immunologically or environmentally adapted to a large section of the East Asian population. It may need to mutate to overcome resistance outside East Asia. We seem to see a slower mutation rate in East Asia than elsewhere, in this initial phase."
He added: "The viral network we have detailed is a snapshot of the early stages of an epidemic, before the evolutionary paths of COVID-19 become obscured by vast numbers of mutations. It's like catching an incipient supernova in the act."
Since today's PNAS study was conducted, the research team has extended its analysis to 1,001 viral genomes. While yet to be peer-reviewed, Forster says the latest work suggests that the first infection and spread among humans of COVID-19 occurred between mid-September and early December.
The phylogenetic network methods used by researchers -- allowing the visualisation of hundreds of evolutionary trees simultaneously in one simple graph -- were pioneered in New Zealand in 1979, then developed by German mathematicians in the 1990s.
These techniques came to the attention of archaeologist Professor Colin Renfrew, a co-author of the new PNAS study, in 1998. Renfrew went on to establish one of the first archaeogenetics research groups in the world at the University of Cambridge.
【 以下文字转载自 Military 讨论区 】
发信人: microyu (yu), 信区: Military
标 题: 美国流行的是最原始的毒株，天朝不是
发信站: BBS 未名空间站 (Thu Apr 9 17:46:21 2020, 美东)
每日邮报也揭底了。一共有A,B,C三种毒株流行。A最原始，B由A突变来，C由B突变来。美帝，澳大利亚以A为主，天朝以B为主，A在武汉少量，C在天朝境外突变。澳大利亚毒株肯定从美国来。如果起源是武汉，为毛不是最原始的A为主？迄今还找不到解释。不
过如果是起源于美帝，那就解释通了。https://www.dailymail.co.uk/sciencetech/article-8204255/There-THREE-separate-types-coronavirus.html
全世界都在反美
太热闹
found in COME place
这是精虫上脑后编的吧
【 在 dragonfly (小蜻蜓-一品御前带刀老中医) 的大作中提到: 】
: 发信人: microyu (yu), 信区: Military
: 标 题: 美国流行的是最原始的毒株，天朝不是
: 发信站: BBS 未名空间站 (Thu Apr 9 17:46:21 2020, 美东)
: 每日邮报也揭底了。一共有A,B,C三种毒株流行。A最原始，B由A突变来，C由B突变来。
: 美帝，澳大利亚以A为主，天朝以B为主，A在武汉少量，C在天朝境外突变。澳大利亚毒
: 株肯定从美国来。如果起源是武汉，为毛不是最原始的A为主？迄今还找不到解释。不
: 过如果是起源于美帝，那就解释通了。
: https://www.dailymail.co.uk/sciencetech/article-8204255/There-THREE-
separate
: -types-coronavirus.html
COVID-19: Genetic network analysis provides 'snapshot' of pandemic origins
Summary:
The first use of phylogenetic techniques shows the 'ancestral' virus genome closest to those in bats was not Wuhan's predominant virus type. The study
charts the 'incipient supernova' of COVID-19 through genetic mutations as it spread from China and Asia to Australia, Europe and North America.
Researchers say their methods could be used to help identify undocumented
infection sources.
Researchers from Cambridge, UK, and Germany have reconstructed the early "
evolutionary paths" of COVID-19 in humans -- as infection spread from Wuhan out to Europe and North America -- using genetic network techniques.
By analysing the first 160 complete virus genomes to be sequenced from human patients, the scientists have mapped some of the original spread of the new coronavirus through its mutations, which creates different viral lineages.
"There are too many rapid mutations to neatly trace a COVID-19 family tree. We used a mathematical network algorithm to visualise all the plausible
trees simultaneously," said geneticist Dr Peter Forster, lead author from
the University of Cambridge.
"These techniques are mostly known for mapping the movements of prehistoric human populations through DNA. We think this is the first time they have
been used to trace the infection routes of a coronavirus like COVID-19."
The team used data from virus genomes sampled from across the world between 24 December 2019 and 4 March 2020. The research revealed three distinct "
variants" of COVID-19, consisting of clusters of closely related lineages,
which they label 'A', 'B' and 'C'.
Forster and colleagues found that the closest type of COVID-19 to the one
discovered in bats -- type 'A', the "original human virus genome" -- was
present in Wuhan, but surprisingly was not the city's predominant virus type.
Mutated versions of 'A' were seen in Americans reported to have lived in
Wuhan, and a large number of A-type viruses were found in patients from the US and Australia.
Wuhan's major virus type, 'B', was prevalent in patients from across East
Asia. However, the variant didn't travel much beyond the region without
further mutations -- implying a "founder event" in Wuhan, or "resistance"
against this type of COVID-19 outside East Asia, say researchers.
The 'C' variant is the major European type, found in early patients from
France, Italy, Sweden and England. It is absent from the study's Chinese
mainland sample, but seen in Singapore, Hong Kong and South Korea.
The new analysis also suggests that one of the earliest introductions of the virus into Italy came via the first documented German infection on January 27, and that another early Italian infection route was related to a "
Singapore cluster."
Importantly, the researchers say that their genetic networking techniques
accurately traced established infection routes: the mutations and viral
lineages joined the dots between known cases.
As such, the scientists argue that these "phylogenetic" methods could be
applied to the very latest coronavirus genome sequencing to help predict
future global hot spots of disease transmission and surge.
"Phylogenetic network analysis has the potential to help identify
undocumented COVID-19 infection sources, which can then be quarantined to
contain further spread of the disease worldwide," said Forster, a fellow of the McDonald Institute of Archaeological Research at Cambridge, as well as
the University's Institute of Continuing Education.
The findings are published today in the journal Proceedings of the National Academy of Sciences (PNAS). The software used in the study, as well as
classifications for over 1,000 coronavirus genomes and counting, is
available free at http://www.fluxus-technology.com.
Variant 'A', most closely related to the virus found in both bats and
pangolins, is described as "the root of the outbreak" by researchers. Type 'B' is derived from 'A', separated by two mutations, then 'C' is in turn a "
daughter" of 'B'.
Researchers say the localisation of the 'B' variant to East Asia could
result from a "founder effect": a genetic bottleneck that occurs when, in
the case of a virus, a new type is established from a small, isolated group of infections.
Forster argues that there is another explanation worth considering. "The
Wuhan B-type virus could be immunologically or environmentally adapted to a large section of the East Asian population. It may need to mutate to
overcome resistance outside East Asia. We seem to see a slower mutation rate in East Asia than elsewhere, in this initial phase."
He added: "The viral network we have detailed is a snapshot of the early
stages of an epidemic, before the evolutionary paths of COVID-19 become
obscured by vast numbers of mutations. It's like catching an incipient
supernova in the act."
Since today's PNAS study was conducted, the research team has extended its
analysis to 1,001 viral genomes. While yet to be peer-reviewed, Forster says the latest work suggests that the first infection and spread among humans
of COVID-19 occurred between mid-September and early December.
The phylogenetic network methods used by researchers -- allowing the
visualisation of hundreds of evolutionary trees simultaneously in one simple graph -- were pioneered in New Zealand in 1979, then developed by German
mathematicians in the 1990s.
These techniques came to the attention of archaeologist Professor Colin
Renfrew, a co-author of the new PNAS study, in 1998. Renfrew went on to
establish one of the first archaeogenetics research groups in the world at
the University of Cambridge.
是外星人更合理
【 在 dragonfly (小蜻蜓-一品御前带刀老中医) 的大作中提到: 】
: 发信人: microyu (yu), 信区: Military
: 标 题: 美国流行的是最原始的毒株，天朝不是
: 发信站: BBS 未名空间站 (Thu Apr 9 17:46:21 2020, 美东)
: 每日邮报也揭底了。一共有A,B,C三种毒株流行。A最原始，B由A突变来，C由B突变来。
: 美帝，澳大利亚以A为主，天朝以B为主，A在武汉少量，C在天朝境外突变。澳大利亚毒
: 株肯定从美国来。如果起源是武汉，为毛不是最原始的A为主？迄今还找不到解释。不
: 过如果是起源于美帝，那就解释通了。
: https://www.dailymail.co.uk/sciencetech/article-8204255/There-THREE-
separate
: -types-coronavirus.html
利用国民英语差自创谣言。用下字典就知道文章说的是：A 来自武汉，A 的变异在美国发现，但是美国的患者来自武汉。这就跟外地人到了上海，在上海的医院确诊了，并且发现患者有不同毒株，来自不同省份。上海就成了发源地了？
【 在 dragonfly (小蜻蜓-一品御前带刀老中医) 的大作中提到: 】
: 发信人: microyu (yu), 信区: Military
: 标 题: 美国流行的是最原始的毒株，天朝不是
: 发信站: BBS 未名空间站 (Thu Apr 9 17:46:21 2020, 美东)
: 每日邮报也揭底了。一共有A,B,C三种毒株流行。A最原始，B由A突变来，C由B突变来。
: 美帝，澳大利亚以A为主，天朝以B为主，A在武汉少量，C在天朝境外突变。澳大利亚毒
: 株肯定从美国来。如果起源是武汉，为毛不是最原始的A为主？迄今还找不到解释。不
: 过如果是起源于美帝，那就解释通了。
: https://www.dailymail.co.uk/sciencetech/article-8204255/There-THREE-
separate
: -types-coronavirus.html
你怎么知道美国的A是从武汉来的，而不是自己境内传的？
【在 jiangyong(酱油)的大作中提到：】
：利用国民英语差自创谣言。用下字典就知道文章说的是：A 来自武汉，A 的变异在美国发现，但是美国的患者来自武汉。这就跟外地人到了上海，在上海的医院确诊了，并且发现患者有不同毒株，来自不同省份。上海就成了发源地了？
：【 在 dragonfly (小蜻蜓-一品御前带刀老中医) 的大作中提到: 】
亚麻男，在武汉呆了一个多月回到雅图，三天后确诊。你说哪里传的
【 在 berryblack(berry) 的大作中提到: 】
: 你怎么知道美国的A是从武汉来的，而不是自己境内传的？
: ：利用国民英语差自创谣言。用下字典就知道文章说的是：A 来自武汉，A 的变异在美
: 国发现，但是美国的患者来自武汉。这就跟外地人到了上海，在上海的医院确诊了，并
: 且发现患者有不同毒株，来自不同省份。上海就成了发源地了？
: ：【 在 dragonfly (小蜻蜓-一品御前带刀老中医) 的大作中提到: 】
谁告诉你这就是真正的美国第一例？说不定都是第两万例了。CDC主任早就承认有流感
死亡实际上是新冠。
【 在 xiaofish (小鱼儿) 的大作中提到: 】
: 亚麻男，在武汉呆了一个多月回到雅图，三天后确诊。你说哪里传的
:
: 你怎么知道美国的A是从武汉来的，而不是自己境内传的？
:
: ：利用国民英语差自创谣言。用下字典就知道文章说的是：A 来自武汉，A 的变
: 异在美
:
: 国发现，但是美国的患者来自武汉。这就跟外地人到了上海，在上海的医院确诊
: 了，并
:
: 且发现患者有不同毒株，来自不同省份。上海就成了发源地了？
:
: ：【 在 dragonfly (小蜻蜓-一品御前带刀老中医) 的大作中提到: 】
:
那是这篇文章里的第一例，你想用这篇文章说明问题就用它的数据，你不想用它的数据想用自己的脑洞就不要拿这篇文章做证据。就这么简单
【 在 liftway(liftway) 的大作中提到: 】
: 谁告诉你这就是真正的美国第一例？说不定都是第两万例了。CDC主任早就承认
有流感
: 死亡实际上是新冠。
Data, show us data that thousands, if not tens of thousands A-type COVID-19 infections in the US.
【 在 liftway (liftway) 的大作中提到: 】
: 谁告诉你这就是真正的美国第一例？说不定都是第两万例了。CDC主任早就承认有流感
: 死亡实际上是新冠。
美国两万例的话 怎么意大利拖了这么久才突然爆发？
按照美国和欧洲的交流频率，美国这么早就有了案例，那意大利不该早没了么。。这点一直很奇怪啊
【 在 liftway (liftway) 的大作中提到: 】
: 谁告诉你这就是真正的美国第一例？说不定都是第两万例了。CDC主任早就承认有流感
: 死亡实际上是新冠。
要是病毒变异的话就合理了，意大利流行的是C,美国现在爆的也是C
原始A如果R0低还极低概率的重症完全可能逃脱侦测
【 在 sapphirewing (Audrey的树) 的大作中提到: 】
: 美国两万例的话 怎么意大利拖了这么久才突然爆发？
: 按照美国和欧洲的交流频率，美国这么早就有了案例，那意大利不该早没了么。。这点
: 一直很奇怪啊