事实上呢？看原文吧：“There are two subclusters of A which are distinguished by the synonymous mutation T29095C. In the T-allele subcluster, four Chinese individuals (from the southern coastal Chinese province of Guangdong) carry the ancestral genome, while three Japanese and two American patients differ from it by a number of mutations. These American patients are reported to have had a history of residence in the presumed source of the outbreak in Wuhan. The C-allele subcluster sports relatively long mutational branches and includes five individuals from Wuhan, two of which are represented in the ancestral node, and eight other East Asians from China and adjacent countries. It is noteworthy that nearly half (15/33) of the types in this subcluster, however, are found outside East Asia, mainly in the United States and Australia.”
事实上呢？看原文吧：“There are two subclusters of A which are distinguished by the synonymous mutation T29095C. In the T-allele subcluster, four Chinese individuals (from the southern coastal Chinese province of Guangdong) carry the ancestral genome, while three Japanese and two American patients differ from it by a number of mutations. These American patients are reported to have had a history of residence in the presumed source of the outbreak in Wuhan. The C-allele subcluster sports relatively long mutational branches and includes five individuals from Wuhan, two of which are represented in the ancestral node, and eight other East Asians from China and adjacent countries. It is noteworthy that nearly half (15/33) of the types in this subcluster, however, are found outside East Asia, mainly in the United States and Australia.”
看到了。那楼主能update 一下有关A型的原文吗？原文说的跟楼主总结的明显不一致啊。明明A型里T C 两种Allele里 ancestal 的病人分别来自广东和武汉，美国和日本等国的都是变异型。
zyskywalker 发表于 4/10/2020 1:31:11 PM
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.
Phylogenetic network analysis has the potential to help identify undocumented COVID-19 infection sources
— Peter Forster
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 one of the first times 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 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.
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.
Phylogenetic network analysis has the potential to help identify undocumented COVID-19 infection sources
— Peter Forster
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 one of the first times 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 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. mindstorm 发表于 4/10/2020 1:41:18 PM
原文在此，其实前面已经有人贴过并翻译了，但是楼主不知为何没看见，反而只是继续引用二手评论 There are two subclusters of A which are distinguished by the synonymous mutation T29095C. In the T-allele subcluster, four Chinese individuals (from the southern coastal Chinese province of Guangdong) carry the ancestral genome, while three Japanese and two American patients differ from it by a number of mutations. These American patients are reported to have had a history of residence in the presumed source of the outbreak in Wuhan. The C-allele subcluster sports relatively long mutational branches and includes five individuals from Wuhan, two of which are represented in the ancestral node, and eight other East Asians from China and adjacent countries. It is noteworthy that nearly half (15/33) of the types in this subcluster, however, are found outside East Asia, mainly in the United States and Australia.
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.
明明说了武汉也有A，只不过不占主导而已。LZ读懂了吗？ “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.”
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. Phylogenetic network analysis has the potential to help identify undocumented COVID-19 infection sources — Peter Forster 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 one of the first times 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 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. mindstorm 发表于 4/10/2020 1:41:00 PM
“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.”
武汉爆发的是B, 那么源头就不在武汉啊！而且A究竟从哪里来，为什么不可能是两个携带A的美国人将病毒带到了武汉？（注意原文，这两个A已经和ancestral A不太一样了）： two American patients differ from it by a number of mutations. These American patients are reported to have had a history of residence in the presumed source of the outbreak in Wuhan. 所以希望科学家们能够继续调查，画清楚整个传染路径。
武汉爆发的是B, 那么源头就不在武汉啊！而且A究竟从哪里来，为什么不可能是两个携带A的美国人将病毒带到了武汉？（注意原文，这两个A已经和ancestral A不太一样了）： two American patients differ from it by a number of mutations. These American patients are reported to have had a history of residence in the presumed source of the outbreak in Wuhan. 所以希望科学家们能够继续调查，画清楚整个传染路径。 happywindveryhappy 发表于 4/10/2020 2:54:04 PM <a href="/showtopic.aspx?topicid=2531578&postid=83551381#83551381" target="_blank"><img src="https://img10.huaren.us/0x0,q50/upload/static/back.gif"></a><img src="http://forums.huaren.us/images/common/back.gif"/>[/url]
A. 武汉也有，但量少，主要是B. 这部分就非常奇怪。美国有很多A. 如果美国的传染来自于中国，当然是非常可能的，但也引起很多解释不了的问题。
There are two subclusters of A which are distinguished by the synonymous mutation T29095C. In the T-allele subcluster, four Chinese individuals (from the southern coastal Chinese province of Guangdong) carry the ancestral genome, while three Japanese and two American patients differ from it by a number of mutations. These American patients are reported to have had a history of residence in the presumed source of the outbreak in Wuhan. The C-allele subcluster sports relatively long mutational branches and includes five individuals from Wuhan, two of which are represented in the ancestral node, and eight other East Asians from China and adjacent countries. It is noteworthy that nearly half (15/33) of the types in this subcluster, however, are found outside East Asia, mainly in the United States and Australia.”
他在文章中清楚地写道：先有四个中国人携带A祖先基因, 三个日本人和两个在武汉的美国人携带了该基因的变异。https://www.pnas.org/content/early/2020/04/07/2004999117 There are two subclusters of A which are distinguished by the synonymous mutation T29095C. In the T-allele subcluster, four Chinese individuals (from the southern coastal Chinese province of Guangdong) carry the ancestral genome, while three Japanese and two American patients differ from it by a number of mutations. These American patients are reported to have had a history of residence in the presumed source of the outbreak in Wuhan. The C-allele subcluster sports relatively long mutational branches and includes five individuals from Wuhan, two of which are represented in the ancestral node, and eight other East Asians from China and adjacent countries. It is noteworthy that nearly half (15/33) of the types in this subcluster, however, are found outside East Asia, mainly in the United States and Australia.
先划重点： 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”.
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.
The findings are published in the journal Proceedings of the National Academy of Sciences (PNAS).
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, the study suggests.
The phylogenetic network methods used by researchers – which looks at evolutionary relationships among biological entities – allowed the visualisation of hundreds of evolutionary trees simultaneously in one simplegraph.
而且目前对西方整个防疫工作影响最大的，就是当初剑桥的那份疫情数学模型吧？
直接影响了差不多整个西方的疫情应对。。
真相不是来了吗？为何故意弄错、混淆视听？英文不好？还是居心叵测？
正常的人，都被你们扣帽子。VOA现在都是中国大外宣了，还有什么不可能的事情呢？
另外，讨论政治的，请滚出本帖。我前面一再声明本贴不是政治贴，不欢迎任何政治回贴。
说的非常好。我也对楼主是否看过原文存疑。明明分析用了160个序列，楼主说用了1000个。
又FBI，好像FBI整天没事干了
看到了。那楼主能update 一下有关A型的原文吗？原文说的跟楼主总结的明显不一致啊。明明A型里T C 两种Allele里 ancestal 的病人分别来自广东和武汉，美国和日本等国的都是变异型。
呵呵，说不过就屏蔽，不够爱岗敬业啊。按你造谣的思路，不传白人，怎么会产生C type？
还有，不好意思，我还真是这方面的从业人员。
啊啊啊啊？什么时候给人涨工资的？难怪这么有干劲。
卧槽 你有什么权利禁止别人回复你什么内容？
我没看，但她只是转发了，为什么是造谣？哎呀，我是看不懂，哪能和您比呢？惭愧呀
广东人心里苦，又双躺枪。
这次不一样啊，涉及到谁要为大瘟疫负责，谁在甩锅的事情，肯定要出手啊，呵呵
凡是回复“抬头看ID的”不用说轮子无疑了。赋诗一首
抬头看ID，低头做鸵鸟。不为讨论故，却道他传谣。大法赐我福，大法传我宝。发帖拿回扣，还嫌有点少。
知道自己智商有短板还算有药可救，再给你补一课，原文里的意思被曲解，就是造谣，lol
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.
Phylogenetic network analysis has the potential to help identify undocumented COVID-19 infection sources
— Peter Forster
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 one of the first times 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 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.
版主呢，為什麼不刪除造謠貼呢
这是别人的总结，我说的是原文。前面一楼已经有引用原文并翻译了。难道你不看原文，只看网上评论？
看起来你也是做科研的，有选择性的取样或者样本有偏颇的的文章得到的结论你会信吗？失去了这个基础，讨论这篇文章的数据还有什么意义呢？
如果只用美国数据，证明美国所有case起源于纽约波士顿西雅图任何一个地方，我没有意见，但是作者用了全世界的数据但是缺了大量某原发国的数据，来试图证明病毒的全球起源，不觉得可笑吗？
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.
从这段文字，1.我想问：1000 个里面多少是国内样本？2.韩国的爆发于武汉而且是武汉带过去这个没问题吧，韩国有C。所以逻辑上站不住脚。
国内有个新闻是销毁样本，相信有版上筒子记得，我觉得中国数据
很有Bias。 抽样不全。哪天中国政府敢于分享所有病毒序列，再来做此争论。
我不HIGHLIGHT这句是有原因的。武汉有A, 但A并不主要的类型。也就是说。A型，是一个祖先菌株，并没有在武汉流行，却在美国流行。
这个是个非常可能引起争议的PARTS，需要看DATA， 或者更多序列来证实这一点或者证明这一点错误。，我们可以一起深入讨论
不好意思，你智商有问题吧，科研文章怎么读怎么评判？你从160 样本读出没在武汉流行，你知道其他样本的型吗。明明此文样本有Bias， 还在那讨论。这篇文章到处为止，胡搅蛮缠无理取闹。对不起 疫情之下很烦躁 讨厌这种打着幌子洗地的行为
你脑子是有水吧。人家平心静气讨论你一上来质疑人家智商。你家教哪里学的？
A. 武汉也有，但量少，主要是B. 这部分就非常奇怪。美国有很多A. 如果美国的传染来自于中国，当然是非常可能的，但也引起很多解释不了的问题。
对啊，如果文中数据属实，B又基本没有传出亚洲，那么美国的那么多A哪里来的？大概率不可能是武汉的少量A传过来的啊。
B的传染性更强，A竞争不过，所以武汉以B为主。美国早期只有A，没有竞争对手，所以A的数量多。
既然要深入讨论，再次请楼主对以下原文和翻译发表意见。明明原文说了A型的两种Allele的ancestal genome是广东病人和武汉病人。楼主是怎么得出你在首楼的结论的？！
There are two subclusters of A which are distinguished by the synonymous mutation T29095C. In the T-allele subcluster, four Chinese individuals (from the southern coastal Chinese province of Guangdong) carry the ancestral genome, while three Japanese and two American patients differ from it by a number of mutations. These American patients are reported to have had a history of residence in the presumed source of the outbreak in Wuhan. The C-allele subcluster sports relatively long mutational branches and includes five individuals from Wuhan, two of which are represented in the ancestral node, and eight other East Asians from China and adjacent countries. It is noteworthy that nearly half (15/33) of the types in this subcluster, however, are found outside East Asia, mainly in the United States and Australia.”
翻译一下：
A株有两种子类，一种叫T，一种叫C。T类里面的上游在四个中国人身上发现，T也在3个日本人，2个美国人身上发现，他们都在武汉居住过。C类有5例武汉的病毒，包括2例被认为是C类中的上游。中国之外的亚洲也有8例。亚洲之外有15/33例，大部分是美国或者澳大利亚。
刚刚在另一楼看都到截图，武汉病例序列只上传了28例。
文章中也说了，中国的变异少。即使测序的，序列相同的，没法上传吧
已经说的很清楚了，选择性失聪，疫情之下我暴躁你也暴躁没家教。大家半斤八两。
变异少所以不需要很多样本，还是样本少导致变异少的结论？
武汉A 少量是多少？占比例多少？美国和澳洲都是A多，多又是多少？占多大比例？160个序列，武汉上传了26个，美国上传了多少？美国前期那些病例我记得都是有武汉旅行史的。
另外考虑时间序列，样本的时间分别都是什么时候？
如果美国和澳洲都是A多，欧美联系这么密切，欧洲怎么可能是C？A传到欧洲就成C了？
不排除样本抽样有偏差，取样错误就能得出错误的结论。
Phylogenetic network analysis of SARS-CoV-2 genomes
https://www.pnas.org/content/early/2020/04/07/2004999117
MetroUK对PNAS的论文做出了解读
https://metro.co.uk/2020/04/10/coronavirus-mutated-three-distinct-strains-spread-across-world-12536852/
The findings are published in the journal Proceedings of the National Academy of Sciences (PNAS).
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, the study suggests.
The phylogenetic network methods used by researchers – which looks at evolutionary relationships among biological entities – allowed the visualisation of hundreds of evolutionary trees simultaneously in one simplegraph.
以蝙蝠和穿山甲提取的病毒为基点来分析，Type A是爆发的根源。中国流行的Type B是A的衍生，有两次变异，C是B的子代。
不懂英文也可以看环球时报的文章
https://news.sina.com.cn/c/2020-04-11/doc-iirczymi5615400.shtml
你啥时候也看混球时报的？不是都是胡叼盘么？
楼主要讨论，那就来讨论一下：原文中附件中有具体的每一个的病毒毒株：
这里我就发一张图，是附表2里面的表二我从新排序了一下，所有的A型按照时间顺序排在一起。
美国的滑了红线。
请问，从那里看出来是美国A型是祖先的？
[table=98%]
[td=87] A [td=87] 29095C [td=296] 50 BetaCov/Wuhan/WH04/2020 [td=87] EPI_ISL_406801 [td=87] 1/5/20
A 29095T 28 BetaCov/Shenzhen/HKU-SZ-002/2020 EPI_ISL_406030 1/10/20
A 29095T 27 BetaCov/Shenzhen/HKU-SZ-005/2020 EPI_ISL_405839 1/11/20
A 29095T 40 BetaCov/Shenzhen/SZTH-002/2020 EPI_ISL_406593 1/13/20
A 29095T 13 BetaCov/Guangdong/20SF012/2020 EPI_ISL_403932 1/14/20
A 29095T 14 BetaCov/Guangdong/20SF013/2020 EPI_ISL_403933 1/15/20
A 29095T 16 BetaCov/Guangdong/20SF025/2020 EPI_ISL_403935 1/15/20
A 29095C 71 BetaCov/Sichuan/IVDC-SC-001/2020 EPI_ISL_408484 1/15/20
A 29095C 266 BetaCov/Wuhan/HBCDC-HB-02/2020 EPI_ISL_412978 1/17/20
A 29095C 68 BetaCov/Yu--an/IVDC-YN-003/2020 EPI_ISL_408480 1/17/20
A 29095C 267 BetaCov/Wuhan/HBCDC-HB-03/2020 EPI_ISL_412979 1/18/20
A 29095C 268 BetaCov/Wuhan/HBCDC-HB-04/2020 EPI_ISL_412980 1/18/20
A 29095C 98 BetaCov/Beijing/IVDC-BJ-005/2020 EPI_ISL_408485 1/18/20
A 29095C 25 BetaCov/USA/WA1/2020 EPI_ISL_404895 1/19/20
A 29095C 157 BetaCov/Fujian/8/2020 EPI_ISL_411060 1/21/20
A 29095C 93 BetaCov/Chongqing/YC01/2020 EPI_ISL_408478 1/21/20
A 29095C 189 BetaCov/Hong Kong/VM20001061/2020 EPI_ISL_412028 1/22/20
A 29095T 32 BetaCov/USA/AZ1/2020 EPI_ISL_406223 1/22/20
A 29095C 30 BetaCov/USA/CA1/2020 EPI_ISL_406034 1/23/20
A 29095C 164 BetaCov/Taiwan/3/2020 EPI_ISL_411926 1/24/20
A 29095C 210 BetaCov/Vietnam/VR03-38142/2020 EPI_ISL_408668 1/24/20
A 29095C 58 BetaCov/Australia/NSW01/2020 EPI_ISL_407893 1/24/20
A 29095C 135 BetaCov/USA/WA1-F6/2020 EPI_ISL_407215 1/25/20
A 29095C 167 BetaCov/South Korea/KCDC03/2020 EPI_ISL_407193 1/25/20
A 29095C 56 BetaCov/USA/WA1-A12/2020 EPI_ISL_407214 1/25/20
A 29095C 147 BetaCov/Australia/QLD01/2020 EPI_ISL_407894 1/28/20
A 29095C 90 BetaCov/USA/IL2/2020 EPI_ISL_410045 1/28/20
A 29095C 54 BetaCov/England/02/2020 EPI_ISL_407073 1/29/20
A 29095C 55 BetaCov/England/01/2020 EPI_ISL_407071 1/29/20
A 29095T 77 BetaCov/Japan/TY-WK-012/2020 EPI_ISL_408665 1/29/20
A 29095C 148 BetaCov/Australia/QLD02/2020 EPI_ISL_407896 1/30/20
A 29095C 228 BetaCov/Korea/KCDC05/2020 EPI_ISL_412869 1/30/20
A 29095C 229 BetaCov/Korea/KCDC06/2020 EPI_ISL_412870 1/30/20
A 29095C 230 BetaCov/Korea/KCDC07/2020 EPI_ISL_412871 1/31/20
A 29095T 78 BetaCov/Japan/TY-WK-501/2020 EPI_ISL_408666 1/31/20
A 29095T 79 BetaCov/Japan/TY-WK-521/2020 EPI_ISL_408667 1/31/20
A 29095C 59 BetaCov/Belgium/GHB-03021/2020 EPI_ISL_407976 2/3/20
A 29095C 143 BetaCov/Australia/QLD03/2020 EPI_ISL_410717 2/5/20
A 29095C 144 BetaCov/Australia/QLD04/2020 EPI_ISL_410718 2/5/20
A 29095C 172 BetaCov/USA/CA7/2020 EPI_ISL_411954 2/6/20
A 29095C 232 BetaCov/Korea/KCDC24/2020 EPI_ISL_412873 2/6/20
A 29095C 270 BetaCov/Wuhan/HBCDC-HB-06/2020 EPI_ISL_412982 2/7/20
A 29095T 174 BetaCov/USA/TX1/2020 EPI_ISL_411956 2/11/20
A 29095C 261 BetaCov/USA/WA2/2020 EPI_ISL_412970 2/24/20
赞拿出数据图表打脸那些胡说八道的。这篇论文明明说的很明白，A型的subcluster C的祖先是中国人，而携带A型的几个美国人的病毒是从中国人那里变异过来的，并且这几个美国人都有武汉居住史。无毛们假装看不见，就是一口咬定A型是美国传出来的，真无耻