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.
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.
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.
先总结两句次要的： 1.意大利病毒来自于新加坡。新加坡人将病毒传染到德国，再传到意大利。 2. 武汉的B株 病毒是病毒的"FOUNDER EFFECT" 3. A 株病毒是病毒爆发的根源。 4. A变异，得到B. B变异，得到了C. 5. 后面再写，能解释的东西太多了，能大概列100项。。。。 mindstorm 发表于 4/10/2020 11:54:21 AM
回复 1楼mindstorm的帖子 你为什么把这两句最关键的隐藏了？ 原文明明是说A来自云南蝙蝠，“ancestral genome”是中国人携带。 美国日本病人携带的是大量变异后的产物 https://www.pnas.org/content/early/2020/04/07/2004999117 Phylogenetic network of 160 SARS-CoV-2 genomes. Node A is the root cluster obtained with the bat (R. affinis) coronavirus isolate BatCoVRaTG13 from Yunnan Province. 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
Phylogenetic network of 160 SARS-CoV-2 genomes. Node A is the root cluster obtained with the bat (R. affinis) coronavirus isolate BatCoVRaTG13 from Yunnan Province.
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 120ParkAve 发表于 4/10/2020 12:35:23 PM <img src="[url=http://forums.huaren.us/images/common/back.gif"/>]http://forums.huaren.us/images/common/back.gif"/>[/url]
ZT 虽然我不是搞生物或者医学方面的，但凭俺当年GRE逻辑满分的水平，读这么一篇论文 还是绰绰有余的，现在俺来解读分析一下，免得一帮拿钱发帖的家伙在此混淆视听。 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. 这段首先说明A类新冠是最早类型，因为它和蝙蝠身上的病毒最接近。武汉有这类病毒 ，但不是主流。 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. 第二段说的是美澳有很多A类病毒，而那些在武汉居住过的美国人里发现A类的变种。 文章后面关于A和B关系的解释： 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. 结合上面两段，唯一可以确证的是新冠病毒来源于蝙蝠。也许是武汉的蝙蝠，也许不是 ，但就算是武汉蝙蝠，该病毒开始对武汉当地人并没有太严重的危害，因为那个市场存 在多年，新冠一直没有大爆发。如果病毒来源是武汉蝙蝠，那么合理推论应该是由于武 毒所和美国的合作，该病毒被送到美国研究，后来在美国泄露，造成病毒在美国人群流 传，并因亚欧人种差异，开始展现严重致病性。然后美国到武汉的人将身体中A类带回 武汉，因为奠基者效应，先发展成A类变种，然后再由此变异成武汉主流B类传到亚洲人 种。 如果不是武汉蝙蝠，那就是美国本土原产病毒，在人群中流传开后，由美国人带到武汉 ，后面变异途径同上段所述一样。 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. 这段说的是B类是东亚主要类型，而且基本只存在于东亚，而出了东亚区域后，再次因 为奠基者效应而变异成C类。 所以，合理的结论是：不管病毒到底是哪里起源的，这个疾病应该是美国首发，然后扩 散至全世界。
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.
这段首先说明A类新冠是最早类型，因为它和蝙蝠身上的病毒最接近。武汉有这类病毒 ，但不是主流。
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.
第二段说的是美澳有很多A类病毒，而那些在武汉居住过的美国人里发现A类的变种。
文章后面关于A和B关系的解释： 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.
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.
Phylogenetic network of 160 SARS-CoV-2 genomes. Node A is the root cluster obtained with the bat (R. affinis) coronavirus isolate BatCoVRaTG13 from Yunnan Province.
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。
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.
这段首先说明A类新冠是最早类型，因为它和蝙蝠身上的病毒最接近。武汉有这类病毒 ，但不是主流。
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.
第二段说的是美澳有很多A类病毒，而那些在武汉居住过的美国人里发现A类的变种。
文章后面关于A和B关系的解释： 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.
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.
论文里的原话：意大利的病例追溯到德国，德国的病例追溯到武汉，而不是楼主说的新加坡 Not only does the network confirm the Italian origin of the Mexican virus (SI Appendix, Fig. S3), but it also implies that this Italian virus derives from the first documented German infection on 27 January 2020 in an employee working for the Webasto company in Munich, who, in turn, had contracted the infection from a Chinese colleague in Shanghai who had received a visit by her parents from Wuhan. This viral journey from Wuhan to Mexico, lasting a month, is documented by 10 mutations in the phylogenetic network.
Not only does the network confirm the Italian origin of the Mexican virus (SI Appendix, Fig. S3), but it also implies that this Italian virus derives from the first documented German infection on 27 January 2020 in an employee working for the Webasto company in Munich, who, in turn, had contracted the infection from a Chinese colleague in Shanghai who had received a visit by her parents from Wuhan. This viral journey from Wuhan to Mexico, lasting a month, is documented by 10 mutations in the phylogenetic network. zyskywalker 发表于 4/10/2020 12:55:58 PM <a href="/showtopic.aspx?topicid=2531578&postid=83549309#83549309" 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]
这是原文：“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”.”
ZT 虽然我不是搞生物或者医学方面的，但凭俺当年GRE逻辑满分的水平，读这么一篇论文 还是绰绰有余的，现在俺来解读分析一下，免得一帮拿钱发帖的家伙在此混淆视听。 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. 这段首先说明A类新冠是最早类型，因为它和蝙蝠身上的病毒最接近。武汉有这类病毒 ，但不是主流。 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. 第二段说的是美澳有很多A类病毒，而那些在武汉居住过的美国人里发现A类的变种。 文章后面关于A和B关系的解释： 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. 结合上面两段，唯一可以确证的是新冠病毒来源于蝙蝠。也许是武汉的蝙蝠，也许不是 ，但就算是武汉蝙蝠，该病毒开始对武汉当地人并没有太严重的危害，因为那个市场存 在多年，新冠一直没有大爆发。如果病毒来源是武汉蝙蝠，那么合理推论应该是由于武 毒所和美国的合作，该病毒被送到美国研究，后来在美国泄露，造成病毒在美国人群流 传，并因亚欧人种差异，开始展现严重致病性。然后美国到武汉的人将身体中A类带回 武汉，因为奠基者效应，先发展成A类变种，然后再由此变异成武汉主流B类传到亚洲人 种。 如果不是武汉蝙蝠，那就是美国本土原产病毒，在人群中流传开后，由美国人带到武汉 ，后面变异途径同上段所述一样。 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. 这段说的是B类是东亚主要类型，而且基本只存在于东亚，而出了东亚区域后，再次因 为奠基者效应而变异成C类。 所以，合理的结论是：不管病毒到底是哪里起源的，这个疾病应该是美国首发，然后扩 散至全世界。 slamdunkfan 发表于 4/10/2020 12:43:07 PM
这是原文：“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”.”
楼主是故意扭曲还是英语不好？ 楼主说：“4. A变异，得到B. B变异，得到了C. 6. 美国是A, 中国是B, 欧洲是C.” 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.” 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。
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.
先总结两句次要的：
1.意大利病毒来自于德国，德国的来自于中国上海同事传染。
2. 武汉的B株 病毒是病毒的"FOUNDER EFFECT"
3. A 株病毒是病毒爆发的根源。
4. A变异，得到B. B变异，得到了C.
5. A来自于云南的蝙蝠
6. 美国是A, 中国是B, 欧洲是C.
后面再写，能解释的东西太多了。。。。
🔥 最新回帖
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
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
你啥时候也看混球时报的？不是都是胡叼盘么？
🛋️ 沙发板凳
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.
这个文章牛啊。
外行看了下，感觉这篇很水，和以前的台湾说差不多啊，用的极早数据，美国病人从武汉来也不说，武汉早期病人数据缺失不说，居然还基于前提是云南的蝙蝠基因
型是A的变种。那更合理的解释就是这个病毒是从美国输入武汉的，然后在武汉变异并
开始流传了。
武汉主要为B病毒，A病毒较少；
美国澳洲主要为A病毒；
欧洲主要为C病毒。
美国或为病毒源头
赵立坚居然蒙对了？
美国的东部主要是意大利来的，我们东北这块最开始发现的都是春假意大利游学回来的
我感觉大家还需要看原文仔细看证据的正确与否。目前就文章的论述的情况来看，感觉事情真相基本出水了
这是为什么能解释一个疑问：为什么纽约死亡率高，真心不怪纽约政府，纽约医生跟医院。
PNAS，基本是学术上，学者们最认可的之一，当然也有灌水。
纠正你一句： 武汉本地有A, 虽然不是 predominant virus type.
type ‘A’, the “original human virus genome” – was present in Wuhan, but surprisingly was not the city’s predominant virus type.
疏忽了这个病毒超级传染性：R值，发病时间顺序；同时不提变异性。模糊视听。
给你说个故事：一个蠢笨的杀人犯每家每户都去行凶，尸体终于被发现，由于没有当场抓住，杀人犯以为有机可趁到处污蔑甩锅陷害，我们来看看会不会成功呢，拭目以待吧！ 我要说一句，国人和华人也是受害者。
感觉我们是不是time travel了？病毒大概是future来的
请不要参杂政治性的东西，我们来讨论证据，文章，你这比喻，就是轮子一直用的。而且请你好好看文章，文章中其实解释了
你们这些SB无毛，到底看不看得懂英文啊？
你们所有知识都来自于微博吗？
没有两个美国院士推荐，文章想水也发不了水啊。。。
MM的猫咪好乖，古人厉害推背图预言过这次大瘟疫。我相信始作佣们清清楚楚知道这个病毒来龙去脉。
等一下
如果光从mutation看，是怎么知道谁先谁后的呢？
为什么不可以是c->b->a?
看文章了吗？文章中说了A 变异株发现于在武汉居住的美国人。。。。
哦
明白了
a和🦇最接近...
可是美国人也不吃🦇，云南的蝙蝠是怎么来美国的呢
C的所有等位位点，在AB上没有，AB的等位位点，在C上全有，C就应当是起源于A--B.
这种结论一般是没有问题的。
可是云南蝙蝠是怎么来美国并跑到人群中的呢？
你自己说。。。。。
现在的论文太水了，武汉病毒序列海外能拿到的有多少？不过微信马上要高潮了……
难道不是相亲男从武汉带了a回来？
这倒是的
一开始西雅图拿到了一点
后来，就没有后来了
讨论政治的，请GO AWAY! 如果你有观点，请直接批文章哪里有问题呗。
PNAS 不见得水。
如果是直接投稿，难度不比CNS 或者大子刊容易。如果院士直接投稿，那就是水。
我的天，你是说PNAS是笑话，美国院士是笑话，你所谓的原始毒株不是笑话？
你有证据有资料，发上来大家看一下，正好一起批这文章。没有任何东西，直接随便说，造谣的人岂不是你？
肯定是美军去云南吃蝙蝠炖穿山甲，然后马上去军运会，还和武汉本地美国人联欢，就是这样，不信你去问痰得塞博士，他们是世界流行病最权威组织，极其可信
赞👍
😿🙀
骂得好，这些五毛根本看不懂英文，收到上头指令就开始发帖甩锅，那片文章清楚说明ancestor genome来自中国，
只是武汉B类更多而已，根本不能得出五毛嘴里“武汉不是病毒源头”的结论
这有什么问题？ 我只划了重点。我完全可以把全文放上，没有任何问题。
你看懂了论文了吗？你说的没有问题，可是你完全没有看懂论文啊。
当人是傻子么，你那个根本就不是什么“重点”好不好，只是你故意截取的片段来“证明”你早有的结论。
再水，也是学术圈里被认可的重要文章，而作者是剑桥大学的实验室
我把你说的内容的中文加到首帖里了。你不用带立场，本帖不欢迎任何政治性的回帖。想讨论政治，请另开一个帖子好吗？
基因的变异可看，谁是parent.
看看这一段。还有问题吗？
Phylogenetic network of 160 SARS-CoV-2 genomes. Node A is the root cluster
obtained with the bat (R. affinis) coronavirus isolate BatCoVRaTG13 from
Yunnan Province.
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。
我不信法轮功，但轮子也不是什么坏人有时候说的话很有道理。我这个比喻是我真实的想法，和政治无关和事实有关。要看懂这篇文章，1: 分析了多少样本，哪些国家的样本 ，每个国家样本的数目，此举需要考虑每个国家感染人数 否则sampling 会有偏差 2. RNA 病毒mutation rate 超高 我不大清楚目前的测序可以判定源头，这是个新病毒，除非大样本分析采集变异规律。
白宫有个super computing task ，看过段时间等那边会不会有报告。
纽约大部分来自欧洲，这个基本是没有问题的。但是这个是世界起源是两码事。
批评的就是整篇文章都是基于各国上传的样本，所以文章的问题是“武汉病毒原始数据缺失”导致结论的不确定性
请问你有什么观点？
因为这些序列是后来的，根本没有上传
所以不更说明这篇文章不是在获得大量序列后全面分析的结论，只是一个片面的推测
文章分析了160的病毒序列，软件可分析1000序列。至于其他的，我前面说了，要看原文的数据
为什么美国不是最早爆发， 不要扯电子烟，那是很无聊的阴谋论。也不可能是以前毒性比现在弱，因为剑桥检测的是现在的毒株。
如果序列没上传，你说怎么样才能不片面呢？
LOL. 你说的没错。我知道的。。。。
这是原文：“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”.”
你说的应当是对的，这里的意思是有两个并行病毒变种
哪里来的一千个序列？原文的Methods部分明明白白写着160个序列。你真的读过原文吗？
你说错了。其他地方讨论这个的已经火爆了，美国放毒是共识了。
你才造谣。你们原来真的不懂英文啊？台湾人，轮子不学英文吗？
我说过了，这文章解释了一切疑问。里面清清楚楚说明了为什么之前不感染白人，为什么现在感染白人。
首先所以数据引用了12月以后的，早期数据为0，早期11月12月初的武汉里有没有大量A，不得而知，其次A在美国依旧爆发了，按照时间推算呢，要知道这是一个传染病，R0的中位数是5.7瞒得了谁？ 要拿电子烟说是的，但是电子烟插管有医护中招么？显然没有显然不是具备传播性
既然如此，为什么在你的总结里，把新加坡的途径醒目地放在第一条，而不提这个武汉的途径？bias?
我说的是华人网，这个网站啥性质还是很清楚的
“A来自云南蝙蝠”这句8 个字的话，难道比你划出的一大片几百字的文章都次要，所以可以忽略？你这个深沉人员，是服务得很好，小看你了。
刷新一下，就看到我改过的了
你是想说华人是大外宣目前还没买下来的网站吗？
地基建在了沙地上，不歪才怪
可能我就不应当加中文进去，这样只讨论政治的就可以GO AWAY....
100万病例，全部测序了吗，全部是变异株吗？
别在我这里露怯了，这篇文章1. 缺乏武汉的大规模样品，2. 那个A也是在武汉居住的华裔
还有这篇文章哪里说不传白人？看你上蹿下跳，包藏祸心很久了。将来各国肯定会彻查病毒来源的，其中带节奏造谣误导的等着FBI上门吧。
如果那时美国有A， 现在也是A， 那时为何不爆发，等到现在？ 如果现在美国爆发的主要是B， 那么就是大陆传来的，大陆是根源。
文章又不是她写的，怎么是她造谣？你这才是造谣
文章中也解释了，这文章几乎解释了现在的所有主要疑问
2. 武汉的B株 病毒是病毒的"FOUNDER EFFECT"
传染性如此严重，指数型增长的病毒，如果12月以后武汉没有大量A，那么早期更不可能有啊
1.他以前造谣不传白人，证据还在；2. 这篇文章数据不足，并且结论被他曲解，也算造谣。Lol，智商是个好东西，btw, 你这样说说明那篇文章你根本看不懂，Lol
100多万都是早期那些蔓延开来的。。追查早期的传播途径显然更重要。。
你是文科生？
根本不是数据不足的问题，就算是原文，也说是A类里面中国毒株的是上游。哪来说的美国的是源头？国内的造谣都是赌大家不去看英语原文
比较原始序列，最早的是蝙蝠和穿三甲的序列
你才造谣。看不懂英文，也没有脑子也好意思出来讨论问题？
给你最后科普一次，然后屏蔽你。病毒在不停变异， 在中国感染中国的人是B TYPE， 同期武汉回来的美国人，感染率很低，C TYPE才是后来引起欧洲的致死菌株，懂了吗？