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.
COVID-19: genetic network analysis provides ‘snapshot’ of pandemic origins
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.
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.
【鱼论】剑桥大学官样文章 新冠源自美国
新冠病毒在全球变异成3种毒株！专家警告正在快速突变
南方都市报
04/10 22:28
英国科学家研究发现，新型冠状病毒在世界各地传播的过程中变异成了3种不同的毒株，而且“正在快速突变，以适应不同人群中的免疫系统抵抗力”。研究还表明，在一些美国人身上发现的病毒变体与蝙蝠中发现的病毒关系最密切。
据英国《太阳报》4月10日报道，来自剑桥大学的研究人员绘制了新冠病毒（Covid-19）最初在人类中传播的地图，发现有三个不同但密切相关的变体。
科学家重建了新冠病毒的早期进化路径，即从中国疫情最严重地区再到欧洲和北美。这项研究结果发表在最新一期《美国国家科学院院刊》(PNAS)上。
这项研究论文主要作者、剑桥大学遗传学家彼得·福斯特（Peter Forster）博士表示，通过分析从患者身上发现的第一批160个完整的病毒基因组序列发现，与在蝙蝠身上发现的最接近的变异主要在来自美国和澳大利亚的患者身上，而不是在中国武汉患者身上。
新冠病毒在全球传播中变异成3种不同毒株
他们使用了2019年12月24日至2020年3月4日期间从世界各地采集的样本数据。数据表明，新冠病毒有三个截然不同但密切相关的变体，被称之为A、B和C。
研究人员发现，与蝙蝠中发现的最接近的冠状病毒类型是A型，即原始的人类病毒基因组。该病毒基因组存在于武汉，但不是武汉地区的主要病毒类型。
在居住于武汉的美国人身上发现了突变的A型病毒，在来自美国和澳大利亚的患者中也发现了大量的A型病毒。
武汉患者的主要病毒类型是B型，并在东亚各地的患者中存在，然而，如果没有进一步的变异，它不会在该地区以外传播太多。
研究人员说，C型病毒是主要的欧洲类型，在来自法国、意大利、瑞典和英国的早期患者中发现。C型病毒没有出现在该研究中的中国大陆患者样本中，但在新加坡、中国香港和韩国都有发现。
分析还表明，该病毒最早传入意大利的途径之一是1月27日通过首例记录在案的德国患者感染，另一条早期的意大利感染途径与“新加坡聚集性”有关。
研究结果认为，A型病毒与蝙蝠和穿山甲中发现的病毒关系最密切，研究人员将其描述为疫情暴发的根源。B型病毒由A型衍生而来，被两个突变分开，然后C型反过来又是B型的“女儿”。
采取“社交隔离”能有效抑制病毒传播（左边为毫无措施传播速度，右边为采取措施传播速度）
福斯特说，病毒有太多的快速突变，无法完整地追踪Covid-19家谱。“但是，我们使用一种数学网络算法来同时可视化所有看似合理的树。这些技术最为人所知的是通过DNA绘制史前人口迁徙地图。我们认为，这是它首次被用来追踪像Covid-19这样的冠状病毒的感染途径。”
专家们警告，新冠病毒正在不断地快速变异，以适应不同人群中的免疫系统抵抗力。
福斯特表示，他们的方法可以应用于最新的冠状病毒基因组测序，以帮助预测未来全球疾病传播和激增的热点。
研究人员使用了系统发育网络方法——观察生物实体之间的进化关系，这样可以在一个简单的图表中同时可视化数百棵进化树。
编译/采写：南都记者 史明磊
COVID-19: genetic network analysis provides ‘snapshot’ of pandemic origins
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更多我的博客文章>>> 剑桥大学官样文章 新冠源自美国 谁不想知道真相？真相离我们越来越近了 美国是新冠毒源 总有一天会真相大白 是美国人害了全世界 包括他们自己 呵呵 这一棍 稳准狠打在七寸上
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.
断章取义最拿手，还喜欢借老外的嘴，因为他们知道自己说的没人信
COVID-19: genetic network analysis provides ‘snapshot’ of pandemic originsStudy 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 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.
同理如果是在美国，那欧洲也会有很多。所以是两种可能，1. 武汉把A病毒传到美，澳。2. 美，澳把A病毒传到武汉
考虑到如果A已经在武汉传播，那军运会就是一个很好的传播途径，如果起源是武汉，那鉴于运动员来自世界各地，这个病毒可能在好多国家都可以找到。但现在只有美，澳。所以更像是传入。运动会一个月后，新冠在武汉全面爆发。
A型在武汉和北美发现， 武汉发现早于北美，病毒从理论上是从武汉传导北美。 文章为了`政治正确，没有直接说出来。。
可悲呀，一切都政治化了。