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本帖最后由 Learnerd 于 2020-4-11 22:05 编辑
驴是念来过倒 发表于 2020-4-11 20:29 
剑桥大学昨天发表论文，认为新冠病毒A类是病毒爆发的根源，而A类集中出现在美国和澳洲，出现于武汉的病毒 ...
好吧, 既然你不贴原文我来贴. 通篇哪有A类在武汉只有极少案例，且来源于在武汉生活过的美国人这种字眼? 还是那句话, 作者我都给你列上来了, 去找作者确认. 只要有一个作者confirm你就算你赢
Zhou et al. (7) recently reported a closely related bat coronavirus, with 96.2% sequence similarity to the human virus. We use this bat virus as an outgroup, resulting in the root of the network being placed in a cluster of lineages which we have labeled “A.” Overall, the network, as expected in an ongoing outbreak, shows ancestral viral genomes existing alongside their newly mutated daughter genomes.
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.
Two derived network nodes are striking in terms of the number of individuals included in the nodal type and in mutational branches radiating from these nodes. We have labeled these phylogenetic clusters B and C.
For type B, all but 19 of the 93 type B genomes were sampled in Wuhan (n = 22), in other parts of eastern China (n = 31), and, sporadically, in adjacent Asian countries (n = 21). Outside of East Asia, 10 B-types were found in viral genomes from the United States and Canada, one in Mexico, four in France, two in Germany, and one each in Italy and Australia. Node B is derived from A by two mutations: the synonymous mutation T8782C and the nonsynonymous mutation C28144T changing a leucine to a serine. Cluster B is striking with regard to mutational branch lengths: While the ancestral B type is monopolized (26/26 genomes) by East Asians, every single (19/19) B-type genome outside of Asia has evolved mutations. This phenomenon does not appear to be due to the month-long time lag and concomitant mutation rate acting on the viral genome before it spread outside of China (Dataset S1, Supplementary Table 2). A complex founder scenario is one possibility, and a different explanation worth considering is that the ancestral Wuhan B-type virus is immunologically or environmentally adapted to a large section of the East Asian population, and may need to mutate to overcome resistance outside East Asia.
Type C differs from its parent type B by the nonsynonymous mutation G26144T which changes a glycine to a valine. In the dataset, this is the major European type (n = 11), with representatives in France, Italy, Sweden, and England, and in California and Brazil. It is absent in the mainland Chinese sample, but evident in Singapore (n = 5) and also found in Hong Kong, Taiwan, and South Korea.
One practical application of the phylogenetic network is to reconstruct infection paths where they are unknown and pose a public health risk. The following cases where the infection history is well documented may serve as illustrations (SI Appendix). On 25 February 2020, the first Brazilian was reported to have been infected following a visit to Italy, and the network algorithm reflects this with a mutational link between an Italian and his Brazilian viral genome in cluster C (SI Appendix, Fig. S1). In another case, a man from Ontario had traveled from Wuhan in central China to Guangdong in southern China and then returned to Canada, where he fell ill and was conclusively diagnosed with coronavirus disease 2019 (COVID-19) on 27 January 2020. In the phylogenetic network (SI Appendix, Fig. S2), his virus genome branches from a reconstructed ancestral node, with derived virus variants in Foshan and Shenzhen (both in Guangdong province), in agreement with his travel history. His virus genome now coexists with those of other infected North Americans (one Canadian and two Californians) who evidently share a common viral genealogy. The case of the single Mexican viral genome in the network is a documented infection diagnosed on 28 February 2020 in a Mexican traveler to Italy. 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.
This viral network is a snapshot of the early stages of an epidemic before the phylogeny becomes obscured by subsequent migration and mutation. The question may be asked whether the rooting of the viral evolution can be achieved at this early stage by using the oldest available sampled genome as a root. As SI Appendix, Fig. S4 shows, however, the first virus genome that was sampled on 24 December 2019 already is distant from the root type according to the bat coronavirus outgroup rooting.
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发表于 2020-4-9 20:21:26
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