文献笔记五十六：武汉新型冠状病毒的进化分析2

论文题目

Evolution of the novel coronavirus from the ongoing Wuhan outbreak and modeling of its spike protein for risk of human transmission 2020年1月21日 SCIENCE CHINA Life Sciences

研究单位

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主要的研究内容

• Evolution of the novel coronavirus from the ongoing Wuhan outbreak 武汉新型冠状病毒的进化分析
• modeling of its spike protein for risk of human transmission 传播风险建模（这部分内容自己暂时还没有看懂）

本篇笔记重点关注论文中对进化树的解释

图一A

• The results showed the Wuhan CoVs were clustered together in the phylogenetic tree, which belong to the Betacoronavirus genera. 武汉新型冠状病毒在进化树上聚在一起，它属于Beta冠状病毒属
• The Wuhan CoV cluster is situated with the groups of SARS/SARS-like coronaviruses, wiht bat coronavirus HKU9-1 as the immediate outgroup. 武汉新型冠状病毒和SARS/SARS-like冠状病毒聚为一大类，bat coronavirus HKU9-1是其最近的外类群。
• Its inner joint neighbors are SARS or SARS-like coronaviruses, including the human-infecting ones. 和武汉新型冠状病毒聚在一起的SARS/SARS-like 冠状病毒中包括可以感染人类的病毒。
• Most of the inner joint neighbors and the outgroups were found in various bats as natural hosts, e.g., bat coronaviruses HKU9-1 and HKU3-1 in Rousettus bats and bat coronavirus HKU5-1 in Pipistrellus bats. 大部分和武汉新型冠状病毒聚在一起的SARS/SARS-like 冠状病毒和最近的外类群的自然宿主是各种各样的蝙蝠
• Thus, bats being the native host of the Wuhan CoV would be the logical and convenient reasoning, though it remains likely there was intermediate host(s) in the transmission cascade from bats to humans. 因此推断武汉新型冠状病毒的自然宿主是蝙蝠是合乎逻辑的（convenient是什么意思是呢？）的理由。但是在蝙蝠向人类传播的过程中可能有中间宿主的存在。
• Based on the unique phylogenetic position of the Wuhan CoVs, it is likely that they share with the SARS/SARS-like coronaviruses, a common ancestor that resembles the bat coronavirus HKU9-1. 根据进化分析的结果，武汉新型冠状病毒可能与SARS/SARS-like 冠状病毒存在共同的祖先，这个共同祖先与 bat冠状病毒HKU9-1相似。

ggtree操作进化树

library(ggtree)
tree<-read.tree("../../Novel_Coronavirus/novelvirus.treefile")
library(ggplot2)
df<-fortify(tree)
df1<-df[which(!df$isTip),]
df1$bootstrap<-ifelse(df1$label>=50,">=50","<50")
df2<-df[which(df$isTip),]
df3_1<-df2[20:25,]
df3_1
df3_2<-df2[c(1:19,26:64),]
df3_1$color<-"A"
df3_2$color<-"B"
df3<-rbind(df3_1,df3_2)
library(dplyr)
df3<-df3%>%
  select(c("label","color"))
df3
p<-ggtree(df,layout = "circular")+
  geom_point(data=df1,aes(x=x,y=y,color=bootstrap),size=5)
p
p1<-p%<+%df3+
  geom_tiplab2(aes(col=color),align=T)+
  scale_color_manual(values=c("darkgreen","skyblue","red","black"))
p1
pdf(file="nv1.pdf",height=20,width=20)
rotate_tree(p1,135)
dev.off()

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过程中遇到的问题

• 使用%<+%操作符后暂时不知道如何修改tiplabel的大小了
• 使用%<+%操作符后geom_cladelabel()函数使用也遇到了问题

以上两个问题暂时还不知道如何解决

• rotate_tree()函数是用来旋转进化树的
• open_tree()函数用来控制开口

文章中用到的序列数据大家可以自己下载，或者直接在我的公众号留言即可！