Phylogenetic network analysis of SARS-CoV-2 genomes
摘要：
In a phylogenetic network analysis of 160 complete human severe acute respiratory syndrome coronavirus 2 (SARS-Cov-2) genomes, we find three central variants distinguished by amino acid changes, which we have named A, B, and C, with A being the ancestral type according to the bat outgroup coronavirus. The A and C types are found in significant proportions outside East Asia, that is, in Europeans and Americans. In contrast, the B type is the most common type in East Asia, and its ancestral genome appears not to have spread outside East Asia without first mutating into derived B types, pointing to founder effects or immunological or environmental resistance against this type outside Asia. The network faithfully traces routes of infections for documented coronavirus disease 2019 (COVID-19) cases, indicating that phylogenetic networks can likewise be successfully used to help trace undocumented COVID-19 infection sources, which can then be quarantined to prevent recurrent spread of the disease worldwide.
Google 翻译：
在对160个完整的人类严重急性呼吸系统综合症冠状病毒2（SARS-Cov-2）基因组进行的系统进化网络分析中，我们发现了三个主要的变异体，它们的氨基酸变化不同，我们将其命名为A，B和C，其中A为根据蝙蝠的外祖先型冠状病毒。 A和C类型在东亚以外地区（即欧洲人和美国人中）的比例很高。相比之下，B型是东亚最常见的类型，其祖先基因组似乎没有先突变成衍生的B型就没有在东亚以外传播，这表明在亚洲以外对该类型的创始人具有影响力或免疫或环境抵抗力。该网络忠实地跟踪了记录在案的冠状病毒病2019（COVID-19）病例的感染途径，这表明系统进化网络同样可以成功地用于帮助跟踪未记录的COVID-19感染源，然后可以对其进行隔离以防止疾病复发全世界。
Fig. 1.
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. Circle areas are proportional to the number of taxa, and each notch on the links represents a mutated nucleotide position. The sequence range under consideration is 56 to 29,797, with nucleotide position (np) numbering according to the Wuhan 1 reference sequence (8). The median-joining network algorithm (2) and the Steiner algorithm (9) were used, both implemented in the software package Network5011CS (https://www.fluxus-engineering.com/), with the parameter epsilon set to zero, generating this network containing 288 most-parsimonious trees of length 229 mutations. The reticulations are mainly caused by recurrent mutations at np11083. The 161 taxa (160 human viruses and one bat virus) yield 101 distinct genomic sequences. The phylogenetic diagram is available for detailed scrutiny in A0 poster format (SI Appendix, Fig. S5) and in the free Network download files.
