Statistics Department, University of Georgia, Athens, GA, USA.
Institute of Bioinformatics, University of Georgia, Athens, GA, USA.
Sci Rep. 2023 Apr 5;13(1):5571. doi: 10.1038/s41598-023-32622-4.
A consensus species tree is reconstructed from 11 gene trees for human, bat, and pangolin beta coronaviruses from samples taken early in the pandemic (prior to April 1, 2020). Using coalescent theory, the shallow (short branches relative to the hosts) consensus species tree provides evidence of recent gene flow events between bat and pangolin beta coronaviruses predating the zoonotic transfer to humans. The consensus species tree was also used to reconstruct the ancestral sequence of human SARS-CoV-2, which was 2 nucleotides different from the Wuhan sequence. The time to most recent common ancestor was estimated to be Dec 8, 2019 with a bat origin. Some human, bat, and pangolin coronavirus lineages found in China are phylogenetically distinct, a rare example of a class II phylogeography pattern (Avise et al. in Ann Rev Eco Syst 18:489-422, 1987). The consensus species tree is a product of evolutionary factors, providing evidence of repeated zoonotic transfers between bat and pangolin as a reservoir for future zoonotic transfers to humans.
从大流行早期（2020 年 4 月 1 日之前）采集的人类、蝙蝠和穿山甲β冠状病毒的 11 个基因树重建共识种系发生树。利用合并理论，浅共识种系发生树（相对于宿主的短分支）为蝙蝠和穿山甲β冠状病毒之间的近期基因流动事件提供了证据，这些事件发生在向人类传播之前。共识种系发生树还用于重建人类 SARS-CoV-2 的祖先序列，该序列与武汉序列有 2 个核苷酸不同。最近共同祖先的时间估计为 2019 年 12 月 8 日，起源于蝙蝠。在中国发现的一些人类、蝙蝠和穿山甲冠状病毒谱系在系统发育上是不同的，这是罕见的第二类系统地理学模式的例子（Avise 等人，在 Ann Rev Eco Syst 18:489-422, 1987）。共识种系发生树是进化因素的产物，为蝙蝠和穿山甲之间反复发生的人畜共患病转移提供了证据，它们是未来向人类传播的人畜共患病的储存库。
