蝙蝠,他们的病毒耐受性,社会行为,和流动性,是新兴病毒的储藏库,包括以遗传灵活性闻名的冠状病毒(CoV)。研究蝙蝠和CoV之间的同系遗传联系为传播动力学和宿主适应提供了重要的见解。先前的研究已经对主机切换等现象产生了有价值的见解,共同物种形成,以及其他有关CoV和蝙蝠之间相互作用的动力学。尽管如此,目前的文献中存在一个明显的差距,涉及比较同系遗传学分析,重点是阐明序列片段对宿主和病毒之间共同进化的贡献。在这项研究中,我们分析了69个宿主病毒连接的同系遗传模式。在所检查的69个宿主病毒链接中,根据ParaFit和PACo分析,47显示出明显的同系发生,确认强有力的协会。专注于两种蛋白质,ORF1ab和spike,我们对宿主和CoV系统发育进行了比较分析。对于ORF1ab,在多个序列比对中的特定窗口(位置520-680、770-870、2930-3070和4910-5080)表现出最低的Robinson-Foulds(RF)距离(即,84.62%),强调其在同系遗传关联中的更高贡献。同样,在尖峰区域内,不同的窗口范围(位置0-140,60-180,100-410,360-550和630-730)显示最低的RF距离为88.46%.我们的分析确定了ORF1ab中的六个重组区(位置360-1390、550-1610、680-1680、700-1710、2060-3090和2130-3250),和4个在刺突蛋白内(位置10-510、50-560、170-710和230-730)。最小RF距离区域与组合区域的融合有力地肯定了重组在病毒适应宿主选择压力中的关键作用。此外,水平基因转移揭示了部分基因转移事件的突出实例,不仅发生在同一宿主物种内的变体中,而且还跨越宿主物种边界。这表明了更复杂的遗传交换模式。通过采用多方面的方法,我们的综合策略提供了控制蝙蝠宿主和CoV之间共同进化动态的复杂相互作用的细微差别的理解。这种更深刻的见解增强了我们对病毒进化和适应机制的理解,揭示了推动病毒多样性的更广泛的动态。
Bats, with their virus tolerance, social behaviors, and mobility, are reservoirs for emerging viruses, including coronaviruses (CoVs) known for genetic flexibility. Studying the cophylogenetic link between
bats and CoVs provides vital insights into transmission dynamics and host adaptation. Prior research has yielded valuable insights into phenomena such as host switching, cospeciation, and other dynamics concerning the interaction between CoVs and
bats. Nonetheless, a distinct gap exists in the current literature concerning a comparative cophylogenetic analysis focused on elucidating the contributions of sequence fragments to the co-evolution between hosts and viruses. In this study, we analyzed the cophylogenetic patterns of 69 host-virus connections. Among the 69 host-virus links examined, 47 showed significant cophylogeny based on ParaFit and PACo analyses, affirming strong associations. Focusing on two proteins, ORF1ab and spike, we conducted a comparative analysis of host and CoV phylogenies. For ORF1ab, the specific window ranged in multiple sequence alignment (positions 520-680, 770-870, 2930-3070, and 4910-5080) exhibited the lowest Robinson-Foulds (RF) distance (i.e., 84.62%), emphasizing its higher contribution in the cophylogenetic association. Similarly, within the spike region, distinct window ranges (positions 0-140, 60-180, 100-410, 360-550, and 630-730) displayed the lowest RF distance at 88.46%. Our analysis identified six recombination regions within ORF1ab (positions 360-1390, 550-1610, 680-1680, 700-1710, 2060-3090, and 2130-3250), and four within the spike protein (positions 10-510, 50-560, 170-710, and 230-730). The convergence of minimal RF distance regions with combination regions robustly affirms the pivotal role of recombination in viral adaptation to host selection pressures. Furthermore, horizontal gene transfer reveals prominent instances of partial gene transfer events, occurring not only among variants within the same host species but also crossing host species boundaries. This suggests a more intricate pattern of genetic exchange. By employing a multifaceted approach, our comprehensive strategy offers a nuanced understanding of the intricate interactions that govern the co-evolutionary dynamics between bat hosts and CoVs. This deeper insight enhances our comprehension of viral evolution and adaptation mechanisms, shedding light on the broader dynamics that propel viral diversity.