The outbreak and spread of new strains of coronavirus (SARS-CoV-2) remain a global threat with increasing cases in affected countries. The evolutionary tree of SARS-CoV-2 revealed that Porcine Reproductive and Respiratory Syndrome virus 2, which belongs to the Beta arterivirus genus from the Arteriviridae family is possibly the most ancient ancestral origin of SARS-CoV-2 and other Coronaviridae. This review focuses on phylogenomic distribution and evolutionary lineage of zoonotic viral cross-species transmission of the Coronaviridae family and the implications of bat microbiome in zoonotic viral transmission and infection. The review also casts light on the role of the human microbiome in predicting and controlling viral infections. The significance of microbiome-mediated interventions in the treatment of viral infections is also discussed. Finally, the importance of synthetic viruses in the study of viral evolution and transmission is highlighted.

新型冠状病毒（SARS-CoV-2）的爆发和传播仍然是全球威胁，受影响国家的病例不断增加。SARS-CoV-2的进化树显示，猪繁殖与呼吸综合征病毒2属于动脉病毒科的β动脉病毒属，可能是SARS-CoV-2和其他冠状病毒科最古老的祖先起源。本综述重点关注冠状病毒科人畜共患病毒跨物种传播的系统发育学分布和进化谱系，以及蝙蝠微生物组在人畜共患病毒传播和感染中的影响。该综述还揭示了人类微生物组在预测和控制病毒感染方面的作用。还讨论了微生物组介导的干预措施在治疗病毒感染中的重要性。最后，强调了合成病毒在病毒进化和传播研究中的重要性。