The emergence of a novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and more recently, the independent evolution of multiple SARS-CoV-2 variants has generated renewed interest in virus evolution and cross-species transmission. While all known human coronaviruses (HCoVs) are speculated to have originated in animals, very little is known about their evolutionary history and factors that enable some CoVs to co-exist with humans as low pathogenic and endemic infections (HCoV-229E, HCoV-NL63, HCoV-OC43, HCoV-HKU1), while others, such as SARS-CoV, MERS-CoV and SARS-CoV-2 have evolved to cause severe disease. In this review, we highlight the origins of all known HCoVs and map positively selected for mutations within HCoV proteins to discuss the evolutionary trajectory of SARS-CoV-2. Furthermore, we discuss emerging mutations within SARS-CoV-2 and variants of concern (VOC), along with highlighting the demonstrated or speculated impact of these mutations on virus transmission, pathogenicity, and neutralization by natural or vaccine-mediated immunity.

中文翻译：

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SARS-CoV-2 的进化轨迹和新出现的变种

新型冠状病毒——严重急性呼吸综合征冠状病毒 2 (SARS-CoV-2) 的出现，以及最近多个 SARS-CoV-2 变体的独立进化，引起了人们对病毒进化和跨物种传播的新兴趣。虽然所有已知的人类冠状病毒 (HCoV) 都被推测起源于动物，但人们对它们的进化历史以及使某些 CoV 作为低致病性和地方性感染与人类共存的因素知之甚少（HCoV-229E、HCoV-NL63） 、HCoV-OC43、HCoV-HKU1），而其他病毒，如 SARS-CoV、MERS-CoV 和 SARS-CoV-2 已经进化到导致严重疾病。在这篇综述中，我们重点介绍了所有已知 HCoV 的起源，并针对 HCoV 蛋白内的突变进行了积极选择的图谱，以讨论 SARS-CoV-2 的进化轨迹。此外，我们还讨论了 SARS-CoV-2 中新出现的突变和相关变体 (VOC)，并强调了这些突变对病毒传播、致病性以及自然或疫苗介导免疫的中和作用已证实或推测的影响。