The severe acute respiratory syndrome coronavirus (SARS-CoV) emerged in humans in 2002. Despite reports showing Chiroptera as the original animal reservoir of SARS-CoV, many argue that Carnivora-hosted viruses are the most likely origin. The emergence of the Middle East respiratory syndrome coronavirus (MERS-CoV) in 2012 also involves Chiroptera-hosted lineages. However, factors such as the lack of comprehensive phylogenies hamper our understanding of host shifts once MERS-CoV emerged in humans and Artiodactyla. Since 2019, the origin of SARS-CoV-2, causative agent of coronavirus disease 2019 (COVID-19), added to this episodic history of zoonotic transmission events. Here we introduce a phylogenetic analysis of 2006 unique and complete genomes of different lineages of Orthocoronavirinae. We used gene annotations to align orthologous sequences for total evidence analysis under the parsimony optimality criterion. Deltacoronavirus and Gammacoronavirus were set as outgroups to understand spillovers of Alphacoronavirus and Betacoronavirus among ten orders of animals. We corroborated that Chiroptera-hosted viruses are the sister group of SARS-CoV, SARS-CoV-2 and MERS-related viruses. Other zoonotic events were qualified and quantified to provide a comprehensive picture of the risk of coronavirus emergence among humans. Finally, we used a 250 SARS-CoV-2 genomes dataset to elucidate the phylogenetic relationship between SARS-CoV-2 and Chiroptera-hosted coronaviruses.

中文翻译：

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所有正冠状病毒亚科的基本进化，包括翼手目冠状病毒的三个致命谱系：SARS-CoV、MERS-CoV 和 SARS-CoV-2


严重急性呼吸综合征冠状病毒 (SARS-CoV) 于 2002 年在人类中出现。尽管有报道显示翼手目动物是 SARS-CoV 的原始动物宿主，但许多人认为食肉目宿主病毒是最有可能的来源。 2012 年出现的中东呼吸综合征冠状病毒 (MERS-CoV) 也涉及翼手目宿主谱系。然而，缺乏全面的系统发育等因素阻碍了我们对中东呼吸综合征冠状病毒在人类和偶蹄目动物中出现后宿主转变的理解。自 2019 年以来，2019 年冠状病毒病 (COVID-19) 的病原体 SARS-CoV-2 的起源，为这段人畜共患病传播事件的历史增添了色彩。在这里，我们介绍了对2006年正冠状病毒亚科不同谱系的独特且完整的基因组的系统发育分析。我们使用基因注释来比对直系同源序列，以在简约最优性标准下进行总体证据分析。将 Delta 冠状病毒和Gamma 冠状病毒设置为外群，以了解Alpha 冠状病毒和Beta 冠状病毒在 10 个动物目中的溢出。我们证实翼手目病毒是 SARS-CoV、SARS-CoV-2 和 MERS 相关病毒的姐妹群。其他人畜共患病事件经过定性和量化，以全面了解人类中出现冠状病毒的风险。最后，我们使用 250 个 SARS-CoV-2 基因组数据集来阐明 SARS-CoV-2 和翼手目冠状病毒之间的系统发育关系。