The pandemic caused by SARS-CoV-2 has had a significant impact on the whole world. In a theory of the origin of SARS-CoV-2, pangolins are considered as a potential intermediate host. To assemble the genome of suspicious coronavirus (CoV) found in pangolins, SARS-CoV-2 was used as a reference in most of the previous studies, implicitly assuming the pangolin CoV and SARS-CoV-2 are the closest neighbors in evolution. However, this assumption may not be true. We investigated how the choice of reference genome affected the resulting CoV genome assembly. We explored various representative CoVs as the reference genome, and found significant differences in the resulting assemblies. The assembly obtained using RaTG13 as a reference showed better statistics in total length, N50, and pairwise distance reconstruction (PDR) scores than the assembly guided by SARS-CoV-2, indicating that RaTG13 may be a better reference. Therefore, RaTG13 should also be considered as a reference for assembling suspicious CoV found in pangolins and other potential intermediate hosts.

中文翻译：

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参考选择对可疑冠状病毒基因组组装的影响

由 SARS-CoV-2 引起的大流行对全世界产生了重大影响。在关于 SARS-CoV-2 起源的理论中，穿山甲被认为是潜在的中间宿主。为了组装在穿山甲中发现的可疑冠状病毒 (CoV) 的基因组，之前的大多数研究都使用 SARS-CoV-2 作为参考，隐含地假设穿山甲 CoV 和 SARS-CoV-2 是进化中最近的邻居。然而，这个假设可能不成立。我们研究了参考基因组的选择如何影响由此产生的 CoV 基因组组装。我们探索了各种具有代表性的 CoV 作为参考基因组，并发现生成的组件存在显着差异。使用 RaTG13 作为参考获得的组件在总长度、N50、和成对距离重建 (PDR) 得分比由 SARS-CoV-2 引导的组装，表明 RaTG13 可能是更好的参考。因此，RaTG13 也应被视为组装穿山甲和其他潜在中间宿主中发现的可疑 CoV 的参考。