Horizontal gene transfer and recombination analysis of SARS-CoV-2 genes helps discover its close relatives and shed light on its origin.
Horizontal gene transfer and recombination analysis of SARS-CoV-2 genes helps discover its close relatives and shed light on its origin.
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DOI：
10.1186/s12862-020-01732-2
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发表时间：
2021-01-21
影响因子：
2.2
通讯作者：
Legendre P
中科院分区：
文献类型：
--
作者：
Makarenkov V;Mazoure B;Rabusseau G;Legendre P
SARS-CoV-2大流行是近年来出现的最大的全球医疗和社会挑战之一。在以前的SARS暴发期间发现的人类冠状病毒毒株被假设通过中间宿主从蝙蝠传播给人类，例如，果子狸传播给SARS冠状病毒，骆驼传播给mers冠状病毒。SARS-CoV-2中间宿主的发现及其在人类中出现的具体机制的确定是具有重要进化意义的主题。在这项研究中，我们研究了SARS-CoV-2的11个主要基因的进化模式。先前的研究表明，SARS-CoV-2的基因组在大多数基因上与马蹄蝠冠状病毒RaTG13高度相似，在刺突蛋白的受体结合（RB）结构域上与某些马来亚穿山甲冠状病毒（CoV）株高度相似。我们提供了统计上显著的水平基因转移和重组事件（基因间和基因内）的详细列表，推断了SARS-CoV-2基因组的11个主要基因。我们的分析表明，SARS-CoV-2基因S和N的两个连续区域可能是由RaTG13与广东穿山甲冠状病毒的基因内重组引起的。在基因S的[1215-1425]区和基因n的[534-727]区发现了RaTG13和GD穿山甲冠状病毒之间具有统计学意义的基因转移重组事件，在SARS-CoV-2的祖先、RaTG13、GD穿山甲冠状病毒和蝙蝠冠状病毒ZC45-ZXC21冠状病毒的ORF1ab、S、ORF3a、ORF7a、ORF8和n基因上发现了具有统计学意义的重组事件。基于拓扑聚类的25种冠状病毒基因树聚类结果显示，冠状病毒基因的三向进化，ORF1ab、S和N基因系统发育形成第一簇，ORF3a、E、M、ORF6、ORF7a、ORF7b和ORF8基因系统发育形成第二簇，ORF10基因系统发育形成第三簇。我们的水平基因转移和重组分析结果表明，SARS-CoV-2不仅可能是由蝙蝠RaTG13和广东穿山甲冠状病毒重组而成的嵌合体病毒，而且可能是蝙蝠CoV ZC45和ZXC21株的近亲。它们还表明GD穿山甲可能是这种危险病毒的中间宿主。
The SARS-CoV-2 pandemic is one of the greatest global medical and social challenges that have emerged in recent history. Human coronavirus strains discovered during previous SARS outbreaks have been hypothesized to pass from bats to humans using intermediate hosts, e.g. civets for SARS-CoV and camels for MERS-CoV. The discovery of an intermediate host of SARS-CoV-2 and the identification of specific mechanism of its emergence in humans are topics of primary evolutionary importance. In this study we investigate the evolutionary patterns of 11 main genes of SARS-CoV-2. Previous studies suggested that the genome of SARS-CoV-2 is highly similar to the horseshoe bat coronavirus RaTG13 for most of the genes and to some Malayan pangolin coronavirus (CoV) strains for the receptor binding (RB) domain of the spike protein. We provide a detailed list of statistically significant horizontal gene transfer and recombination events (both intergenic and intragenic) inferred for each of 11 main genes of the SARS-CoV-2 genome. Our analysis reveals that two continuous regions of genes S and N of SARS-CoV-2 may result from intragenic recombination between RaTG13 and Guangdong (GD) Pangolin CoVs. Statistically significant gene transfer-recombination events between RaTG13 and GD Pangolin CoV have been identified in region [1215–1425] of gene S and region [534–727] of gene N. Moreover, some statistically significant recombination events between the ancestors of SARS-CoV-2, RaTG13, GD Pangolin CoV and bat CoV ZC45-ZXC21 coronaviruses have been identified in genes ORF1ab, S, ORF3a, ORF7a, ORF8 and N. Furthermore, topology-based clustering of gene trees inferred for 25 CoV organisms revealed a three-way evolution of coronavirus genes, with gene phylogenies of ORF1ab, S and N forming the first cluster, gene phylogenies of ORF3a, E, M, ORF6, ORF7a, ORF7b and ORF8 forming the second cluster, and phylogeny of gene ORF10 forming the third cluster. The results of our horizontal gene transfer and recombination analysis suggest that SARS-CoV-2 could not only be a chimera virus resulting from recombination of the bat RaTG13 and Guangdong pangolin coronaviruses but also a close relative of the bat CoV ZC45 and ZXC21 strains. They also indicate that a GD pangolin may be an intermediate host of this dangerous virus.
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影响因子：
10.7
作者：
Castresana, J
通讯作者：
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