Molecular Epidemiology of Human Coronavirus OC43 Reveals Evolution of Different Genotypes over Time and Recent Emergence of a Novel Genotype due to Natural Recombination
Molecular Epidemiology of Human Coronavirus OC43 Reveals Evolution of Different Genotypes over Time and Recent Emergence of a Novel Genotype due to Natural Recombination
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DOI：
10.1128/jvi.05512-11
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发表时间：
2011-11-01
影响因子：
5.4
通讯作者：
Yuen, Kwok-Yung
中科院分区：
文献类型：
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作者：
Lau, Susanna K. P.;Lee, Paul;Yuen, Kwok-Yung
虽然人类冠状病毒OC 43-OC 43（HCoV-OC 43）是最常见的与人类感染相关的冠状病毒，但对其分子流行病学和进化知之甚少。我们进行了一项分子流行病学研究，以调查不同的基因型和潜在的重组HCoV-OC 43。从2004年至2011年收集的鼻咽抽吸物中的29株HCoV-OC 43菌株进行了RNA依赖性RNA聚合酶（RdRp）、刺突和核衣壳基因分析。系统发育分析表明，至少有三个不同的簇HCoV-OC 43，虽然10个不寻常的菌株显示不一致的系统发育位置之间的RdRp和刺突基因。这表明存在四种HCoV-OC 43基因型（A至D），其中基因型D最可能由重组引起。C、D基因型的全基因组测序和bootscan分析表明，在D基因型的产生过程中，基因型B和C之间发生了重组事件。在29株菌株中，没有一株属于更古老的基因型A，2004年的5株属于基因型B，2004 - 2006年的15株属于基因型C，2004年的1株和2008 - 2011年的所有8株属于重组基因型D。使用刺突和核衣壳基因的分子钟分析将所有基因型的最近共同祖先追溯到20世纪50年代，基因型B和C追溯到20世纪80年代，基因型B追溯到20世纪90年代，基因型C追溯到20世纪90年代末至21世纪初，而重组基因型D菌株早在2004年就被检测到。这是第一项描述HCoV-OC 43中自然重组和不同基因型随时间演变的研究，导致新基因型D的出现，该基因型与我们老年人群中的肺炎相关。
Although human coronavirus OC43-OC43 (HCoV-OC43) is the coronavirus most commonly associated with human infections, little is known about its molecular epidemiology and evolution. We conducted a molecular epidemiology study to investigate different genotypes and potential recombination in HCoV-OC43. Twenty-nine HCoV-OC43 strains from nasopharyngeal aspirates, collected from 2004 to 2011, were subjected to RNA-dependent RNA polymerase (RdRp), spike, and nucleocapsid gene analysis. Phylogenetic analysis showed at least three distinct clusters of HCoV-OC43, although 10 unusual strains displayed incongruent phylogenetic positions between RdRp and spike genes. This suggested the presence of four HCoV-OC43 genotypes (A to D), with genotype D most likely arising from recombination. The complete genome sequencing of two genotype C and D strains and bootscan analysis showed recombination events between genotypes B and C in the generation of genotype D. Of the 29 strains, none belonged to the more ancient genotype A, 5 from 2004 belonged to genotype B, 15 from 2004 to 2006 belonged to genotype C, and 1 from 2004 and all 8 from 2008 to 2011 belonged to the recombinant genotype D. Molecular clock analysis using spike and nucleocapsid genes dated the most recent common ancestor of all genotypes to the 1950s, genotype B and C to the 1980s, genotype B to the 1990s, and genotype C to the late 1990s to early 2000s, while the recombinant genotype D strains were detected as early as 2004. This represents the first study to describe natural recombination in HCoV-OC43 and the evolution of different genotypes over time, leading to the emergence of novel genotype D, which is associated with pneumonia in our elderly population.