Origin and host adaptation of the novel canine coronavirus (CCoV-HuPn-2018) isolated from a human pneumonia patient

从人类肺炎患者身上分离出的新型犬冠状病毒（CCoV-HuPn-2018）的起源和宿主适应

• 批准号: 10593314
• 负责人: Nicola Decaro
• 金额: $ 20.56万
• 依托单位: OHIO STATE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-08-23 至 2025-07-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10593314
• 关键词: 2019-nCoV; Acute; Address; Adult; Affect; Biological; Biological Process; Canis familiaris; Cells; Child; Chiroptera; Clinical; Collaborations; Collection; Coronavirus; Coronavirus nucleocapsid protein; Country; Disease; Evolution; Family Felidae; Family suidae; Genbank; Genes; Genetic; Genetic Markers; Genome; Genomics; Genotype; Haiti; Human; Immune; Immune response; Infant; Infection; Innate Immune Response; Interferon Type I; Interferons; Knowledge; Malaysia; Modeling; Molecular; Molecular Biology; Mutation; Pathogenicity; Patients; Phenotype; Phosphorylation; Phylogenetic Analysis; Play; Pneumonia; Population; Production; Proteins; Public Health; RNA Binding; Recombinants; Role; SARS coronavirus; SARS-CoV N protein; Signal Transduction; Syndrome; Thailand; Virion; Virus; Zoonoses; comparative; genome sequencing; genome-wide; genome-wide analysis; genomic RNA; genomic data; geographically distant; high risk; human pathogen; molecular clock; next generation sequencing; novel; respiratory; response; reverse genetics; trait; transcriptome; transcriptomics; transmission process

1 Project Summary 2 There is growing evidence that canine coronaviruses (CCoVs) can infect humans and be associated with 3 clinical (mostly acute respiratory) illness in children and adults. Human infections with CCoVs with recombinant 4 canine-feline-porcine spike proteins (hCFPL-CoVs) have been confirmed in several countries including Haiti 5 (2017), Malaysia (2018), the USA (2014) and Thailand (2003). The high sequence identity (SI, 99.4%) observed 6 between hCFPL-CoVs from geographically distant Malaysia (CCoV-HuPn-2018) and Haiti (HuCCoV-Z19) 7 suggests that they may be capable of human-to-human transmission or represents temporal clustering. CCoVs 8 have not been recognized previously as human pathogens, and the threat they pose to public health is unknown 9 and may be underappreciated. While complete genome sequencing demonstrated hCFPL-CoVs are canine- 10 feline recombinant alphacoronaviruses, it failed to identify potential ancestral strains likely due to scarcity of 11 CCoV genomic data (only 17 complete genome sequences are available in the GenBank). To address that, we 12 will conduct complete genomic sequencing of up to 200 new CCoVs (from Dr. Decaro) and additional hCFPL- 13 CoVs (if identified in Dr. Gray’s ongoing study). 14 A unique 36 nt (12-aa) deletion identified in the N protein in the SR-rich domain (ΔSR-N) of CCoV-HuPn- 15 2018 may be associated with a recent zoonotic transmission of CCoV-HuPn-2018 and certain biological 16 functions acquired or lost by the virus. While such deletions in the SR-rich region of the N-protein were not 17 previously found in CCoVs, presence of a similar deletion was demonstrated in severe acute respiratory 18 syndrome coronavirus (SARS-CoV) strains early following their emergence into human population but not in 19 SARS-CoV-like bat strains. This deletion was shown to be associated with the altered cellular localization of the 20 N-protein and increased pathogenicity of the SARS-CoV strains bearing them. Because SARS-CoV N-protein 21 plays an important role in inhibition of type I interferon (IFN) production, deletions in it may alter innate immune 22 responses against SARS-CoV as well as other CoVs including CCoV-HuPn-2018. Using reverse genetics, we 23 will evaluate the biological function of this mutation. We propose the following Specific Aims to study the 24 genomics, evolution and human emergence mechanisms of hCFPL-CoVs. Aim 1. Conduct genome-wide 25 analysis of historic and current CCoV strains a) to determine the evolutionary relationship between hCFPL-CoVs 26 and their potentially ancestral strains and b) to identify genetic features associated with CCoV-HuPn-2018 27 infectivity or pathogenicity to human host. Aim 2. To generate and use CCoV-HuPn-2018 infectious clone to 28 investigate the effect of the identified N- deletion (ΔSR-N) on CCoV-HuPn-2018 cellular localization, replication 29 dynamics and the host transcriptome response. These studies will identify the genomic features associated with 30 hCFPL-CoV/CCoV infectivity to humans and generate essential fundamental knowledge regarding the common 31 mechanisms regulating zoonotic transmission of CoVs.

1个项目摘要 越来越多的证据表明，犬冠状病毒(CCoV)可以感染人类，并与 3儿童和成人的临床疾病(主要是急性呼吸道疾病)。重组人感染冠状病毒 包括海地在内的几个国家已经确认了4种犬-猫-猪尖峰蛋白(hCFPL-CoV) 5(2017)、马来西亚(2018)、美国(2014)和泰国(2003)。观察到高序列同源性(SI，99.4%) 6地理位置遥远的马来西亚(CCoV-HuPn-2018)和海地(HuCCoV-Z19)的hCFPL-CoV之间 7表明它们可能能够在人与人之间传播，或者代表着时间上的聚集性。CCoV 8以前没有被确认为人类病原体，它们对公共卫生构成的威胁尚不清楚 9，并可能被低估。虽然完整的基因组测序表明hCFPL-CoV是犬科动物- 10种猫科重组甲型冠状病毒，它未能识别出潜在的祖先株，可能是由于缺乏 11个冠状病毒基因组数据(GenBank中只有17个完整的基因组序列)。为了解决这个问题，我们 12将对多达200个新的CCoV(来自Decaro博士)和额外的hCFPL-进行完整的基因组测序- 13个CoV(如果在Gray博士正在进行的研究中发现的话)。 14在冠状病毒富含SR结构域(ΔSR-N)的N蛋白中发现一个独特的36个核苷酸(12-aa)缺失。 15 2018年可能与最近的CCoV-HuPn-2018人畜传播和某些生物 病毒获得或丢失的16种功能。而N蛋白的SR富集区的这种缺失则不是 17以前在CCoV中发现的，在严重急性呼吸道疾病中也发现了类似的缺失 18株SARS冠状病毒(SARS-CoV)在进入人群后早期出现，但在 19株类SARS冠状病毒蝙蝠。这种缺失被证明与细胞定位的改变有关 20 N蛋白和携带它们的SARS-CoV毒株的致病性增强。因为SARS冠状病毒N蛋白 21在抑制I型干扰素的产生中起着重要作用，它的缺失可能会改变天然免疫。 22针对SARS-CoV以及包括CCoV-HuPn-2018在内的其他CoV的答复。利用反向遗传学，我们 23日将评估这种突变的生物学功能。我们建议以下具体目标来研究 24人CFPL-CoV的基因组学、进化和人类羽化机制。目标1.进行全基因组 25)对历史和当前冠状病毒株的分析，以确定hCFPL-CoV之间的进化关系 26及其潜在的祖先毒株以及b)确定与CCoV-HuPn-2018相关的遗传特征 27对人类宿主的感染性或致病性。目的2.制备和使用CCoV-HuPn-2018感染性克隆 28研究已确定的N-缺失(ΔSR-N)对冠状病毒-HuPn-2018细胞定位、复制的影响 29动态和寄主转录组反应。这些研究将确定与以下基因相关的基因组特征 30hCFPL-CoV/CCoV对人类的传染性，并产生关于常见疾病的基本基础知识 31个调节人畜共患冠状病毒传播的机制。