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; 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 2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3个临床（主要是急性呼吸道疾病）。与重组的CCOV感染的人类感染 在包括海地在内的几个国家中，已经确认了4个犬 - 五孢子菌峰值蛋白（HCFPL-COV） 5（2017），马来西亚（2018），美国（2014）和泰国（2003）。观察到的高序列身份（SI，99.4％） 6从地理上遥远的马来西亚（CCOV-HUPN-2018）和海地（Huccov-Z19）的HCFPL-COV之间 7表明它们可能能够进行人类到人类的传播或代表临时聚类。 CCOV 8以前尚未被认为是人类病原体，他们对公共卫生构成的威胁尚不清楚 9，可能被低估了。虽然完整的基因组测序表明hcfpl-cov是犬 - 10个猫重组字母瘤病毒，它未能识别出可能由于稀缺性造成的潜在祖传菌株 11 CCOV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将进行多达200个新CCOV（来自Decaro博士）的完整基因组测序，并进行其他HCFPL- 13个COV（如果在Gray博士正在进行的研究中确定）。 14在CCOV-HUPN-的N蛋白中鉴定出的独特的36 NT（12-AA）缺失（ΔSR-N） 15 2018可能与CCOV-HUPN-2018的最近人畜共患病和某些生物学有关 病毒获得或丢失的16个功能。虽然在N蛋白的SR富区域中的此类缺失不是 17先前在CCOV中发现的，在严重的急性呼吸道中证明了相似的缺失 18综合征冠状病毒（SARS-COV）菌株在人口中出现后，但没有 19个类似SARS-COV的蝙蝠菌株。该缺失显示与改变的细胞定位有关 20 N蛋白质并增加了带有它们的SARS-COV菌株的致病性。因为SARS-COV N蛋白 21在抑制I型干扰素（IFN）生产中起重要作用，其中缺失可能会改变先天免疫 22针对SARS-COV以及包括CCOV-HUPN-2018在内的其他COV的响应。使用反向遗传学，我们 23将评估该突变的生物学功能。我们提出了以下具体目的，以研究 24 HCFPL-COV的基因组，进化和人类出现机制。目标1。进行全基因组进行 25对历史和当前CCOV菌株的分析a）确定HCFPL-COV之间的进化关系 26及其潜在的祖先菌株和b）确定与CCOV-HUPN-2018相关的遗传特征 27对人类宿主的感染或致病性。目标2。生成和使用CCOV-HUPN-2018感染克隆 28研究已鉴定的N-缺失（ΔSR-N）对CCOV-HUPN-2018细胞定位的影响 29动力学和主机转录组响应。这些研究将确定与 30 HCFPL-COV/CCOV感染人类，并产生有关共同的基本知识 31种调节COV人畜共动物传播的机制。