Jie Cui

Jie Cui
Institut Pasteur of Shanghai, Chinese Academy of Sciences · Pathogen Bioinformatics Unit

PhD

About

160
Publications
43,707
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Introduction
I'm a professor and principal investigator in Pathogen Bioinformatics Unit, at Institut Pasteur of Shanghai, Chinese Academy of Sciences. My lab is interested in virus evolution, reconstructing the evolutionary process leading to the emergence of pathogens, exploring the virosphere and developing viromics, mNGS and bioinformatics tools.
Additional affiliations
March 2019 - present
Institut Pasteur of Shanghai, Chinese Academy of Sciences
Position
  • Professor (Full)

Publications

Publications (160)
Article
Full-text available
Coronaviruses, such as severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV), are highly transmissible pathogens, and they can be lethal in humans. Bats are believed to be the original sources of these lethal pathogens. In December 2019, a cluster of pneumonia cases was reported in Wuha...
Article
Full-text available
The SARS-CoV-2 epidemic started in late December 2019 in Wuhan, China, and has since impacted a large portion of China and raised major global concern. Herein, we investigated the extent of molecular divergence between SARS-CoV-2 and other related coronaviruses. Although we found only 4% variability in genomic nucleotides between SARS-CoV-2 and a b...
Article
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Malacostracan crustaceans (order Malacostraca), such as crabs, lobsters, and shrimp, are essential secondary producers, as well as major carriers of viruses, in marine ecosystems and are widely distributed from the intertidal belt to the deep seabed, functioning as ideal models for studies of virus transmission between marine layers. They are of gr...
Article
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Ocean viromes remain poorly understood and little is known about the ecological factors driving aquatic RNA virus evolution. In this study, we used a meta-transcriptomic approach to characterize the viromes of 58 marine invertebrate species across three seas. This revealed the presence of 315 newly identified RNA viruses in nine viral families or o...
Article
Retroviruses are widely distributed in all vertebrates, as are their endogenous forms, endogenous retroviruses (ERV), which serve as “fossil” evidence to trace the ancient origins and history of virus-host interactions over millions of years. The retroviral envelope (Env) plays a significant role in host range determination, but major information o...
Article
Significance We discovered a dual role of vimentin underlying Zika virus (ZIKV) replication. The vimentin network reorganizes to surround the replication complex. Depletion of vimentin resulted in drastic segregation of viral proteins and subsequent defective infection, indicating its function as an “organizer” that ensures the concentration of all...
Preprint
Full-text available
Retroviruses are widely distributed in all vertebrates, as are their endogenous form, endogenous retrovirus (ERV), which serves as “fossil” evidence to trace the ancient origins and history of virus-host interactions over millions of years. The retroviral envelope (Env) plays a significant role in host range determination, but major information on...
Article
Full-text available
In late 2020, we detected 32 highly pathogenic avian influenza A(H5N8) viruses in migratory ducks in Shanghai, China. Phylogenetic analysis of 5 representative isolates identified 2 sublineages of clade 2.3.4.4b. Each sublineage formed separate clusters with isolates from East Asia and Europe.
Article
RNA interference (RNAi) is the major antiviral mechanism in plants and invertebrates, but the absence of detectable viral (v)siRNAs in mammalian cells upon viral infection has questioned the functional relevance of this pathway in mammalian immunity. We designed a series of peptides specifically targeting enterovirus A71 (EV-A71)-encoded protein 3A...
Article
Full-text available
Foamy viruses (FVs) are complex retroviruses that can infect humans and other animals. In this study, by integrating transcriptomic and genomic data, we discovered 412 FVs from 6 lineages in amphibians, which significantly increased the known set of FVs in amphibians. Among these lineages, salamander FVs maintained a co-evolutionary pattern with th...
Preprint
Emerging microbe infections such as Zika virus (ZIKV) pose an increasing threat to human health. Current investigations on ZIKV replication have revealed the construction of replication compartments (RCs) and the utilization of host cellular endomembranes, without careful examination of the cytoskeletal network. Here, we investigated the function o...
Preprint
Full-text available
Ocean viromes remain poorly understood and little is known about the ecological factors driving aquatic RNA virus evolution. In this study, we used a meta-transcriptomic approach to characterize the viromes of 58 marine invertebrate species across three seas. This revealed the presence of 315 newly identified RNA viruses in nine viral families or o...
Article
Full-text available
Human endogenous retroviruses (HERVs) were formed via ancient integration of exogenous retroviruses into the human genome and are considered to be viral “fossils”. The human genome is embedded with a considerable amount of HERVs, witnessing the long-term evolutionary history of the viruses and the host. Most HERVs have lost coding capability during...
Article
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病毒组学是一门借助Meta-genomics或Meta-transcriptomics的手段,对样品中所携带的所有病毒进行系统性分析的学科。随着高通量测序技术的兴起,以及其在病原生物学领域的广泛应用,人们对于病毒组的认识有了极大的拓展,其研究可以辅助预测病毒性传染病、了解病毒的进化和基因组的多样性、探究病毒在宿主或地域间的跨物种传播现象,是描绘病毒生态圈的理论基础。本实验方法旨在从目标样品中提取核酸并进行文库构建和高通量测序,从测序结果中挖掘新病毒信息,并做病毒组分析。
Preprint
Full-text available
Foamy viruses (FVs) are complex retroviruses that can infect humans and other animals. In this study, by integrating transcriptomic and genomic data, we discovered 412 FVs from 6 lineages in amphibians, which significantly increased the known set of FVs in amphibians. Among these lineages, salamander FVs maintained a co-evolutionary pattern with th...
Article
Full-text available
Although artemisinin combination therapies have succeeded in reducing the global burden of malaria, multidrug resistance of the deadliest malaria parasite, Plasmodium falciparum , is emerging worldwide. Innovative antimalarial drugs that kill all life-cycle stages of malaria parasites are urgently needed. Here, we report the discovery of the compou...
Article
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Enteroviruses (EVs) species A are a major public health issue in the Asia–Pacific region and cause frequent epidemics of hand, foot andmouth disease (HFMD) inChina.Mild infections are common in children; however,HFMDcan also cause severe illness that affects the central nervous system. Tomolecularly characterize EVs, a prospective HFMDvirological s...
Article
Enteroviruses (EVs) species A are a major public health issue in the Asia–Pacific region and cause frequent epidemics of hand, foot and mouth disease (HFMD) in China. Mild infections are common in children; however, HFMD can also cause severe illness that affects the central nervous system. To molecularly characterize EVs, a prospective HFMD virolo...
Article
Full-text available
Hendra virus (HeV) and Cedar virus (CedV) are henipaviruses, which fall into the Paramyxoviridae family of single-stranded, negative-sense RNA viruses. HeV is classified as a Biosafety Level-4 (BSL-4) agent, as it is highly pathogenic and is often fatal to humans. To date, no HeV prevention or treatment methods for human are available. In contrast,...
Article
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Background: H6 subtype influenza viruses were prevalent in domestic poultry and wild birds, which also could pose potential threat to humans. However, little is known about the prevalence of H6 subtype viruses in wild birds in eastern China, a crucial stopover or wintering site for migratory wild birds along the East Asian-Australasian Flyway. Me...
Preprint
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Bats are recognized as important reservoirs of viruses deadly to other mammals, including humans. These infections are typically nonpathogenic in bats raising questions about innate immune differences that might exist between bats and other mammals. Tetherin is an important restriction factor which inhibits the release of a diverse range of viruses...
Article
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We miscalculated identities of several genes, and the corrected Table 1 should be as follows.
Article
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Porcine endogenous retroviruses (PERVs) are proviruses that have medical value in xenotransplantation. However, the evolutionary process leading to the generation of modern PERVs is not well understood. In this study, we in silico mined 14 pig genomes and other available 304 mammalian genomes, which led to the documentation of 185 full-length PERVs...
Article
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Background: Epigenetic regulation is essential in regulating gene expression across a variety of biological processes. Many high-throughput sequencing technologies have been widely used to generate epigenetic data, such as histone modification, transcription factor binding sites, DNA modifications, chromatin accessibility, and etc. A large scale o...
Article
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Mosquito-borne flaviviruses infect both mammals and mosquitoes. RNA interference (RNAi) has been demonstrated as an anti-flavivirus mechanism in mosquitoes; however, whether and how flaviviruses induce and antagonize RNAi-mediated antiviral immunity in mammals remains unknown. We show that the nonstructural protein NS2A of dengue virus-2 (DENV2) ac...
Article
Formins and tropomyosins (Tpms) are two central components of the microfilaments. Formins are involved in the nucleation and polymerization of actin filaments, and Tpms form along the actin stress fibers to regulate their dynamics. However, the correlation between formins and Tpms remains unclear. Here, we elucidated the function of distinct formin...
Preprint
Full-text available
Background: Porcine endogenous retroviruses (PERVs) are proviruses that can replicate in human cells. However, the evolutionary process leading to the generation of modern PERVs is not well understood. Results: We mined 14 pig genomes and other available 304 mammalian genomes in silico, which led to the documentation of 185 full-length PERVs. Notab...
Article
Full-text available
A history of long-term co-divergence means that foamy viruses (family Retroviridae) provide an ideal framework to understanding virus-host evolution over extended time periods. Endogenous foamy viruses (EndFVs) are rare, and to date have only been described in a limited number of mammals, amphibians, reptiles and fish genomes. By screening 414 avia...
Preprint
Full-text available
A history of long-term co-divergence means that foamy viruses (family Retroviridae) provide an ideal framework to understanding virus-host evolution over extended time-periods. Endogenous foamy viruses (EFVs) are rare, and to date have only been found in a limited number of genomes from mammals, amphibians, reptiles and fish. By screening 510 avian...
Article
Bats, unique among mammals with powered flight, have many species with the longest size-proportionate lifespan of all mammals. Evolutionary adaptations would have been required to survive the elevated body temperatures during flight. Heat shock protein (HSP), highly conserved master regulators of cell stress, expression was examined across tissues...
Article
The re-emergence of Zika virus (ZIKV) in the Western Hemisphere has resulted in global public health crisis since 2015. ZIKV preferentially infects and targets human neural progenitor cells (hNPCs) and causes fetal microcephaly upon maternal infection. hNPCs not only play critical roles during fetal brain development, but also persist in adult brai...
Article
Full-text available
Endogenous retroviruses (ERVs) represent host genomic ‘fossils’ of ancient viruses. Foamy viruses, including those that form endogenous copies, provide strong evidence for virus-host co-divergence across the vertebrate phylogeny. Endogenous foamy viruses (EFVs) have previously been discovered in mammals, amphibians, and fish. Here we report a novel...
Article
Bats are the natural reservoirs of severe acute respiratory syndrome coronavirus (SARS-CoV) which caused the outbreak of human SARS in 2002–2003. We introduce the genetic diversity of SARS-related coronaviruses (SARSr-CoVs) discovered in bats and provide insights on the bat origin of human SARS. We also analyze the viral geographical structure that...
Article
Endogenous retroviruses (ERVs) arise from the infection and integration of past retroviruses into animal hosts. We performed large-scale genomic mining of 101 avian genomes for discovery of ERVs having none-avian origin and investigated the cross-species transmission events. Phylogenetic analysis of the reverse transcriptase (RT) of polymerase gene...
Article
Full-text available
Severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV) are two highly transmissible and pathogenic viruses that emerged in humans at the beginning of the 21st century. Both viruses likely originated in bats, and genetically diverse coronaviruses that are related to SARS-CoV and MERS-CoV...
Preprint
Full-text available
Background Xenotransplantation may overcome significant shortage of human allotransplant. Porcine organs are considered favorable for xenotransplantation duo to similar size and function to human organ. However, porcine endogenous retroviruses (PERVs) are potential infectious agents during xenotransplantation as they are able to infect and horizont...
Preprint
Full-text available
Endogenous retroviruses (ERVs) represent host genomic fossils of ancient viruses. Foamy viruses, including those that form endogenous copies, provide strong evidence for virus-host co-divergence across the vertebrate phylogeny. Endogenous foamy viruses (EFV) have previously been discovered in mammals, amphibians and fish. Here we report a novel end...
Article
Full-text available
The yellow fever virus (YFV) recently reemerged in the large outbreaks in Africa and Brazil, and the first imported patients into Asia have recalled the concerns of YFV evolution. Here we show phylogenomics of YFV with serial clinical samples of the 2016 YFV infections. Phylogenetics exhibited that the 2016 strains were close to Angola 1971 strains...
Article
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A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper.
Article
Full-text available
Bats have attracted attention in recent years as important reservoirs of viruses deadly to humans and other mammals. These infections are typically nonpathogenic in bats raising questions about innate immune differences that might exist between bats and other mammals. The APOBEC3 gene family encodes antiviral DNA cytosine deaminases with important...
Article
Background: During 2016-2017, the previously rare GII.P16-GII.2 norovirus suddenly emerged as the predominant genotype causing gastroenteritis outbreaks in China and other countries. Its origin, phylodynamics, and mechanism behind the predominance remain unclear. Methods: Bayesian phylogenetic analyses were performed on 180 full capsid and 150 p...
Article
Full-text available
There have been five waves of H7N9 avian influenza virus (AIV) infection in humans since its initial emergence in China in 2013, posing a significant threat to public health. Hubei province was free local transmission during the first four waves of H7N9 AIV. However, multiple cases of human H7N9 infection were reported in Hubei during January 2017....
Article
Compared with terrestrial mammals, bats have a longer lifespan and greater capacity to co-exist with a variety of viruses. In addition to cytosolic DNA generated by these viral infections, the metabolic demands of flight cause DNA damage and the release of self-DNA into the cytoplasm. However, whether bats have an altered DNA sensing/defense system...
Article
Full-text available
A large number of SARS-related coronaviruses (SARSr-CoV) have been detected in horseshoe bats since 2005 in different areas of China. However, these bat SARSr-CoVs show sequence differences from SARS coronavirus (SARS-CoV) in different genes (S, ORF8, ORF3, etc) and are considered unlikely to represent the direct progenitor of SARS-CoV. Herein, we...
Data
Distribution of SARSr-CoVs highly similar to SARS-CoV in the variable S, ORF3 and ORF8 genes in the single cave. (DOCX)
Data
Alignment of amino acid sequences of the receptor-binding motif (corresponding to aa 424–495 of SARS-CoV S protein). Two clades of the SARSr-CoVs identified from bats in the studied cave are indicated with vertical lines on the left. (PPTX)
Data
Alignment of nucleotide sequences of a genomic region covering ORF6 to ORF7a. ORFX is located between ORF6 and ORF7a in the genomes of WIV1, WIV16, Rs7327 and Rs4874. The start codon and stop codon of ORFX are marked with red boxes. The deletion responsible for the long ORFX in Rs7327 and Rs4874 is marked with the blue box. (PPTX)
Data
Detection of potential recombination events by similarity plot and boot scan analysis. (A) Full-length genome sequence of SARSr-CoV Rs4084 was used as query sequence and RsSHC014, Rf4092 and Rs4081 as reference sequences. (B) Full-length genome sequence of SARSr-CoV Rs4237 was used as query sequence and SARSr-CoV Rs4247, Rs4081 and Rs3367 as refere...
Data
Quantification of SARSr-CoV in individual bat fecal samples. The number of genome copies of SARSr-CoV per gram of bat feces was determined by quantitative real-time PCR targeting the RdRp gene. Samples from which the SARSr-CoV RBD sequences were successfully amplified are indicated in red. (PPTX)
Data
Alignment of amino acid sequences of ORF3b protein. (PPTX)
Data
Chinese provinces where bat SARSr-CoVs have been detected. (PPTX)
Data
Full-length genome sequences of bat SARSr-CoVs newly identified in this study. (FAS)
Data
Phylogenetic analyses based on nucleotide sequences of the S gene (A), ORF3a (B) and ORF8 (C). The trees were constructed by the maximum likelihood method using the LG model with bootstrap values determined by 1000 replicates. Only bootstraps > 50% are shown. Rs, Rhinolophus sinicus; Rf, Rhinolophus ferremequinum; Rm, Rhinolophus macrotis; Ra, Rhin...
Data
The successful or failed rescue of the chimeric SARSr-CoVs. (A) Cytopathic effects in Vero E6 cells transfected with the infectious BAC clones constructed with the backbone of WIV1 and various S genes of different bat SARSr-CoV strains. Microphotographs were taken 24 hours post transfection. (B) The culture media supernatant collected from the cell...
Data
Spike substitution strategy. The original fragments E and F were shortened to leave spike gene as an independent fragment. The new fragments were designated as Es and Fs. BsaI or BsmBI sites were introduced into the junctions of Es/Spike and Spike/Fs. Then any spike could be substituted into the genome of SARSr-CoV WIV1 through this strategy. (TIF)
Data
Comparison of the novel bat SARSr-CoVs identified in this study with human/civet SARS-CoVs and previously described bat SARSr-CoVs. (DOCX)
Article
Full-text available
The worldwide infection rate of herpesvirus is high, but the detailed prevalence in China, especially the central area, remains unclear. In the present study, the prevalence of Herpes simplex virus (HSV), Epstein-Barr virus (EBV), and human cytomegalovirus (HCMV) was investigated in 303 healthy adults in Wuhan, a representative city in Central Chin...
Article
Full-text available
Since its emergence in 2013, the H7N9 low-pathogenic avian influenza virus (LPAIV) has been circulating in domestic poultry in China, causing five waves of human infections. A novel H7N9 highly pathogenic avian influenza virus (HPAIV) variant possessing multiple basic amino acids at the cleavage site of the hemagglutinin (HA) protein was first repo...
Data
The ceRNA network, including lncRNAs, circRNAs, miRNAs, and mRNAs, in cervical cancer. The ceRNA network is based on lncRNA/miRNA, circRNA/miRNA, and miRNA/mRNA interactions. The size of each node is proportional to the calculated functional connectivity of each node.