Exploring viral infection using single-cell sequencing.

Abstract:

:Single-cell sequencing (SCS) has emerged as a valuable tool to study cellular heterogeneity in diverse fields, including virology. By studying the viral and cellular genome and/or transcriptome, the dynamics of viral infection can be investigated at single cell level. Most studies have explored the impact of cell-to-cell variation on the viral life cycle from the point of view of the virus, by analyzing viral sequences, and from the point of view of the cell, mainly by analyzing the cellular host transcriptome. In this review, we will focus on recent studies that use single-cell sequencing to explore viral diversity and cell variability in response to viral replication.

journal_name

Virus Res

journal_title

Virus research

authors

Rato S,Golumbeanu M,Telenti A,Ciuffi A

doi

10.1016/j.virusres.2016.10.016

subject

Has Abstract

pub_date

2017-07-15 00:00:00

pages

55-68

eissn

0168-1702

issn

1872-7492

pii

S0168-1702(16)30388-4

journal_volume

239

pub_type

杂志文章,评审
  • Trends in plant virus epidemiology: opportunities from new or improved technologies.

    abstract::This review focuses on new or improved technologies currently being applied, or likely to be applied in the future, to worldwide research on plant virus epidemiology. Recent technological advances and innovations provide many opportunities to improve understanding of the way diverse types of plant virus epidemics deve...

    journal_title:Virus research

    pub_type: 杂志文章,评审

    doi:10.1016/j.virusres.2013.11.003

    authors: Jones RA

    更新日期:2014-06-24 00:00:00

  • Allopurinol, an inhibitor of purine catabolism, enhances susceptibility of tobacco to Tobacco mosaic virus.

    abstract::Tobacco (cv. Xanthi nn) plants were watered with allopurinol [4-hydroxypyrazolo (3,4-d) pyrimidine, HPP], a xanthine oxidoreductase (XOR) inhibitor, to investigate its effects on infection by Tobacco mosaic virus engineered to express the green fluorescent protein (TMV.GFP). TMV.GFP infection was monitored by examinat...

    journal_title:Virus research

    pub_type: 杂志文章

    doi:10.1016/j.virusres.2008.05.018

    authors: Silvestri S,Murphy AM,Buonaurio R,Carr JP

    更新日期:2008-11-01 00:00:00

  • The key molecular events during Macrobrachium rosenbergii nodavirus (MrNV) infection and replication in Sf9 insect cells.

    abstract::In this study we demonstrated that Macrobrachium rosenbergii nodavirus (MrNV) was able to internalize and replicate in Sf9 insect cells, with levels of infection altered by substances affecting the caveolin-(CAV) mediated endocytosis pathway. The use of Sf9 cells for efficient MrNV replication and propagation was demo...

    journal_title:Virus research

    pub_type: 杂志文章

    doi:10.1016/j.virusres.2016.06.012

    authors: Somrit M,Watthammawut A,Chotwiwatthanakun C,Weerachatyanukul W

    更新日期:2016-09-02 00:00:00

  • Prevalence and diversity of mycoviruses infecting the plant pathogen Ustilaginoidea virens.

    abstract::Rice false smut caused by Ustilaginoidea virens is a destructive disease in many rice-growing areas. Mycoviruses have been described in many fungal species, but there is little information regarding mycoviruses in U. virens. In this study, double-stranded (ds) RNA banding patterns were assessed in 198 wild-type isolat...

    journal_title:Virus research

    pub_type: 杂志文章

    doi:10.1016/j.virusres.2014.08.022

    authors: Jiang Y,Zhang T,Luo C,Jiang D,Li G,Li Q,Hsiang T,Huang J

    更新日期:2015-01-02 00:00:00

  • Human group C rotavirus: completion of the genome sequence and gene coding assignments of a non-cultivatable rotavirus.

    abstract::Genome segments 1 and 2 of human group C rotavirus 'Bristol' strain were sequenced and their gene-protein coding properties assigned. This work completed the genome sequence of a human group C rotavirus (17,910 bp) and allowed the full gene-protein coding assignment of the 11 segments of dsRNA. Gene 1 is 3309 bp in si...

    journal_title:Virus research

    pub_type: 杂志文章

    doi:10.1016/s0168-1702(01)00442-7

    authors: Chen Z,Lambden PR,Lau J,Caul EO,Clarke IN

    更新日期:2002-02-26 00:00:00

  • Analysis of codon usage bias in potato virus Y non-recombinant strains.

    abstract::Potato virus Y (PVY) is a member of the genus Potyvirus, family Potyviridae, is considered one of the most devastating pest affecting economically important crops, such as potato, tobacco, tomato and pepper, representing a serious threat due to high incidence and worldwide distribution. Its economic significance as we...

    journal_title:Virus research

    pub_type: 杂志文章

    doi:10.1016/j.virusres.2020.198077

    authors: Gómez MM,de Mello Volotão E,Assandri IR,Peyrou M,Cristina J

    更新日期:2020-09-01 00:00:00

  • Complete genome sequence of Oryctes rhinoceros nudivirus isolated from the coconut rhinoceros beetle in Solomon Islands.

    abstract::Oryctes rhinoceros nudivirus (OrNV) has been an effective biocontrol agent against the insect pest Oryctes rhinoceros (Coleoptera: Scarabaeidae) for decades, but there is evidence that resistance could be evolving in some host populations. We detected OrNV infection in O. rhinoceros from Solomon Islands and used Oxfor...

    journal_title:Virus research

    pub_type: 杂志文章

    doi:10.1016/j.virusres.2020.197864

    authors: Etebari K,Filipović I,Rašić G,Devine GJ,Tsatsia H,Furlong MJ

    更新日期:2020-03-01 00:00:00

  • The Tat protein of the human immunodeficiency virus type 1 (HIV-1) interacts with the EGF-like repeats of the Notch proteins and the EGF precursor.

    abstract::Employing the yeast two-hybrid system, the Tat protein of the human immunodeficiency virus (HIV) was shown to interact with a region spanning the EGF-like repeats 1-6 of the mouse Notch1, the human Notch2 and the Drosophila Notch. This observation was confirmed in mammalian cells by demonstrating an interaction betwee...

    journal_title:Virus research

    pub_type: 杂志文章

    doi:10.1016/j.virusres.2003.08.016

    authors: Shoham N,Cohen L,Yaniv A,Gazit A

    更新日期:2003-12-01 00:00:00

  • Stimulating effect of heat shock on the early stage of human cytomegalovirus replication cycle.

    abstract::The effect of mild heat shock on the replication of human cytomegalovirus (HCMV) was studied in human embryo fibroblasts. Treatment of cell cultures at 44 degrees C for 10 min just before infection or at 24 h post infection (p.i.) shortened HCMV eclipse period and enhanced viral replication, while heat shock performed...

    journal_title:Virus research

    pub_type: 杂志文章

    doi:10.1016/0168-1702(86)90070-5

    authors: Zerbini M,Musiani M,La Placa M

    更新日期:1986-12-01 00:00:00

  • Evolutionary relationships of virus species belonging to a distinct lineage within the Ampelovirus genus.

    abstract::A study of the evolutionary relationships of GLRaV-4,-5,-6 and -9, and two new Ampelovirus isolates (GLRaV-Pr and -De) related to grapevine leafroll disease was conducted based on molecular variability, positive selection analysis and maximum likelihood phylogenetic reconstructions. Sequences corresponding to the N-te...

    journal_title:Virus research

    pub_type: 杂志文章

    doi:10.1016/j.virusres.2008.02.015

    authors: Maliogka VI,Dovas CI,Katis NI

    更新日期:2008-07-01 00:00:00

  • Induction of virus-specific neutralizing immune response against West Nile and Japanese encephalitis viruses by chimeric peptides representing T-helper and B-cell epitopes.

    abstract::West Nile virus (WNV) and Japanese encephalitis virus (JEV), the members of JEV serocomplex group are pathogens of global health concern. The co-circulation of these viruses poses challenges in effective diagnostics due to antigenic similarity between the E-protein of these viruses. The present study aimed to design c...

    journal_title:Virus research

    pub_type: 杂志文章

    doi:10.1016/j.virusres.2011.08.008

    authors: Gangwar RS,Shil P,Sapkal GN,Khan SA,Gore MM

    更新日期:2012-01-01 00:00:00

  • Resolution of cassava-infecting alphaflexiviruses: Molecular and biological characterization of a novel group of potexviruses lacking the TGB3 gene.

    abstract::Several potexviruses (Family Alphaflexiviridae) have been reported infecting cassava (Manihot esculenta Crantz) in the Americas. They were isolated from severely diseased plants during the last 30-40 years and include: Cassava common mosaic virus (CsCMV), Cassava Caribbean mosaic virus (CsCaMV), Cassava Colombian symp...

    journal_title:Virus research

    pub_type: 杂志文章

    doi:10.1016/j.virusres.2017.03.019

    authors: Lozano I,Leiva AM,Jimenez J,Fernandez E,Carvajal-Yepes M,Cuervo M,Cuellar WJ

    更新日期:2017-09-15 00:00:00

  • Nuclear transport of influenza virus polymerase PA protein.

    abstract::The subcellular distribution of influenza polymerase PA subunit has been studied using a SV40-recombinant virus (SVPA76), which allows the expression and accumulation of this protein in COS-1 cells. In contrast to the complete nuclear localization observed for the PA subunit several hours after influenza virus infecti...

    journal_title:Virus research

    pub_type: 杂志文章

    doi:10.1016/0168-1702(92)90031-4

    authors: Nieto A,de la Luna S,Bárcena J,Portela A,Valcárcel J,Melero JA,Ortín J

    更新日期:1992-06-01 00:00:00

  • Evaluation on antiviral activity of a novel arctigenin derivative against multiple rhabdoviruses in aquaculture.

    abstract::Rhabdoviruses cause devastating diseases in aquaculture, resulting in enormous economic losses. Our previous studies indicated that imidazole arctigenin derivatives possessed antiviral activities against aquatic rhabdoviruses. Based on the data of structure-activity relationship, a new imidazole arctigenin derivative,...

    journal_title:Virus research

    pub_type: 杂志文章

    doi:10.1016/j.virusres.2020.198019

    authors: Shen YF,Liu YH,Li BY,Liu TQ,Wang GX

    更新日期:2020-08-01 00:00:00

  • LncRNA, miRNA and lncRNA-miRNA interaction in viral infection.

    abstract::Noncoding RNAs (ncRNAs) are key components of the transcriptome and play an important role in both normal biological activity and pathological processes such as viral infection and tumorigenesis. LncRNAs and miRNAs are the most important elements of ncRNAs and function as vital regulatory elements. Their complex regul...

    journal_title:Virus research

    pub_type: 杂志文章,评审

    doi:10.1016/j.virusres.2018.08.018

    authors: Chen L,Zhou Y,Li H

    更新日期:2018-09-15 00:00:00

  • Evidence for the assignment of two strains of SPLV to the genus Potyvirus based on coat protein and 3' non-coding region sequence data.

    abstract::The use of potyvirus-specific primers and subsequent application of the RACE procedure allowed the cloning of the 3' terminal 1088 nucleotides of the genomic RNA of the Taiwan isolate of sweetpotato latent virus (SPLV-T) and the 3' genomic 1085 nucleotides of a SPLV-like virus from China (SPLV-CH). The sequence of an ...

    journal_title:Virus research

    pub_type: 杂志文章

    doi:10.1016/s0168-1702(97)01456-1

    authors: Colinet D,Kummert J,Lepoivre P

    更新日期:1997-05-01 00:00:00

  • Activation of PI3K/Akt pathway limits JNK-mediated apoptosis during EV71 infection.

    abstract::Apoptosis is frequently induced to inhibit virus replication during infection of Enterovirus 71 (EV71). On the contrary, anti-apoptotic pathway, such as PI3K/Akt pathway, is simultaneously exploited by EV71 to accomplish the viral life cycle. The relationship by which EV71-induced apoptosis and PI3K/Akt signaling path...

    journal_title:Virus research

    pub_type: 杂志文章

    doi:10.1016/j.virusres.2014.07.026

    authors: Zhang H,Li F,Pan Z,Wu Z,Wang Y,Cui Y

    更新日期:2014-11-04 00:00:00

  • Correlation of cellular factors and differential scrapie prion permissiveness in ovine microglia.

    abstract::Prion diseases are fatal neurodegenerative disorders by which the native cellular prion protein (PrPC) is misfolded into an accumulating, disease-associated isoform (PrPD). To improve the understanding of prion pathogenesis and develop effective treatments, it is essential to elucidate factors contributing to cellular...

    journal_title:Virus research

    pub_type: 杂志文章

    doi:10.1016/j.virusres.2017.07.016

    authors: Dinkel KD,Schneider DA,Muñoz-Gutiérrez JF,McElliott VR,Stanton JB

    更新日期:2017-08-15 00:00:00

  • Adaptability costs in immune escape variants of vesicular stomatitis virus.

    abstract::We have used vesicular stomatitis virus (VSV) to determine the cost of antiserum resistance during escape from a polyclonal immune response. Replication of VSV in the presence of polyclonal antiserum resulted in the selection of antibody-escape mutants, as shown by increased fitness in the presence of antiserum and by...

    journal_title:Virus research

    pub_type: 杂志文章

    doi:10.1016/j.virusres.2004.06.007

    authors: Novella IS,Gilbertson DL,Borrego B,Domingo E,Holland JJ

    更新日期:2005-01-01 00:00:00

  • Development of a stable insect cell line constitutively expressing rotavirus VP2.

    abstract::An insect High-Five cell line was generated constitutively and stably expressing the VP2 protein of rotavirus RF strain leading to the formation of core-like particles. The integration of the VP2 gene was confirmed by PCR, Real-time PCR and Southern blot, and the protein expression was confirmed by Western blot and im...

    journal_title:Virus research

    pub_type: 杂志文章

    doi:10.1016/j.virusres.2012.12.015

    authors: Shoja Z,Tagliamonte M,Jalilvand S,Mokhtari-Azad T,Hamkar R,Shahmahmoodi S,Rezaei F,Tornesello M,Buonaguro FM,Buonaguro L,Nategh R

    更新日期:2013-03-01 00:00:00

  • Use of a neural network secondary structure prediction to define targets for mutagenesis of herpes simplex virus glycoprotein B.

    abstract::Herpes simplex virus glycoprotein B (HSV gB) is essential for penetration of virus into cells, for cell-to-cell spread of virus, and for cell-cell fusion. Every member of the family Herpesviridae has a gB homolog, underlining its importance. The antigenic structure of gB has been studied extensively, but little is kno...

    journal_title:Virus research

    pub_type: 杂志文章

    doi:10.1016/s0168-1702(98)00030-6

    authors: Norton DD,Dwyer DS,Muggeridge MI

    更新日期:1998-05-01 00:00:00

  • RING finger proteins of infectious spleen and kidney necrosis virus (ISKNV) function as ubiquitin ligase enzymes.

    abstract::Infectious spleen and kidney necrosis virus (ISKNV) is the etiological agent that causes a pandemic and severe disease in fish characteristic of enlarged and damaged spleen and kidney. To identify viral proteins involved in infection and pathogenesis, we characterized five open reading frames (ORFs) of the ISKNV genom...

    journal_title:Virus research

    pub_type: 杂志文章

    doi:10.1016/j.virusres.2006.09.003

    authors: Xie J,Zhu J,Yang H,Weng S,Chen C,Chen H,Xie Q,Li M,He J

    更新日期:2007-02-01 00:00:00

  • Picobirnaviruses encode a protein with repeats of the ExxRxNxxxE motif.

    abstract::Picobirnaviruses possess a bisegmented double-stranded RNA genome. While the segment 2 encodes the RNA-dependent RNA polymerase, the segment 1 displays two open reading frames (ORFs). ORF2 was recently shown to code the capsid precursor and ORF1 product has not been characterized. In this study, we show that the three...

    journal_title:Virus research

    pub_type: 杂志文章

    doi:10.1016/j.virusres.2011.02.018

    authors: Da Costa B,Duquerroy S,Tarus B,Delmas B

    更新日期:2011-06-01 00:00:00

  • Viral modulation of stress granules.

    abstract::Following viral infection, the host responds by mounting a robust anti-viral response with the aim of creating an unfavorable environment for viral replication. As a countermeasure, viruses have elaborated mechanisms to subvert the host response in order to maintain viral protein synthesis and production. In the last ...

    journal_title:Virus research

    pub_type: 杂志文章,评审

    doi:10.1016/j.virusres.2012.06.004

    authors: Valiente-Echeverría F,Melnychuk L,Mouland AJ

    更新日期:2012-11-01 00:00:00

  • Expression of fluorescent proteins within the repeat long region of the Marek's disease virus genome allows direct identification of infected cells while retaining full pathogenicity.

    abstract::Marek's disease virus (MDV) is a lymphotropic alphaherpesvirus and causes Marek's disease (MD) in chickens. RLORF4 is an MDV-specific gene located in the repeat long (RL) regions of the genome and is directly involved in attenuation. In this report, we generated recombinant (r)MDVs in which eGFP or mRFP was inserted i...

    journal_title:Virus research

    pub_type: 杂志文章

    doi:10.1016/j.virusres.2015.02.012

    authors: Jarosinski KW,Donovan KM,Du G

    更新日期:2015-04-02 00:00:00

  • Naturally occurring NS3 resistance-associated variants in hepatitis C virus genotype 1: Their relevance for developing countries.

    abstract::Hepatitis C virus (HCV) is a major cause of global morbidity and mortality, with an estimated 130-150 million infected individuals worldwide. HCV is a leading cause of chronic liver diseases including cirrhosis and hepatocellular carcinoma. Current treatment options in developing countries involve pegylated interferon...

    journal_title:Virus research

    pub_type: 杂志文章

    doi:10.1016/j.virusres.2016.07.008

    authors: Echeverría N,Betancour G,Gámbaro F,Hernández N,López P,Chiodi D,Sánchez A,Boschi S,Fajardo A,Sóñora M,Moratorio G,Cristina J,Moreno P

    更新日期:2016-09-02 00:00:00

  • Negative-strand RNA viruses: the plant-infecting counterparts.

    abstract::While a large number of negative-strand (-)RNA viruses infect animals and humans, a relative small number have plants as their primary host. Some of these have been classified within families together with animal/human infecting viruses due to similarities in particle morphology and genome organization, while others h...

    journal_title:Virus research

    pub_type: 杂志文章,评审

    doi:10.1016/j.virusres.2011.09.028

    authors: Kormelink R,Garcia ML,Goodin M,Sasaya T,Haenni AL

    更新日期:2011-12-01 00:00:00

  • The capsid protein of vesicular exanthema of swine virus serotype A48: relationship to the capsid protein of other animal caliciviruses.

    abstract::Vesicular exanthema of swine virus (VESV), the prototype calicivirus, is the etiologic agent of the porcine disease vesicular exanthema of swine (VES). VES is characterized by vesicle formation on the extremities, mouth and snout and causes abortions and stillbirths if infection occurs during pregnancy. VESV is consid...

    journal_title:Virus research

    pub_type: 杂志文章

    doi:10.1016/s0168-1702(98)00013-6

    authors: Neill JD,Meyer RF,Seal BS

    更新日期:1998-03-01 00:00:00

  • DNA sequence of the simian varicella virus (SVV) gH gene and analysis of the SVV and varicella zoster virus gH transcripts.

    abstract::The varicella zoster virus (VZV) glycoprotein H (gH) stimulates VZV-specific immune responses and may be involved in virus penetration. This study reports the genomic map position and the DNA sequence of a simian varicella virus (SVV) homologue of the VZV gH gene. A 32P-labeled VZV gH-specific DNA probe hybridized to ...

    journal_title:Virus research

    pub_type: 杂志文章

    doi:10.1016/0168-1702(95)00049-v

    authors: Pumphrey CY,Gray WL

    更新日期:1995-09-01 00:00:00

  • A novel tetraspanin C189 upregulated in C6/36 mosquito cells following dengue 2 virus infection.

    abstract::Dengue (Den) viruses cause apoptosis in mammalian cells, but usually result in high progeny yields without evident damage in mosquito cells. By using subtractive hybridization, 13 potentially virus-induced genes were selected in Den-2 virus-infected Aedes albopictus C6/36 cells. Based on semi-quantitative and real-tim...

    journal_title:Virus research

    pub_type: 杂志文章

    doi:10.1016/j.virusres.2006.11.002

    authors: Lin CC,Yang CF,Tu CH,Huang CG,Shih YT,Chuang CK,Chen WJ

    更新日期:2007-03-01 00:00:00