Cytosine deamination and selection of CpG suppressed clones are the two major independent biological forces that shape codon usage bias in coronaviruses.

Abstract:

:Using the complete genome sequences of 19 coronavirus genomes, we analyzed the codon usage bias, dinucleotide relative abundance and cytosine deamination in coronavirus genomes. Of the eight codons that contain CpG, six were markedly suppressed. The mean NNU/NNC ratio of the six amino acids using either NNC or NNU as codon is 3.262, suggesting cytosine deamination. Among the 16 dinucleotides, CpG was most markedly suppressed (mean relative abundance 0.509). No correlation was observed between CpG abundance and mean NNU/NNC ratio. Among the 19 coronaviruses, CoV-HKU1 showed the most extreme codon usage bias and extremely high NNU/NNC ratio of 8.835. Cytosine deamination and selection of CpG suppressed clones by the immune system are the two major independent biochemical and biological selective forces that shape codon usage bias in coronavirus genomes. The underlying mechanism for the extreme codon usage bias, cytosine deamination and G+C content in CoV-HKU1 warrants further studies.

journal_name

Virology

journal_title

Virology

authors

Woo PC,Wong BH,Huang Y,Lau SK,Yuen KY

doi

10.1016/j.virol.2007.08.010

subject

Has Abstract

pub_date

2007-12-20 00:00:00

pages

431-42

issue

2

eissn

0042-6822

issn

1096-0341

pii

S0042-6822(07)00516-8

journal_volume

369

pub_type

杂志文章

相关文献

VIROLOGY文献大全
  • Induction of type-specific neutralizing antibodies by capsomeres of human papillomavirus type 33.

    abstract::The immunogenicity of capsomeres of human papillomavirus type 33 was evaluated in a dose-response analysis. Capsomeres were obtained free of capsids by expression of L1 carrying the single point mutation C427S. Neutralizing antibodies were detected using an in vitro pseudoinfection assay. Capsomeres induced type-speci...

    journal_title:Virology

    pub_type: 杂志文章

    doi:10.1006/viro.2000.0875

    authors: Fligge C,Giroglou T,Streeck RE,Sapp M

    更新日期:2001-05-10 00:00:00

  • Geographic classification of dengue-2 virus strains by antigen signature analysis.

    abstract::Dengue-2 virus strains from different locations were compared by T1-RNAse-resistant oligonucleotide fingerprinting and antigen signature analysis. The latter technique involved construction of radioimmunoassays using monoclonal antibodies that recognize nine distinct dengue-2 type-specific and flavivirus cross-reactiv...

    journal_title:Virology

    pub_type: 杂志文章

    doi:10.1016/0042-6822(86)90457-5

    authors: Monath TP,Wands JR,Hill LJ,Brown NV,Marciniak RA,Wong MA,Gentry MK,Burke DS,Grant JA,Trent DW

    更新日期:1986-10-30 00:00:00

  • Identification of two independent neutralization domains on the VP4 trypsin cleavage products VP5* and VP8* of human rotavirus ST3.

    abstract::The antigenic structure of the VP4 protein of human rotavirus (HRV) strains Wa and ST3 was studied by using a panel of Wa- and ST3-derived VP4-specific neutralizing monoclonal antibodies (NMAbs) and NMAb-resistant variants. The VP4-coding genes from three Wa and three ST3 variants were sequenced. For Wa VP4, one homot...

    journal_title:Virology

    pub_type: 杂志文章

    doi:10.1016/s0042-6822(95)80029-8

    authors: Padilla-Noriega L,Dunn SJ,López S,Greenberg HB,Arias CF

    更新日期:1995-01-10 00:00:00

  • Temperature-sensitive mutants in the vaccinia virus 4b virion structural protein assemble malformed, transcriptionally inactive intracellular mature virions.

    abstract::Two noncomplementing vaccinia virus temperature-sensitive mutants, Cts8 and Cts26, were mapped to the A3L gene, which encodes the major virion structural protein, 4b. The two ts mutants display normal patterns of gene expression, DNA replication, telomere resolution, and protein processing during infection. Morphogene...

    journal_title:Virology

    pub_type: 杂志文章

    doi:10.1016/j.virol.2004.08.038

    authors: Kato SE,Strahl AL,Moussatche N,Condit RC

    更新日期:2004-12-05 00:00:00

  • Tomato spotted wilt Tospovirus genome reassortment and genome segment-specific adaptation.

    abstract::A system to associate specific genome segments with viral phenotypes and to study factors influencing genome reassortment was developed for tomato spotted wilt Tospovirus (TSWV). Reassortant isolates were generated by co-inoculating a TSWV isolate, TSWV-D, with TSWV-10 or TSWV-MD. The parental origin of each genome se...

    journal_title:Virology

    pub_type: 杂志文章

    doi:10.1006/viro.1998.9131

    authors: Qiu WP,Geske SM,Hickey CM,Moyer JW

    更新日期:1998-04-25 00:00:00

  • Helicase ATPase activity of the Tobacco mosaic virus 126-kDa protein modulates replicase complex assembly.

    abstract::Mutations disrupting helicase domain motifs of the Tobacco mosaic virus 126/183-kDa proteins were investigated for their effect on replicase function and assembly. These mutations inhibited virus replication but did not affect 126-kDa induced N gene resistance or RNAi suppression. However, in vivo expressed 126-kDa mo...

    journal_title:Virology

    pub_type: 杂志文章

    doi:10.1016/j.virol.2010.03.019

    authors: Wang X,Kelman Z,Culver JN

    更新日期:2010-07-05 00:00:00

  • Selection and characterisation of acyclovir-resistant herpes simplex virus type 1 mutants inducing altered DNA polymerase activities.

    abstract::A collection of TK+, ACV-resistant mutants of herpes simplex virus type 1 (HSV-1) has been derived using a selection system based on biochemically transformed cells. Evidence is presented suggesting that most of these mutants induce resistant DNA polymerase activities and are thus likely to express variant DNA polymer...

    journal_title:Virology

    pub_type: 杂志文章

    doi:10.1016/0042-6822(85)90009-1

    authors: Larder BA,Darby G

    更新日期:1985-10-30 00:00:00

  • Infection, replication, and cytopathology of human papillomavirus type 31 in trophoblasts.

    abstract::Human papillomavirus (HPV) DNA is preferentially found in spontaneous abortions, specifically residing in trophoblasts, and transfected HPV-16 DNA replicates and produces progeny in 3A trophoblasts in culture. In this study 3A trophoblasts were shown to display both HPV receptors and infection by HPV-31b and HPV-6 vir...

    journal_title:Virology

    pub_type: 杂志文章

    doi:10.1016/j.virol.2003.08.020

    authors: You H,Liu Y,Agrawal N,Prasad CK,Chiriva-Internati M,Lowery CL,Kay HH,Hermonat PL

    更新日期:2003-11-25 00:00:00

  • Cellular uptake and nuclear delivery of recombinant adenovirus penton base.

    abstract::An Ad2 capsid component, the penton base, expressed as recombinant protein, was found to be capable of affecting the entire entry pathway of adenovirion in HeLa cells, i.e., cell attachment, endocytosis, vesicular escape, intracytoplasmic movement, and translocation through the nuclear pore complex. Data with pentamer...

    journal_title:Virology

    pub_type: 杂志文章

    doi:10.1006/viro.1999.9864

    authors: Hong SS,Gay B,Karayan L,Dabauvalle MC,Boulanger P

    更新日期:1999-09-15 00:00:00

  • Single oral immunization with replication deficient recombinant adenovirus elicits long-lived transgene-specific cellular and humoral immune responses.

    abstract::Oral-gastric delivery of vaccines is a preferred route of immunization and is particularly relevant to the development of vaccine-vector systems. We have investigated the ability of a replication deficient (E1-deleted) adenovirus construct (RAd68), which efficiently expresses the measles virus nucleocapsid (N) protein...

    journal_title:Virology

    pub_type: 杂志文章

    doi:10.1006/viro.2001.1281

    authors: Sharpe S,Fooks A,Lee J,Hayes K,Clegg C,Cranage M

    更新日期:2002-02-15 00:00:00

  • Failure of neutralizing antibody to regulate CAE lentivirus expression in vivo.

    abstract::Sequential isolates of caprine arthritis-encephalitis lentivirus (CAEV) were obtained from clinically arthritic carpal joints of three Saanen goats between 36.4 and 44.9 months after infection with biologically cloned CAEV isolate 63. These virus isolates and the CAEV-63 inoculum were evaluated for neutralization by a...

    journal_title:Virology

    pub_type: 杂志文章

    doi:10.1006/viro.1993.1542

    authors: Cheevers WP,McGuire TC,Norton LK,Cordery-Cotter R,Knowles DP

    更新日期:1993-10-01 00:00:00

  • In vivo and in vitro infection with two different molecular clones of visna virus.

    abstract::The behavior of two genetically different molecular clones of visna virus KV1772-kv72/67 and LV1-1KS1 was compared in vivo and in vitro. On intracerebral inoculation, clone KV1772-kv72/67 induced a similar response in five sheep as has already been reported with neurovirulent derivates of visna virus. Virus was freque...

    journal_title:Virology

    pub_type: 杂志文章

    doi:10.1006/viro.1996.8428

    authors: Torsteinsdóttir S,Agnarsdóttir G,Matthíasdóttir S,Rafnar B,Andrésdóttir V,Andrésson OS,Staskus K,Pétursson G,Pálsson PA,Georgsson G

    更新日期:1997-03-17 00:00:00

  • Development of reassortant viruses between pathogenic hantavirus strains.

    abstract::Segment reassortment of negative strand viruses is an important mechanism for the development of new virus strains with altered pathogenicity. This study reports on in vitro generation of reassortants between Andes (ANDV) and Sin Nombre (SNV) viruses. Although they both cause hantavirus pulmonary syndrome (HPS), ANDV ...

    journal_title:Virology

    pub_type: 杂志文章

    doi:10.1016/j.virol.2004.07.012

    authors: Rizvanov AA,Khaiboullina SF,St Jeor S

    更新日期:2004-10-01 00:00:00

  • Analysis of Hantaan virus RNA: evidence for a new genus of bunyaviridae.

    abstract::Hantaan virus, the prototype virus of hemorrhagic fever with renal syndrome, was examined for nucleic acid characteristics which would support its previously proposed inclusion in the virus family Bunyaviridae. Nucleocapsid RNA from Hantaan virions and a control bunyavirus were examined for ribonuclease A (RNase A) se...

    journal_title:Virology

    pub_type: 杂志文章

    doi:10.1016/0042-6822(83)90514-7

    authors: Schmaljohn CS,Dalrymple JM

    更新日期:1983-12-01 00:00:00

  • Different recombinant murine leukemia viruses use different cell surface receptors.

    abstract::Retroviruses can be grouped by viral interference measurements into classes which use common cell surface receptors. We previously tested a large number of isolates of mink cell focus-inducing (MCF) murine leukemia viruses (MuLVs), and reported that all of them share a distinct receptor on NIH/3T3 cells (A. Rein, Viro...

    journal_title:Virology

    pub_type: 杂志文章

    doi:10.1016/0042-6822(84)90255-1

    authors: Rein A,Schultz A

    更新日期:1984-07-15 00:00:00

  • Nucleotide sequences within the U5 region of the viral RNA genome are the major determinants for an human immunodeficiency virus type 1 to maintain a primer binding site complementary to tRNA(His).

    abstract::The initiation of reverse transcription of the human immunodeficiency virus type 1 (HIV-1) genome requires cellular tRNA(Lys,3) as a primer and occurs at a site in the viral RNA genome, designated as the primer binding site (PBS), which is complementary to the 3'-terminal 18 nucleotides of tRNA(Lys,3). We previously d...

    journal_title:Virology

    pub_type: 杂志文章

    doi:10.1006/viro.1996.0658

    authors: Zhang Z,Kang SM,LeBlanc A,Hajduk SL,Morrow CD

    更新日期:1996-12-15 00:00:00

  • In vitro fidelity of the prototype primate foamy virus (PFV) RT compared to HIV-1 RT.

    abstract::We compared the in vitro fidelity of wild-type human immunodeficiency virus type-1 (HIV-1) reverse transcriptase (RT) and the prototype foamy virus (PFV) RT. Both enzymes had similar error rates for single nucleotide substitutions; however, PFV RT did not appear to make errors at specific hotspots, like HIV-1 RT. In a...

    journal_title:Virology

    pub_type: 杂志文章

    doi:10.1016/j.virol.2007.05.034

    authors: Boyer PL,Stenbak CR,Hoberman D,Linial ML,Hughes SH

    更新日期:2007-10-25 00:00:00

  • Sequence conservation and divergence of hepatitis delta virus RNA.

    abstract::The complete RNA sequence of the hepatitis delta virus (HDV) obtained from the Nauru Island in the Pacific was determined by cDNA cloning and amplification by polymerase chain reaction (PCR). The sequence showed 14-17% divergence from the two known HDV RNA sequences. There are three highly conserved domains: the regio...

    journal_title:Virology

    pub_type: 杂志文章

    doi:10.1016/0042-6822(90)90335-o

    authors: Chao YC,Chang MF,Gust I,Lai MM

    更新日期:1990-10-01 00:00:00

  • Transforming properties of Felis catus papillomavirus type 2 E6 and E7 putative oncogenes in vitro and their transcriptional activity in feline squamous cell carcinoma in vivo.

    abstract::Felis catus papillomavirus type 2 (FcaPV2) DNA is found in feline cutaneous squamous cell carcinomas (SCCs); however, its biological properties are still uncharacterized. In this study, we successfully expressed FcaPV2 E6 and E7 putative oncogenes in feline epithelial cells and demonstrated that FcaPV2 E6 binds to p53...

    journal_title:Virology

    pub_type: 杂志文章

    doi:10.1016/j.virol.2016.05.017

    authors: Altamura G,Corteggio A,Pacini L,Conte A,Pierantoni GM,Tommasino M,Accardi R,Borzacchiello G

    更新日期:2016-09-01 00:00:00

  • In vivo priming and activation of memory cytotoxic T-lymphocytes (CTL) by a chimeric simian virus 40 T antigen expressing an eight amino acid residue herpes simplex virus gB CTL epitope.

    abstract::The simian virus 40 (SV40) large T antigen was used as an immunogenic vector to express a herpes simplex virus type 1 (HSV-1) glycoprotein B (gB), H-2Kb-restricted cytotoxic T lymphocyte (CTL) recognition epitope corresponding to amino acid residues 498-505. Immunization of naive, C57BL/6 mice with a cell line, B6/350...

    journal_title:Virology

    pub_type: 杂志文章

    doi:10.1006/viro.1993.1657

    authors: Bonneau RH,Fu TM,Tevethia SS

    更新日期:1993-12-01 00:00:00

  • Characterization of multiple molecular interactions between human cytomegalovirus (HCMV) and human immunodeficiency virus type 1 (HIV-1).

    abstract::In transient gene expression assays we observed an increase in expression of the bacterial chloramphenicol acetyl-transferase (CAT) gene, under the transcriptional control of the HIV-1 LTR (pLTR-CAT), when this plasmid was cotransfected into Vero or MRC-5 cells with a plasmid containing either the HCMV immediate early...

    journal_title:Virology

    pub_type: 杂志文章

    doi:10.1016/0042-6822(90)90233-h

    authors: Rando RF,Srinivasan A,Feingold J,Gonczol E,Plotkin S

    更新日期:1990-05-01 00:00:00

  • Mason-Pfizer monkey virus Gag proteins interact with the human sumo conjugating enzyme, hUbc9.

    abstract::Retroviral Gag proteins function during early and late stages of the viral life cycle. To gain additional insight into the cellular requirements for viral replication, a two-hybrid screen was used to identify cellular proteins that interact with the Mason-Pfizer monkey virus Gag protein. One of the cellular proteins f...

    journal_title:Virology

    pub_type: 杂志文章

    doi:10.1016/s0042-6822(03)00348-9

    authors: Weldon RA Jr,Sarkar P,Brown SM,Weldon SK

    更新日期:2003-09-15 00:00:00

  • Detection of visna virus antigens and RNA in glial cells in foci of demyelination.

    abstract::Visna is a slow virus infection of sheep in which the characteristic pathological change is demyelination in foci of inflammation. The latter is thought to be the result of an immunopathological process directed against cellular and antigenic targets that have been difficult to define because of restricted viral gene ...

    journal_title:Virology

    pub_type: 杂志文章

    doi:10.1016/0042-6822(85)90264-8

    authors: Stowring L,Haase AT,Petursson G,Georgsson G,Palsson P,Lutley R,Roos R,Szuchet S

    更新日期:1985-03-01 00:00:00

  • Increased gelatinase B/matrix metalloproteinase 9 (MMP-9) activity in a murine model of acute coxsackievirus B4-induced pancreatitis.

    abstract::Infection of mice with coxsackievirus B4 results within days in a severe acute necrotizing pancreatitis, which resolves completely within weeks. Gelatinase B or matrix metalloproteinase 9 (MMP-9) has previously been shown to be involved in several models of pancreatitis, but its role in virus-induced pancreatitis has ...

    journal_title:Virology

    pub_type: 杂志文章

    doi:10.1016/j.virol.2008.08.046

    authors: De Palma AM,Verbeken E,Van Aelst I,Van den Steen PE,Opdenakker G,Neyts J

    更新日期:2008-12-05 00:00:00

  • SV40 vectors carrying minimal sequence of viral origin with exchangeable capsids.

    abstract::Polyomaviral vectors are generated by transfecting 293T cells with three sets of DNAs: DNA for the expression of simian virus 40 (SV40) T antigen; DNA for the expression of SV40 capsid proteins, and vector DNA harboring a reporter gene expression cassette carrying a SV40 origin. The vector DNA harbors a minimal sequen...

    journal_title:Virology

    pub_type: 杂志文章

    doi:10.1016/j.virol.2008.06.032

    authors: Nakanishi A,Chapellier B,Maekawa N,Hiramoto M,Kuge T,Takahashi RU,Handa H,Imai T

    更新日期:2008-09-15 00:00:00

  • Oligomeric organization and strain-specific proteolytic modification of the virion M2 protein of influenza A H1N1 viruses.

    abstract::The M2 protein of influenza A H1N1 strains PR8, WS, and WSN is present in homooligomeric forms in virions grown in the allantoic cavity of embryonated eggs. The bulk of the virion M2 is detected as tetramers and dimers. The oligomeric forms of PR8 virions differ from those of WS and WSN not only in apparent molecular ...

    journal_title:Virology

    pub_type: 杂志文章

    doi:10.1016/0042-6822(92)90096-8

    authors: Panayotov PP,Schlesinger RW

    更新日期:1992-01-01 00:00:00

  • The structure of adeno-associated virus serotype 3B (AAV-3B): insights into receptor binding and immune evasion.

    abstract::Adeno-associated viruses (AAVs) are leading candidate vectors for human gene therapy. AAV serotypes have broad cellular tropism and use a variety of cellular receptors. AAV serotype 3 binds to heparan sulfate proteoglycan prior to cell entry and is serologically distinct from other serotypes. The capsid features that ...

    journal_title:Virology

    pub_type: 杂志文章

    doi:10.1016/j.virol.2010.03.027

    authors: Lerch TF,Xie Q,Chapman MS

    更新日期:2010-07-20 00:00:00

  • Comparison of the genomes of attenuated equine herpesvirus-1 strains with their parent virulent strain.

    abstract::To elucidate the virulence factors of equine herpesvirus-1 (EHV-1), we compared the genomic architecture of the HH1 strain, a Japanese isolate of EHV-1, with that of its four descendant strains obtained by serial passage in bovine kidney (BK) cells, i.e. BK77, BK161, BK271, and BK343. In preliminary studies high-passa...

    journal_title:Virology

    pub_type: 杂志文章

    doi:10.1006/viro.1994.1228

    authors: Kirisawa R,Ui S,Takahashi A,Kawakami Y,Iwai H

    更新日期:1994-05-01 00:00:00

  • Residues in the PB2 and PA genes contribute to the pathogenicity of avian H7N3 influenza A virus in DBA/2 mice.

    abstract::Replication and transmission of avian influenza virus in humans poses a pandemic threat. The molecular determinants that facilitate this process are not well understood. We used DBA/2 mice to identify viral factors that mediate the difference in pathogenesis between a virulent (H7N3) and a non-virulent (H7N9) avian in...

    journal_title:Virology

    pub_type: 杂志文章

    doi:10.1016/j.virol.2016.04.013

    authors: DesRochers BL,Chen RE,Gounder AP,Pinto AK,Bricker T,Linton CN,Rogers CD,Williams GD,Webby RJ,Boon AC

    更新日期:2016-07-01 00:00:00

  • Identification and characterization of a new base substitution in the vaccine strain of Sabin 3 poliovirus.

    abstract::The complete RNA sequence of Sabin 3 (LED3) used in vaccine in the United States has been determined. The LED3 Sabin 3 sequence contains the attenuating mutations at bases 472 and 2034 but differs from that published by Stanway et al. (Nucleic Acids Res., 11, 5629-5643, 1983) at two other base positions, 2493 and 6061...

    journal_title:Virology

    pub_type: 杂志文章

    doi:10.1016/0042-6822(91)90576-w

    authors: Weeks-Levy C,Tatem JM,DiMichele SJ,Waterfield W,Georgiu AF,Mento SJ

    更新日期:1991-12-01 00:00:00