Codon usage bias of the phosphoprotein gene of spring viraemia of carp virus and high codon adaptation to the host.

Abstract:

:In this study, we calculated the relative synonymous codon usage (RSCU) value and the effective number of codons (ENC) value to carry out principal component analysis (PCA) and correlation analysis of the codon usage pattern of the phosphoprotein gene (P gene) of spring viraemia of carp virus (SVCV). The synonymous codon usage pattern in P genes is geography-specific, based on PCA analysis. The high correlation between (G + C)1,2 % and (G + C)3 % suggests that mutational pressure rather than natural selection is the main factor that determines the codon usage and base components in P genes. At least 40 out of 59 synonymous codons are similarly selected in all functional genes within five complete SVCV genomes, and the hosts based on the RSCU data. These results not only provide insight into variations in the codon usage pattern of SVCV but also may help in understanding the processes governing the evolution of SVCV.

journal_name

Arch Virol

journal_title

Archives of virology

authors

Ma YP,Zhou ZW,Liu ZX,Hao L,Ma JY,Feng GQ,Liang ZL,Ke H

doi

10.1007/s00705-014-2000-z

subject

Has Abstract

pub_date

2014-07-01 00:00:00

pages

1841-7

issue

7

eissn

0304-8608

issn

1432-8798

journal_volume

159

pub_type

杂志文章
  • Selective syncytium formation by murine leukemia virus in rat 3Y1 fibroblasts transformed by adenovirus type 12 or its E1A gene.

    abstract::3Y1 rat fibroblasts transformed by adenovirus type 12 or by its E1A gene formed syncytia when cocultivated with the Friend as well as other ecotropic murine leukemia-virus-producing cells. In contrast, the parental 3Y1 cells and those transformed by other tumor viruses or by a chemical carcinogen exhibited no syncytiu...

    journal_title:Archives of virology

    pub_type: 杂志文章

    doi:10.1007/BF01310628

    authors: Momozaki N,Ogura H,Matsuhashi S,Joh K,Tabuchi K,Kimura G,Hori K

    更新日期:1990-01-01 00:00:00

  • Induction of apoptosis in a T lymphoblastoid cell line infected with feline immunodeficiency virus.

    abstract::The mechanism of cell death induced by feline immunodeficiency virus (FIV) infection was investigated in an interleukin 2(IL-2)-dependent T-lymphoblastoid cell line (MYA-1). DNA extracted from FIV-infected MYA-1 cells showed a ladder of nucleosomal DNA, indicating that the cytopathic effect (CPE) observed in these cel...

    journal_title:Archives of virology

    pub_type: 杂志文章

    doi:10.1007/BF01309772

    authors: Ohno K,Okamoto Y,Miyazawa T,Mikami T,Watari T,Goitsuka R,Tsujimoto H,Hasegawa A

    更新日期:1994-01-01 00:00:00

  • A novel East African monopartite begomovirus-betasatellite complex that infects Vernonia amygdalina.

    abstract::The complete genomes of a monopartite begomovirus (genus Begomovirus, family Geminiviridae) and an associated betasatellite found infecting Vernonia amygdalina Delile (family Compositae) in Uganda were cloned and sequenced. Begomoviruses isolated from two samples showed the highest nucleotide sequence identity (73.1% ...

    journal_title:Archives of virology

    pub_type: 杂志文章

    doi:10.1007/s00705-016-3175-2

    authors: Mollel HG,Ndunguru J,Sseruwagi P,Alicai T,Colvin J,Navas-Castillo J,Fiallo-Olivé E

    更新日期:2017-04-01 00:00:00

  • Mutational analysis of the activator of late transcription, Alt, in the lactococcal bacteriophage TP901-1.

    abstract::An activator protein, Alt, synthesized during the early state of lytic infection is required for transcription of the late operon in the lactococcal phage TP901-1. In order to identify amino acid residues in the Alt protein required for activation of the TP901-1 late promoter, P(late), hydroxylamine mutagenesis was pe...

    journal_title:Archives of virology

    pub_type: 杂志文章

    doi:10.1007/s00705-006-0851-7

    authors: Pedersen M,Hammer K

    更新日期:2007-02-01 00:00:00

  • Piperacillin and ceftazidime produce the strongest synergistic phage-antibiotic effect in Pseudomonas aeruginosa.

    abstract::The combined use of phage and antibiotics can show synergistic antimicrobial effects, so-called phage-antibiotic synergy (PAS). Here, we screened and examined PAS against Pseudomonas aeruginosa in vitro. Testing four different phages infecting P. aeruginosa, phage KPP22 classified within the family Myoviridae genus Pb...

    journal_title:Archives of virology

    pub_type: 杂志文章

    doi:10.1007/s00705-018-3811-0

    authors: Uchiyama J,Shigehisa R,Nasukawa T,Mizukami K,Takemura-Uchiyama I,Ujihara T,Murakami H,Imanishi I,Nishifuji K,Sakaguchi M,Matsuzaki S

    更新日期:2018-07-01 00:00:00

  • Influenza A/Fujian/411/02(H3N2)-lineage viruses in Finland: genetic diversity, epidemic activity and vaccination-induced antibody response.

    abstract::The first sporadic cases of Fujian/411/02-lineage viruses were recorded in Finland in winter 2001-2002. The first protracted but low-intensity outbreak occurred here during the first half of 2003, and the second outbreak early in autumn 2003, after detection of sporadic influenza A cases in the summer. The calculated ...

    journal_title:Archives of virology

    pub_type: 杂志文章

    doi:10.1007/s00705-005-0635-5

    authors: Ikonen N,Pyhälä R,Toivonen M,Korpela H

    更新日期:2006-02-01 00:00:00

  • Effect of treatment with certain flavonoids on Mengo virus-induced encephalitis in mice.

    abstract::Among the four flavonoids tested quercetin and morin proved to be significantly effective against lethal Mengo virus-induced encephalitis in mice when the drugs were adminsitered orally (p.o.). With subcutaneous (s.c.) administration all four drugs failed to prevent mortality in the infected mice. Quercetin produced m...

    journal_title:Archives of virology

    pub_type: 杂志文章

    doi:10.1007/BF01315089

    authors: Veckenstedt A,Béládi I,Mucsi I

    更新日期:1978-01-01 00:00:00

  • Complete nucleotide sequence of a new isolate of passion fruit woodiness virus from Western Australia.

    abstract::We determined the complete genome sequence of the passion fruit woodiness virus Gld-1 isolate (PWV-Gld-1) from Australia and compared it with that of PWV-MU-2, another Australian isolate of PWV. The genomes shared high sequence identity in both the complete nucleotide sequence and the ORF amino acid sequence. All of t...

    journal_title:Archives of virology

    pub_type: 杂志文章

    doi:10.1007/s00705-013-1670-2

    authors: Fukumoto T,Nakamura M,Wylie SJ,Chiaki Y,Iwai H

    更新日期:2013-08-01 00:00:00

  • Preparation and characterization of a neutralizing monoclonal antibody directed to VP4 of rotavirus strain K8 which has unique VP4 neutralization epitopes.

    abstract::For selecting the neutralizing monoclonal antibodies (N-MAbs) directed to VP4 of rotavirus strain K8, which has unique VP4 neutralization epitopes, we prepared several reassortant viruses by mixed infection of two different strains K8 (serotype 1) and P (serotype 3) in vitro: three reassortant clones having VP4 of K8 ...

    journal_title:Archives of virology

    pub_type: 杂志文章

    doi:10.1007/BF01316751

    authors: Kobayashi N,Taniguchi K,Urasawa T,Urasawa S

    更新日期:1991-01-01 00:00:00

  • Complete nucleotide sequence and genome organization of Pelargonium flower break virus.

    abstract::The complete nucleotide sequence of Pelargonium flower break virus (PFBV) has been determined. The genomic RNA is 3923 nucleotides (nt) long and contains five open reading frames (ORFs). The 5'-proximal ORF encodes a 27 kDa protein (p27) and terminates with an amber codon which may be read-through into an in-frame p56...

    journal_title:Archives of virology

    pub_type: 杂志文章

    doi:10.1007/s00705-003-0231-5

    authors: Rico P,Hernández C

    更新日期:2004-03-01 00:00:00

  • Molecular characterization of a novel reovirus isolated from Pekin ducklings in China.

    abstract::The complete genome sequence of a novel duck orthoreovirus, designated DRV strain TH11(DRV-TH11), was determined and characterized. The DRV-TH11 genome is comprised of 23,417 bp and its genome organization is more similar to that of avian orthoreoviruses (ARVs) of chicken origin than other reoviruses. The results of c...

    journal_title:Archives of virology

    pub_type: 杂志文章

    doi:10.1007/s00705-014-2241-x

    authors: Zhu YQ,Li CF,Bi ZL,Chen ZY,Meng CC,Wang GJ,Ding C,Liu GQ

    更新日期:2015-01-01 00:00:00

  • Transcriptional control of the HERV-H LTR element of the GSDML gene in human tissues and cancer cells.

    abstract::Long terminal repeats (LTRs) of human endogenous retroviruses (HERVs) have been reported to serve as alternative promoters in functional genes. The GSDML (gasdermin-like protein) gene located on human chromosome 17q21 has been found to be an oncogenomic recombination hotspot. Here, we identified the LTR element of HER...

    journal_title:Archives of virology

    pub_type: 杂志文章

    doi:10.1007/s00705-006-0764-5

    authors: Sin HS,Huh JW,Kim DS,Kang DW,Min DS,Kim TH,Ha HS,Kim HH,Lee SY,Kim HS

    更新日期:2006-10-01 00:00:00

  • Abortive infection of influenza virus in Ehrlich ascites tumor cells. Unusual fragility of virus particles.

    abstract::Noninfectious virus particles were produced in Ehrlich ascites tumor cells infected intraperitoneally with fowl plague virus. The PFU yield of virus per cell was less than 0.1 and the ratio PFU/HA units in the progeny virus was less than 10(3). The virus particles had the same morphology and size as egg-grown virus bu...

    journal_title:Archives of virology

    pub_type: 杂志文章

    doi:10.1007/BF01315278

    authors: Bukrinskaya AG,Gitelman AK,Martynenko VB

    更新日期:1978-01-01 00:00:00

  • Serological analysis of hemorrhagic fever with renal syndrome (HFRS) patients in Far Eastern Russia and identification of the causative hantavirus genotype.

    abstract::Hemorrhagic fever with renal syndrome (HFRS) is endemic in East Asia and Europe. The disease is caused by several viruses belonging to the genus Hantavirus, including the Hantaan virus (HTNV), Seoul virus (SEOV), Dobrava Belgrade virus (DOBV), and Puumala virus (PUUV). Recently, HTNV-related viruses, Amur (AMR) and Fa...

    journal_title:Archives of virology

    pub_type: 杂志文章

    doi:10.1007/s00705-003-0113-x

    authors: Miyamoto H,Kariwa H,Araki K,Lokugamage K,Hayasaka D,Cui BZ,Lokugamage N,Ivanov LI,Mizutani T,Iwasa MA,Yoshimatsu K,Arikawa J,Takashima I

    更新日期:2003-08-01 00:00:00

  • The role of the C-terminal region of olive latent virus 1 coat protein in host systemic infection.

    abstract::A full-length cDNA clone of olive latent virus 1 (OLV-1), a member of the genus Necrovirus, family Tombusviridae, was subjected to site-directed mutagenesis, and coat protein gene mutants were constructed. A mutant clone, denoted Delta3297, was obtained by deleting the nucleotide in position 3297, thus inducing a fram...

    journal_title:Archives of virology

    pub_type: 杂志文章

    doi:10.1007/s00705-006-0767-2

    authors: Pantaleo V,Grieco F,Di Franco A,Martelli GP

    更新日期:2006-10-01 00:00:00

  • Computational analysis of the effect of polymerase acidic (PA) gene mutation F35L in the 2009 pandemic influenza A (H1N1) virus on binding aspects of mononucleotides in the endonuclease domain.

    abstract::An F35L mutation in the N-terminal domain of the polymerase acidic protein (PA-Nter), which contains the active site of the endonuclease, has been reported to result in higher polymerase activity in mouse-adapted strains of the 2009 pandemic influenza A H1N1 virus. We modeled wild and mutant complexes of uridine 5'-mo...

    journal_title:Archives of virology

    pub_type: 杂志文章

    doi:10.1007/s00705-017-3681-x

    authors: Bhoye D,Cherian SS

    更新日期:2018-04-01 00:00:00

  • Human cytomegalovirus persists in cells treated with interferon. Brief report.

    abstract::Human cytomegalovirus disappeared from cultures continuously exposed to interferon. When interferon was removed, high titers of virus reappeared. Cytomegalovirus was thus able to persist in potentially infectious form in cells protected by interferon. ...

    journal_title:Archives of virology

    pub_type: 杂志文章

    doi:10.1007/BF01309276

    authors: Rodriguez JE,Loepfe TR,Stinski MF

    更新日期:1983-01-01 00:00:00

  • The intestine is a site of passage for potato leafroll virus from the gut lumen into the haemocoel in the aphid vector, Myzus persicae Sulz.

    abstract::Four detection techniques, three of which gave reliable identification of the virus particles, were used to locate potato leafroll virus (PLRV) in the alimentary canal of its main aphid vector, Myzus persicae Sulz: immunofluorescence on cryostat sections, conventional transmission electron microscopy on ultrathin sect...

    journal_title:Archives of virology

    pub_type: 杂志文章

    doi:10.1007/BF01378639

    authors: Garret A,Kerlan C,Thomas D

    更新日期:1993-01-01 00:00:00

  • The complete nucleotide sequence of turnip mosaic virus RNA Japanese strain.

    abstract::The complete nucleotide sequence of the RNA genome of turnip mosaic virus Japanese strain (TuMV-J) has been determined from five overlapping cDNA clones and by direct sequencing of viral RNA. The RNA sequence was 9833 nucleotides in length, excluding a 3' terminal poly(A) tail. An AUG triplet at position 130-132 was a...

    journal_title:Archives of virology

    pub_type: 杂志文章

    doi:10.1007/BF01718209

    authors: Ohshima K,Tanaka M,Sako N

    更新日期:1996-01-01 00:00:00

  • Molecular phylogenetic analysis of Barley yellow mosaic virus.

    abstract::Complete nucleotide sequences of three strains (I, III, and IV) of Barley yellow mosaic virus (BaYMV) isolated in Japan were determined. The length of the genome was the same among the three strains; RNA1 was 7,642 nt and RNA2 was 3,585 nt. The molecular phylogenetic analysis showed that strain I was most closely rela...

    journal_title:Archives of virology

    pub_type: 杂志文章

    doi:10.1007/s00705-008-0163-1

    authors: Nishigawa H,Hagiwara T,Yumoto M,Sotome T,Kato T,Natsuaki T

    更新日期:2008-01-01 00:00:00

  • Characterization of the structural proteins of hemorrhagic enteritis virus.

    abstract::The structural proteins of hemorrhagic enteritis (HEV), a turkey adenovirus, were analyzed by polyacrylamide gel electrophoresis (PAGE) and Western blotting using polyspecific, monospecific and monoclonal antibodies for detection. In purified HEV preparations, eleven polypeptides with apparent molecular weights rangin...

    journal_title:Archives of virology

    pub_type: 杂志文章

    doi:10.1007/BF01309695

    authors: van den Hurk JV

    更新日期:1992-01-01 00:00:00

  • Can HCV affect the efficacy of anti-HIV treatment?

    abstract::To evaluate the impact of new antiretroviral combinations (HAART: Highly Active Anti Retroviral Therapy) on HCV replication and liver enzyme levels, we analysed the changes in HCV viremia and aminotransferase levels in HIV and HCV co-infected patients. Moreover, to evaluate the influence of HCV infection on the effica...

    journal_title:Archives of virology

    pub_type: 杂志文章

    doi:10.1007/s007050050685

    authors: Filippini P,Coppola N,Scolastico C,Liorre G,Nocera R,Sagnelli E,Piccinino F

    更新日期:2000-01-01 00:00:00

  • Complete genome sequence analysis of a genetic variant of grapevine virus L from the grapevine cultivar Blanc du Bois.

    abstract::The complete genome sequences of two grapevine virus L (GVL) isolates collected from the wine grape cultivar Blanc du Bois (Vitis spp.: 'Florida D 6-148'×'Cardinal') in Texas were determined. The two genome sequences (excluding the polyA tail) were each 7594 nucleotide long and 99.7% identical to each other, but they ...

    journal_title:Archives of virology

    pub_type: 杂志文章

    doi:10.1007/s00705-020-04682-8

    authors: Alabi OJ,Appel DN,McBride S,Al Rwahnih M,Pontasch FM

    更新日期:2020-08-01 00:00:00

  • Tryptic peptide analysis of the structural proteins of a temperature-sensitive mutant derived from an HVJ (Sendai virus) carrier culture.

    abstract::The individual structural polypeptides of HVJ (haemagglutinating virus of Japan--the Sendai strain of parainfluenza 1 virus) were examined by tryptic peptide analysis. [3H]-methionine-labelled structural proteins of the wild-type virus of HVJ (HVJ-W) and [35S]-methionine-labelled corresponding constituent proteins of ...

    journal_title:Archives of virology

    pub_type: 杂志文章

    doi:10.1007/BF01320600

    authors: Kimura Y

    更新日期:1979-01-01 00:00:00

  • Ljungan virus is endemic in rodents in the UK.

    abstract::Ljungan virus is a recently identified member of the family Picornaviridae that was isolated from bank voles in Sweden. LjV has been associated with [corrected] type 1 diabetes-like symptoms and myocarditis in bank voles (Myodes glareolus), and it has been suggested that it has zoonotic potential. Here, we show for th...

    journal_title:Archives of virology

    pub_type: 杂志文章

    doi:10.1007/s00705-013-1731-6

    authors: Salisbury AM,Begon M,Dove W,Niklasson B,Stewart JP

    更新日期:2014-03-01 00:00:00

  • Identification of host factors potentially involved in RTM-mediated resistance during potyvirus long distance movement.

    abstract::The long distance movement of potyviruses is a poorly understood step of the viral cycle. Only factors inhibiting this process, referred to as "Restricted TEV Movement" (RTM), have been identified in Arabidopsis thaliana. On the virus side, the potyvirus coat protein (CP) displays determinants required for long-distan...

    journal_title:Archives of virology

    pub_type: 杂志文章

    doi:10.1007/s00705-017-3292-6

    authors: Sofer L,Cabanillas DG,Gayral M,Téplier R,Pouzoulet J,Ducousso M,Dufin L,Bréhélin C,Ziegler-Graff V,Brault V,Revers F

    更新日期:2017-07-01 00:00:00

  • Sequence variability within the 3'-proximal part of the Sweet potato mild mottle virus genome.

    abstract::Sweet potato mild mottle virus (SPMMV) is the type member of the genus Ipomovirus (family Potyviridae) and is only known to occur in East Africa. In Uganda, SPMMV is the third most prevalent virus infecting sweet potato. The sequence variability of SPMMV was studied by cloning and sequencing a 1.8-kb fragment represen...

    journal_title:Archives of virology

    pub_type: 杂志文章

    doi:10.1007/s00705-002-0930-3

    authors: Mukasa SB,Rubaihayo PR,Valkonen JP

    更新日期:2003-03-01 00:00:00

  • Immunogenicity of non-structural proteins of foot-and-mouth disease virus: differences between infected and vaccinated swine.

    abstract::Non-structural as well as VP1 recombinant proteins of foot-and-mouth disease virus (FMDV) produced in E. coli, have been used to study the specific antibody response of infected or vaccinated swine. An analysis of sera from infected pigs, using a direct ELISA, showed that polypeptide 3ABC (spanning non-structural prot...

    journal_title:Archives of virology

    pub_type: 杂志文章

    doi:10.1007/BF01538822

    authors: Rodríguez A,Dopazo J,Sáiz JC,Sobrino F

    更新日期:1994-01-01 00:00:00

  • Purification of mengovirus by freon extraction and chromatography on protein-coated controlled pore glass.

    abstract::Mengovirus, extracted from infected L-cell cultures with Freon 113 and concentrated from the aqueous phase with polyethyleneglycol, was chromatographed on protein-coated controlled pore glass (CPG). The covalent binding of protein to CPG is described. Further purification and concentration of mengovirus was achieved b...

    journal_title:Archives of virology

    pub_type: 杂志文章

    doi:10.1007/BF01315283

    authors: Gschwender HH,Traub P

    更新日期:1978-01-01 00:00:00

  • Complete nucleotide sequences of M and L RNAs from a new pepper-infecting tospovirus, Pepper chlorotic spot virus.

    abstract::Pepper chlorotic spot virus (PCSV), newly found in Taiwan, was identified as a new tospovirus based on the molecular characterization of its S RNA. In this study, the complete M and L RNA sequences of PCSV were determined. The M RNA has 4795 nucleotides (nts), encoding the NSm protein of 311 aa (34.5 kDa) in the viral...

    journal_title:Archives of virology

    pub_type: 杂志文章

    doi:10.1007/s00705-017-3260-1

    authors: Huang KS,Tai CH,Cheng YH,Lin SH,Chen TC,Jan FJ

    更新日期:2017-07-01 00:00:00