An extensive evaluation of codon usage pattern and bias of structural proteins p30, p54 and, p72 of the African swine fever virus (ASFV)

Indrabalan, Uma Bharathi; Suresh, Kuralayanapalya Puttahonnappa; Shivamallu, Chandan; Patil, Sharanagouda S.

doi:10.1007/s13337-021-00719-x

Cited by 13 publications

(11 citation statements)

References 33 publications

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“…In this plot, the splashes will fall near the curve when the CUB patterns are mainly driven by mutational effects. Instead, if the codon preference is determined by selection or other factors, the points will be distant from the curve [ 70 , 71 , 72 ].…”

Section: Methodsmentioning

confidence: 99%

Codon Usage Analyses Reveal the Evolutionary Patterns among Plastid Genes of Saxifragales at a Larger-Sampling Scale

Han

Zhou

et al. 2023

Genes

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Saxifragales is a 15-family order of early-divergent Eudicots with a rich morphological diversity and an ancient rapid radiation. Codon usage bias (CUB) analyses have emerged as an essential tool for understanding the evolutionary dynamics in genes. Thus far, the codon utilization patterns had only been reported in four separate genera within Saxifragales. This study provides a comprehensive assessment of the codon manipulation based on 50 plastid genes, covering 11 constituent families at a larger sampling scale. Our results first showed a high preference for AT bases and AT-ending codons. We then used effective number of codons (ENC) to assess a range of codon bias levels in the plastid genes. We also detected high-informative intrafamilial differences of ENC in three families. Subsequently, parity rule 2 (PR2) plot analyses revealed both family-unique and order-shared bias patterns. Most importantly, the ENC plots and neutrality analyses collectively supported the dominant roles of selection in the CUB of Saxifragales plastid genes. Notably, the phylogenetic affinities inferred by both ML and BI methods were consistent with each other, and they all comprised two primary clades and four subclades. These findings significantly enhance our understanding of the evolutionary processes of the Saxifrage order, and could potentially inspire more CUB analyses at higher taxonomic levels.

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Section: Methodsmentioning

confidence: 99%

Codon Usage Analyses Reveal the Evolutionary Patterns among Plastid Genes of Saxifragales at a Larger-Sampling Scale

Han

Zhou

et al. 2023

Genes

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“…Monoclonal antibodies (mAbs) against the major ASFV shell protein p72 and the structural hyperimmunogenic protein p30 have been used as targets in serological assays to detect ASFV infection [19,20]. The p54 protein, a type II transmembrane protein that is produced following infection, is also a potentially important target for the detection of ASFV [21,22]. Moreover, p54 inoculation induces high titers of anti-p54 antibodies [23,24].…”

Section: Introductionmentioning

confidence: 99%

A Novel Linear B-Cell Epitope on the P54 Protein of African Swine Fever Virus Identified Using Monoclonal Antibodies

Zheng

Hou

Chen

et al. 2023

Viruses

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The African swine fever virus (ASFV) is a highly infectious viral pathogen that presents a major threat to the global pig industry. No effective vaccine is available for the virus. The p54 protein, a major structural component of ASFV, is involved in virus adsorption and entry to target cells and also plays a key role in ASFV vaccine development and disease prevention. Here, we generated species-specific monoclonal antibodies (mAbs), namely 7G10A7F7, 6E8G8E1, 6C3A6D12, and 8D10C12C8 (subtype IgG1/kappa type), against the ASFV p54 protein and characterized the specificity of these mAbs. Peptide scanning techniques were used to determine the epitopes that are recognized by the mAbs, which defined a new B-cell epitope, TMSAIENLR. Amino acid sequence comparison showed that this epitope is conserved among all reference ASFV strains from different regions of China, including the widely prevalent, highly pathogenic strain Georgia 2007/1 (NC_044959.2). This study reveals important signposts for the design and development of ASFV vaccines and also provides critical information for the functional studies of the p54 protein via deletion analysis.

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“…MAbs against ASFV's major capsid protein p72 and the structural and highly immunogenic protein p30 have been used as targets for detection of ASFV infection in serological assays [11,12]. The type II transmembrane protein p54, which plays a key role in virus morphogenesis and viral infection, was also suggested as an important detection target [13,14]. ASFV infection or p54 replicon inoculation both induced high titers of anti-p54 antibodies [15][16][17][18][19].…”

Section: Introductionmentioning

confidence: 99%

Preparation of Monoclonal Antibodies against the Viral p54 Protein and a Blocking ELISA for Detection of the Antibody against African Swine Fever Virus

Gao

Xia

Bai

et al. 2022

Viruses

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African swine fever virus (ASFV) causes a highly contagious viral disease in domestic and wild pigs, leading to serious economic losses. As there are no vaccines or drugs available, early accurate diagnosis and eradiation of infected animals are the most important measures for ASFV prevention and control. Therefore, improvement of available diagnostic assays and development of novel effective techniques are required. This study is devoted to generating a new detection platform of blocking monoclonal antibody−based enzyme−linked immunosorbent assay (ELISA) against ASFV p54 protein. Seven monoclonal antibodies against recombinant p54 protein were produced and four epitopes were identified. Three blocking ELISAs were developed with 6A5 and 6F9 mAbs labeled with HRP, respectively, of which the 6A5/6F9−based blocking ELISA displayed the best detection performance, with an AUC of 0.986, sensitivity of 98.36% and specificity of 92.36% in ROC analysis. Moreover, it has an excellent agreement at 96.59% (198/205) when compared to the commercial blocking ELISA (kappa value = 0.920). The method also has high repeatability, with CV <10%, and no cross reaction with the serum antibodies against PRV, PRRSV, CSFV, PCV2 or SVA. This indicates that the 6A5/6F9−based blocking ELISA has high accuracy with good sensitivity and specificity, suitable for viral detection, field surveillance and epidemiological studies.

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An extensive evaluation of codon usage pattern and bias of structural proteins p30, p54 and, p72 of the African swine fever virus (ASFV)

Cited by 13 publications

References 33 publications

Codon Usage Analyses Reveal the Evolutionary Patterns among Plastid Genes of Saxifragales at a Larger-Sampling Scale

Codon Usage Analyses Reveal the Evolutionary Patterns among Plastid Genes of Saxifragales at a Larger-Sampling Scale

A Novel Linear B-Cell Epitope on the P54 Protein of African Swine Fever Virus Identified Using Monoclonal Antibodies

Preparation of Monoclonal Antibodies against the Viral p54 Protein and a Blocking ELISA for Detection of the Antibody against African Swine Fever Virus

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