Establishment and application of a multiplex PCR for rapid and simultaneous detection of six viruses in swine

Zeng, Zhiyong; Liu, Zhijie; Wang, Weicheng; Tang, Deyuan; Hai-ying, Liang; Zhao, Liang

doi:10.1016/j.jviromet.2014.08.001

Cited by 41 publications

(35 citation statements)

References 14 publications

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“…This result is analogous to those of previous studies, which found that some RNA viruses, such as hepatitis A virus, bovine viral diarrhea virus, SARS-coronavirus, Newcastle disease virus, Marburg virus, and swine fever virus, also show a weak codon usage bias [22, 34–38]. A possible explanation for this is that the low codon usage bias may be beneficial for the efficient transcription and translation of virus genes in host cells [22].…”

Section: Resultssupporting

confidence: 90%

Analysis of Synonymous Codon Usage Bias of Zika Virus and Its Adaption to the Hosts

et al. 2016

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Zika virus (ZIKV) is a mosquito-borne virus (arbovirus) in the family Flaviviridae, and the symptoms caused by ZIKV infection in humans include rash, fever, arthralgia, myalgia, asthenia and conjunctivitis. Codon usage bias analysis can reveal much about the molecular evolution and host adaption of ZIKV. To gain insight into the evolutionary characteristics of ZIKV, we performed a comprehensive analysis on the codon usage pattern in 46 ZIKV strains by calculating the effective number of codons (ENc), codon adaptation index (CAI), relative synonymous codon usage (RSCU), and other indicators. The results indicate that the codon usage bias of ZIKV is relatively low. Several lines of evidence support the hypothesis that translational selection plays a role in shaping the codon usage pattern of ZIKV. The results from a correspondence analysis (CA) indicate that other factors, such as base composition, aromaticity, and hydrophobicity may also be involved in shaping the codon usage pattern of ZIKV. Additionally, the results from a comparative analysis of RSCU between ZIKV and its hosts suggest that ZIKV tends to evolve codon usage patterns that are comparable to those of its hosts. Moreover, selection pressure from Homo sapiens on the ZIKV RSCU patterns was found to be dominant compared with that from Aedes aegypti and Aedes albopictus. Taken together, both natural translational selection and mutation pressure are important for shaping the codon usage pattern of ZIKV. Our findings contribute to understanding the evolution of ZIKV and its adaption to its hosts.

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Section: Resultssupporting

confidence: 90%

Analysis of Synonymous Codon Usage Bias of Zika Virus and Its Adaption to the Hosts

et al. 2016

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“…PCV2 infections by themselves generally cause only mild disease; however, their frequent association with co‐infections with other porcine viruses, such as classical swine fever virus (CSFV), porcine respiratory and reproductive syndrome virus (PRRSV) and porcine parvovirus (PPV), can result in damage to the porcine immune system and more serious disease (Chen et al., ; Zeng et al., ). A study of simultaneous infection of pigs with CSFV and PCV2 showed a higher PCV2 load in organs and substantially different pathologic lesions as compared to infection with PCV2 only (Jacobsen et al., ).…”

Section: Discussionmentioning

confidence: 99%

Retrospective study of porcine circovirus type 2 infection reveals a novel genotype PCV2f

Bao

Luo

et al. 2017

Transbound Emerg Dis

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Porcine postweaning multisystemic wasting syndrome (PMWS) caused by porcine circovirus type 2 (PCV2) is a disease causing severe economic losses annually worldwide to the pig industry. PCV2 infection was first reported in China in 2000, and currently has three major genotypes, PCV2a, b and d, circulating in this country. To further elucidate the origin and prevalence of PCV2 in China, 123 clinical pig tissue samples collected in 25 provinces between 1990 and 1999 were analysed by PCV2-specific PCR, resulting in identification of 23 PCV2 strains collected between 1996 and 1999. Phylogenetic analysis based on the nucleotide sequences of open reading frame 2 (ORF2) showed that 20 of the 23 grouped within PCV2a, while the remaining three strains formed an independent clade, so far unreported and therefore named PCV2f. This genotype shared lower sequence identity with other known genotypes. This study provides further understanding of the genetic diversity and evolution of PCV2 and has tracked PCV2 infection in China back to 1996 rather than 2000.

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“…Traditional methods for CSFV detection relied on virus isolation or serological diagnosis. Recently, several molecular assays have been developed to detect CSFV and replace classical assays and are in wide use252627. However, few of these methods could discriminate between wild-type CSFV strains and vaccine strains.…”

Section: Discussionmentioning

confidence: 99%

Visual detection and differentiation of Classic Swine Fever Virus strains using nucleic acid sequence-based amplification (NASBA) and G-quadruplex DNAzyme assay

Shi

et al. 2017

Sci Rep

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The split G-quadruplex DNAzyme has emerged as a valuable tool for visual DNA detection. Here, we successfully integrated colorimetric split G-quadruplex DNAzyme assay with nucleic acid sequence-based amplification to generate a novel detection approach, allowing visual and rapid detection for the RNA of Shimen and HCLV strains of Classic Swine Fever Virus (CSFV). CSFV is a RNA virus that causes a highly contagious disease in domestic pigs and wild boar. With this method, we were able to detect as little as 10 copies/ml of CSF viral RNA within 3 h in serum samples taken from the field. No interference was encountered in the amplification and detection of Classic Swine Fever Virus in the presence of non-target RNA or DNA. Moreover, Shimen and HCLV strains of Classic Swine Fever Virus could be easily differentiated using the NASBA-DNAzyme system. These findings indicate the NASBA-DNAzyme system is a rapid and practical technique for detecting and discriminating CSFV strains and may be applied to the detection of other RNA viruses.

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Establishment and application of a multiplex PCR for rapid and simultaneous detection of six viruses in swine

Cited by 41 publications

References 14 publications

Analysis of Synonymous Codon Usage Bias of Zika Virus and Its Adaption to the Hosts

Analysis of Synonymous Codon Usage Bias of Zika Virus and Its Adaption to the Hosts

Retrospective study of porcine circovirus type 2 infection reveals a novel genotype PCV2f

Visual detection and differentiation of Classic Swine Fever Virus strains using nucleic acid sequence-based amplification (NASBA) and G-quadruplex DNAzyme assay

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