Detection of a novel porcine circovirus 4 in Korean pig herds using a loop-mediated isothermal amplification assay

Kim, Da‐Young; Kim, Hye‐Ryung; Park, Jong‐Hyun; Kwon, Na-Young; Kim, Jong Min; Kim, Jae-Kyeom; Park, Jihoon; Lee, Kyoung-Ki; Kim, Seong‐Hee; Kim, Won-Il; Lyoo, Young S.; Park, Choi‐Kyu

doi:10.1016/j.jviromet.2021.114350

Cited by 26 publications

(32 citation statements)

References 33 publications

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“…This fact was also confirmed by the data obtained from the other analysis in the current study, such as the higher number of commonly used preferred codons, less bias on natural selection and mutation pressure, and relative lower natural selection pressure compared with the PCV-1, PCV-2 and PCV-3. However, the higher adaptability for PCV-1 and PCV-4 may lead to the competition of the translation resource with their host during protein translation and result in low translation efficiency, which may be a reason for the low prevalence of PCV-1 and PCV-4 [3,38,39]. A previous study on Crimean-Congo hemorrhagic fever virus also indicated that although the high CAI value represents a better adaption to the host, it exhibits a lower translation efficiency [22].…”

Section: Discussionmentioning

confidence: 99%

Comprehensive Analysis of Codon Usage Patterns in Chinese Porcine Circoviruses Based on Their Major Protein-Coding Sequences

Feng

Segalés

Wang

et al. 2022

Viruses

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Porcine circoviruses (PCVs) are distributed in swine herds worldwide and represent a threat to the health of domestic pigs and the profits of the swine industry. Currently, four PCV species, including PCV-1, PCV-2, PCV-3 and PCV-4, have been identified in China. Considering the ubiquitous characteristic of PCVs, the new emerged PCV-4 and the large scale of swine breeding in China, an overall analysis on codon usage bias for Chinese PCV sequences was performed by using the major proteins coding sequences (ORF1 and ORF2) to better understand the relationship of these viruses with their host. The data from genome nucleotide frequency composition and relative synonymous codon usage (RSCU) analysis revealed an overrepresentation of AT pair and the existence of a certain codon usage bias in all PCVs. However, the values of an effective number of codons (ENC) revealed that the bias was of low magnitude. Principal component analysis, ENC-plot, parity rule two analysis and correlation analysis suggested that natural selection and mutation pressure were both involved in the shaping of the codon usage patterns of PCVs. However, a neutrality plot revealed a stronger effect of natural selection than mutation pressure on codon usage patterns. Good host adaptation was also shown by the codon adaptation index analysis for all these viruses. Interestingly, obtained data suggest that PCV-4 might be more adapted to its host compared to other PCVs. The present study obtained insights into the codon usage pattern of PCVs based on ORF1 and ORF2, which further helps the understanding the molecular evolution of these swine viruses.

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Section: Discussionmentioning

confidence: 99%

Comprehensive Analysis of Codon Usage Patterns in Chinese Porcine Circoviruses Based on Their Major Protein-Coding Sequences

Feng

Segalés

Wang

et al. 2022

Viruses

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“…Since 2019, PCV4 has been reported in several provinces of China, including Hunan, Henan, Jiangsu, Anhui, Shanxi, Guangxi, and Inner Mongolia [ 3 , 4 , 10 – 14 ]. Furthermore, PCV4 was also detected in domestic swine in Korea [ 15 , 16 ]. Notwithstanding, based on failure to detect PCV4 DNA in swine samples (sera and tissues) from Europe (Italy and Spain) [ 17 ], it seems PCV4 appears to have a limited geographic distribution.…”

Section: Evolution and Genetic Diversity Of Pcv4mentioning

confidence: 99%

Current knowledge on epidemiology and evolution of novel porcine circovirus 4

Wang

Mai

Yang

et al. 2022

Vet Res

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Porcine circovirus type 4 (PCV4) is a newly emerging virus, with both PCV4 genomic DNA and specific antibodies detected in swine herds in several provinces in China and South Korea. Although the virus was first identified in 2019 in Hunan, China, retrospective research suggests that serum samples collected as early as 2008 were positive for PCV4 antibody. Infections with only PCV4 or co-infections with other pathogens have been associated with several clinical manifestations, but its pathogenesis remains to be determined. The purpose of this review was the following: (1) to characterize PCV4 epidemiology by assessing evolutionary dynamics and genetic diversity of PCV4 strains circulating in swine herds; (2) to reconstruct a computerized 3D model to analyze PCV4 Cap properties; (3) and to summarize the current evidence of PCV4-associated clinical-pathological manifestations. The origin of PCV4 is apparently distinct from other PCV, based on analysis of phylogenetic trees. Of note, PCV4 shares an ancient common ancestor with mink circoviruses. Furthermore, the amino acid residue at position 27 of the PCV4 Cap is a key benchmark to distinguish PCV4a (27S) from PCV4b (27 N), based on PCV4 strains currently available, and variation of this residue may alter Cap antigenicity. In addition, the capsid surface of PCV4 has characteristics of increased polar residues, compared to PCV2, which raises the possibility that PCV4 may target negatively charged host receptors to promote virus infection. Further studies are required, including virus isolation and culture, and more detailed characterization of molecular epidemiology and genetic diversity of PCV4 in swine herds.

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“…The most recently reported PCV, namely, PCV4, was first identified in Chinese farmed pigs with severe clinical disease in 2019 [ 5 ]. Thereafter, several groups have conducted epidemiological investigations on PCV4 and found that PCV4 also exists widely in pigs [ 6 , 7 , 8 , 9 , 10 , 11 , 12 ]. Kim et al found that the positive rates of PCV4 in individual pig samples and at the farm level were 39.3% and 45.7%, respectively [ 9 ].…”

Section: Introductionmentioning

confidence: 99%

“…Thereafter, several groups have conducted epidemiological investigations on PCV4 and found that PCV4 also exists widely in pigs [ 6 , 7 , 8 , 9 , 10 , 11 , 12 ]. Kim et al found that the positive rates of PCV4 in individual pig samples and at the farm level were 39.3% and 45.7%, respectively [ 9 ]. The virus can be detected in all age groups and aborted fetuses, with the highest titer in the sow group [ 8 ].…”

Section: Introductionmentioning

confidence: 99%

Porcine Circovirus Type 4 Strains Circulating in China Are Relatively Stable and Have Higher Homology with Mink Circovirus than Other Porcine Circovirus Types

Chen

Niu

et al. 2022

IJMS

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Porcine circovirus type 4 (PCV4) is a newly identified porcine circovirus (PCV) belonging to the Circovirus genus Circoviridae family. Although several groups have conducted epidemiological investigations on PCV4 and found that PCV4 also exists widely in pigs, there are few reports on the origin and evolution of PCV4. In this study, the genetic relationship between PCV4, mink circovirus (MiCV), bat circovirus (BtCV), PCV1, PCV2, and PCV3 was analyzed, and the consistency of viral proteins in three-dimensional (3D) structure and epitopes was predicted. We found that the genome and protein structure of PCV4 was relatively stable among current circulating PCV4 strains. Furthermore, PCV4 was more similar to MiCV in terms of its genome, protein structure, and epitope levels than other PCVs and BtCVs, suggesting that PCV4 may be derived from MiCV or have a common origin with MiCV, or mink may be an intermediate host of PCV4, which may pose a great threat to other animals and/or even human beings. Therefore, it is necessary to continuously monitor the infection and variation of PCV4, analyze the host spectrum of PCV4, and establish the prevention and treatment methods of PCV4 infection in advance.

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Detection of a novel porcine circovirus 4 in Korean pig herds using a loop-mediated isothermal amplification assay

Cited by 26 publications

References 33 publications

Comprehensive Analysis of Codon Usage Patterns in Chinese Porcine Circoviruses Based on Their Major Protein-Coding Sequences

Comprehensive Analysis of Codon Usage Patterns in Chinese Porcine Circoviruses Based on Their Major Protein-Coding Sequences

Current knowledge on epidemiology and evolution of novel porcine circovirus 4

Porcine Circovirus Type 4 Strains Circulating in China Are Relatively Stable and Have Higher Homology with Mink Circovirus than Other Porcine Circovirus Types

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