In silico analyses of antigenicity and surface structure variation of an emerging porcine circovirus genotype 2b mutant, prevalent in southern China from 2013 to 2015

Zhan, Yang; Wang, Naidong; Zhu, Zhe; Wang, Zhanfeng; Wang, Aibing; Deng, Zhibang; Yang, Yi

doi:10.1099/jgv.0.000398

Cited by 19 publications

(21 citation statements)

References 46 publications

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“…Meanwhile, compared with the traditional PCV2a/PCV2b strain, the PCV2d strain contains seven unique amino acids (53I, 59 K, 68 N, 89 L, 90 T, 134 N, 169R) in the Cap protein sequence, and these amino acids are mostly distributed along the surface of the viral nucleocapsid. This new surface conformation also renders the antibodies raised against the SH and LG vaccines unable to neutralize the virus [29]. In the present study, several aa mutations occurred at epitopes in the Cap protein.…”

Section: Sequence Alignment Of Orf2mentioning

confidence: 59%

Molecular epidemiology and genetic variation analyses of porcine circovirus type 2 isolated from Yunnan Province in China from 2016-2019

Zhu

et al. 2020

BMC Vet Res

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Background: Porcine circovirus type 2 (PCV2) is the causative agent of porcine circovirus-associated disease (PCVAD). Its prevalence in swine herds was first reported in China in 2000. PCV2 infection causes immunosuppression that leads to multiple diseases, causing serious economic problems for the swine industry in China. Since information on the genetic variation of PCV2 in Yunnan province is limited, this study aims to investigate the molecular epidemiological and evolutionary characteristics of PCV2 from 2016 to 2019. Methods: A total of 279 clinical samples were collected from different regions of Yunnan between 2016 to 2019, and PCV2 was detected by PCR. We then amplified full genomes from the positive samples, and the sequences were analysed for homology and genetic evolution. Results: Overall, 60.93% (170/279) of the screened swine herd samples were positive for PCV2. We sequenced 15 Yunnan province PCV2 strains from positive samples. Analyses of the complete genomes and Cap genes led to the classification of the 15 Yunnan PCV2 strains into PCV2a (2 of 15), PCV2b (1of 15) and PCV2d (12 of 15). All strains shared 94.3-99.9% of their identities with the nucleotide sequences of complete genomes in this study and shared 94.2-99.9% identity with the reference sequences. All strains share 89.4-100% and 86.8-100% of their identities with the nucleotide and amino acid (aa) sequences of Cap, respectively. Conclusions: The results of this study provide evidence that PCV2a, PCV2b and PCV2d genotypes coexisted in Yunnan Province from 2016 to 2019, and the priority prevalence genotype was PCV2d. The data provide evidence for the increased genetic diversity and insights into the molecular epidemiology of PCV2. This study also provides basic data for the Yunnan province PCV2 molecular epidemiological survey and accumulates effective materials for the development of PCV2 vaccines.

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Section: Sequence Alignment Of Orf2mentioning

confidence: 59%

Molecular epidemiology and genetic variation analyses of porcine circovirus type 2 isolated from Yunnan Province in China from 2016-2019

Zhu

et al. 2020

BMC Vet Res

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“…PCV2 CS structure 13 and other structures previously determined by Cryo-EM 18 or by homology modeling methods. 16 , 17 The amino acid sequence of PCV2 (KT719404) presented 99% of identity when compared with PCV2 CS . Furthermore, our model presented a root mean square deviation (RMSD) value of 0.962 Å in comparison with the crystallographic structure ( Fig.…”

Section: Resultsmentioning

confidence: 99%

“… 12 , 13 Also, several studies described a number of amino acids in different regions with possible role in antibody recognition. 12 , 14 , 15 In this sense, the PCV2 capsid and these epitopes have been used as a target for in silico structural analyses 16 , 17 and in experimental structural studies by Cryo electron microscopy 18 and X-ray crystallography. 13 …”

Section: Introductionmentioning

confidence: 99%

Structure analysis of capsid protein of Porcine circovirus type 2 from pigs with systemic disease

Gava

Serrão

Fernandes

et al. 2018

Brazilian Journal of Microbiology

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Economic losses with high mortality rate associated with Porcine circovirus type 2 (PCV2) is reported worldwide. PCV2 commercial vaccine was introduced in 2006 in U.S. and in 2008 in Brazil. Although PCV2 vaccines have been widely used, cases of PCV2 systemic disease have been reported in the last years. Eleven nursery or fattening pigs suffering from PCV2 systemic disease were selected from eight PCV2-vaccinated farms with historical records of PCV2 systemic disease in Southern Brazil. PCV2 genomes were amplified and sequenced from lymph node samples of selected pigs. The comparison among the ORF2 amino acid sequences of PCV2 isolates revealed three amino acid substitutions in the positions F57I, N178S and A190T, respectively. Using molecular modeling, a structural model for the capsid protein of PCV2 was built. Afterwards, the mutated residues positions were identified in the model. The structural analysis of the mutated residues showed that the external residue 190 is close to an important predicted region for antibodies recognition. Therefore, changes in the viral protein conformation might lead to an inefficient antibody binding and this could be a relevant mechanism underlying the recent vaccine failures observed in swine farms in Brazil.

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“…Experimental reports about a higher PCV-2d virulence are contradictory [29][30][31], likely because of the multifactorial nature of PCVD. More consistent evidence is present regarding differential cross-protection among strains belonging to different genotypes due to the variability in epitopic domains [9,[32][33][34]. While the efficacy of currently available PCV-2a-based commercial vaccines to protect against clinical sign onset was demonstrated in several experimental trials [30,35,36], differences have been highlighted in terms of immune response and viremia.…”

Section: Discussionmentioning

confidence: 97%

Free to Circulate: An Update on the Epidemiological Dynamics of Porcine Circovirus 2 (PCV-2) in Italy Reveals the Role of Local Spreading, Wild Populations, and Foreign Countries

et al. 2020

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Porcine circovirus 2 (PCV-2) is one of the most impactful and widespread pathogens of the modern swine industry. Unlike other DNA viruses, PCV-2 is featured by a remarkable genetic variability, which has led to the emergence and recognition of different genotypes, some of which (PCV-2a, 2b, and 2d) have alternated over time. Currently, PCV-2d is considered the most prevalent genotype, and some evidence of differential virulence and vaccine efficacy have been reported. Despite the potential practical relevance, the data on PCV-2 epidemiology in Italy are quite outdated and do not quantify the actual circulation of this genotype in Italy. In the present study, 82 complete ORF2 sequences were obtained from domestic pigs and wild boars sampled in Northern Italy in the period 2013–2018 and merged with those previously obtained from Italy and other countries. A combination of phylogenetic, haplotype network, and phylodynamic analyses were used to genotype the collected strains and evaluate the temporal trend and the spatial and host spread dynamics. A rising number of PCV-2d detections was observed in domestic pigs, particularly since 2013, reaching a detection frequency comparable to PCV-2b. A similar picture was observed in wild boars, although a lower sequence number was available. Overall, the present study demonstrates the extreme complexity of PCV-2 molecular epidemiology in Italy, the significant spread across different regions, the recurrent introduction from foreign countries, and the frequent occurrence of recombination events. Although a higher viral flux occurred from domestic to wild populations than vice versa, wild boars seem to maintain PCV-2 infection and spread it over relatively long distances.

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In silico analyses of antigenicity and surface structure variation of an emerging porcine circovirus genotype 2b mutant, prevalent in southern China from 2013 to 2015

Cited by 19 publications

References 46 publications

Molecular epidemiology and genetic variation analyses of porcine circovirus type 2 isolated from Yunnan Province in China from 2016-2019

Molecular epidemiology and genetic variation analyses of porcine circovirus type 2 isolated from Yunnan Province in China from 2016-2019

Structure analysis of capsid protein of Porcine circovirus type 2 from pigs with systemic disease

Free to Circulate: An Update on the Epidemiological Dynamics of Porcine Circovirus 2 (PCV-2) in Italy Reveals the Role of Local Spreading, Wild Populations, and Foreign Countries

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