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Simultaneous detection and phylogenetic analysis of porcine epidemic diarrhea virus and porcine circovirus 4 in Henan province, China

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Abstract

Porcine circovirus 4 (PCV4) is a recently discovered circovirus that was first reported in 2019 in several pigs in Hunan province of China and has also been identified in pigs infected with porcine epidemic diarrhea virus (PEDV). To further investigate the coinfection and genetic diversity of these two viruses, 65 clinical samples (including feces and intestinal tissues) were collected from diseased piglets on 19 large-scale pig farms in Henan province of China, and a duplex SYBR Green I–based quantitative real-time polymerase chain reaction (qPCR) assay was developed for detecting PEDV and PCV4 simultaneously. The results showed that the limit of detection was 55.2 copies/μL and 44.1 copies/μL for PEDV and PCV4, respectively. The detection rate for PEDV and PCV4 was 40% (26/65) and 38% (25/65), respectively, and the coinfection rate for the two viruses was 34% (22/65). Subsequently, the full-length spike (S) gene of eight PEDV strains and a portion of the genome containing the capsid (Cap) gene of three PCV4 strains were sequenced and analyzed. Phylogenetic analysis showed that all of the PEDV strains from the present study clustered in the G2a subgroup and were closely related to most of the PEDV reference strains from China from 2011 to 2021, but they differed genetically from a vaccine strain (CV777), a Korean strain (virulent DR1), and two Chinese strains (SD-M and LZC). It is noteworthy that two PEDV strains (HEXX-24 and HNXX-24XIA) were identified in one sample, and the HNXX-24XIA strain had a large deletion at amino acids 31-229 of the S protein. Moreover, a recombination event was observed in strain HEXX-24. Phylogenetic analysis based on the amino acid sequence of the PCV4 Cap protein revealed that PCV4 strains were divided into three genotypes: PCV4a1, PCV4a2, and PCV4b. Three strains in the present study belonged to PCV4a1, and they had a high degree of sequence similarity (>98% identity) to other PCV4 reference strains. This study not only provides technical support for field investigation of PEDV and PCV4 coinfection but also provides data for their prevention and control.

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Data availability

The data that support the findings of this study are openly available in this manuscript and in the Supporting Information attached.

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Acknowledgements

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Funding

Funding was supported by National Key Research and Development Program (no. 2021YFD1801105), Henan open competition mechanism to select the best candidates to undertake key research projects (no. 211110111000), Program for Scientific and Technological Innovation Talents in Universities of Ministry of Education of Henan Province (no. 21HASTIT039).

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  1. Hong-Xuan Li, Xi-Meng Chen, You-Yi Zhao contributed equally to this work.

Authors and Affiliations

  1. International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengdong New District Longzi Lake 15#, Zhengzhou, 450046, Henan, People’s Republic of China

    Hong-Xuan Li, Xi-Meng Chen, You-Yi Zhao, Hong-Lei Zhang, Lan-Lan Zheng, Lin-Qing Wang, Shi-jie Ma & Hong-Ying Chen

  2. Department of Life Science, Zhengzhou Normal University, Zhengzhou, 450044, Henan, People’s Republic of China

    Lin-Qing Wang

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Contributions

LHX and CHY contributed significantly to the conception, design, acquisition, and analysis of the work. CXM and ZYY carried out the interpretation of data. ZYY, ZHL, and ZLL discussed and prepared the final report. LHX and WLQ drafted the work. ZLL and MSJ substantively reviewed and revised it. All of the authors have read and approved the final manuscript.

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Correspondence to Shi-jie Ma or Hong-Ying Chen.

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705_2023_5791_MOESM1_ESM.jpg

Supplementary file1 Supplementary Fig. S1 Identification of possible recombination events in HEXX-24 using RDP4 (using six recombination detection programs: RDP, BOOTSCAN, MaxChi, Chimaera, SiScan, and 3Seq). One putative recombinant region (P < 0.01) was located at nt position 58 and nt position 665 in the S gene. The analysis was performed with an RDP distance model and a window size of 20 (JPG 1139 KB)

705_2023_5791_MOESM2_ESM.jpg

Supplementary file2 Supplementary Fig. S2 Recombination analysis of HEXX-24 using the Simplot program. The green and yellow curves represent the parental strains (PC22A and HUBY, respectively) of HEXX-24 (JPG 620 KB)

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Li, HX., Chen, XM., Zhao, YY. et al. Simultaneous detection and phylogenetic analysis of porcine epidemic diarrhea virus and porcine circovirus 4 in Henan province, China. Arch Virol 168, 161 (2023). https://doi.org/10.1007/s00705-023-05791-w

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