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Detection and phylogenetic analysis of porcine circovirus 3 in part of northern China from 2016 to 2018

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Abstract

Porcine circovirus 3 (PCV3) is a recently identified virus that is associated with reproductive failure, porcine dermatitis and nephropathy syndrome, and multi-systemic inflammation. To investigate the molecular epidemic characteristics and genetic evolution of PCV3 in northern China, a commercial TaqMan-based real-time quantitative PCR kit was used to detect PCV3 in 435 tissue specimens collected from pigs with various clinical signs from 105 different swine farms in northern China. The results showed that 48 out of 105 (45.7%) farms and 97 out of 435 (22.3%) samples tested positive for PCV3. Of the 97 PCV3-positive samples, 80 (82.5%) tested positive for other pathogens. PCV3 was found more frequently in pigs with reproductive failure than in those with other clinical signs. This study is the first to detect PCV3 in Tianjin. The complete genome sequences of six PCV3 isolates and the capsid (Cap) protein gene sequences of 11 isolates were determined. Based on the predicted amino acids at positions 24 and 27 of the Cap protein and their evolutionary relationships, the 17 PCV3 strains obtained from northern China and 49 reference strains downloaded from the GenBank database were divided into four major groups (3a-3d). An analysis of selection pressure and polymorphism indicated that the PCV3 Cap protein seems to be evolving under balancing selection, that the population is in dynamic equilibrium, and that no population expansion occurred during the study period. Our results provide new information about the molecular epidemiology and evolution of PCV3.

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Acknowledgements

This research was supported by the Program of the Modern Agriculture Industry Technology System Foundation of Hebei Province (HBCT2018110207), Science and Technology Innovation Program of Hebei Province for Graduate Students (CXZZBS2019095), and Key R & D Projects in Hebei Province, China (19226622D).

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Author notes

  1. Wenyuan Gu and Qiankai Shi contributed equally to this work.

Authors and Affiliations

  1. College of Veterinary Medicine, Hebei Agricultural University, Baoding, 071001, China

    Wenyuan Gu, Qiankai Shi, Jianlou Zhang, Guangfu Yuan, Shaojie Chen, Yuzhu Zuo & Jinghui Fan

  2. Animal Diseases Control Center of Hebei, Shijiazhuang, 050053, China

    Wenyuan Gu

  3. Department of Veterinary Clinical Medicine and the Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Illinois, Urbana, Illinois, 61802, USA

    Leyi Wang

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  1. Wenyuan Gu
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  2. Qiankai Shi
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  4. Jianlou Zhang
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  5. Guangfu Yuan
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Correspondence to Yuzhu Zuo or Jinghui Fan.

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Appendix 1

Appendix 1

No.

Strain name

GenBank accession no.

Collection location

Collection date

Gene type

1

PCV3/CH/HB/CZ-2/2017

MG727537

Hebei

2017

Complete genome

2

PCV3/CH/HB/BD/2017

MG727538

Hebei

2017

Complete genome

3

PCV3/CH/HB/CZ-1/2017

MG727539

Hebei

2017

Complete genome

4

PCV3/CH/HB/SJZ/2017

MG727540

Hebei

2017

Complete genome

5

PCV3/CH/HB/HD/2017

MH101645

Hebei

2017

Complete genome

6

PCV3/CH/Tianjin-1/2018

MH547276

Tianjin

2018

Complete genome

7

PCV3/CH/Liaoning-1/2018

MH547277

Liaoning

2018

Full-length cap gene

8

PCV3/CH/Beijing-1/2016

MH547278

Beijing

2016

Full-length cap gene

9

PCV3/CH/Beijing-2/2018

MH547279

Beijing

2018

Full-length cap gene

10

PCV3/CH/Shanxi-1/2018

MH547280

Shanxi

2018

Full-length cap gene

11

PCV3/CH/Shanxi-2/2018

MH548436

Shanxi

2018

Full-length cap gene

12

PCV3/CH/Shandong-1/2018

MH548437

Shandong

2018

Full-length cap gene

13

PCV3/CH/Liaoning-2/2018

MH548438

Liaoning

2018

Full-length cap gene

14

PCV3/CH/Tianjin-2/2017

MH579786

Tianjin

2017

Full-length cap gene

15

PCV3/CH/HB-CD/2018

MH636587

Hebei

2018

Full-length cap gene

16

PCV3/CH/HB-ZJK/2018

MH636589

Hebei

2018

Full-length cap gene

17

PCV3/CH/HB-TS/2018

MH636590

Hebei

2018

Full-length cap gene

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Gu, W., Shi, Q., Wang, L. et al. Detection and phylogenetic analysis of porcine circovirus 3 in part of northern China from 2016 to 2018. Arch Virol 165, 2003–2011 (2020). https://doi.org/10.1007/s00705-020-04709-0

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  • DOI: https://doi.org/10.1007/s00705-020-04709-0

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