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27.08.2022 | Original Article

Genomic characterization and pathogenicity analysis of a porcine deltacoronavirus strain isolated in western China

verfasst von: Zemei Wang, Shuxian Li, Yongheng Shao, Yabin Lu, Chen Tan, Yaru Cui, Guangming Ding, Yuguang Fu, Guangliang Liu, Jianing Chen, Yonghao Hu

Erschienen in: Archives of Virology | Ausgabe 11/2022

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Abstract

Porcine deltacoronavirus (PDCoV) is an enteric virus that was first identified in 2012. Although PDCoV has been detected worldwide, there is little information about its circulation in western China. In this study, fecal samples were collected from piglets with watery diarrhea in western China between 2015 and 2018 for the detection of PDCoV. The positive rate was 29.9%. A PDCoV strain (CHN/CQ/BN23/2016, BN23) was isolated and selected for further investigation. Phylogenetic analysis showed that this strain formed an individual cluster between the early Chinese lineage and the Chinese lineage. RDP4 and SimPlot analysis demonstrated that strain BN23 is a recombinant of Thailand/S5015L/2015 and CHN-AH-2004. The pathogenicity of BN23 was evaluated in 3-day-old piglets. Challenged piglets developed serious clinical signs and died at 3 days post-inoculation. Our data show that PDCoV is prevalent in western China and that strain BN23 is highly pathogenic to newborn piglets. Therefore, more attention should be paid to emerging PDCoV strains in western China.

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Saeng-Chuto K, Jermsutjarit P, Stott CJ, Vui DT, Tantituvanont A, Nilubol D (2020) Retrospective study, full-length genome characterization and evaluation of viral infectivity and pathogenicity of chimeric porcine deltacoronavirus detected in Vietnam. Transbound Emerg Dis 67:183–198CrossRef

Vitosh-Sillman S, Loy JD, Brodersen B, Kelling C, Doster A, Topliff C, Nelson E, Bai J, Schirtzinger E, Poulsen E, Meadors B, Anderson J, Hause B, Anderson G, Hesse R (2016) Experimental infection of conventional nursing pigs and their dams with Porcine deltacoronavirus. J Vet Diagnostic Investig 28:486–497CrossRef

Lee S, Lee C (2014) Complete genome characterization of Korean porcine deltacoronavirus strain KOR/KNU14-04/2014. Genome Announcements 2

Li G, Chen Q, Harmon KM, Yoon KJ, Schwartz KJ, Hoogland MJ, Gauger PC, Main RG, Zhang J (2014) Full-length genome sequence of porcine deltacoronavirus strain USA/IA/2014/8734. Genome Announcements 2

Woo PC, Lau SK, Lam CS, Lau CC, Tsang AK, Lau JH, Bai R, Teng JL, Tsang CC, Wang M, Zheng BJ, Chan KH, Yuen KY (2012) Discovery of seven novel Mammalian and avian coronaviruses in the genus deltacoronavirus supports bat coronaviruses as the gene source of alphacoronavirus and betacoronavirus and avian coronaviruses as the gene source of gammacoronavirus and deltacoronavirus. J Virol 86:3995–4008CrossRef

Wang L, Byrum B, Zhang Y (2014) Detection and genetic characterization of deltacoronavirus in pigs, Ohio, USA, 2014. Emerg Infect Dis 20:1227–1230CrossRef

Niederwerder MC, Hesse RA (2018) Swine enteric coronavirus disease: a review of 4 years with porcine epidemic diarrhoea virus and porcine deltacoronavirus in the United States and Canada. Transbound Emerg Dis 65:660–675CrossRef

Lee JH, Chung HC, Nguyen VG, Moon HJ, Kim HK, Park SJ, Lee CH, Lee GE, Park BK (2016) Detection and phylogenetic analysis of porcine deltacoronavirus in Korean Swine Farms, 2015. Transbound Emerg Dis 63:248–252CrossRef

Suzuki T, Shibahara T, Imai N, Yamamoto T, Ohashi S (2018) Genetic characterization and pathogenicity of Japanese porcine deltacoronavirus. Infect Genet Evolut 61:176–182CrossRef

10.

Le VP, Song S, An BH, Park GN, Pham NT, Le DQ, Nguyen VT, Vu TTH, Kim KS, Choe S, An DJ (2018) A novel strain of porcine deltacoronavirus in Vietnam. Arch Virol 163:203–207CrossRef

11.

Janetanakit T, Lumyai M, Bunpapong N, Boonyapisitsopa S, Chaiyawong S, Nonthabenjawan N, Kesdaengsakonwut S, Amonsin A (2016) Porcine deltacoronavirus, Thailand, 2015. Emerg Infect Dis 22:757–759CrossRef

12.

Lorsirigool A, Saeng-Chuto K, Madapong A, Temeeyasen G, Tripipat T, Kaewprommal P, Tantituvanont A, Piriyapongsa J, Nilubol D (2017) The genetic diversity and complete genome analysis of two novel porcine deltacoronavirus isolates in Thailand in 2015. Virus Genes 53:240–248CrossRef

13.

Chen F, Zhu Y, Wu M, Ku X, Yao L, He Q (2015) Full-length genome characterization of Chinese porcine deltacoronavirus strain CH/SXD1/2015. Genome announcements 3

14.

Wang YW, Yue H, Fang W, Huang YW (2015) Complete genome sequence of porcine deltacoronavirus strain CH/Sichuan/S27/2012 from Mainland China. Genome Announcements 3

15.

Dong N, Fang L, Yang H, Liu H, Du T, Fang P, Wang D, Chen H, Xiao S (2016) Isolation, genomic characterization, and pathogenicity of a Chinese porcine deltacoronavirus strain CHN-HN-2014. Vet Microbiol 196:98–106CrossRef

16.

Hsueh FC, Hsu FY, Chen YH, Shih HC, Lin WH, Yang CY, Lin CF, Chiou MT, Lin CN (2021) Phylogenetic classification of global porcine deltacoronavirus (PDCoV) reference strains and molecular characterization of PDCoV in Taiwan. Viruses 13

17.

Huang H, Li Y, Wang W, Zheng M, Cao L, Sun W, Lu H (2020) Detection and molecular characterization of novel porcine bufaviruses in Guangxi province. Infect Genet Evolut 82:104286CrossRef

18.

Huang H, Yin Y, Wang W, Cao L, Sun W, Shi K, Lu H, Jin N (2020) Emergence of Thailand-like strains of porcine deltacoronavirus in Guangxi Province, China. Vet Med Sci 6:854–859CrossRef

19.

Jin XH, Zhang YF, Yuan YX, Han L, Zhang GP, Hu H (2021) Isolation, characterization and transcriptome analysis of porcine deltacoronavirus strain HNZK-02 from Henan Province, China. Mol Immunol 134:86–99CrossRef

20.

Liu BJ, Zuo YZ, Gu WY, Luo SX, Shi QK, Hou LS, Zhong F, Fan JH (2018) Isolation and phylogenetic analysis of porcine deltacoronavirus from pigs with diarrhoea in Hebei province, China. Transbound Emerg Dis 65:874–882CrossRef

21.

Ding G, Fu Y, Li B, Chen J, Wang J, Yin B, Sha W, Liu G (2020) Development of a multiplex RT-PCR for the detection of major diarrhoeal viruses in pig herds in China. Transbound Emerg Dis 67:678–685CrossRef

22.

Katoh K, Standley DM (2013) MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 30:772–780CrossRef

23.

Lole KS, Bollinger RC, Paranjape RS, Gadkari D, Kulkarni SS, Novak NG, Ingersoll R, Sheppard HW, Ray SC (1999) Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination. J Virol 73:152–160CrossRef

24.

Martin DP, Murrell B, Golden M, Khoosal A, Muhire B (2015) RDP4: detection and analysis of recombination patterns in virus genomes. Virus Evol 1:vev003CrossRef

25.

Martin D, Rybicki E (2000) RDP: detection of recombination amongst aligned sequences. Bioinformatics (Oxford, England) 16:562–563CrossRef

26.

Padidam M, Sawyer S, Fauquet CM (1999) Possible emergence of new geminiviruses by frequent recombination. Virology 265:218–225CrossRef

27.

Gibbs MJ, Armstrong JS, Gibbs AJ (2000) Sister-scanning: a Monte Carlo procedure for assessing signals in recombinant sequences. Bioinformatics (Oxford, England) 16:573–582CrossRef

28.

Smith JM (1992) Analyzing the mosaic structure of genes. J Mol Evol 34:126–129CrossRef

29.

Boni MF, Posada D, Feldman MW (2007) An exact nonparametric method for inferring mosaic structure in sequence triplets. Genetics 176:1035–1047CrossRef

30.

Holmes EC, Worobey M, Rambaut A (1999) Phylogenetic evidence for recombination in dengue virus. Mol Biol Evol 16:405–409CrossRef

31.

Song D, Zhou X, Peng Q, Chen Y, Zhang F, Huang T, Zhang T, Li A, Huang D, Wu Q, He H, Tang Y (2015) Newly emerged porcine deltacoronavirus associated with diarrhoea in swine in China: identification, prevalence and full-length genome sequence analysis. Transbound Emerg Dis 62:575–580CrossRef

32.

Zhai SL, Wei WK, Li XP, Wen XH, Zhou X, Zhang H, Lv DH, Li F, Wang D (2016) Occurrence and sequence analysis of porcine deltacoronaviruses in southern China. Virol J 13:136CrossRef

33.

Zhang F, Luo S, Gu J, Li Z, Li K, Yuan W, Ye Y, Li H, Ding Z, Song D, Tang Y (2019) Prevalence and phylogenetic analysis of porcine diarrhea associated viruses in southern China from 2012 to 2018. BMC Vet Res 15:470CrossRef

34.

Zhang H, Liang Q, Li B, Cui X, Wei X, Ding Q, Wang Y, Hu H (2019) Prevalence, phylogenetic and evolutionary analysis of porcine deltacoronavirus in Henan Province, China. Prev Vet Med 166:8–15CrossRef

35.

Kong F, Wang Q, Kenney SP, Jung K, Vlasova AN, Saif LJ (2022) Porcine deltacoronaviruses: origin, evolution, cross-species transmission and zoonotic potential. Pathogens (Basel, Switzerland) 11

36.

Dong N, Fang L, Zeng S, Sun Q, Chen H, Xiao S (2015) Porcine deltacoronavirus in mainland China. Emerg Infect Dis 21:2254–2255CrossRef

37.

Wang M, Wang Y, Baloch AR, Pan Y, Tian L, Xu F, Shivaramu S, Chen S, Zeng Q (2018) Detection and genetic characterization of porcine deltacoronavirus in Tibetan pigs surrounding the Qinghai-Tibet Plateau of China. Transbound Emerg Dis 65:363–369CrossRef

38.

Chen Q, Gauger P, Stafne M, Thomas J, Arruda P, Burrough E, Madson D, Brodie J, Magstadt D, Derscheid R, Welch M, Zhang J (2015) Pathogenicity and pathogenesis of a United States porcine deltacoronavirus cell culture isolate in 5-day-old neonatal piglets. Virology 482:51–59CrossRef

39.

Wang L, Hayes J, Sarver C, Byrum B, Zhang Y (2016) Porcine deltacoronavirus: histological lesions and genetic characterization. Arch Virol 161:171–175CrossRef

40.

Li J, Zhou J, Zhao S, Guo R, Zhong C, Xue T, Peng Q, Zhang B, Fan B, Liu C, Ni Y, Ren L, Zhu X, Li B (2022) Pathogenicity, infective dose and altered gut microbiota in piglets infected with porcine deltacoronavirus. Virology 567:26–33CrossRef

41.

Wang H, Qin Y, Zhao W, Yuan T, Yang C, Mi X, Zhao P, Lu Y, Lu B, Chen Z, He Y, Yang C, Yi X, Wu Z, Chen Y, Wei Z, Huang W, Ouyang K (2021) Genetic characteristics and pathogenicity of a novel porcine deltacoronavirus Southeast Asia-Like Strain Found in China. Front Vet Sci 8:701612CrossRef

42.

Zhou X, Zhou L, Zhang P, Ge X, Guo X, Han J, Zhang Y, Yang H (2021) A strain of porcine deltacoronavirus: genomic characterization, pathogenicity and its full-length cDNA infectious clone. Transbound Emerg Dis 68:2130–2146CrossRef

43.

Zhang Q, Yoo D (2016) Immune evasion of porcine enteric coronaviruses and viral modulation of antiviral innate signaling. Virus Res 226:128–141CrossRef

44.

Zhang K, Lin S, Li J, Deng S, Zhang J, Wang S (2022) Modulation of innate antiviral immune response by porcine enteric coronavirus. Front Microbiol 13:845137CrossRef

Titel: Genomic characterization and pathogenicity analysis of a porcine deltacoronavirus strain isolated in western China
verfasst von: Zemei Wang
Shuxian Li
Yongheng Shao
Yabin Lu
Chen Tan
Yaru Cui
Guangming Ding
Yuguang Fu
Guangliang Liu
Jianing Chen
Yonghao Hu
Publikationsdatum: 27.08.2022
Verlag: Springer Vienna
Erschienen in: Archives of Virology / Ausgabe 11/2022
Print ISSN: 0304-8608
Elektronische ISSN: 1432-8798
DOI: https://doi.org/10.1007/s00705-022-05549-w

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Genomic characterization and pathogenicity analysis of a porcine deltacoronavirus strain isolated in western China

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