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The genetic diversity and complete genome analysis of two novel porcine deltacoronavirus isolates in Thailand in 2015

Abstract

Porcine deltacoronavirus (PDCoV) was identified in intestinal samples collected from piglets with diarrhea in Thailand in 2015. Two Thai PDCoV isolates, P23_15_TT_1115 and P24_15_NT1_1215, were isolated and identified. The full-length genome sequences of the P23_15_TT_1115 and P24_15_NT1_1215 isolates were 25,404 and 25,407 nucleotides in length, respectively, which were relatively shorter than that of US and China PDCoV. The phylogenetic analysis based on the full-length genome demonstrated that Thai PDCoV isolates form a new cluster separated from US and China PDCoV but relatively were more closely related to China PDCoV than US isolates. The genetic analyses demonstrated that Thai PDCoVs have 97.0–97.8 and 92.2–94.0% similarities with China PDCoV at nucleotide and amino acid levels, respectively, but share 97.1–97.3 and 92.5–93.0 similarity with US PDCoV at the nucleotide and amino acid levels, respectively. Thai PDCoV possesses two discontinuous deletions of five amino acids in ORF1a/b region. One additional deletion of one amino acid was identified in P23_15_TT_1115. The variation analyses demonstrated that six regions (nt 1317–1436, 2997–3096, 19,737–19,836, 20,277–20,376, 21,177–21,276, and 22,371–22,416) in ORF1a/b and spike genes exhibit high sequence variation between Thai and other PDCoV. The analyses of amino acid changes suggested that they could potentially be from different lineages.

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Acknowledgements

This work was supported by the National Research Council of Thailand [Grant Number 5080001], and Agricultural research development agency (Public organization). The funding provided by Special Task Force for Activating Research (STAR), swine viral evolution and vaccine research (SVEVR), Chulalongkorn University.

Authors’ contribution

C.J.S. and D.N. conceived and designed the experiments; C.J.S., G.T. and T.T. performed the experiments; C.J.S. and K.S. analyzed the data; C.J.S., T.T. and A.T. contributed reagents/materials/analysis tools; C.J.S. and D.N. composed the manuscript.

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Correspondence to Dachrit Nilubol.

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All applicable international, national, and/or institutional guidelines for the care and use of animals were followed.

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Edited by Keizo Tomonaga.

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Lorsirigool, A., Saeng-chuto, K., Madapong, A. et al. The genetic diversity and complete genome analysis of two novel porcine deltacoronavirus isolates in Thailand in 2015. Virus Genes 53, 240–248 (2017). https://doi.org/10.1007/s11262-016-1413-z

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Keywords

  • Porcine deltacoronavirus
  • Full-length genome
  • Thailand