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. 2015 Jan;79(1):8-15.

Genetic variation analyses of porcine epidemic diarrhea virus isolated in mid-eastern China from 2011 to 2013

Pan-Deng Zhao  1 , Chen Tan  1 , Yanpen Dong  1 , Yufeng Li  1 , Xiaoli Shi  1 , Juan Bai  1 , Ping Jiang  1
Affiliations

Genetic variation analyses of porcine epidemic diarrhea virus isolated in mid-eastern China from 2011 to 2013

Pan-Deng Zhao et al. Can J Vet Res. 2015 Jan.

Abstract
in English, French

Porcine diarrhea outbreaks caused by porcine epidemic diarrhea virus (PEDV) has occurred in China with significant losses of piglets since 2010. In this study, the complete S and ORF3 genes of 15 field PEDV isolates in mid-eastern China from 2011 to 2013 were detected and compared with other reference strains. Based on S gene, all of the PEDV strains could be assigned to 3 genogroups. Only 1 isolate, JS120103, belonged to genogroup 1 and showed a close relationship with previous Chinese strains DX and JS-2004-2, European strain CV777, and Korean strain DR13. The other 14 isolates belonged to genogroup 3 and showed a close relationship with other Chinese strains isolated after 2010. The S genes of those isolates were 9 nucleotides longer in length than JS120103 and the other reference strains in genogroup 1, with 15 bp insertion and 6 bp deletion. Homology analyses revealed that all of the Chinese field isolates, except JS120103, are 97.6% to 100% (95.8% to 100%) identical in nucleotide (deduced amino acid) sequence to each other. Meanwhile, based on the ORF3 gene, all of the PEDV isolates could be separated into 3 genogroups. Eleven of the 15 field isolates in this study belonged to genogroup 3 and were 95.8% to 100% identical in nucleotide sequence or 95.6% to 100% in deduced amino acid sequence to each other. Our results indicate that the variant PEDV strain spread wildly in mid-eastern China. This will be useful to take into consideration in the control and prevention of this disease.

Des épidémies de diarrhée porcine due au virus de la diarrhée épidémique porcine (VDEP) sont présentes en Chine et ont causé des pertes significatives de porcelets depuis 2010. Dans la présente étude, les gènes S et ORF3 de 15 isolats de champs de VDEP provenant de la portion moyen-orientale de la Chine isolés entre 2011 et 2013 furent détectés et comparés à des souches de référence. Sur la base du gène S, toutes les souches de VDEP pouvaient être réparties dans trois génogroupes. Un seul isolat, JS120103, appartenait au génogroupe 1 et montrait une proche parenté avec les souches chinoises précédentes DX et JS-2004-2, la souche européenne CV777, et la souche coréenne DR13. Les 14 autres isolats appartenaient au génogroupe 3, et montraient une proche parenté avec d’autres souches chinoises isolées après 2010. Les gènes S de ces isolats étaient plus longs de 9 nucléotides que JS120103 et les autres souches de référence du génogroupe 1, avec une insertion de 15 paires de base et une délétion de 6 paires de base. Les analyses d’homologie ont révélé que tous les isolats de champs chinois, sauf JS120103, sont 97,6 % à 100 % (95,8 % à 100 %) identiques entre eux en séquence de nucléotides (d’acides aminés déduits). Également, sur la base du gène ORF3, tous les isolats de VDEP pouvaient être séparés en 3 génogroupes. Onze des 15 isolats de champs de la présente étude appartenaient au génogroupe 3 et étaient 95,8 % à 100 % identiques entre eux en séquence de nucléotides ou 95,6 % à 100 % en séquence d’acides aminés déduits. Ces résultats indiquent que les variants des souches de VDEP sont largement dispersés dans la partie moyenne-orientale de la Chine. Ces données seront utiles à prendre en considération pour la prévention et la maitrise de cette maladie.(Traduit par Docteur Serge Messier).

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Figures

Figure 1
Figure 1
Amino acid sequence alignment of the S genes of the field isolates in mid-eastern China and porcine epidemic diarrhea virus (PEDV) reference strains. The dashes (-) indicate the deleted sequences. Insertion and deletion in PEDV isolates are shaded. Putative signal sequences (solid boxes) are indicated.
Figure 1
Figure 1
Amino acid sequence alignment of the S genes of the field isolates in mid-eastern China and porcine epidemic diarrhea virus (PEDV) reference strains. The dashes (-) indicate the deleted sequences. Insertion and deletion in PEDV isolates are shaded. Putative signal sequences (solid boxes) are indicated.
Figure 1
Figure 1
Amino acid sequence alignment of the S genes of the field isolates in mid-eastern China and porcine epidemic diarrhea virus (PEDV) reference strains. The dashes (-) indicate the deleted sequences. Insertion and deletion in PEDV isolates are shaded. Putative signal sequences (solid boxes) are indicated.
Figure 1
Figure 1
Amino acid sequence alignment of the S genes of the field isolates in mid-eastern China and porcine epidemic diarrhea virus (PEDV) reference strains. The dashes (-) indicate the deleted sequences. Insertion and deletion in PEDV isolates are shaded. Putative signal sequences (solid boxes) are indicated.
Figure 2
Figure 2
Phylogenetic analysis based on the full length of the S genes of 15 field isolates of porcine epidemic diarrhea virus (PEDV) in mid-eastern China and other PEDV reference strains. The 15 field isolates in this study are marked by closed circle symbols. Unrooted phylogenetic trees were generated by the distance-based neighbor-joining method using computer software [MEGA 5.05(25)]. Bootstrap values (based on 1000 replicates) for each node are given if > 60%.
Figure 3
Figure 3
Phylogenetic analysis based on the full length of the ORF3 gene of the 11 field isolates of porcine epidemic diarrhea virus (PEDV) in mid-eastern China and other PEDV reference strains. The 11 field isolates in this study are marked by closed triangle symbols. Unrooted phylogenetic trees were generated by the distance-based neighbor-joining method using computer software [MEGA 5.05(25)]. Bootstrap values (based on 1000 replicates) for each node are given if > 60%.
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