Classification of Emergent U.S. Strains of Porcine Epidemic Diarrhea Virus by Phylogenetic Analysis of Nucleocapsid and ORF3 Genes

A retrospective study of porcine epidemic diarrhoea virus (PEDV) reveals the presence of swine enteric coronavirus (SeCoV) since 1993 and the recent introduction of a recombinant PEDV‐SeCoV in Spain

“…When the complete genome sequences were analysed, the PEDV isolates were grouped based on their S-gene genogroup SeCoV reported in these isolates was described previously (Valkó et al, 2017(Valkó et al, , 2019 and might provide some advantages, as the S protein is a key target for PEDV neutralizing antibodies (Li et al, 2017;Okda et al, 2017). Besides, the comparison of the sequences of this recombinant region indicated that the SP4 subgroup clusters together with the more modern SeCoV strains (after 2009), but not with the older Spanish ones (1993)(1994)(1995)(1996)(1997)(1998)(1999), reinforcing the notion With regard to the tree topology based on the S-gene, there were no significant differences regarding the complete genome tree with the exception of the position of several isolated strains, supporting the use of the complete S-gene sequences to infer the phylogenetic relationships of PEDV as previously proposed (Sung et al, 2015;Zhang, Chen, Gauger, Harmon, & Yoon, 2014). However,…”

“…With regard to the tree topology based on the S-gene, there were no significant differences regarding the complete genome tree with the exception of the position of several isolated strains, supporting the use of the complete S-gene sequences to infer the phylogenetic relationships of PEDV as previously proposed (Sung et al, 2015;Zhang, Chen, Gauger, Harmon, & Yoon, 2014). However,…”

Analysis of the spike, ORF3, and nucleocapsid genes of porcine epidemic diarrhea virus circulating on Thai swine farms, 2011–2016

“…One-third of the S gene among the new variants G1b shared greater than 95% identity to the classical G1a strain, while the remaining two-thirds possessed greater than 99% similarity to highly virulent G2 strains. Therefore, S INDEL variants resemble recombination strains between G1a and G2 (Huang et al, 2013; Wang et al, 2014). Infection by some S-INDEL variants was reported to produce decreased symptom severity including moderate diarrhea, lower titers of viral shedding, and reduced mortality (Murakami et al, 2015; Vlasova et al, 2014).…”

Reply to “Classification of Emergent U.S. Strains of Porcine Epidemic Diarrhea Virus by Phylogenetic Analysis of Nucleocapsid and ORF3 Genes”

“…However, Wang et al wrote a letter to the editor (Classification of Emergent U.S. Strains of Porcine Epidemic Diarrhea Virus by Phylogenetic Analysis of Nucleocapsid and ORF3 Genes [3]) to dispute our viewpoint and concluded "In summary, the phylogenetic reconstructions may indicate that the N and ORF3 genes should be given significant focus in the evaluation of genetic diversity of PEDV strains emerging in the United States." Upon request from the Journal of Clinical Microbiology, we provide the following responses to the letter of Wang et al…”