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. 2021 Feb 25:8:651999.
doi: 10.3389/fvets.2021.651999. eCollection 2021.

Detection and Genetic Diversity of Porcine Coronavirus Involved in Diarrhea Outbreaks in Spain

Héctor Puente  1 , Héctor Argüello  1 , Óscar Mencía-Ares  1 , Manuel Gómez-García  1 , Pedro Rubio  1 , Ana Carvajal  1
Affiliations

Detection and Genetic Diversity of Porcine Coronavirus Involved in Diarrhea Outbreaks in Spain

Héctor Puente et al. Front Vet Sci. .

Abstract

Porcine enteric coronaviruses include some of the most relevant viral pathogens to the swine industry such as porcine epidemic diarrhea virus (PEDV) or porcine transmissible gastroenteritis virus (TGEV) as well as several recently identified virus such as swine enteric coronavirus (SeCoV), porcine deltacoronavirus (PDCoV) or swine enteric alphacoronavirus (SeACoV). The aim of this study is the identification and characterization of enteric coronaviruses on Spanish pig farms between 2017 and 2019. The study was carried out on 106 swine farms with diarrhea outbreaks where a viral etiology was suspected by using two duplex RT-PCRs developed for the detection of porcine enteric coronaviruses. PEDV was the only coronavirus detected in our research (38.7% positive outbreaks, 41 out of 106) and neither TGEV, SeCoV, PDCoV nor SeACoV were detected in any of the samples. The complete S-gene of all the PEDV isolates recovered were obtained and compared to PEDV and SeCoV sequences available in GenBank. The phylogenetic tree showed that only PEDV of the INDEL 2 or G1b genogroup has circulated in Spain between 2017 and 2019. Three different variants were detected, the recombinant PEDV-SeCoV being the most widespread. These results show that PEDV is a relevant cause of enteric disorders in pigs in Spain while new emerging coronavirus have not been detected so far. However, the monitoring of these virus is advisable to curtail their emergence and spread.

Keywords: INDEL strain; PEDV; S or Spike gene; pig; swine coronavirus.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

Figure 1
Figure 1
Map showing the distribution of the viral suspected diarrhea outbreaks investigated in this research (shaded area). The number of farms sampled (blue circle) and PEDV positive farms per province (orange circle) are given.
Figure 2
Figure 2
Distribution of the viral suspected diarrhea outbreaks and PEDV positive outbreaks from January, 2017 to March, 2019. The number of sampled farms and PEDV-positive farms is shown above the columns. The percentage of PEDV-positive outbreaks in each trimester studied. The percentage of PEDV-positive outbreaks in each trimester studied is showed.
Figure 3
Figure 3
Phylogenetic tree based on the complete S-gene sequences including enteric porcine coronaviruses available in GenBank. Numbers along the tree represent the confidence value for a given internal branch based on 500 Bootstrap replicates (only values >70 are shown). The symbols above the strains highlight the Spanish PEDV isolates of this study. The filled circles identified the isolates sequenced in this research while the filled triangles identified isolates previously sequenced by de Nova et al. (15). GenBank accession number, country and year of the outbreak are also shown below the strains. The genogroups and subgroups referred in the text are included on the right of the tree. Scale bars indicate nucleotide substitutions per site.
Figure 4
Figure 4
Phylogenetic tree based on the complete S-gene sequences including all Spanish enteric porcine coronaviruses available in GenBank. Numbers along the tree represents the confidence value for a given internal branch based on 500 Bootstrap replicates (only values >70 are shown). The symbols above the strains stand out the Spanish PEDV isolates of this study. The filled circles identified the isolates sequenced in this research and the filled triangles identified the isolates previously sequenced by de Nova et al. (15). GenBank accession number, province and year of the outbreak are also shown below the strains. The genogroups and subgroups referred in the text are included on the right of the tree. Scale bars indicate nucleotide substitutions per site. Black, pre-2000 isolates; Red, 2014 isolates; Gray, 2015 isolates; Purple, 2016 isolates; Yellow, 2017 isolates; Green, 2018 isolates; Blue, 2019 isolates.
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