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

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Analysis of the spike, ORF3, and nucleocapsid genes of porcine epidemic diarrhea virus circulating on Thai swine farms, 2011–2016 https://t.co/xdNOsH9vDQ https://t.co/I4wwvBI2Zc
Microbiology

Main article text

 

Introduction

Materials and Methods

Samples

Reverse-transcription polymerase chain reaction

Nucleotide and amino acid sequence analyses

Results

Analysis of the S gene

Analysis of the ORF3 gene

Analysis of the N gene

Discussion

Conclusion

Supplemental Information

Farm locations and provincial origins of 769 samples in this study.

DOI: 10.7717/peerj.6843/supp-1

The percentage detection and provincial origins of 95 PEDV strains.

The percentage detection of each provinces are determined and represent in pie chart. NP, Nakhon Pathom; RB, Ratchaburi; CS, Chachoengsao; CB, Chon Buri; UD, Udon Thani; AY, Phra Nakhon Si Ayutthaya; KR, Kanchanaburi; and PJ, Prachuap Khiri Khan.

DOI: 10.7717/peerj.6843/supp-2

Amino acid sequence alignment of the partial S gene encompassing the COE domain of the Thai PEDV strains and the prototypic CV777.

Numbers indicate residue position. Identical residues are dotted. Strain NP-68/12 differed most from CV777 which showed in gray highlight.

DOI: 10.7717/peerj.6843/supp-3

Amino acid sequence alignment of the partial S gene encompassing the COE domain of the Thai PEDV strains and the prototypic CV777.

Numbers indicate residue position. Identical residues are dotted. Strain NP-68/12 differed most from CV777 which showed in gray highlight.

DOI: 10.7717/peerj.6843/supp-4

Amino acid sequence alignment of the partial S gene encompassing the COE domain of the Thai PEDV strains and the prototypic CV777.

Numbers indicate residue position. Identical residues are dotted. Strain NP-68/12 differed most from CV777 which showed in gray highlight.

DOI: 10.7717/peerj.6843/supp-5

Amino acid sequence alignment of the partial S gene encompassing the COE domain of the Thai PEDV strains and the prototypic CV777.

Numbers indicate residue position. Identical residues are dotted. Strain NP-68/12 differed most from CV777 which showed in gray highlight.

DOI: 10.7717/peerj.6843/supp-6

Amino acid sequence alignment of the partial N gene from Thai PEDV strains with deletions.

Numbers indicate residue position. Identical residues are dotted. Deletions are noted with dashed lines covered by the red boxes.

DOI: 10.7717/peerj.6843/supp-7

Nucleotide sequence primers.

Nucleotide primers used to amplify the PEDV genes.

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Nucleotide accession numbers of the Thai PEDV strains.

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The details of provincial origin and year collection of 95 PEDV strains.

NP, Nakorn Pathom; RB, Ratchaburi; CS, Chachoengsao; CB, Chonburi; UD, Udon Thani; AY, Phra Nakhon Si Ayutthaya; PJ, Prachuap Khiri Khan; NR, Nakhon Ratchasima; and n/a, unknown farm location.

DOI: 10.7717/peerj.6843/supp-10

Comparison of amino acid identities between the Thai PEDV and the vaccine strains.

The COE domain of Thai PEDVs had the most sequence variation compared to vaccine strains, while ORF3 and N genes are more conserved.

DOI: 10.7717/peerj.6843/supp-11

Residue differences within the S, ORF3, and N of the Thai PEDV, CV777, and other vaccine strains.

Vaccine strains include Attenuated DR13, 94P4-C6, and P-5V (strain KPEDV-9, 83P-5 were excluded because their sequence not available).

DOI: 10.7717/peerj.6843/supp-12

The subtypes of 95 Thai PEDV strains.

S gene is sub-divided into subgroup 1 and 3, subgroup 1 and 2 for N gene, whereas major groups of ORF3 gene are not sub-divided into subgroup.

DOI: 10.7717/peerj.6843/supp-13

Spike gene sequences.

Spike gene sequence with accession number of 95 PEDV strains.

DOI: 10.7717/peerj.6843/supp-14

ORF3 gene sequences.

ORF3 gene sequence with accession number of 95 PEDV strains.

DOI: 10.7717/peerj.6843/supp-15

Nucleocapsid gene sequences.

Nucleocapsid gene sequence with accession number of 95 PEDV strains.

DOI: 10.7717/peerj.6843/supp-16

Additional Information and Declarations

Competing Interests

The authors declare that they have no competing interests.

Author Contributions

Supansa Tuanthap conceived and designed the experiments, performed the experiments, analyzed the data, prepared figures and/or tables.

Sompong Vongpunsawad prepared figures and/or tables, authored or reviewed drafts of the paper.

Cherdpong Phupolphan contributed reagents/materials/analysis tools, sample collections and preparations.

Ausanee Duang-in performed the experiments.

Suphot Wattanaphansak contributed reagents/materials/analysis tools.

Pornchalit Assavacheep contributed reagents/materials/analysis tools.

Apiradee Theamboonlers contributed reagents/materials/analysis tools.

Supol Luengyosluechakul conceived and designed the experiments, contributed reagents/materials/analysis tools, prepared figures and/or tables, authored or reviewed drafts of the paper.

Alongkorn Amonsin conceived and designed the experiments, analyzed the data, contributed reagents/materials/analysis tools, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.

Yong Poovorawan conceived and designed the experiments, analyzed the data, contributed reagents/materials/analysis tools, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.

Ethics

The following information was supplied relating to ethical approvals (i.e., approving body and any reference numbers):

The Institutional Animal Care and Use Committee of Chulalongkorn University (IACUC number 1731020) and the Institutional Biosafety Committee (IBC number 1731008) of Chulalongkorn University approved this study.

DNA Deposition

The following information was supplied regarding the deposition of DNA sequences:

The DNA sequences are available in the Genbank database (https://www.ncbi.nlm.nih.gov/). The accession numbers are listed below:

for S gene

MF139511MF139512

MF139376MF139377

MF138383

KC858259KC858262

KX911490KX911510

KX911512KX911530

KX911532KX911533

KX911543KX911546

KX911548

KX911550KX911552

KX911554KX911556

KX911559

KX911561KX911564

KX911567KX911568

KX911570KX911571

KX911573KX911575

and MH744158MH744346 for ORF3 and N genes.

Data Availability

The following information was supplied regarding data availability:

The raw data of 3 gene sequences and their accession numbers are available in Datasets S1S3.

Funding

The Chulalongkorn University graduate scholarship to commemorate the 72nd Anniversary of his Majesty King Bhumibol Adulyadej, The 100th Anniversary Chulalongkorn University Fund for a doctoral scholarship was granted to Supansa Tuanthap, the Research Chair Grant from NSTDA (P-15-50004), Thailand Research Fund (RTA6080012) and the Center of Excellence in Clinical Virology (GCE 59-009-30-005). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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