Phylogenetic and Genetic Variation Analysis of Porcine Epidemic Diarrhea Virus in East Central China during 2020–2023
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Clinical Sample Information
2.2. Primer Design
2.3. Real-Time PCR Detection and S Gene Sequencing
2.4. Phylogenetic Analyses
2.5. Recombinant Analyses
3. Results
3.1. Identity and Homology Analysis of S Gene Sequence
3.2. Phylogenetic Analysis of PEDV Based on Nucleotide Sequences of the S Gene
3.3. Recombination Analysis of PEDV Based on Nucleotide Sequences of the S Gene
3.4. Comparative Analysis of Amino Acid Sequences of S Protein
3.5. Different Antigenic Index of PEDV S Protein
4. Discussion
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Name | Sequence (5′-3′) | Product Length/bp |
---|---|---|
PEDV-SF | CATACAGTACTTGTACCGGGTGA | 384 |
PEDV-SR | AGACTTGGACCATTTCTA | |
PEDV-S1F | GAAGAATGGTAAGTTGCTAGTG | 1100 |
PEDV-S1R | GAAGTACAATTGAGCCTTCAGC | |
PEDV-S2F | GGCCATTCCTAAGATTTATGG | 1400 |
PEDV-S2R | CACCTATGTTACTATACACC | |
PEDV-S3F | GATGATGATATAGTGGGTG | 1200 |
PEDV-S3R | CTGTACCAGAGAGAAAATG | |
PEDV-S4F | ACTAAGTATACTGAGGTTC | 1000 |
PEDV-S4R | TGGAACTACATTGAGCTC |
Name of Strain | Access. No. | Location | Date | |
---|---|---|---|---|
1 | SM98 | GU937797 | South Korea | 2010 |
2 | CHM2013 | KM887144 | China | 2013 |
3 | CV777 | AF353511 | Switzerland | 2001 |
4 | Virulent-DR13 | JQ023161 | South Korea | 2011 |
5 | Attenuated-DR13 | JQ023162 | South Korea | 2011 |
6 | SD-M | JX560761 | China | 2012 |
7 | Vaccine-CV777 | KT323979 | China | 2015 |
8 | AH-M | KJ158152 | China | 2011 |
9 | ZL29 | KU847996 | China | 2016 |
10 | GER/L00719/2014 | LM645058 | Germany | 2014 |
11 | USA/Iowa106/2013 | KJ645695 | USA | 2013 |
12 | MYZ-1/JPN/2013 | LC063846 | Japan | 2013 |
13 | CH/SCCZ/2018 | MH593148 | China | 2018 |
14 | CH/HNBR/01/2021 | MZ161067 | China | 2021 |
15 | K13JA12-1 | KJ539151 | South Korea | 2013 |
16 | IA2 | KF468754 | USA | 2014 |
17 | BJ-2011-1 | JN825712 | China | 2011 |
18 | AH2012 | KC210145 | China | 2012 |
19 | YN90 | KTO21231 | China | 2014 |
20 | AJ1102 | JX188454 | China | 2012 |
21 | GD-A | JX112709 | China | 2012 |
22 | CHSD2014 | KX791060 | China | 2014 |
23 | CHN-SC2021 | OM505025 | China | 2021 |
24 | CH/HNWMB/2021 | ON960077 | China | 2021 |
25 | CH/HNLH/2015 | KT199103 | China | 2015 |
26 | CH/HNAY/2015 | KR809885 | China | 2015 |
27 | JSnt2020 | OR808012 | China (Jiangsu) | 2020 |
28 | JSyc2021 | OR808013 | China (Jiangsu) | 2021 |
29 | JSxz2021 | OR808014 | China (Jiangsu) | 2021 |
30 | JSsq2021 | OR808015 | China (Jiangsu) | 2021 |
31 | AHbz2022 | OR808016 | China (Anhui) | 2022 |
32 | JSxz2023 | OR808017 | China (Jiangsu) | 2023 |
33 | AHfy2023 | OR808018 | China (Anhui) | 2023 |
34 | AHbz2023-1 | OR808019 | China (Anhui) | 2023 |
35 | AHbz2023-2 | OR808020 | China (Anhui) | 2023 |
36 | GDS21 | MH726371 | China (Anhui) | 2014 |
37 | GD22 | MH726368 | China (Jiangsu) | 2012 |
38 | GDS23 | MH107322 | China (Jiangsu) | 2012 |
39 | GDS25 | MH726365 | China (Jiangsu) | 2013 |
40 | GDS27 | MH726380 | China (Anhui) | 2014 |
41 | GDS31 | MH726394 | China (Jiangsu) | 2015 |
42 | JSS01 | KU646831 | China (Anhui) | 2012 |
43 | JSS12 | KY070587 | China (Jiangsu) | 2016 |
44 | FR0012014 | KR011756.1 | France | 2014 |
45 | NLGD0022014 | KR011122.1 | The Netherlands | 2014 |
PEDV Strains (Subgroup) | Percentage of Nucleotide (Amino Acid) Identity (%) | |||||
---|---|---|---|---|---|---|
CV777 | Vaccine-CV777 | CH/HNBR/01/2021 | AH2012 | AJ1102 | CHN-SC2021 | |
JSyc2021 | 94.0 | 93.7 | 95.7 | 98.1 | 97.7 | 98.5 |
(G2c) | (93.3) | (92.7) | (95.1) | (97.9) | (98.2) | (98.1) |
JSxz2021 | 93.9 | 93.6 | 95.8 | 98.1 | 97.3 | 98.5 |
(G2c) | (93.6) | (93.0) | (95.7) | (98.4) | (98.1) | (98.6) |
JSsq2021 | 94.1 | 93.8 | 96.5 | 98.3 | 97.5 | 98.9 |
(G2c) | (93.6) | (92.9) | (95.7) | (98.3) | (98.1) | (98.6) |
AHbz2022 | 94.1 | 93.8 | 96.3 | 98.2 | 97.4 | 98.8 |
(G2c) | (93.8) | (93.0) | (95.7) | (98.1) | (98.0) | (98.3) |
AHfy2023 | 94.0 | 93.8 | 96.1 | 98.3 | 97.4 | 98.7 |
(G2c) | (93.2) | (92.6) | (95.4) | (98.1) | (97.8) | (98.2) |
JSxz2023 | 94.1 | 93.7 | 96.4 | 98.3 | 97.4 | 98.7 |
(G2c) | (93.7) | (92.9) | (95.9) | (98.4) | (98.2) | (98.7) |
JSnt2020 | 94.9 | 94.9 | 99.3 | 95.9 | 95.1 | 96.3 |
(G1c) | (94.9) | (94.4) | (99.1) | (95.6) | (95.4) | (95.7) |
AHbz2023-1 | 95.0 | 95.2 | 99.0 | 96.2 | 95.2 | 96.5 |
(G1c) | (95.0) | (94.5) | (98.9) | (95.8) | (95.3) | (95.9) |
AHbz2023-2 | 94.7 | 94.9 | 98.7 | 96.1 | 95.1 | 96.3 |
(G1c) | (94.6) | (94.1) | (98.4) | (95.4) | (94.9) | (95.5) |
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Sun, L.; Li, D.; Yan, C.; Wu, C.; Han, F.; Bo, Z.; Shen, M.; Sun, Y.; Wang, L.; Zheng, H.; et al. Phylogenetic and Genetic Variation Analysis of Porcine Epidemic Diarrhea Virus in East Central China during 2020–2023. Animals 2024, 14, 2185. https://doi.org/10.3390/ani14152185
Sun L, Li D, Yan C, Wu C, Han F, Bo Z, Shen M, Sun Y, Wang L, Zheng H, et al. Phylogenetic and Genetic Variation Analysis of Porcine Epidemic Diarrhea Virus in East Central China during 2020–2023. Animals. 2024; 14(15):2185. https://doi.org/10.3390/ani14152185
Chicago/Turabian StyleSun, Liumei, Duo Li, Caijie Yan, Chengyue Wu, Feng Han, Zongyi Bo, Manman Shen, Yiwei Sun, Liyan Wang, Haoqin Zheng, and et al. 2024. "Phylogenetic and Genetic Variation Analysis of Porcine Epidemic Diarrhea Virus in East Central China during 2020–2023" Animals 14, no. 15: 2185. https://doi.org/10.3390/ani14152185
APA StyleSun, L., Li, D., Yan, C., Wu, C., Han, F., Bo, Z., Shen, M., Sun, Y., Wang, L., Zheng, H., Wang, M., & Zhang, Z. (2024). Phylogenetic and Genetic Variation Analysis of Porcine Epidemic Diarrhea Virus in East Central China during 2020–2023. Animals, 14(15), 2185. https://doi.org/10.3390/ani14152185