Phylogenetic Analysis of Porcine Epidemic Diarrhea Virus (PEDV) during 2020–2022 and Isolation of a Variant Recombinant PEDV Strain
Abstract
:1. Introduction
2. Results
2.1. Prevalence of PEDV in Clinical Samples from Diarrheal Pigs
2.2. Virus Isolation and Identification
2.3. Phylogenetic Analysis and Alignment of the Genome and S Gene of PEDV/SC/2022
2.4. Recombination within the PEDV/SC/2022 ORF1b Gene
3. Discussion
4. Materials and Methods
4.1. Cells, Antibodies, and Clinical Samples
4.2. RNA Extraction and Detection of PEDV
4.3. Amplification and Sequencing of PEDV S Gene
4.4. Virus Isolation and RT-PCR Identification
4.5. TCID50 Assay
4.6. IFA
4.7. Electron Microscopy Analysis
4.8. Phylogenetic and Recombination Analysis
4.9. Growth Kinetics
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Total | Sample Type | Total | PEDV Positive Rate Positive/Sample (%) | |
---|---|---|---|---|
Small Intestine Tissue | Feces | |||
Sichuan | 198 | 95 | 293 | 151/293 (51.54%) |
Guizhou | 1 | 4 | 5 | 5/5 (100%) |
Chongqing | 1 | 0 | 1 | 1/1 (100%) |
Inner Mongolia | 0 | 16 | 16 | 10/16 (62.5%) |
Henan | 0 | 14 | 14 | 14/14 (100%) |
Jiangsu | 0 | 5 | 5 | 5/5 (100%) |
Guangxi | 0 | 13 | 13 | 13/13 (100%) |
Total | 200 | 147 | 347 | 199/347 (57.35%) |
Strain | GenBank No. | Location | Year |
---|---|---|---|
CV777 | AF353511 | Belgium | 1977 |
LZC | EF185992 | China | 2007 |
JS2008 | KC109141 | China | 2013 |
SD-M | JX560761 | China | 2012 |
SC1402 | KP162057 | China | 2014 |
CHHNAY2015 | KR809885 | China | 2015 |
SNJ_P | MK702008 | China | 2018 |
OH851 | KJ399978 | USA | 2014 |
GER/L00719/2014 | LM645058 | Germany | 2014 |
OH1414 | KJ408801 | USA | 2014 |
IA1 | KF468753 | USA | 2013 |
IA2 | KF468754 | USA | 2013 |
AH2012 | KC210145 | China | 2012 |
LWL | MK392335 | China | 2019 |
FL2013 | KP765609 | China | 2014 |
FJzz1 | MK288006 | China | 2011 |
AJ1102 | JX188454 | China | 2011 |
Primer | Sequence | Lenth (bp) |
---|---|---|
PEDV-N-F | 5′-CACAGATAGTGAGAAAGTGCTTCA-3′ | 1434 |
PEDV-N-R | 5′-CAGTAATAACAGTGTAATGGCACT-3′ | |
PEDV-S-1-F | 5′-TTTGTGGTTTTTCTAATCATTTGGTCAACG-3′ | 1659 |
PEDV-S-1-R | 5′-GAACTAAACCCATTGATAGTAGTGTCA-3′ | |
PEDV-S-2-F | 5′-GTCACAATTAATTTCACTGGTC-3′ | 1716 |
PEDV-S-2-R | 5′-CTGTAGAACATCCGTCTGTAG-3′ | |
PEDV-S-3-F | 5′-GCAGATATAGTCTGTGCAC-3′ | 1551 |
PEDV-S-3-R | 5′-AGAAGTAGATAAAAACACTGGTG-3′ |
Strain | GenBank No. | Location | Year |
---|---|---|---|
CV777 | AF353511 | Belgium | 1977 |
DR13 | DQ862099 | South Korea | 1999 |
LZC | EF185992 | China | 2006 |
KNU-0802 | GU180143 | South Korea | 2008 |
KNU-0902 | GU180145 | South Korea | 2009 |
SM98 | GU937797 | South Korea | 2011 |
CNU-091222-01 | JN184634 | South Korea | 2009 |
CH/S | JN547228 | China | 1986 |
BJ-2011-1 | JN825712 | China | 2011 |
CHGD-01 | JN980698 | China | 2011 |
virulent_DR13 | JQ023161 | South Korea | 2009 |
attenuated_DR13 | JQ023162 | South Korea | 2002 |
GD_B | JX088695 | China | 2012 |
AJ1102 | JX188454 | China | 2011 |
LC | JX489155 | China | 2011 |
ZJCZ4 | JX524137 | China | 2011 |
SD-M | JX560761 | China | 2012 |
GD-1 | JX647847 | China | 2011 |
JS2008 | KC109141 | China | 2013 |
CH/ZMDZY/11 | KC196276 | China | 2011 |
AH2012 | KC210145 | China | 2012 |
JS-HZ2012 | KC210147 | China | 2012 |
USA/Colorado/2013 | KF272920 | USA | 2013 |
NCH/GDGZ/2012 | KF384500 | China | 2012 |
USA/Indiana/17846/2013 | KF452323 | USA | 2013 |
MN | KF468752 | USA | 2013 |
IA1 | KF468753 | USA | 2013 |
IA2 | KF468754 | USA | 2013 |
CH/JX-1/2013 | KF760557 | China | 2013 |
CH/YNKM-8/2013 | KF761675 | China | 2013 |
KPEDV-9 | KF898124 | South Korea | 1997 |
SHQP/YM/2013 | KJ196348 | China | 2013 |
OH851 | KJ399978 | USA | 2014 |
OH1414 | KJ408801 | USA | 2014 |
KNU-1303 | KJ451038 | South Korea | 2013 |
KNU-1401 | KJ451047 | South Korea | 2014 |
KNU-1402 | KJ451048 | South Korea | 2014 |
CH/JX-2/2013 | KJ526096 | China | 2013 |
K13JA12-1 | KJ539151 | South Korea | 2014 |
K14JB01 | KJ539154 | South Korea | 2014 |
USA/Kansas29/2013 | KJ645637 | USA: Kansas | 2013 |
USA/Iowa107/2013 | KJ645696 | USA | 2013 |
MEX/124/2014 | KJ645700 | Mexico | 2014 |
USA/Minnesota52/2013 | KJ645704 | USA | 2013 |
VN/VAP1113_1 | KJ960179 | Viet Nam | 2013 |
GDS01 | KM089829 | China | 2014 |
KNU-1406-1 | KM403155 | South Korea | 2014 |
CHM2013 | KM887144 | China | 2013 |
USA/IA/2013/19321 | KM975738 | USA | 2013 |
SC1402 | KP162057 | China | 2014 |
Hawaii/39249/2014 | KP688354 | USA | 2013 |
SQ2014 | KP728470 | China | 2013 |
FL2013 | KP765609 | China | 2014 |
CH/HNYF/14 | KP890336 | China | 2015 |
15V010/BEL/2015 | KR003452 | Belgium | 2015 |
FR/001/2014 | KR011756 | France | 2014 |
PC21A | KR078299 | USA | 2013 |
CH/HNQX-3/14 | KR095279 | China | 2015 |
EAS1 | KR610991 | Thailand | 2015 |
EAS2 | KR610992 | Thailand | 2014 |
CBR1 | KR610993 | Thailand | 2014 |
CH/HNAY/2015 | KR809885 | China | 2015 |
YN1 | KT021227 | China | 2013 |
YN15 | KT021228 | China | 2013 |
CH/HNLH/2015 | KT199103 | China | 2015 |
CV777 | KT323979 | China | 1998 |
HUA-14PED96 | KT941120 | Viet Nam | 2014 |
YC2014 | KU252649 | China | 2014 |
SLO/JH-11/2015 | KU297956 | Slovenia | 2015 |
ZJU/G1/2013 | KU664503 | China | 2013 |
CH/SCCD/2014 | KU975389 | China | 2014 |
JSLS-1/2015 | KX534205 | China | 2015 |
KB2013-4 | KX580953 | China | 2013 |
85-7 | KX839246 | China | 2013 |
CH/GX/2015/750A | KY793536 | China | 2015 |
AVCT12 | LC053455 | Thailand | 2010 |
IWT-1/JPN/2014 | LC063834 | Japan | 2014 |
OKN-1/JPN/2013 | LC063836 | Japan | 2013 |
MYG-1/JPN/2014 | LC063838 | Japan | 2014 |
MYZ-1/JPN/2013 | LC063846 | Japan | 2013 |
L00721/GER/2014 | LM645057 | Germany | 2014 |
GER/L00719/2014 | LM645058 | Germany | 2014 |
PEDV/GER/L01020-K01_15-10/2015 | LT898413 | Germany | 2015 |
PEDV/GER/L01014-K01_15-04/2015 | LT898420 | Germany | 2015 |
PEDV/GER/L00906-K16_14-01/2014 | LT898430 | Germany | 2014 |
CH/JXJA/2017 | MF375374 | China | 2017 |
NW8 | MF782687 | China | 2015 |
PPC 14 | MG781192 | South Korea | 2014 |
CH/SCZY44/2017 | MH061338 | China | 2017 |
CH/SCDY523/2018 | MH593144 | China | 2018 |
JS-A | MH748550 | China | 2017 |
FJzz1 | MK288006 | China | 2011 |
LW/L | MK392335 | China | 2010 |
SNJ-P | MK702008 | China | 2018 |
PEDV-1556-Valencia-Requena | MN692763 | Spain | 2014 |
PEDV-1611-Murcia-Lorca | MN692768 | Spain | 2015 |
PEDV-1613-Murcia-Fuentealamo | MN692769 | Spain | 2015 |
CH-HNAY-2016 | MN893406 | China | 2016 |
CH-HNAY-2017 | MN893407 | China | 2017 |
CH-HNHB-1-2017 | MN893408 | China | 2017 |
CH-HNHB-2-2017 | MN893409 | China | 2017 |
CH-HNJY-2017 | MN893410 | China | 2017 |
CH-HNLH-2016 | MN893411 | China | 2016 |
CH-HNLH-2017 | MN893412 | China | 2017 |
CH-HNNY-2017 | MN893413 | China | 2017 |
CH-HNPDS-1-2018 | MN893414 | China | 2018 |
CH-HNPDS-2-2018 | MN893415 | China | 2018 |
CH-HNPY-2016 | MN893416 | China | 2016 |
CH-HNSMX-2016 | MN893417 | China | 2016 |
CH-HNXX-2017 | MN893418 | China | 2017 |
CH-HNXY-1-2017 | MN893419 | China | 2017 |
CH-HNXY-2-2017 | MN893420 | China | 2017 |
CH-HNXY-3-2018 | MN893421 | China | 2018 |
CH-HNZK-1-2017 | MN893422 | China | 2017 |
CH-HNZK-2-2018 | MN893423 | China | 2018 |
CH-HNZK-3-2018 | MN893424 | China | 2018 |
CH-HNZK-4-2017 | MN893425 | China | 2017 |
CH-HNZMD-2017 | MN893426 | China | 2017 |
CH-HNZZ-2017 | MN893427 | China | 2017 |
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Peng, Q.; Fu, P.; Zhou, Y.; Lang, Y.; Zhao, S.; Wen, Y.; Wang, Y.; Wu, R.; Zhao, Q.; Du, S.; et al. Phylogenetic Analysis of Porcine Epidemic Diarrhea Virus (PEDV) during 2020–2022 and Isolation of a Variant Recombinant PEDV Strain. Int. J. Mol. Sci. 2024, 25, 10878. https://doi.org/10.3390/ijms252010878
Peng Q, Fu P, Zhou Y, Lang Y, Zhao S, Wen Y, Wang Y, Wu R, Zhao Q, Du S, et al. Phylogenetic Analysis of Porcine Epidemic Diarrhea Virus (PEDV) during 2020–2022 and Isolation of a Variant Recombinant PEDV Strain. International Journal of Molecular Sciences. 2024; 25(20):10878. https://doi.org/10.3390/ijms252010878
Chicago/Turabian StylePeng, Qianling, Ping Fu, Yutong Zhou, Yifei Lang, Shan Zhao, Yiping Wen, Yiping Wang, Rui Wu, Qin Zhao, Senyan Du, and et al. 2024. "Phylogenetic Analysis of Porcine Epidemic Diarrhea Virus (PEDV) during 2020–2022 and Isolation of a Variant Recombinant PEDV Strain" International Journal of Molecular Sciences 25, no. 20: 10878. https://doi.org/10.3390/ijms252010878