Whole-Genome, Recombinant, and Phylogenetic Analysis of Porcine Epidemic Diarrhea Virus Strain CH/JSXZ/2015

Table 3

Nucleotide and amino acid sequence identity (%) of different PEDV CH/JSXZ/2015 genome regions compared with the other strains.

	CH/JSXZ/2015
	Strain	GenBank accession no.	Location	Date	Genome	S aa	ORF3 aa
1	JSXZ	MT625963.1	China	2015	100.0	100.0	100.0
2	CV777	AF353511.1	Switzerland	2001	93.6	92.4	98.5
3	85–7-C40	KY486714.1	China	2017	93.6	90.8	96.1
4	85-7-mutant1	KX839247.1	China	2016	93.5	90.8	95.4
5	AH2012/12	KU646831.1	China	2016	96.9	97.4	96.9
6	AJ1102	JX188454.1	China	2012	98.0	98.2	97.3
7	B5-HB2017	MF807952.1	China	2017	98.5	98.0	100.0
8	BJ−2011–1	JN825712.1	China	2011	98.9	99.0	99.6
9	CH/FJND−3/2011	JQ282909.1	China	2011	98.2	97.2	99.6
10	CH/FJZZ−9/2012	KC140102.1	China	2012	98.2	98.1	99.6
11	CH/GDZHDM/1401	KR153326.1	China	2014	99.5	99.8	100.0
12	CH/GDZHDM/1401	KX016034.1	China	2014	99.5	99.8	100.0
13	CH/HNLH/2015	KT199103.1	China	2015	99.2	99.4	99.6
14	CH/HNZZ47/2016	KX981440.1	China	2016	98.9	98.2	100.0
15	CH/JLDH/2016	MF346935.1	China	2017	98.8	98.8	96.4
16	CH/JXJA/2017	MF375374.1	China	2017	99.0	99.1	100.0
17	CH/S	JN547228.1	China	2011	94.2	91.1	100.0
18	CH/YNKM−8/2013	KF761675.1	China	2013	98.2	98.3	98.2
19	CH/ZJCX−1/2012	KF840537.1	China	2013	98.9	99.3	100.0
20	CHN/SH−2016−4/2016	MG837012.1	China	2018	99.1	98.7	100.0
21	CO/P14/IC	KU558702.1	America	2016	98.8	98.1	98.9
22	FR/001/2014	KR011756.1	France	2015	98.1	95.1	99.6
23	GDS23	MH107322.1	China	2018	98.8	98.6	98.2
24	JS-HZ2012	KC210147.1	China	2012	98.9	99.1	100.0
25	LNCT2	KT323980.1	China	2015	98.9	98.6	100.0
26	MEX/104/2013	KJ645708.1	America	2014	98.8	99.1	100.0
27	NPL-PEDv/2013	KJ778615.1	America	2014	98.8	99.1	100.0
28	OH8593−14	KP641662.1	America	2015	98.8	98.7	100.0
29	OH9097−14	KP641663.1	America	2015	98.8	98.6	100.0
30	OH15962	KJ584361.1	America	2014	98.7	99.1	100.0
31	PC21A	KR078299.1	America	2015	98.7	99.2	100.0
32	PC22A-P100-C6	KU893871.1	America	2016	98.6	98.1	98.7
33	PC273/O	MG837058.1	America	2018	98.6	99.2	99.6
34	PEDV 1842/2016 ITA	KY111278.1	Italy	2016	97.9	94.7	99.6
35	PEDV/MEX/PUE/01/2015	MH004421.1	Mexico	2018	98.6	98.5	100.0
36	PEDV/MEX/QRO/02/2017	MH013466.1	Mexico	2018	98.6	98.7	100.0
37	PEDV/USA/Minnesota125/2015	KU982980.1	America	2016	98.7	98.5	99.2
38	PEDV/USA/NorthDakota93/2015	KU982970.1	America	2016	98.7	99.1	100.0
39	PEDV/USA/Oklahoma133/2015	KU982968.1	America	2016	98.8	98.5	100.0
40	PEDV-LNsy	KY007140.1	China	2016	99.0	98.5	100.0
41	PEDV-SX	KY420075.1	China	2017	94.0	92.3	98.6
42	PEDV-WS	KM609213.1	China	2014	99.3	99.4	100.0
43	TC PC168-P2	KM392226.1	America	2014	98.7	99.1	100.0
44	USA/2014/IL/20697 P7	KT591944.1	America	2015	98.5	95.0	95.1
45	USA/Colorado/2013	KF272920.1	America	2013	98.9	99.2	99.6
46	USA/IL20697/2014 Passage 5	KT860508.1	America	2015	98.5	95.0	100.0
47	USA/Illinois98/2013	KJ645690.1	America	2014	98.7	99.0	100.0
48	USA/Illinois259/2014 from USA	KR265785.1	America	2015	98.8	99.1	100.0
49	USA/Indiana34/2013&America	KJ645641.1	America	2014	98.8	98.9	100.0
50	USA/Iowa/18984/2013	KF804028.1	America	2013	98.7	99.1	100.0
51	USA/Kansas46/2013	KJ645650.1	America	2014	98.9	99.0	100.0
52	USA/Kansas431/2014 from USA	KR265819.1	America	2015	98.9	98.9	100.0
53	USA/Minnesota76/2013	KJ645671.1	America	2014	98.7	99.0	100.0
54	USA/Minnesota90/2013	KJ645682.1	America	2014	98.8	99.1	99.6
55	USA/Missouri373/2014 from USA	KR265844.1	America	2015	98.7	98.7	100.0
56	USA/MO/2014/03293	KM975741.1	America	2014	98.2	94.9	100.0
57	USA/NC/2013/35140	KM975735.1	America	2014	98.9	99.0	100.0
58	USA/Nebraska287/2014 from USA	KR265765.1	America	2015	98.7	99.0	100.0
59	USA/Nebraska288/2014 from USA	KR265803.1	America	2015	98.7	99.0	100.0
60	USA/NorthCarolina66/2013	KJ645662.1	America	2014	98.9	99.1	99.6
61	USA/Ohio123/2014	KJ645699.1	America	2014	98.8	99.1	100.0
62	USA/OK10240−8/2017	MG334555.1	America	2017	98.8	99.0	100.0
63	USA/Tennesse56/2013	KJ645654.1	America	2014	98.7	98.7	100.0
64	YN90	KT021231.1	China	2015	98.1	97.8	91.2
65	PEDV/Pig-wt/ESP/Calaf-1/2014	MT602520.1	Spain	2020	98.0	95.3	99.1
66	HNAY2016	MT338518.1	China	2021	99.0	99.5	99.2
67	CH/HNXX/2016	MT338517.1	China	2021	98.5	97.9	98.2
68	CH/SXWS/2018	MT090146.1	China	2020	99.1	99.2	100.0
69	SH1302	MT843277.1	China	2020	94.0	98.6	92.4
70	MSCH	MT683617.1	China	2021	98.7	97.9	98.2

Abbreviations: aa, amino acid.