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LOC_000L5S3.1
Download
Download FASTA
Download metadata TSV
South_Africa/LOC_000L5S3.1/2018-01-01
C. MacIntyre
University of Pretoria, Medical Virology
Sample details
Collection date
2018
Earliest release date
2025-11-23
Sampling location
South Africa
Isolate name
ZRU029/18
Data use terms
Data use terms
OPEN
(history)
Data use terms URL
https://#TODO-MVP/open
INSDC
NCBI release date
2025-11-23
NCBI update date
2025-11-23
INSDC accession
OR879082.1
Host
Host
domestic horse; equine; horse (Equus caballus)
Submission details
Submission ID
OR879082.1
Submitting group
Automated Ingest from INSDC/NCBI Virus by Loculus
Date submitted
2026-09-03 08:13:39 UTC
Date released
2026-09-03 08:32:48 UTC
Lineage
Lineage
2
Files
Annotations
LOC_000L5S3.1.embl
Alignment and QC
Total SNPs
2130
Total inserted nucs
28
Total deleted nucs
13
Total unknown nucs
530
Total frame shifts
1
Frame shifts
NS4B:20-22(nt:6973-6981)
Length
10801 (93%)
Amino Acid Mutations from founder clade
2K:
S
19
G
NS1:
E
173
D
NS1:
V
188
I
NS1:
R
256
G
NS2A:
A
19
V
NS2A:
R
98
K
NS2A:
K
122
R
NS2A:
S
192
I
NS2A:
A
224
V
NS2B:
A
106
T
NS2B:
Q
127
H
NS3:
G
103
R
NS3:
K
187
R
NS3:
I
352
V
NS3:
K
367
R
NS3:
S
421
N
NS4B:
S
14
G
NS4B:
-
28
L
Show more
Variant
True
Nucleotide mutations
Mutations called relative to the
NC_009942.1
reference
Substitutions
A
82
G
C
86
T
T
100
C
C
123
T
G
126
A
G
128
A
A
156
G
C
160
T
T
167
G
G
168
A
T
180
A
T
199
C
C
204
T
C
210
T
C
216
G
G
222
C
A
231
C
T
234
C
Show more
Deletions
6982-6985, 10470, 10487-10494
Insertions
ins_6972:AAGCT, ins_6976:AC, ins_10467:AGATAGCATTATAGTTA, ins_10483:GCT, ins_10501:T
Amino acid substitutions
Substitutions called relative to the
NC_009942.1
reference
Substitutions
2K
2K:
M
15
L
2K:
S
19
G
NS1
NS1:
S
9
G
NS1:
Y
34
F
NS1:
K
51
A
NS1:
V
71
I
NS1:
E
94
N
NS1:
S
99
A
NS1:
T
105
A
NS1:
I
113
M
NS1:
L
123
I
NS1:
V
135
I
NS1:
K
141
E
NS1:
Q
146
A
NS1:
L
153
M
NS1:
K
170
R
NS1:
V
171
I
NS1:
E
173
D
NS1:
S
174
T
NS1:
V
188
I
Show more
NS2A
NS2A:
A
19
V
NS2A:
M
34
I
NS2A:
L
38
M
NS2A:
I
39
L
NS2A:
S
68
A
NS2A:
R
98
K
NS2A:
N
104
S
NS2A:
V
112
A
NS2A:
H
119
Y
NS2A:
Q
123
N
NS2A:
I
124
V
NS2A:
L
126
S
NS2A:
I
129
V
NS2A:
A
137
S
NS2A:
T
147
S
NS2A:
T
150
N
NS2A:
R
167
K
NS2A:
I
183
V
Show more
NS2B
NS2B:
A
41
V
NS2B:
S
61
T
NS2B:
V
103
A
NS2B:
A
106
T
NS2B:
V
120
I
NS2B:
Q
127
H
NS3
NS3:
Q
92
H
NS3:
G
103
R
NS3:
F
130
Y
NS3:
D
172
E
NS3:
I
175
A
NS3:
K
187
R
NS3:
R
203
K
NS3:
R
215
K
NS3:
A
233
S
NS3:
P
249
H
NS3:
N
253
S
NS3:
V
283
I
NS3:
S
302
A
NS3:
S
331
A
NS3:
L
336
M
NS3:
S
347
T
NS3:
I
352
V
NS3:
T
356
V
Show more
NS4A
NS4A:
I
6
V
NS4A:
K
11
R
NS4A:
T
64
S
NS4A:
M
65
L
NS4A:
A
85
V
NS4A:
V
86
I
NS4A:
V
89
A
NS4B
NS4B:
S
11
N
NS4B:
S
14
G
NS4B:
F
17
L
NS4B:
Q
19
H
NS4B:
N
26
T
NS4B:
F
27
T
NS4B:
S
28
L
NS4B:
T
116
A
NS4B:
I
168
V
NS4B:
L
183
M
NS4B:
K
193
R
NS4B:
A
198
V
NS4B:
I
202
T
NS4B:
T
241
M
NS5
NS5:
Q
18
H
NS5:
T
25
I
NS5:
I
33
T
NS5:
K
45
R
NS5:
V
49
I
NS5:
I
78
V
NS5:
R
101
K
NS5:
C
139
A
NS5:
C
140
S
NS5:
I
162
V
NS5:
R
177
K
NS5:
V
181
I
NS5:
L
197
T
NS5:
R
224
H
NS5:
V
229
I
NS5:
V
233
I
NS5:
R
247
K
NS5:
Y
254
F
Show more
capsid
capsid:
S
2
P
capsid:
S
11
N
capsid:
P
22
S
capsid:
V
24
G
capsid:
S
100
T
capsid:
K
108
T
capsid:
T
109
A
capsid:
I
111
F
capsid:
A
112
T
capsid:
V
113
I
capsid:
M
114
L
capsid:
I
115
L
capsid:
S
120
C
capsid:
V
121
A
env
env:
E
55
D
env:
T
64
S
env:
K
71
R
env:
D
83
E
env:
R
93
K
env:
S
122
T
env:
I
126
T
env:
R
128
W
env:
T
129
I
env:
L
131
Q
env:
V
159
I
env:
T
162
A
env:
L
167
F
env:
A
172
S
env:
I
196
T
env:
T
198
I
env:
N
199
S
env:
T
205
S
Show more
prM
prM:
T
17
I
prM:
V
19
T
prM:
D
21
G
prM:
M
44
L
prM:
D
46
E
prM:
V
55
A
prM:
S
57
A
prM:
A
73
S
prM:
M
112
L
prM:
A
117
V
prM:
V
156
A
prM:
V
157
I
Deletions
NS4B
NS4B:23, NS4B:24
Insertions
NS4B
ins_NS4B:28:G
Nucleotide sequence
Aligned nucleotide sequence
Aligned amino acid sequences
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