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GS_0067517.1
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Display Name: USA/GS_0067517.1/2025-04-21
E. B. Fox,
J. M. Garrigues &
N. M. Green
Submission details
Submission ID
PV717447.1.seg1/PV717448.1.seg2/PV717449.1.seg3/PV717450.1.seg4/PV717451.1.seg5/PV717452.1.seg6/PV717453.1.seg7/PV717454.1.seg8
Submitting group
Automated Ingest from INSDC/NCBI Virus by Loculus
Date submitted
2025-06-30 20:41:51 UTC
Date released
2025-07-01 07:20:49 UTC
Authors
Author affiliations
Los Angeles County Public Health Lab microbial pathogen submission group, Los Angeles County Public Health Laboratories
Clade
Clade HA
6B.1A.5a.2a.1
Clade NA
C.5.3.1
Alignment states and QC metrics seg1
Completeness seg1
83.77%
Length seg1
2280
Total ambiguous nucs seg1
0
Total deleted nucs seg1
0
Total frame shifts seg1
0
Total inserted nucs seg1
0
Total SNPs seg1
69
Total unknown nucs seg1
370
Alignment states and QC metrics seg2
Completeness seg2
94.68%
Length seg2
2274
Total ambiguous nucs seg2
0
Total deleted nucs seg2
0
Total frame shifts seg2
0
Total inserted nucs seg2
0
Total SNPs seg2
69
Total unknown nucs seg2
121
Alignment states and QC metrics seg3
Completeness seg3
90.56%
Length seg3
2151
Total ambiguous nucs seg3
0
Total deleted nucs seg3
0
Total frame shifts seg3
0
Total inserted nucs seg3
0
Total SNPs seg3
69
Total unknown nucs seg3
203
Alignment states and QC metrics seg4
Completeness seg4
97.09%
Length seg4
1701
Total ambiguous nucs seg4
0
Total deleted nucs seg4
0
Total frame shifts seg4
0
Total inserted nucs seg4
0
Total SNPs seg4
104
Total unknown nucs seg4
0
Alignment states and QC metrics seg5
Completeness seg5
100.00%
Length seg5
1497
Total ambiguous nucs seg5
0
Total deleted nucs seg5
0
Total frame shifts seg5
0
Total inserted nucs seg5
0
Total SNPs seg5
60
Total unknown nucs seg5
0
Alignment states and QC metrics seg6
Completeness seg6
98.39%
Length seg6
1410
Total ambiguous nucs seg6
0
Total deleted nucs seg6
0
Total frame shifts seg6
0
Total inserted nucs seg6
0
Total SNPs seg6
18
Total unknown nucs seg6
0
Alignment states and QC metrics seg7
Completeness seg7
100.00%
Length seg7
982
Total ambiguous nucs seg7
0
Total deleted nucs seg7
0
Total frame shifts seg7
0
Total inserted nucs seg7
0
Total SNPs seg7
29
Total unknown nucs seg7
0
Alignment states and QC metrics seg8
Completeness seg8
100.00%
Length seg8
863
Total ambiguous nucs seg8
0
Total deleted nucs seg8
0
Total frame shifts seg8
0
Total inserted nucs seg8
0
Total SNPs seg8
33
Total unknown nucs seg8
0
Sample details
Collection country
USA
Collection subdivision level 1
California
Collection date
2025-04-21
Isolate name
A/California/LACPHL-INF01995/2025
Host
Host name scientific
Homo sapiens
Host taxon id
9606
INSDC
INSDC accession seg1
PV717447.1
INSDC accession seg2
PV717448.1
INSDC accession seg3
PV717449.1
INSDC accession seg4
PV717450.1
INSDC accession seg5
PV717451.1
INSDC accession seg6
PV717452.1
INSDC accession seg7
PV717453.1
INSDC accession seg8
PV717454.1
NCBI release date
2025-06-02
INSDC seg4
Subtype seg4
H1
INSDC seg6
Subtype seg6
N1
Nucleotide mutations
Mutations called relative to the
NC_026438.1
,
NC_026435.1
,
NC_026437.1
,
CY121680.1
,
NC_026436.1
,
MW626056.1
,
NC_026431.1
&
NC_026432.1
references
Substitutions
seg1
seg1:
A
18
G
seg1:
G
66
A
seg1:
A
90
C
seg1:
A
96
G
seg1:
A
108
G
seg1:
A
132
G
seg1:
A
138
G
seg1:
G
161
A
seg1:
A
174
G
seg1:
T
201
C
seg1:
A
225
G
seg1:
A
226
T
seg1:
C
242
T
seg1:
A
243
G
seg1:
C
261
T
seg1:
C
285
A
seg1:
A
291
G
seg1:
C
309
T
Show more
seg2
seg2:
G
42
A
seg2:
A
159
G
seg2:
G
168
A
seg2:
G
180
A
seg2:
C
192
T
seg2:
C
201
T
seg2:
T
207
A
seg2:
T
210
C
seg2:
T
222
C
seg2:
G
225
A
seg2:
C
297
T
seg2:
G
312
A
seg2:
T
324
A
seg2:
G
354
A
seg2:
A
366
G
seg2:
C
447
T
seg2:
T
450
C
seg2:
G
461
A
Show more
seg3
seg3:
G
40
A
seg3:
R
53
A
seg3:
T
81
C
seg3:
G
84
C
seg3:
A
88
G
seg3:
C
90
T
seg3:
C
99
T
seg3:
A
114
T
seg3:
C
153
T
seg3:
C
162
T
seg3:
C
165
T
seg3:
G
187
A
seg3:
G
204
A
seg3:
G
298
A
seg3:
G
423
A
seg3:
G
498
A
seg3:
G
504
A
seg3:
G
597
A
Show more
seg4
seg4:
C
42
A
seg4:
A
47
G
seg4:
G
57
A
seg4:
A
119
G
seg4:
T
161
C
seg4:
C
164
T
seg4:
G
188
A
seg4:
G
209
A
seg4:
A
231
C
seg4:
C
281
A
seg4:
C
293
G
seg4:
C
318
T
seg4:
G
322
A
seg4:
G
360
A
seg4:
G
416
A
seg4:
A
429
G
seg4:
C
443
T
seg4:
A
456
G
Show more
seg5
seg5:
A
33
G
seg5:
G
42
T
seg5:
C
87
T
seg5:
A
97
G
seg5:
C
141
A
seg5:
C
171
T
seg5:
T
177
C
seg5:
C
180
T
seg5:
C
249
A
seg5:
A
288
C
seg5:
G
298
A
seg5:
C
303
T
seg5:
G
309
A
seg5:
T
314
C
seg5:
G
315
A
seg5:
R
341
A
seg5:
T
365
A
seg5:
A
390
G
Show more
seg6
seg6:
T
68
C
seg6:
C
301
T
seg6:
C
452
A
seg6:
G
607
A
seg6:
A
785
G
seg6:
T
799
C
seg6:
A
818
G
seg6:
C
893
T
seg6:
G
914
T
seg6:
A
1049
G
seg6:
A
1064
G
seg6:
C
1187
T
seg6:
A
1193
G
seg6:
A
1208
G
seg6:
A
1304
G
seg6:
G
1365
A
seg6:
T
1403
C
seg6:
G
1415
T
seg7
seg7:
G
48
A
seg7:
G
75
A
seg7:
T
123
C
seg7:
C
124
A
seg7:
G
238
A
seg7:
G
258
A
seg7:
A
293
G
seg7:
G
306
A
seg7:
G
339
A
seg7:
G
342
A
seg7:
C
375
A
seg7:
T
432
C
seg7:
G
441
T
seg7:
G
492
A
seg7:
C
507
A
seg7:
A
574
G
seg7:
C
622
A
seg7:
G
660
A
Show more
seg8
seg8:
C
6
A
seg8:
C
42
T
seg8:
C
54
T
seg8:
G
60
A
seg8:
T
99
C
seg8:
C
108
A
seg8:
T
159
C
seg8:
G
163
A
seg8:
C
192
T
seg8:
C
204
T
seg8:
A
238
G
seg8:
G
250
A
seg8:
C
264
T
seg8:
C
268
A
seg8:
C
315
T
seg8:
A
367
G
seg8:
A
375
T
seg8:
A
391
G
Show more
Deletions
None
Insertions
None
Amino acid mutations
Mutations called relative to the
NC_026438.1
,
NC_026435.1
,
NC_026437.1
,
CY121680.1
,
NC_026436.1
,
MW626056.1
,
NC_026431.1
&
NC_026432.1
references
Substitutions
HA1
HA1:
K
54
Q
HA1:
S
74
R
HA1:
P
83
S
HA1:
S
84
N
HA1:
D
97
N
HA1:
T
120
A
HA1:
N
129
D
HA1:
K
130
N
HA1:
P
137
S
HA1:
K
142
R
HA1:
N
156
K
HA1:
L
161
I
HA1:
S
162
N
HA1:
K
163
Q
HA1:
S
164
T
HA1:
S
183
P
HA1:
S
185
I
HA1:
A
186
T
Show more
HA2
HA2:
E
29
D
HA2:
I
45
V
HA2:
E
47
K
HA2:
I
91
V
HA2:
S
124
H
HA2:
I
133
T
HA2:
E
172
K
HA2:
E
179
D
HA2:
V
193
A
M1
M1:
L
42
I
M1:
V
80
I
M1:
K
98
R
M1:
M
192
V
M1:
Q
208
K
M1:
K
230
R
M2
M2:
R
18
K
M2:
D
21
G
M2:
S
23
N
M2:
I
28
T
NA
NA:
A
98
V
NA:
S
200
N
NA:
I
264
T
NA:
V
453
M
NA:
K
469
N
NEP
NEP:
D
2
E
NEP:
N
29
S
NEP:
T
48
A
NEP:
M
83
I
NP
NP:
E
14
D
NP:
I
33
V
NP:
V
100
I
NP:
M
105
T
NP:
X
114
E
NP:
L
122
Q
NP:
I
136
L
NP:
V
217
I
NP:
V
425
I
NP:
S
498
N
NS1
NS1:
D
2
E
NS1:
E
55
K
NS1:
T
80
A
NS1:
V
84
I
NS1:
L
90
I
NS1:
I
123
V
NS1:
E
125
D
NS1:
K
131
E
NS1:
A
155
T
NS1:
N
205
S
PA
PA:
V
14
I
PA:
X
18
E
PA:
I
30
V
PA:
V
63
I
PA:
V
100
I
PA:
P
224
S
PA:
S
225
C
PA:
R
262
K
PA:
I
438
V
PA:
I
505
V
PA-X
PA-X:
V
14
I
PA-X:
X
18
E
PA-X:
I
30
V
PA-X:
V
63
I
PA-X:
V
100
I
PA-X:
R
199
K
PA-X:
N
204
S
PA-X:
R
206
K
PA-X:
R
221
Q
PA-X:
L
229
S
PB1
PB1:
G
154
D
PB1:
K
386
R
PB1:
I
397
M
PB1:
I
435
T
PB1:
P
454
S
PB1:
D
729
E
PB1:
K
757
R
PB2
PB2:
R
54
K
PB2:
T
76
S
PB2:
T
81
M
PB2:
G
225
S
PB2:
R
293
K
PB2:
R
299
K
PB2:
S
453
T
PB2:
L
475
M
PB2:
I
559
M
PB2:
V
667
I
PB2:
V
731
I
SigPep
SigPep:
L
8
M
SigPep:
A
13
T
Deletions
None
Insertions
None
Load sequences