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Influenza A/H1N1pdm
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GSD_0060JFE.1
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USA/GSD_0060JFE.1/2026-01-14
E. B. Fox,
J. M. Garrigues &
N. M. Green
Los Angeles County Public Health Lab microbial pathogen submission group, Los Angeles County Public Health Laboratories
Submission details
Submission ID
PZ147482.1.seg1/PZ147483.1.seg2/PZ147484.1.seg3/PZ147485.1.seg4/PZ147486.1.seg5/PZ147487.1.seg6/PZ147488.1.seg7/PZ147489.1.seg8
Submitting group
Automated Ingest from INSDC/NCBI Virus by Loculus
Date submitted
2026-03-16 10:11:18 UTC
Date released
2026-03-16 13:36:41 UTC
Clade
Clade HA
D.3.1
Clade NA
D.2
Sample details
Collection country
USA
Collection subdivision level 1
California
Collection date
2026-01-14
Isolate name
A/California/LACPHL-INF02340/2026
Host
Host
Homo sapiens
INSDC
INSDC accession seg1
PZ147482.1
INSDC accession seg2
PZ147483.1
INSDC accession seg3
PZ147484.1
INSDC accession seg4
PZ147485.1
INSDC accession seg5
PZ147486.1
INSDC accession seg6
PZ147487.1
INSDC accession seg7
PZ147488.1
INSDC accession seg8
PZ147489.1
NCBI release date
2026-03-13
INSDC seg4
Subtype seg4
H1
INSDC seg6
Subtype seg6
N1
Alignment and QC
Length seg1
2280 (100%)
Total SNPs seg1
88
Length seg2
2274 (99.9%)
Total ambiguous nucs seg2
3
Total SNPs seg2
71
Length seg3
2151 (100%)
Total SNPs seg3
84
Length seg4
1701 (97.1%)
Total SNPs seg4
105
Length seg5
1497 (100%)
Total SNPs seg5
60
Length seg6
1410 (98.4%)
Total SNPs seg6
21
Length seg7
982 (100%)
Total SNPs seg7
27
Length seg8
863 (100%)
Total SNPs seg8
36
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
A
18
G
G
25
A
A
30
G
A
90
C
A
96
G
A
108
G
A
138
G
G
144
A
G
161
A
A
174
G
G
198
A
T
201
C
A
225
G
C
242
T
A
243
G
C
285
A
A
291
G
C
309
T
Show more
seg2
G
42
A
A
159
G
G
168
A
G
180
A
C
192
T
T
207
A
T
210
C
T
222
C
G
225
A
T
231
C
C
297
T
G
312
A
A
345
G
A
366
G
T
384
C
T
397
C
C
447
T
T
450
C
Show more
seg3
G
40
A
C
42
T
R
53
A
T
81
C
G
84
C
A
88
G
C
90
T
C
99
T
A
114
T
G
126
A
C
153
T
C
162
T
C
165
T
G
187
A
G
204
A
G
270
A
G
298
A
G
423
A
Show more
seg4
C
42
A
A
47
G
G
57
A
A
119
G
T
161
C
C
164
T
G
188
A
A
231
C
C
293
G
C
318
T
G
322
A
G
360
A
A
408
C
G
416
A
A
429
G
C
443
T
A
456
G
A
461
T
Show more
seg5
A
33
G
G
42
T
C
87
T
A
97
G
C
141
A
C
171
T
T
177
C
C
180
T
C
249
A
A
288
C
G
298
A
G
309
A
T
314
C
G
315
A
R
341
A
T
365
A
A
390
G
T
402
C
Show more
seg6
T
50
C
G
65
A
A
144
G
G
163
A
T
188
C
C
434
T
C
452
A
G
607
A
A
785
G
T
799
C
A
818
G
C
831
T
C
893
T
G
914
T
T
1016
C
A
1049
G
C
1187
T
A
1193
G
Show more
seg7
T
36
C
G
75
A
C
124
A
G
238
A
G
258
A
A
293
G
G
306
A
G
339
A
C
375
A
T
432
C
G
441
T
T
465
C
G
492
A
C
507
A
A
574
G
G
600
A
C
622
A
G
660
A
Show more
seg8
C
6
A
C
42
T
C
54
T
C
57
T
T
99
C
C
108
A
T
150
A
C
153
T
T
159
C
G
163
A
C
192
T
C
204
T
A
238
G
G
250
A
C
264
T
C
268
A
C
315
T
G
363
A
Show more
Deletions
N/A
Insertions
N/A
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:
D
21
G
M2:
S
23
N
NA
NA:
I
46
V
NA:
S
52
N
NA:
S
200
N
NA:
I
264
T
NA:
H
275
Y
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:
N
377
S
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:
N
321
K
PA:
I
330
V
PA:
A
337
T
PA:
K
339
N
PA:
R
362
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:
V
200
I
PB1:
K
386
R
PB1:
I
397
M
PB1:
I
435
T
PB1:
K
737
R
PB1:
K
757
R
PB2
PB2:
D
9
N
PB2:
R
54
K
PB2:
M
66
I
PB2:
T
81
M
PB2:
D
195
N
PB2:
G
225
S
PB2:
R
293
K
PB2:
R
299
K
PB2:
V
344
M
PB2:
I
354
L
PB2:
S
453
T
PB2:
L
475
M
PB2:
T
524
A
PB2:
V
667
I
PB2:
V
731
I
SigPep
SigPep:
L
8
M
SigPep:
A
13
T
Deletions
N/A
Insertions
N/A
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