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Influenza A/H1N1pdm
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GS_00GU2V2.1
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Display Name: USA/GS_00GU2V2.1/2025-12-01
P. C. Gauger,
G. S. Silva &
D. C. Linhares
Submission details
Submission ID
PX879962.1.seg1/PX879965.1.seg3/PX879963.1.seg4/PX879966.1.seg5/PX879964.1.seg6/PX879967.1.seg7/PX879961.1.seg8
Submitting group
Automated Ingest from INSDC/NCBI Virus by Loculus
Date submitted
2026-01-17 04:29:50 UTC
Date released
2026-01-17 04:30:45 UTC
Authors
Author affiliations
University of Pennsylvania Center of Excellence for Influenza Research and Response (CEIRR), CEIRR Influenza Data Processing and Communication Center
INSDC
Bioproject accession
PRJNA818275
INSDC accession seg1
PX879962.1
INSDC accession seg3
PX879965.1
INSDC accession seg4
PX879963.1
INSDC accession seg5
PX879966.1
INSDC accession seg6
PX879964.1
INSDC accession seg7
PX879967.1
INSDC accession seg8
PX879961.1
NCBI release date
2026-01-16
Clade
Clade HA
1
Alignment states and QC metrics seg1
Completeness seg1
100.00%
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
191
Total unknown nucs seg1
0
Alignment states and QC metrics seg3
Completeness seg3
100.00%
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
185
Total unknown nucs seg3
0
Alignment states and QC metrics seg4
Completeness seg4
97.09%
Length seg4
1695
Total ambiguous nucs seg4
0
Total deleted nucs seg4
6
Total frame shifts seg4
0
Total inserted nucs seg4
0
Total SNPs seg4
276
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
57
Total unknown nucs seg5
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
28
Total unknown nucs seg7
0
Alignment states and QC metrics seg8
Completeness seg8
97.10%
Length seg8
838
Total ambiguous nucs seg8
0
Total deleted nucs seg8
0
Total frame shifts seg8
0
Total inserted nucs seg8
0
Total SNPs seg8
61
Total unknown nucs seg8
0
Sample details
Collection country
USA
Collection date
2025-12-01
Isolate name
A/swine/Nebraska/Q121292/2025
Host
Host name scientific
Sus scrofa
Host taxon id
9823
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:
G
21
A
seg1:
T
27
C
seg1:
A
105
G
seg1:
T
106
A
seg1:
G
114
A
seg1:
A
117
G
seg1:
C
129
T
seg1:
G
161
A
seg1:
A
177
G
seg1:
C
180
A
seg1:
G
207
A
seg1:
A
216
G
seg1:
A
219
G
seg1:
A
239
G
seg1:
A
255
G
seg1:
A
258
G
seg1:
A
264
T
seg1:
G
267
A
Show more
seg3
seg3:
C
9
T
seg3:
A
21
G
seg3:
R
53
A
seg3:
G
75
T
seg3:
C
82
T
seg3:
G
84
A
seg3:
C
90
T
seg3:
A
93
G
seg3:
T
96
C
seg3:
T
105
C
seg3:
A
120
G
seg3:
T
123
C
seg3:
T
132
C
seg3:
T
150
C
seg3:
C
153
T
seg3:
C
162
T
seg3:
G
163
A
seg3:
G
170
A
Show more
seg4
seg4:
C
33
T
seg4:
A
35
G
seg4:
G
36
T
seg4:
A
38
G
seg4:
T
41
C
seg4:
C
42
T
seg4:
T
48
C
seg4:
T
54
C
seg4:
C
62
T
seg4:
T
78
A
seg4:
A
110
T
seg4:
C
113
T
seg4:
A
119
T
seg4:
C
122
T
seg4:
A
128
G
seg4:
C
129
T
seg4:
A
134
G
seg4:
T
161
C
Show more
seg5
seg5:
A
33
G
seg5:
C
75
T
seg5:
T
99
C
seg5:
G
111
A
seg5:
T
159
A
seg5:
A
162
G
seg5:
A
282
G
seg5:
T
326
C
seg5:
R
341
A
seg5:
T
365
A
seg5:
T
405
C
seg5:
C
408
T
seg5:
G
459
A
seg5:
A
474
G
seg5:
C
483
T
seg5:
A
486
G
seg5:
C
492
T
seg5:
A
513
G
Show more
seg7
seg7:
A
12
C
seg7:
C
45
A
seg7:
G
48
A
seg7:
T
114
C
seg7:
C
163
T
seg7:
A
180
G
seg7:
A
252
G
seg7:
G
258
A
seg7:
G
270
A
seg7:
G
324
A
seg7:
C
396
T
seg7:
G
414
T
seg7:
A
489
G
seg7:
T
501
A
seg7:
A
528
G
seg7:
G
630
A
seg7:
T
642
C
seg7:
C
672
T
Show more
seg8
seg8:
C
12
T
seg8:
C
15
T
seg8:
A
16
G
seg8:
T
39
C
seg8:
T
51
C
seg8:
G
60
A
seg8:
A
63
G
seg8:
G
70
A
seg8:
C
96
T
seg8:
A
114
G
seg8:
T
127
C
seg8:
A
129
G
seg8:
A
131
T
seg8:
G
151
A
seg8:
G
152
A
seg8:
C
153
T
seg8:
T
159
C
seg8:
A
186
G
Show more
Deletions
seg4:444-449
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:
L
3
I
HA1:
R
45
G
HA1:
V
47
K
HA1:
A
48
S
HA1:
H
51
Y
HA1:
I
61
L
HA1:
L
70
I
HA1:
S
71
L
HA1:
A
73
V
HA1:
P
83
S
HA1:
D
94
S
HA1:
I
96
T
HA1:
D
97
N
HA1:
R
113
K
HA1:
K
119
I
HA1:
T
120
E
HA1:
S
122
P
HA1:
S
128
Y
Show more
HA2
HA2:
E
29
D
HA2:
L
38
Q
HA2:
N
43
R
HA2:
E
47
G
HA2:
V
55
I
HA2:
I
56
V
HA2:
H
72
N
HA2:
K
75
R
HA2:
K
82
R
HA2:
I
91
V
HA2:
Y
110
F
HA2:
S
124
N
HA2:
K
127
R
HA2:
D
158
N
HA2:
P
160
L
HA2:
A
166
S
HA2:
E
179
D
HA2:
I
183
V
HA2:
Y
184
H
HA2:
V
200
L
M1
M1:
A
227
T
M2
M2:
T
11
I
M2:
D
21
G
M2:
S
22
L
M2:
V
27
A
NEP
NEP:
M
6
V
NEP:
E
26
G
NEP:
S
37
A
NEP:
S
60
K
NEP:
M
83
V
NEP:
A
115
T
NP
NP:
D
53
E
NP:
I
109
T
NP:
X
114
E
NP:
L
122
Q
NP:
S
287
N
NP:
M
316
V
NP:
N
370
S
NP:
N
377
S
NP:
V
425
I
NP:
K
452
R
NS1
NS1:
M
6
V
NS1:
D
24
N
NS1:
K
44
I
NS1:
G
51
N
NS1:
S
73
F
NS1:
E
75
D
NS1:
L
77
I
NS1:
R
78
K
NS1:
V
84
A
NS1:
S
87
P
NS1:
S
91
A
NS1:
L
115
F
NS1:
L
119
M
NS1:
M
124
L
NS1:
V
129
I
NS1:
I
145
V
NS1:
V
157
I
NS1:
Y
171
N
Show more
PA
PA:
X
18
E
PA:
P
28
S
PA:
D
55
N
PA:
R
57
Q
PA:
I
85
T
PA:
F
105
L
PA:
I
118
V
PA:
S
186
G
PA:
T
208
K
PA:
K
213
R
PA:
P
224
S
PA:
N
254
S
PA:
K
256
Q
PA:
T
263
I
PA:
L
275
P
PA:
H
277
S
PA:
I
322
V
PA:
V
323
I
Show more
PA-X
PA-X:
X
18
E
PA-X:
P
28
S
PA-X:
D
55
N
PA-X:
R
57
Q
PA-X:
I
85
T
PA-X:
F
105
L
PA-X:
I
118
V
PA-X:
S
186
G
PA-X:
S
193
N
PA-X:
K
195
R
PA-X:
Q
200
R
PA-X:
L
205
S
PA-X:
R
206
K
PA-X:
Q
208
K
PA-X:
L
210
P
PA-X:
S
213
G
PA-X:
*
233
W
PB2
PB2:
S
36
T
PB2:
R
54
K
PB2:
D
60
E
PB2:
K
80
R
PB2:
A
184
T
PB2:
G
225
S
PB2:
V
292
I
PB2:
I
315
M
PB2:
V
356
I
PB2:
E
391
D
PB2:
C
409
R
PB2:
S
453
P
PB2:
N
456
S
PB2:
T
471
A
PB2:
K
482
R
PB2:
I
559
S
PB2:
V
560
L
PB2:
K
574
R
Show more
SigPep
SigPep:
V
6
L
SigPep:
Y
10
H
SigPep:
F
12
L
Deletions
HA1:125, HA1:126
Insertions
None
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