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Influenza A/H1N1pdm
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GS_00H6T0C.1
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USA/GS_00H6T0C.1/2026-02-05
R. S. Cox,
G. Goodwin,
J. Freeman,
G. Godfrey &
D. Hook
South Carolina Dept. of Public Health, South Carolina Dept. of Public Health
Submission details
Submission ID
PZ052278.1.seg2/PZ052277.1.seg3/PZ052267.1.seg4/PZ052273.1.seg5/PZ052271.1.seg6/PZ052269.1.seg7/PZ052275.1.seg8
Submitting group
Automated Ingest from INSDC/NCBI Virus by Loculus
Date submitted
2026-02-26 04:33:21 UTC
Date released
2026-02-26 04:35:30 UTC
INSDC
Bioproject accession
PRJNA1428227
Biosample accession
SAMN55949453
INSDC accession seg2
PZ052278.1
INSDC accession seg3
PZ052277.1
INSDC accession seg4
PZ052267.1
INSDC accession seg5
PZ052273.1
INSDC accession seg6
PZ052271.1
INSDC accession seg7
PZ052269.1
INSDC accession seg8
PZ052275.1
NCBI release date
2026-02-25
SRA run accession
SRR37362116
Clade
Clade HA
D.3.1
Clade NA
D
Sample details
Collection country
USA
Collection subdivision level 1
South Carolina
Collection date
2026-02-05
Isolate name
A/South Carolina/SCPHL-FLU26-0045/2026
Host
Host
Homo sapiens
INSDC seg4
Subtype seg4
H1
INSDC seg6
Subtype seg6
N1
Alignment and QC
Length seg2
2274 (100%)
Total SNPs seg2
73
Length seg3
2151 (100%)
Total SNPs seg3
87
Length seg4
1701 (97.1%)
Total SNPs seg4
110
Length seg5
1497 (100%)
Total SNPs seg5
59
Length seg6
1410 (98.3%)
Total ambiguous nucs seg6
1
Total SNPs seg6
24
Length seg7
982 (100%)
Total SNPs seg7
34
Length seg8
838 (97.1%)
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
seg2
seg2:
G
42
A
seg2:
A
63
G
seg2:
T
81
C
seg2:
A
159
G
seg2:
G
168
A
seg2:
G
180
A
seg2:
C
192
A
seg2:
G
204
A
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:
A
345
G
seg2:
A
366
G
seg2:
T
384
C
seg2:
C
447
T
Show more
seg3
seg3:
G
40
A
seg3:
R
53
A
seg3:
A
56
G
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:
C
468
T
seg3:
G
477
A
Show more
seg4
seg4:
A
38
G
seg4:
C
42
A
seg4:
A
47
G
seg4:
G
57
A
seg4:
C
113
T
seg4:
A
119
G
seg4:
T
161
C
seg4:
C
164
T
seg4:
G
188
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
409
A
seg4:
G
416
A
seg4:
A
429
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:
C
285
T
seg6:
A
392
G
seg6:
T
413
C
seg6:
C
452
A
seg6:
G
607
A
seg6:
G
659
A
seg6:
C
728
A
seg6:
G
748
A
seg6:
A
785
G
seg6:
T
799
C
seg6:
A
818
G
seg6:
C
893
T
seg6:
G
914
T
seg6:
C
929
T
seg6:
G
950
A
seg6:
T
1010
C
seg6:
T
1016
C
seg6:
A
1049
G
Show more
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:
G
414
A
seg7:
T
429
C
seg7:
T
432
C
seg7:
G
441
T
seg7:
G
492
A
seg7:
C
507
A
seg7:
A
574
G
Show more
seg8
seg8:
C
6
A
seg8:
C
42
T
seg8:
C
54
T
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
226
T
seg8:
T
230
C
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
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:
R
113
K
HA1:
T
120
A
HA1:
N
129
D
HA1:
K
130
N
HA1:
P
137
S
HA1:
A
139
D
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
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:
P
93
S
NA:
S
200
N
NA:
S
247
N
NA:
I
264
T
NA:
M
314
I
NA:
V
453
M
NA:
K
469
N
NEP
NEP:
D
2
E
NEP:
M
14
T
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
76
S
NS1:
L
77
P
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:
P
164
S
NS1:
N
205
S
PA
PA:
V
14
I
PA:
X
18
E
PA:
K
19
R
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:
K
19
R
PA-X:
I
30
V
PA-X:
V
63
I
PA-X:
V
100
I
PA-X:
R
199
K
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
757
R
SigPep
SigPep:
L
8
M
SigPep:
A
13
T
Deletions
None
Insertions
None
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