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GS_00HJRNC.1
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USA/GS_00HJRNC.1/2025-12-22
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
PZ194955.1.seg1/PZ194923.1.seg2/PZ194896.1.seg3/PZ194754.1.seg4/PZ194859.1.seg5/PZ194824.1.seg6/PZ194789.1.seg7
Submitting group
Automated Ingest from INSDC/NCBI Virus by Loculus
Date submitted
2026-03-26 04:37:20 UTC
Date released
2026-03-26 04:40:45 UTC
INSDC
Bioproject accession
PRJNA1419886
Biosample accession
SAMN56688414
INSDC accession seg1
PZ194955.1
INSDC accession seg2
PZ194923.1
INSDC accession seg3
PZ194896.1
INSDC accession seg4
PZ194754.1
INSDC accession seg5
PZ194859.1
INSDC accession seg6
PZ194824.1
INSDC accession seg7
PZ194789.1
NCBI release date
2026-03-25
SRA run accession
SRR37749230
Clade
Clade HA
K
Clade NA
None
Sample details
Collection country
USA
Collection subdivision level 1
South Carolina
Collection date
2025-12-22
Isolate name
A/South Carolina/SCPHL-FLU26-0080/2025
Host
Host
Homo sapiens
INSDC seg4
Subtype seg4
H3
INSDC seg6
Subtype seg6
N2
Alignment and QC
Length seg1
2280 (97.4%)
Total SNPs seg1
103
Length seg2
2274 (97.1%)
Total SNPs seg2
110
Length seg3
2151 (96.3%)
Total SNPs seg3
86
Length seg4
1701 (97.9%)
Total SNPs seg4
125
Length seg5
1497 (95.6%)
Total SNPs seg5
57
Length seg6
1410 (98%)
Total SNPs seg6
18
Length seg7
982 (95.6%)
Total SNPs seg7
26
Nucleotide mutations
Mutations called relative to the
NC_007373.1
,
NC_007372.1
,
NC_007371.1
,
CY163680.1
,
NC_007369.1
,
CY114383.1
,
NC_007367.1
&
NC_007370.1
references
Substitutions
seg1
C
54
T
G
57
A
T
75
C
G
87
A
C
192
T
C
198
T
T
255
C
A
282
G
C
289
A
A
336
G
G
343
A
G
347
A
A
369
G
G
375
A
A
402
G
T
417
C
T
426
C
T
438
C
Show more
seg2
C
46
T
G
57
A
C
84
A
A
129
G
A
132
T
A
135
G
C
141
T
T
171
C
A
179
G
G
180
A
A
213
T
A
219
G
G
258
A
C
282
T
C
306
T
T
327
C
G
336
A
A
342
T
Show more
seg3
A
99
G
A
120
C
C
144
T
A
156
G
T
174
C
T
177
C
G
210
A
T
222
C
G
243
A
A
324
T
A
333
G
C
340
T
A
342
G
A
345
G
G
363
A
T
369
C
A
396
G
A
435
G
Show more
seg4
A
24
G
T
42
A
G
56
T
A
71
C
C
72
A
T
74
A
C
77
T
C
89
T
G
120
T
G
155
A
A
163
G
C
189
T
G
199
A
C
203
A
C
208
T
G
213
A
G
214
A
G
222
A
Show more
seg5
G
81
A
G
96
A
T
180
G
G
207
A
G
219
A
G
237
A
C
249
T
G
324
A
A
351
G
A
387
G
G
390
A
G
432
T
G
436
T
T
447
C
A
451
C
C
459
T
G
492
A
A
513
G
Show more
seg6
C
40
T
A
64
G
T
100
C
C
349
A
G
456
A
G
517
A
A
721
G
C
797
A
C
994
T
T
1015
C
A
1044
G
A
1079
G
A
1160
G
G
1206
A
G
1342
A
G
1390
A
A
1410
G
T
1413
C
seg7
A
37
T
C
188
T
G
205
A
G
214
T
A
241
G
T
292
C
T
298
C
A
466
G
A
481
G
C
493
T
A
517
G
G
523
A
A
637
G
A
658
G
G
680
A
C
697
T
T
703
C
C
787
T
Show more
Deletions
N/A
Insertions
N/A
Amino acid mutations
Mutations called relative to the
NC_007373.1
,
NC_007372.1
,
NC_007371.1
,
CY163680.1
,
NC_007369.1
,
CY114383.1
,
NC_007367.1
&
NC_007370.1
references
Substitutions
HA1
HA1:
K
2
N
HA1:
L
3
I
HA1:
A
19
S
HA1:
Q
33
R
HA1:
S
45
N
HA1:
T
48
I
HA1:
G
50
K
HA1:
D
53
N
HA1:
E
62
G
HA1:
K
83
E
HA1:
K
92
R
HA1:
Y
94
N
HA1:
N
96
S
HA1:
N
121
K
HA1:
T
131
K
HA1:
T
135
K
HA1:
S
138
A
HA1:
R
142
G
Show more
HA2
HA2:
I
32
R
HA2:
N
46
D
HA2:
I
77
V
HA2:
R
121
K
HA2:
G
155
E
HA2:
D
160
N
HA2:
I
193
M
HA2:
V
200
I
M1
M1:
V
219
I
M2
M2:
P
25
L
M2:
S
31
N
M2:
L
54
F
M2:
N
82
S
M2:
D
88
A
NA
NA:
R
150
H
NA:
H
264
N
NA:
D
346
G
NA:
N
358
D
NA:
N
385
D
NA:
R
400
K
NA:
H
468
R
NA:
I
469
T
NP
NP:
A
131
S
NP:
I
136
L
NP:
V
197
I
NP:
R
236
K
NP:
T
472
A
PA
PA:
N
142
K
PA:
I
155
M
PA:
K
158
R
PA:
S
208
T
PA:
K
222
N
PA:
K
256
Q
PA:
N
272
S
PA:
I
311
M
PA:
Y
321
C
PA:
D
382
E
PA:
D
396
E
PA:
N
409
S
PA:
I
421
V
PA:
Y
437
H
PA:
I
602
V
PA:
K
605
R
PA:
V
668
I
PA:
N
675
K
PA-X
PA-X:
N
142
K
PA-X:
I
155
M
PA-X:
K
158
R
PA-X:
E
209
G
PA-X:
V
212
A
PA-X:
N
222
T
PB1
PB1:
K
52
R
PB1:
V
113
A
PB1:
V
423
I
PB1:
L
576
I
PB1:
R
586
K
PB1:
A
587
T
PB1:
E
618
D
PB1:
N
667
I
PB1:
*
758
Q
PB1-F2
PB1-F2:
E
4
G
PB1-F2:
Q
5
L
PB1-F2:
D
6
G
PB1-F2:
P
8
L
PB1-F2:
I
18
T
PB1-F2:
R
21
E
PB1-F2:
H
32
L
PB1-F2:
N
34
S
PB1-F2:
S
47
N
PB1-F2:
T
55
I
PB1-F2:
S
63
F
PB1-F2:
V
70
A
PB1-F2:
R
73
K
PB1-F2:
H
75
L
PB1-F2:
S
82
P
PB1-F2:
K
85
R
PB1-F2:
W
88
*
PB2
PB2:
A
106
T
PB2:
S
107
N
PB2:
I
147
T
PB2:
E
249
G
PB2:
R
299
G
PB2:
K
340
R
PB2:
E
341
Y
PB2:
K
353
R
PB2:
I
451
V
PB2:
V
560
I
PB2:
I
588
T
PB2:
T
613
A
PB2:
L
648
I
SigPep
SigPep:
T
3
A
SigPep:
Y
9
N
Deletions
N/A
Insertions
N/A
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