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Influenza A/H3N2
Influenza B/Victoria
Dengue 1
Dengue 2
Dengue 3
Dengue 4
Influenza A/H1N1pdm
Influenza A/H3N2
Influenza A/H5N1
Influenza A
Influenza B
RSV-A
RSV B
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GS_00G4CLR.1
Download
Download FASTA
Download metadata TSV
Display Name: USA/GS_00G4CLR.1/2025-06-23
Direct Submission
Submission details
Submission ID
PX400166.1.seg1/PX400162.1.seg2/PX400164.1.seg3/PX400161.1.seg4/PX400163.1.seg5/PX400165.1.seg6/PX400160.1.seg7/PX400167.1.seg8
Submitting group
Automated Ingest from INSDC/NCBI Virus by Loculus
Date submitted
2025-09-22 21:24:33 UTC
Date released
2025-09-22 21:38:46 UTC
Authors
Author affiliations
Center for Research on Influenza Pathogenesis (CRIP), CEIRS Data Processing and Coordinating Center
INSDC
Bioproject accession
PRJNA470648
INSDC accession seg1
PX400166.1
INSDC accession seg2
PX400162.1
INSDC accession seg3
PX400164.1
INSDC accession seg4
PX400161.1
INSDC accession seg5
PX400163.1
INSDC accession seg6
PX400165.1
INSDC accession seg7
PX400160.1
INSDC accession seg8
PX400167.1
NCBI release date
2025-09-22
Clade
Clade HA
3C.2a1b.2a.2a.3a.1
Clade NA
B.4.2
Alignment states and QC metrics seg1
Completeness seg1
100.00%
Length seg1
2341
Total ambiguous nucs seg1
0
Total deleted nucs seg1
0
Total frame shifts seg1
0
Total inserted nucs seg1
0
Total SNPs seg1
97
Total unknown nucs seg1
0
Alignment states and QC metrics seg2
Completeness seg2
100.00%
Length seg2
2341
Total ambiguous nucs seg2
0
Total deleted nucs seg2
0
Total frame shifts seg2
0
Total inserted nucs seg2
0
Total SNPs seg2
113
Total unknown nucs seg2
0
Alignment states and QC metrics seg3
Completeness seg3
100.00%
Length seg3
2233
Total ambiguous nucs seg3
0
Total deleted nucs seg3
0
Total frame shifts seg3
0
Total inserted nucs seg3
0
Total SNPs seg3
85
Total unknown nucs seg3
0
Alignment states and QC metrics seg4
Completeness seg4
100.00%
Length seg4
1762
Total ambiguous nucs seg4
0
Total deleted nucs seg4
0
Total frame shifts seg4
0
Total inserted nucs seg4
25
Total SNPs seg4
117
Total unknown nucs seg4
0
Alignment states and QC metrics seg5
Completeness seg5
100.00%
Length seg5
1565
Total ambiguous nucs seg5
0
Total deleted nucs seg5
1
Total frame shifts seg5
0
Total inserted nucs seg5
0
Total SNPs seg5
54
Total unknown nucs seg5
0
Alignment states and QC metrics seg6
Completeness seg6
100.00%
Length seg6
1466
Total ambiguous nucs seg6
0
Total deleted nucs seg6
0
Total frame shifts seg6
0
Total inserted nucs seg6
30
Total SNPs seg6
80
Total unknown nucs seg6
0
Alignment states and QC metrics seg7
Completeness seg7
100.00%
Length seg7
1027
Total ambiguous nucs seg7
0
Total deleted nucs seg7
0
Total frame shifts seg7
0
Total inserted nucs seg7
0
Total SNPs seg7
26
Total unknown nucs seg7
0
Alignment states and QC metrics seg8
Completeness seg8
100.00%
Length seg8
890
Total ambiguous nucs seg8
0
Total deleted nucs seg8
0
Total frame shifts seg8
0
Total inserted nucs seg8
0
Total SNPs seg8
27
Total unknown nucs seg8
0
Sample details
Collection country
USA
Collection date
2025-06-23
Isolate name
A/New York City/PX22305/2025
Host
Host name scientific
Homo sapiens
Host taxon id
9606
INSDC seg4
Subtype seg4
H3
INSDC seg6
Subtype seg6
N2
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
seg1:
T
27
C
seg1:
C
54
T
seg1:
G
57
A
seg1:
T
75
C
seg1:
C
192
T
seg1:
C
198
T
seg1:
T
255
C
seg1:
A
282
G
seg1:
C
289
A
seg1:
A
330
G
seg1:
A
336
G
seg1:
G
343
A
seg1:
G
347
A
seg1:
A
369
G
seg1:
G
375
A
seg1:
A
402
G
seg1:
T
426
C
seg1:
T
438
C
Show more
seg2
seg2:
C
46
T
seg2:
G
57
A
seg2:
C
84
A
seg2:
A
129
G
seg2:
A
132
T
seg2:
A
135
G
seg2:
C
141
T
seg2:
T
171
C
seg2:
A
179
G
seg2:
G
180
A
seg2:
A
213
T
seg2:
A
219
G
seg2:
G
249
A
seg2:
G
258
A
seg2:
C
288
T
seg2:
T
297
C
seg2:
C
306
T
seg2:
G
336
A
Show more
seg3
seg3:
G
22
A
seg3:
A
99
G
seg3:
A
120
C
seg3:
C
144
T
seg3:
A
156
G
seg3:
T
177
C
seg3:
T
222
C
seg3:
G
243
A
seg3:
A
324
T
seg3:
A
333
G
seg3:
C
340
T
seg3:
A
342
G
seg3:
A
345
G
seg3:
G
363
A
seg3:
T
369
C
seg3:
A
396
G
seg3:
A
435
G
seg3:
C
450
A
Show more
seg4
seg4:
A
24
G
seg4:
T
42
A
seg4:
G
56
T
seg4:
C
72
A
seg4:
T
74
A
seg4:
C
77
T
seg4:
C
89
T
seg4:
G
155
A
seg4:
A
163
G
seg4:
C
189
T
seg4:
G
192
A
seg4:
G
199
A
seg4:
C
203
A
seg4:
C
208
T
seg4:
G
213
A
seg4:
G
214
A
seg4:
G
222
A
seg4:
G
226
A
Show more
seg5
seg5:
A
16
G
seg5:
C
29
T
seg5:
A
40
C
seg5:
G
96
A
seg5:
C
162
T
seg5:
G
207
A
seg5:
G
219
A
seg5:
C
249
T
seg5:
T
255
C
seg5:
A
345
C
seg5:
A
351
G
seg5:
G
390
A
seg5:
G
432
T
seg5:
G
436
T
seg5:
T
447
C
seg5:
A
451
C
seg5:
C
459
T
seg5:
G
492
A
Show more
seg6
seg6:
T
15
C
seg6:
C
51
A
seg6:
A
60
G
seg6:
A
73
T
seg6:
T
88
C
seg6:
C
144
T
seg6:
A
177
T
seg6:
C
205
T
seg6:
T
245
C
seg6:
G
270
A
seg6:
A
280
G
seg6:
A
281
G
seg6:
T
303
C
seg6:
C
345
A
seg6:
C
380
T
seg6:
G
408
A
seg6:
C
429
T
seg6:
G
442
A
Show more
seg7
seg7:
A
37
T
seg7:
G
100
A
seg7:
C
188
T
seg7:
G
205
A
seg7:
G
214
T
seg7:
A
241
G
seg7:
T
292
C
seg7:
T
298
C
seg7:
G
427
A
seg7:
A
466
G
seg7:
A
481
G
seg7:
C
493
T
seg7:
A
517
G
seg7:
A
637
G
seg7:
A
658
G
seg7:
G
680
A
seg7:
C
697
T
seg7:
T
703
C
Show more
seg8
seg8:
C
53
T
seg8:
G
102
A
seg8:
A
104
C
seg8:
C
116
T
seg8:
C
123
A
seg8:
T
125
C
seg8:
G
192
T
seg8:
T
205
C
seg8:
T
218
C
seg8:
A
238
G
seg8:
T
271
C
seg8:
C
275
G
seg8:
T
311
C
seg8:
G
398
A
seg8:
G
416
A
seg8:
G
430
A
seg8:
A
442
G
seg8:
A
464
G
Show more
Deletions
seg5:1545
Insertions
ins_seg4:0:AGCAAAAGCAGG, ins_seg4:1737:CCTTGTTTCTACT, ins_seg6:0:AGCAAAAGCAGGAGTA, ins_seg6:1436:TCCTTGTTTCTACT
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:
L
3
I
HA1:
Q
33
R
HA1:
V
43
I
HA1:
S
45
N
HA1:
T
48
I
HA1:
G
50
K
HA1:
D
53
N
HA1:
S
54
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
A
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:
I
32
V
M2:
L
54
F
M2:
N
82
S
NA
NA:
M
24
L
NA:
L
81
P
NA:
N
93
G
NA:
P
126
L
NA:
D
147
N
NA:
V
194
I
NA:
I
215
V
NA:
K
220
N
NA:
E
221
D
NA:
S
245
N
NA:
S
247
T
NA:
I
262
V
NA:
T
267
K
NA:
L
285
P
NA:
V
303
I
NA:
Y
310
R
NA:
S
315
R
NA:
N
329
S
Show more
NP
NP:
A
131
S
NP:
I
136
L
NP:
V
197
I
NP:
R
236
K
NP:
T
472
A
NS1
NS1:
E
26
N
NS1:
L
33
I
NS1:
A
56
S
NS1:
V
60
A
NS1:
E
71
G
NS1:
V
82
A
NS1:
M
124
I
NS1:
S
135
N
NS1:
D
139
G
NS1:
I
171
V
NS1:
K
221
E
NS1:
K
229
E
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:
M
171
I
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:
R
44
K
PB1-F2:
S
47
N
PB1-F2:
S
57
F
PB1-F2:
L
60
P
PB1-F2:
S
63
F
PB1-F2:
R
73
K
PB1-F2:
H
75
P
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:
T
292
A
PB2:
K
340
R
PB2:
K
353
R
PB2:
I
588
T
PB2:
T
613
A
SigPep
SigPep:
T
3
A
SigPep:
Y
9
N
Deletions
None
Insertions
None
Load sequences