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Influenza A/H5N1
Influenza B/Victoria
Influenza A/H1N1pdm
Influenza A/H3N2
Influenza A/H5N1
Influenza A
Influenza B
RSV-A
RSV B
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GS_0029NMH.1
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Display Name: USA/GS_0029NMH.1/2025-02-11
Kirby,
M. K.; Garten,
R.; Davis,
T.; Dugan,
V.; Sheffield,
S.; Liddell,
J.; Frederick,
J. C.; Di,
H.; Wilson,
M.; De La Cruz,
J.; Keong,
L.; Lacek,
K. A.; Shu,
B.; Schatzman,
S.; Nguyen,
H.; Matzinger,
S.; Rossheim,
A.; Donaghy,
D.; Cassidy,
F.; Wellbrock,
A.; Owen,
M.; Aragon,
D.
Submission details
Submission ID
PV177837.1.seg1/PV177835.1.seg2/PV177839.1.seg3/PV177834.1.seg4/PV177841.1.seg5/PV177836.1.seg6/PV177838.1.seg7/PV177840.1.seg8
Submitting group
Automated Ingest from INSDC/NCBI Virus by Loculus
Date submitted
2025-03-05 13:13:12 UTC
Date released
2025-03-05 14:09:01 UTC
Authors
Author affiliations
Centers for Disease Control and Prevention, Influenza Division
INSDC
Bioproject accession
PRJNA1095491
INSDC accession seg1
PV177837.1
INSDC accession seg2
PV177835.1
INSDC accession seg3
PV177839.1
INSDC accession seg4
PV177834.1
INSDC accession seg5
PV177841.1
INSDC accession seg6
PV177836.1
INSDC accession seg7
PV177838.1
INSDC accession seg8
PV177840.1
NCBI release date
2025-02-26
Clade
Clade
2.3.4.4b
Alignment states and QC metrics seg1
Completeness seg1
70.23%
Length seg1
2316
Total ambiguous nucs seg1
1
Total deleted nucs seg1
0
Total frame shifts seg1
0
Total inserted nucs seg1
0
Total SNPs seg1
257
Total unknown nucs seg1
671
Alignment states and QC metrics seg2
Completeness seg2
55.32%
Length seg2
2316
Total ambiguous nucs seg2
0
Total deleted nucs seg2
0
Total frame shifts seg2
0
Total inserted nucs seg2
0
Total SNPs seg2
123
Total unknown nucs seg2
1021
Alignment states and QC metrics seg3
Completeness seg3
50.11%
Length seg3
2208
Total ambiguous nucs seg3
0
Total deleted nucs seg3
0
Total frame shifts seg3
0
Total inserted nucs seg3
0
Total SNPs seg3
118
Total unknown nucs seg3
1089
Alignment states and QC metrics seg4
Completeness seg4
99.55%
Length seg4
1749
Total ambiguous nucs seg4
0
Total deleted nucs seg4
3
Total frame shifts seg4
0
Total inserted nucs seg4
0
Total SNPs seg4
175
Total unknown nucs seg4
0
Alignment states and QC metrics seg5
Completeness seg5
98.40%
Length seg5
1540
Total ambiguous nucs seg5
0
Total deleted nucs seg5
0
Total frame shifts seg5
0
Total inserted nucs seg5
0
Total SNPs seg5
174
Total unknown nucs seg5
0
Alignment states and QC metrics seg6
Completeness seg6
97.67%
Length seg6
1425
Total ambiguous nucs seg6
0
Total deleted nucs seg6
0
Total frame shifts seg6
0
Total inserted nucs seg6
1
Total SNPs seg6
214
Total unknown nucs seg6
0
Alignment states and QC metrics seg7
Completeness seg7
97.57%
Length seg7
1002
Total ambiguous nucs seg7
0
Total deleted nucs seg7
0
Total frame shifts seg7
0
Total inserted nucs seg7
0
Total SNPs seg7
60
Total unknown nucs seg7
0
Alignment states and QC metrics seg8
Completeness seg8
100.00%
Frame shifts seg8
NS1:23-26(nt:80-92)
Length seg8
865
Total ambiguous nucs seg8
0
Total deleted nucs seg8
2
Total frame shifts seg8
1
Total inserted nucs seg8
2
Total SNPs seg8
246
Total unknown nucs seg8
0
Sample details
Collection country
USA
Collection subdivision level 1
Colorado
Collection date
2025-02-11
Isolate name
EPI_ISL_19749443
Host
Host name scientific
Homo sapiens
Host taxon id
9606
INSDC seg4
Subtype seg4
H5
INSDC seg6
Subtype seg6
N1
Nucleotide mutations
Mutations called relative to the
NC_007357.1
,
NC_007358.1
,
NC_007359.1
,
NC_007362.1
,
NC_007360.1
,
NC_007361.1
,
NC_007363.1
&
NC_007364.1
references
Substitutions
seg1
seg1:
T
17
A
seg1:
A
33
G
seg1:
A
48
G
seg1:
G
63
A
seg1:
C
69
T
seg1:
A
90
C
seg1:
G
102
T
seg1:
T
105
C
seg1:
T
108
C
seg1:
A
126
G
seg1:
A
141
G
seg1:
G
147
A
seg1:
T
159
A
seg1:
A
165
G
seg1:
T
192
C
seg1:
A
211
C
seg1:
G
222
A
seg1:
T
228
C
Show more
seg2
seg2:
A
70
G
seg2:
T
75
C
seg2:
T
96
C
seg2:
A
129
G
seg2:
C
141
A
seg2:
T
171
C
seg2:
A
177
G
seg2:
G
183
A
seg2:
G
195
A
seg2:
G
204
A
seg2:
T
207
C
seg2:
C
216
T
seg2:
T
225
C
seg2:
G
228
A
seg2:
A
237
G
seg2:
T
252
C
seg2:
T
255
C
seg2:
G
258
A
Show more
seg3
seg3:
T
63
C
seg3:
C
114
T
seg3:
G
120
T
seg3:
A
126
G
seg3:
T
129
C
seg3:
C
132
T
seg3:
G
144
T
seg3:
C
147
T
seg3:
A
150
G
seg3:
A
171
G
seg3:
C
180
T
seg3:
T
183
C
seg3:
C
206
T
seg3:
A
211
G
seg3:
A
213
G
seg3:
C
228
A
seg3:
T
235
C
seg3:
T
238
C
Show more
seg4
seg4:
A
9
T
seg4:
T
10
C
seg4:
A
12
C
seg4:
C
14
T
seg4:
A
30
C
seg4:
G
52
A
seg4:
C
54
T
seg4:
T
57
C
seg4:
C
63
T
seg4:
C
102
T
seg4:
A
123
G
seg4:
T
141
C
seg4:
T
144
C
seg4:
G
174
A
seg4:
A
175
G
seg4:
T
183
C
seg4:
C
195
T
seg4:
A
207
G
Show more
seg5
seg5:
A
40
C
seg5:
G
57
A
seg5:
T
72
C
seg5:
G
81
A
seg5:
A
96
G
seg5:
T
111
C
seg5:
G
117
A
seg5:
T
147
C
seg5:
T
153
C
seg5:
G
159
A
seg5:
T
162
C
seg5:
T
165
C
seg5:
A
183
G
seg5:
C
195
T
seg5:
C
198
T
seg5:
T
201
C
seg5:
A
207
G
seg5:
T
216
C
Show more
seg6
seg6:
G
35
A
seg6:
T
43
C
seg6:
C
47
T
seg6:
T
50
C
seg6:
A
53
G
seg6:
T
62
C
seg6:
G
69
A
seg6:
G
74
A
seg6:
T
80
A
seg6:
C
83
T
seg6:
T
84
C
seg6:
A
87
G
seg6:
T
90
C
seg6:
G
101
A
seg6:
C
122
T
seg6:
G
137
A
seg6:
A
140
T
seg6:
G
143
A
Show more
seg7
seg7:
A
25
G
seg7:
A
76
G
seg7:
G
112
A
seg7:
C
142
T
seg7:
A
196
G
seg7:
A
205
G
seg7:
G
268
A
seg7:
C
274
T
seg7:
T
275
C
seg7:
T
292
C
seg7:
T
301
C
seg7:
T
307
C
seg7:
T
316
C
seg7:
G
319
A
seg7:
A
322
G
seg7:
A
327
G
seg7:
G
331
A
seg7:
C
332
T
Show more
seg8
seg8:
G
9
A
seg8:
G
29
T
seg8:
A
30
G
seg8:
A
32
G
seg8:
A
33
T
seg8:
C
35
A
seg8:
T
36
A
seg8:
C
37
G
seg8:
G
38
C
seg8:
T
50
C
seg8:
T
53
C
seg8:
A
55
T
seg8:
A
59
T
seg8:
C
65
T
seg8:
A
66
G
seg8:
A
68
C
seg8:
A
69
C
seg8:
A
71
C
Show more
Deletions
seg4:1054-1056, seg8:90, seg8:93
Insertions
ins_seg8:79:TG, ins_seg6:17:T
Amino acid mutations
Mutations called relative to the
NC_007357.1
,
NC_007358.1
,
NC_007359.1
,
NC_007362.1
,
NC_007360.1
,
NC_007361.1
,
NC_007363.1
&
NC_007364.1
references
Substitutions
HA
HA:
K
3
N
HA:
V
11
I
HA:
T
52
A
HA:
R
69
K
HA:
N
88
R
HA:
K
98
R
HA:
S
100
N
HA:
D
110
S
HA:
F
111
L
HA:
T
124
I
HA:
Q
131
L
HA:
S
139
P
HA:
D
142
E
HA:
A
143
T
HA:
S
145
L
HA:
S
149
A
HA:
H
154
Q
HA:
R
156
A
Show more
M1
M1:
K
101
R
M1:
T
140
A
M1:
F
144
L
M1:
M
165
I
M1:
K
230
R
M1:
N
232
D
M1:
K
242
N
M1:
M
248
L
M2
M2:
N
13
T
M2:
E
14
G
M2:
K
18
N
M2:
V
28
I
M2:
I
51
V
M2:
R
61
S
NA
NA:
I
8
T
NA:
V
17
I
NA:
M
23
V
NA:
H
44
N
NA:
Q
45
H
NA:
A
46
P
NA:
P
48
T
NA:
I
53
V
NA:
V
62
M
NA:
V
67
I
NA:
F
74
L
NA:
L
75
I
NA:
T
76
A
NA:
K
78
Q
NA:
A
81
D
NA:
S
82
P
NA:
T
84
A
NA:
V
99
I
Show more
NP
NP:
V
105
M
NP:
M
136
L
NP:
A
353
V
NP:
S
450
N
NP:
S
451
A
NS1
NS1:
I
6
V
NS1:
T
7
S
NS1:
Y
14
F
NS1:
I
18
V
NS1:
L
21
R
NS1:
L
22
F
NS1:
C
28
G
NS1:
D
33
L
NS1:
A
42
S
NS1:
K
44
R
NS1:
L
54
I
NS1:
R
55
E
NS1:
V
56
T
NS1:
M
59
R
NS1:
E
60
A
NS1:
K
63
Q
NS1:
D
67
R
NS1:
K
70
E
Show more
NS2
NS2:
I
6
V
NS2:
T
7
S
NS2:
Q
14
M
NS2:
E
22
G
NS2:
V
26
E
NS2:
E
36
K
NS2:
R
37
S
NS2:
I
40
L
NS2:
S
48
A
NS2:
M
49
V
NS2:
N
60
S
NS2:
A
63
E
NS2:
T
64
K
NS2:
N
67
G
NS2:
E
68
Q
NS2:
A
81
E
NS2:
C
83
V
NS2:
N
85
H
Show more
PA
PA:
T
61
I
PA:
I
63
V
PA:
L
504
I
PA:
R
536
K
PA:
R
544
E
PA:
I
545
V
PA:
E
553
A
PA:
P
585
L
PA:
F
586
L
PA:
K
626
R
PA:
R
716
K
PAX
PAX:
T
61
I
PAX:
I
63
V
PB1
PB1:
N
16
D
PB1:
E
96
D
PB1:
T
478
S
PB1:
C
490
F
PB1:
M
535
I
PB1:
D
536
N
PB1:
P
558
T
PB1:
P
598
L
PB1:
A
609
V
PB1:
G
610
C
PB1:
E
614
D
PB1:
N
694
S
PB1:
G
754
R
PB1:
*
758
Y
PB2
PB2:
K
340
R
PB2:
K
355
R
PB2:
A
471
T
PB2:
V
478
I
PB2:
Q
508
R
PB2:
S
579
P
PB2:
S
590
G
PB2:
E
627
K
PB2:
P
628
Q
PB2:
R
699
K
PB2:
M
727
G
PB2:
F
741
S
Deletions
HA:344, NS1:27
Insertions
None
Load sequences