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Influenza A/H5N1
Influenza A/H5N1
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GS_001E9GY.1
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Display Name: GS_001E9GY.1/2024-10-18
Kirby,
M. K.; Steel,
J.; Garten,
R.; Davis,
T.; Dugan,
V.; DaSilva,
J.; Liddell,
J.; Frederick,
J. C.; Di,
H.; Sheffield,
S.; Radford,
K.; De La Cruz,
J.; Keong,
L.; Lacek,
K. A.; Shu,
B.; Lopez,
D.; Seliskar,
L.; Le,
H.; Cadiz,
V.; Hua,
C.; Hok,
S.; Millena,
S.
Submission details
Submission ID
PQ524077.1.seg1/PQ524076.1.seg2/PQ524075.1.seg3/PQ524079.1.seg4/PQ524078.1.seg5/PQ524082.1.seg6/PQ524081.1.seg7/PQ524080.1.seg8
Submitting group
Automated Ingest from INSDC/NCBI Virus by Loculus
Date submitted
2024-12-11 16:47:38 UTC
Date released
2024-12-11 17:24:58 UTC
Data use terms
Data use terms
OPEN
✕
Data Use Terms History
Changed
User
Data Use Terms
2024-12-11 16:48
insdc_ingest_user
OPEN
Close
(history)
Authors
Author affiliations
Centers for Disease Control and Prevention, WHO Collaborating Center for Surveillance, Epidemiology and Control of Influenza, Influenza Division
INSDC
Bioproject accession
PRJNA1095491
INSDC accession seg1
PQ524077.1
INSDC accession seg2
PQ524076.1
INSDC accession seg3
PQ524075.1
INSDC accession seg4
PQ524079.1
INSDC accession seg5
PQ524078.1
INSDC accession seg6
PQ524082.1
INSDC accession seg7
PQ524081.1
INSDC accession seg8
PQ524080.1
NCBI release date
2024-10-28
Clade
Clade
2.3.4.4b
Alignment states and QC metrics seg1
Completeness seg1
98.93%
Length seg1
2316
Total ambiguous nucs seg1
0
Total deleted nucs seg1
0
Total frame shifts seg1
0
Total inserted nucs seg1
0
Total SNPs seg1
366
Total unknown nucs seg1
0
Alignment states and QC metrics seg2
Completeness seg2
98.93%
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
270
Total unknown nucs seg2
0
Alignment states and QC metrics seg3
Completeness seg3
98.88%
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
164
Total unknown nucs seg3
0
Alignment states and QC metrics seg4
Completeness seg4
98.64%
Length seg4
1733
Total ambiguous nucs seg4
0
Total deleted nucs seg4
3
Total frame shifts seg4
0
Total inserted nucs seg4
0
Total SNPs seg4
188
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
183
Total unknown nucs seg5
0
Alignment states and QC metrics seg6
Completeness seg6
98.29%
Length seg6
1433
Total ambiguous nucs seg6
0
Total deleted nucs seg6
0
Total frame shifts seg6
0
Total inserted nucs seg6
0
Total SNPs seg6
152
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
64
Total unknown nucs seg7
0
Alignment states and QC metrics seg8
Completeness seg8
100.00%
Length seg8
865
Total ambiguous nucs seg8
0
Total deleted nucs seg8
11
Total frame shifts seg8
0
Total inserted nucs seg8
11
Total SNPs seg8
217
Total unknown nucs seg8
0
Sample details
Collection country
USA
Collection subdivision level 1
California
Collection date
2024-10-18
Isolate name
EPI_ISL_19512044
Host
Host name scientific
Homo sapiens
Host taxon id
9606
Nucleotide mutations
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:
G
147
A
seg1:
T
159
A
seg1:
A
211
C
seg1:
G
222
A
seg1:
T
228
C
seg1:
G
243
A
seg1:
G
255
C
seg1:
T
258
C
Show more
seg2
seg2:
T
42
C
seg2:
T
48
C
seg2:
A
54
G
seg2:
G
60
T
seg2:
T
75
C
seg2:
T
81
C
seg2:
T
93
G
seg2:
C
138
T
seg2:
C
153
T
seg2:
G
180
A
seg2:
G
195
A
seg2:
A
199
T
seg2:
G
204
A
seg2:
T
207
C
seg2:
A
210
G
seg2:
C
216
T
seg2:
G
228
A
seg2:
C
241
T
Show more
seg3
seg3:
C
20
T
seg3:
A
22
C
seg3:
G
81
A
seg3:
A
117
G
seg3:
G
120
A
seg3:
G
144
A
seg3:
A
171
G
seg3:
C
180
T
seg3:
T
189
C
seg3:
G
195
A
seg3:
C
206
T
seg3:
A
207
G
seg3:
A
211
G
seg3:
C
228
A
seg3:
G
249
A
seg3:
A
255
G
seg3:
G
270
A
seg3:
A
277
G
Show more
seg4
seg4:
A
30
C
seg4:
C
54
T
seg4:
T
57
C
seg4:
C
63
T
seg4:
C
102
T
seg4:
G
114
A
seg4:
A
123
G
seg4:
T
141
C
seg4:
G
174
A
seg4:
T
183
C
seg4:
C
192
A
seg4:
T
198
C
seg4:
A
207
G
seg4:
T
216
A
seg4:
C
219
G
seg4:
G
225
A
seg4:
G
227
A
seg4:
A
228
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
199
C
seg5:
T
201
C
seg5:
A
207
G
Show more
seg6
seg6:
A
15
T
seg6:
T
17
C
seg6:
G
35
A
seg6:
T
43
C
seg6:
G
69
A
seg6:
A
78
G
seg6:
T
80
C
seg6:
T
90
C
seg6:
A
92
G
seg6:
C
122
T
seg6:
T
125
C
seg6:
T
134
C
seg6:
G
137
A
seg6:
C
150
T
seg6:
A
155
G
seg6:
G
156
C
seg6:
T
179
C
seg6:
T
185
C
Show more
seg7
seg7:
A
25
G
seg7:
A
76
G
seg7:
G
112
A
seg7:
A
127
G
seg7:
C
142
T
seg7:
A
196
G
seg7:
A
205
G
seg7:
G
268
A
seg7:
T
275
C
seg7:
A
279
G
seg7:
A
285
C
seg7:
T
292
C
seg7:
T
301
C
seg7:
T
307
C
seg7:
G
310
A
seg7:
T
316
C
seg7:
C
320
T
seg7:
A
322
G
Show more
seg8
seg8:
G
9
A
seg8:
A
30
T
seg8:
C
34
G
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
seg8:
G
74
A
seg8:
T
76
G
seg8:
C
78
T
seg8:
T
83
A
seg8:
A
84
C
seg8:
T
85
C
Show more
Deletions
seg4:1054-1056, seg8:36-38, seg8:90, seg8:93, seg8:181, seg8:239-242, seg8:494
Insertions
ins_seg8:28:TGT, ins_seg8:510:C, ins_seg8:221:GAGG, ins_seg8:176:G, ins_seg8:79:TG
Amino acid mutations
Substitutions
HA
HA:
K
3
N
HA:
R
69
K
HA:
N
88
R
HA:
K
98
R
HA:
S
100
N
HA:
D
104
G
HA:
D
110
S
HA:
F
111
L
HA:
L
120
M
HA:
T
124
I
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
HA:
S
157
P
Show more
M2
M2:
E
14
G
M2:
K
18
N
M2:
V
28
I
M2:
I
51
V
M2:
R
61
G
M2:
D
88
N
NA
NA:
I
8
T
NA:
V
17
I
NA:
I
20
V
NA:
H
44
Y
NA:
A
46
P
NA:
V
67
I
NA:
N
71
S
NA:
T
76
A
NA:
K
78
Q
NA:
A
81
T
NA:
T
84
A
NA:
V
99
I
NA:
H
100
Y
NA:
H
155
Y
NA:
T
188
I
NA:
M
258
I
NA:
L
269
M
NA:
E
287
D
Show more
NP
NP:
Y
52
H
NP:
V
105
M
NP:
I
119
V
NP:
M
136
L
NP:
A
353
V
NP:
S
450
N
NP:
S
451
A
NP:
S
482
N
NS2
NS2:
I
6
V
NS2:
T
7
L
NS2:
Q
14
M
NS2:
E
22
G
NS2:
V
26
E
NS2:
R
37
S
NS2:
I
40
L
NS2:
S
48
A
NS2:
M
49
V
NS2:
N
60
S
NS2:
A
63
G
NS2:
T
64
K
NS2:
N
67
G
NS2:
E
68
Q
NS2:
A
81
E
NS2:
C
83
V
NS2:
N
85
H
NS2:
I
86
R
Show more
PAX
PAX:
T
61
M
PAX:
I
63
V
PAX:
T
85
A
PAX:
K
113
R
PAX:
T
129
I
PAX:
S
193
N
PAX:
G
209
E
PAX:
L
210
P
PAX:
S
219
F
PAX:
L
221
R
PAX:
I
222
T
PAX:
N
228
T
PAX:
R
250
Q
PAX:
K
252
R
PB1
PB1:
T
59
S
PB1:
E
75
D
PB1:
K
134
N
PB1:
M
171
V
PB1:
G
177
E
PB1:
M
179
I
PB1:
I
182
T
PB1:
R
430
K
PB1:
E
460
Q
PB1:
T
478
S
PB1:
C
490
F
PB1:
M
535
I
PB1:
D
536
N
PB1:
P
558
T
PB1:
A
587
P
PB1:
P
598
L
PB1:
A
609
V
PB1:
G
610
C
PB1:
G
754
R
PB2
PB2:
V
109
I
PB2:
V
139
I
PB2:
N
334
S
PB2:
K
340
R
PB2:
K
355
R
PB2:
E
362
G
PB2:
D
441
N
PB2:
A
471
T
PB2:
V
478
I
PB2:
V
495
I
PB2:
Q
508
R
PB2:
I
562
V
PB2:
S
579
P
PB2:
S
590
G
PB2:
P
628
Q
PB2:
M
631
L
PB2:
V
649
I
PB2:
K
670
R
Show more
Deletions
HA:344
Insertions
None
Load sequences