GenSpectrum
Influenza A/H5N1
Influenza A/H5N1
RSV-A
RSV B
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GS_001EJGP.1
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Display Name: GS_001EJGP.1/2024-11-07
Kirby,
M. K.; Steel,
J.; Garten,
R.; Davis,
T.; Dugan,
V.; Sheffield,
S.; Liddell,
J.; Frederick,
J. C.; Di,
H.; Radford,
K.; De La Cruz,
J.; Keong,
L.; Lacek,
K. A.; Shu,
B.; Schatzman,
S.; Nguyen,
H.; Molinar,
B.; Wright,
C.; Guevara,
H.; Pan,
C.-Y.; Morales,
C.; Wadford,
D.; Waswa,
B.; Eliamani,
...,
J.
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Submission details
Submission ID
PQ687559.1.seg3/PQ687558.1.seg4/PQ687561.1.seg5/PQ687556.1.seg6/PQ687557.1.seg7/PQ687560.1.seg8
Submitting group
Automated Ingest from INSDC/NCBI Virus by Loculus
Date submitted
2024-12-07 00:12:42 UTC
Date released
2024-12-07 00:13:20 UTC
Data use terms
Data use terms
OPEN
✕
Data Use Terms History
Changed
User
Data Use Terms
2024-12-07 00:12
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 seg3
PQ687559.1
INSDC accession seg4
PQ687558.1
INSDC accession seg5
PQ687561.1
INSDC accession seg6
PQ687556.1
INSDC accession seg7
PQ687557.1
INSDC accession seg8
PQ687560.1
NCBI release date
2024-12-06
Clade
Clade
2.3.4.4b
Alignment states and QC metrics seg3
Completeness seg3
98.79%
Length seg3
2208
Total ambiguous nucs seg3
2
Total deleted nucs seg3
0
Total frame shifts seg3
0
Total inserted nucs seg3
0
Total SNPs seg3
166
Total unknown nucs seg3
0
Alignment states and QC metrics seg4
Completeness seg4
97.61%
Length seg4
1715
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
184
Total unknown nucs seg5
0
Alignment states and QC metrics seg6
Completeness seg6
52.54%
Length seg6
766
Total ambiguous nucs seg6
0
Total deleted nucs seg6
0
Total frame shifts seg6
0
Total inserted nucs seg6
0
Total SNPs seg6
75
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
866
Total ambiguous nucs seg8
0
Total deleted nucs seg8
11
Total frame shifts seg8
0
Total inserted nucs seg8
12
Total SNPs seg8
218
Total unknown nucs seg8
0
Sample details
Collection country
USA
Collection subdivision level 1
California
Collection date
2024-11-07
Isolate name
EPI_ISL_19590704
Host
Host name scientific
Homo sapiens
Host taxon id
9606
Nucleotide mutations
Substitutions
seg3
seg3:
C
20
T
seg3:
G
81
A
seg3:
A
117
G
seg3:
G
120
A
seg3:
G
144
A
seg3:
T
168
C
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
226
T
seg3:
C
228
A
seg3:
G
249
A
seg3:
A
255
G
seg3:
G
270
A
Show more
seg4
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
seg4:
T
231
C
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
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seg6
seg6:
A
689
T
seg6:
C
690
T
seg6:
G
704
A
seg6:
A
716
T
seg6:
T
719
C
seg6:
T
731
C
seg6:
T
737
C
seg6:
T
740
C
seg6:
C
752
T
seg6:
T
761
C
seg6:
G
782
A
seg6:
A
791
G
seg6:
G
794
A
seg6:
A
797
G
seg6:
A
809
T
seg6:
T
812
C
seg6:
C
821
T
seg6:
T
825
A
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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
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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_seg8:865:C, ins_seg8:221:GAGG, ins_seg8:176:G, ins_seg8:79:TG
Amino acid mutations
Substitutions
HA
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:
V
147
M
HA:
S
149
A
HA:
R
156
A
HA:
S
157
P
HA:
S
171
D
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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:
M
258
I
NA:
L
269
M
NA:
E
287
D
NA:
T
289
M
NA:
V
321
I
NA:
G
336
S
NA:
V
338
M
NA:
S
339
P
NA:
P
340
S
NA:
N
366
S
NA:
G
382
E
NA:
A
395
E
NA:
I
418
M
NA:
S
434
N
NA:
D
460
G
NP
NP:
Y
52
H
NP:
V
105
M
NP:
I
119
V
NP:
M
136
L
NP:
A
353
V
NP:
Q
357
R
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:
P
68
S
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
Deletions
HA:344
Insertions
None
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