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Influenza A/H1N1pdm
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RSV-A
RSV B
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GS_00DCQ8R.1
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Display Name: USA/GS_00DCQ8R.1/2025-03-18
Rothstein,
A. P.; Collins,
S.; Muir,
G.; Simas,
A.; Lu,
B.; Cosca,
B.; Girinathan,
B.; Leeson,
P.; Philipson,
C. W.; Plocik,
A. M.; Simen,
B.
Submission details
Submission ID
PV543857.1.seg2/PV543856.1.seg3/PV543853.1.seg4/PV543854.1.seg5/PV543855.1.seg8
Submitting group
Automated Ingest from INSDC/NCBI Virus by Loculus
Date submitted
2025-04-18 21:10:37 UTC
Date released
2025-04-18 21:10:49 UTC
Authors
Author affiliations
Ginkgo Bioworks, Ginkgo Biosecurity
Clade
Clade HA
V1A.3a.2
Alignment states and QC metrics seg3
Completeness seg3
100.00%
Length seg3
2291
Total ambiguous nucs seg3
0
Total deleted nucs seg3
0
Total frame shifts seg3
0
Total inserted nucs seg3
46
Total SNPs seg3
44
Total unknown nucs seg3
0
Alignment states and QC metrics seg4
Completeness seg4
99.20%
Length seg4
1861
Total ambiguous nucs seg4
0
Total deleted nucs seg4
9
Total frame shifts seg4
0
Total inserted nucs seg4
0
Total SNPs seg4
53
Total unknown nucs seg4
0
Alignment states and QC metrics seg5
Completeness seg5
100.00%
Length seg5
1817
Total ambiguous nucs seg5
0
Total deleted nucs seg5
0
Total frame shifts seg5
0
Total inserted nucs seg5
67
Total SNPs seg5
34
Total unknown nucs seg5
0
Alignment states and QC metrics seg8
Completeness seg8
99.62%
Length seg8
1066
Total ambiguous nucs seg8
0
Total deleted nucs seg8
0
Total frame shifts seg8
0
Total inserted nucs seg8
4
Total SNPs seg8
21
Total unknown nucs seg8
0
Sample details
Collection country
USA
Collection subdivision level 1
New York
Collection date
2025-03-18
Isolate name
GKISBBBE29444
Host
Host name scientific
Homo sapiens
Host taxon id
9606
INSDC
INSDC accession seg2
PV543857.1
INSDC accession seg3
PV543856.1
INSDC accession seg4
PV543853.1
INSDC accession seg5
PV543854.1
INSDC accession seg8
PV543855.1
NCBI release date
2025-04-18
Alignment states and QC metrics seg2
Length seg2
2376
INSDC seg4
Lineage seg4
vic
Nucleotide mutations
Mutations called relative to the
CY115157.1
,
CY115158.1
,
CY115156.1
,
KX058884.1
,
CY115154.1
,
CY073894.1
,
CY115152.1
&
CY115155.1
references
Substitutions
seg3
seg3:
T
111
C
seg3:
C
117
T
seg3:
T
339
C
seg3:
G
414
A
seg3:
T
423
C
seg3:
C
426
T
seg3:
G
549
A
seg3:
T
606
C
seg3:
A
618
G
seg3:
T
654
C
seg3:
A
771
G
seg3:
C
813
T
seg3:
G
867
A
seg3:
C
897
T
seg3:
A
935
G
seg3:
G
936
A
seg3:
C
1006
T
seg3:
A
1054
G
Show more
seg4
seg4:
C
252
A
seg4:
G
267
A
seg4:
C
270
T
seg4:
G
297
A
seg4:
G
312
T
seg4:
A
318
G
seg4:
A
351
G
seg4:
C
375
T
seg4:
C
378
T
seg4:
A
427
G
seg4:
A
438
G
seg4:
C
441
T
seg4:
T
444
C
seg4:
G
457
A
seg4:
G
460
A
seg4:
A
463
G
seg4:
A
484
G
seg4:
C
509
T
Show more
seg5
seg5:
C
3
T
seg5:
T
46
C
seg5:
C
178
T
seg5:
A
224
G
seg5:
A
228
C
seg5:
A
235
G
seg5:
T
298
C
seg5:
C
313
T
seg5:
G
361
A
seg5:
A
373
G
seg5:
C
380
T
seg5:
G
412
A
seg5:
A
454
G
seg5:
C
523
T
seg5:
A
553
G
seg5:
C
608
T
seg5:
A
634
G
seg5:
A
763
G
Show more
seg8
seg8:
G
6
A
seg8:
G
26
A
seg8:
A
118
G
seg8:
C
160
T
seg8:
T
163
C
seg8:
G
190
A
seg8:
T
341
C
seg8:
A
352
C
seg8:
T
391
C
seg8:
C
419
T
seg8:
G
478
A
seg8:
C
604
T
seg8:
A
610
T
seg8:
C
632
T
seg8:
G
661
A
seg8:
C
666
T
seg8:
T
775
C
seg8:
G
818
A
Show more
Deletions
seg4:562-570
Insertions
ins_seg8:1066:TAAA, ins_seg5:0:GCATTTTCTTGTAAACTCCA, ins_seg5:1750:CATTTGGAATATGGGTGTTTATTCTCATTAAAATAAATATAAAAAAT, ins_seg3:2241:AGAAAC, ins_seg3:2245:ATCAAAAATGCTCGTGTTTCTAC, ins_seg3:0:GCGTTTGATTTATCATA
Amino acid mutations
Mutations called relative to the
CY115157.1
,
CY115158.1
,
CY115156.1
,
KX058884.1
,
CY115154.1
,
CY073894.1
,
CY115152.1
&
CY115155.1
references
Substitutions
HA1
HA1:
I
117
V
HA1:
A
127
T
HA1:
E
128
K
HA1:
N
129
D
HA1:
K
136
E
HA1:
P
144
L
HA1:
N
150
K
HA1:
A
154
T
HA1:
E
183
K
HA1:
G
184
E
HA1:
N
197
E
HA1:
A
199
T
HA1:
A
202
V
HA1:
K
203
R
HA1:
R
279
K
HA2
HA2:
R
151
K
NEP
NEP:
L
30
S
NEP:
S
93
P
NP
NP:
T
66
A
NP:
Q
67
P
NP:
V
453
A
NS1
NS1:
Y
104
H
NS1:
K
107
N
NS1:
L
130
F
NS1:
H
201
Y
NS1:
A
212
V
NS1:
V
263
M
PA
PA:
K
312
R
PA:
T
352
A
PA:
S
530
T
PA:
F
709
V
PA:
N
714
S
PA:
I
723
V
Deletions
HA1:162-164
Insertions
None
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