GS_00DCQ9P.1

Display Name: USA/GS_00DCQ9P.1/2025-03-06
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
PV543863.1.seg1/PV543864.1.seg2/PV543862.1.seg3/PV543858.1.seg4/PV543860.1.seg5/PV543859.1.seg7/PV543861.1.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
55
Total unknown nucs seg3
0

Alignment states and QC metrics seg4

Completeness seg4
98.14%
Length seg4
1841
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
1828
Total ambiguous nucs seg5
0
Total deleted nucs seg5
0
Total frame shifts seg5
0
Total inserted nucs seg5
78
Total SNPs seg5
33
Total unknown nucs seg5
0

Alignment states and QC metrics seg7

Completeness seg7
100.00%
Length seg7
1155
Total ambiguous nucs seg7
0
Total deleted nucs seg7
0
Total frame shifts seg7
0
Total inserted nucs seg7
8
Total SNPs seg7
16
Total unknown nucs seg7
0

Alignment states and QC metrics seg8

Completeness seg8
99.62%
Length seg8
1083
Total ambiguous nucs seg8
0
Total deleted nucs seg8
0
Total frame shifts seg8
0
Total inserted nucs seg8
21
Total SNPs seg8
22
Total unknown nucs seg8
0

Sample details

Collection country
USA
Collection subdivision level 1
New York
Collection date
2025-03-06
Isolate name
GKISBBBE37560

Host

Host name scientific
Homo sapiens
Host taxon id
9606

INSDC

INSDC accession seg1
PV543863.1
INSDC accession seg2
PV543864.1
INSDC accession seg3
PV543862.1
INSDC accession seg4
PV543858.1
INSDC accession seg5
PV543860.1
INSDC accession seg7
PV543859.1
INSDC accession seg8
PV543861.1
NCBI release date
2025-04-18

Alignment states and QC metrics seg1

Length seg1
2355

Alignment states and QC metrics seg2

Length seg2
2382

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:T15C
  • seg3:T88C
  • seg3:T111C
  • seg3:C117T
  • seg3:T339C
  • seg3:G414A
  • seg3:T423C
  • seg3:G549A
  • seg3:A618G
  • seg3:T654C
  • seg3:C756A
  • seg3:A771G
  • seg3:C813T
  • seg3:G867A
  • seg3:C897T
  • seg3:A935G
  • seg3:G936A
  • seg3:A987G

    • seg4

  • seg4:G39A
  • seg4:T135C
  • seg4:C252A
  • seg4:C270T
  • seg4:C282T
  • seg4:G297A
  • seg4:G312T
  • seg4:A318G
  • seg4:A351G
  • seg4:C375T
  • seg4:C378T
  • seg4:A427G
  • seg4:A435G
  • seg4:C441T
  • seg4:T444C
  • seg4:T456C
  • seg4:G457A
  • seg4:A484G

    • seg5

  • seg5:C3T
  • seg5:T46C
  • seg5:A55G
  • seg5:A121G
  • seg5:C178T
  • seg5:A224G
  • seg5:A235G
  • seg5:G244A
  • seg5:T298C
  • seg5:C313T
  • seg5:G361A
  • seg5:A373G
  • seg5:C380T
  • seg5:A454G
  • seg5:C523T
  • seg5:C608T
  • seg5:A634G
  • seg5:G715T

    • seg7

  • seg7:C33T
  • seg7:C46T
  • seg7:A83G
  • seg7:T113C
  • seg7:T125A
  • seg7:C287G
  • seg7:G316A
  • seg7:A419G
  • seg7:G482A
  • seg7:G500T
  • seg7:G521A
  • seg7:G536A
  • seg7:A566G
  • seg7:C656T
  • seg7:A919G
  • seg7:A967G

    • seg8

  • seg8:G26A
  • seg8:C94T
  • seg8:A118G
  • seg8:C151T
  • seg8:T163C
  • seg8:G190A
  • seg8:T197C
  • seg8:T274C
  • seg8:T341C
  • seg8:A352C
  • seg8:T355C
  • seg8:T391C
  • seg8:C419T
  • seg8:C604T
  • seg8:A610T
  • seg8:C632T
  • seg8:G661A
  • seg8:T775C
    • Deletions
    seg4:562-570
    Insertions
    ins_seg8:1066:TAAAAATCCTCTTGTTACTAC, ins_seg7:0:TTCTTA, ins_seg7:1147:AA, ins_seg5:0:GCATTTTCTTGTGAACTCCA, ins_seg5:1750:CGTTTGGAATATGGGTGTTTATTCTCATTAAAATAAATATAAAAAATGCTGTTGTTTC, ins_seg3:2241:ATAAAC, ins_seg3:2245:ATCAAAAATGCTCGTGTTTCTAC, ins_seg3:0:GCGTTTGATTTATCAGA

    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:I117V
  • HA1:A127T
  • HA1:K136E
  • HA1:P144L
  • HA1:N150K
  • HA1:G184E
  • HA1:N197E
  • HA1:K203R
  • HA1:R279K

    • M1

  • M1:T15I
  • M1:R105K

    • NEP

  • NEP:L30S
  • NEP:S93P
  • NEP:I95M

    • NP

  • NP:I9M
  • NP:T66A
  • NP:V323I
  • NP:V453A

    • NS1

  • NS1:Y104H
  • NS1:K107N
  • NS1:L130F
  • NS1:H201Y

    • PA

  • PA:K312R
  • PA:T352A
  • PA:S530T
  • PA:F709V
  • PA:N714S
  • PA:I723V
    • Deletions
    HA1:162-164
    Insertions
    None