GS_00DCQCH.1

Display Name: USA/GS_00DCQCH.1/2025-03-12
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
PV543883.1.seg1/PV543879.1.seg4/PV543881.1.seg5/PV543880.1.seg6/PV543882.1.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
Clade NA
B.7.3

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
55
Total unknown nucs seg4
0

Alignment states and QC metrics seg5

Completeness seg5
100.00%
Length seg5
1829
Total ambiguous nucs seg5
0
Total deleted nucs seg5
0
Total frame shifts seg5
0
Total inserted nucs seg5
79
Total SNPs seg5
30
Total unknown nucs seg5
0

Alignment states and QC metrics seg6

Completeness seg6
100.00%
Length seg6
1542
Total ambiguous nucs seg6
0
Total deleted nucs seg6
0
Total frame shifts seg6
0
Total inserted nucs seg6
141
Total SNPs seg6
35
Total unknown nucs seg6
0

Alignment states and QC metrics seg8

Completeness seg8
99.62%
Length seg8
1084
Total ambiguous nucs seg8
0
Total deleted nucs seg8
0
Total frame shifts seg8
0
Total inserted nucs seg8
22
Total SNPs seg8
16
Total unknown nucs seg8
0

Sample details

Collection country
USA
Collection subdivision level 1
New York
Collection date
2025-03-12
Isolate name
GKISBBBE48428

Host

Host name scientific
Homo sapiens
Host taxon id
9606

INSDC

INSDC accession seg1
PV543883.1
INSDC accession seg4
PV543879.1
INSDC accession seg5
PV543881.1
INSDC accession seg6
PV543880.1
INSDC accession seg8
PV543882.1
NCBI release date
2025-04-18

Alignment states and QC metrics seg1

Length seg1
2344

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

seg4

  • seg4:T195C
  • seg4:C252A
  • seg4:C265T
  • seg4:C270T
  • seg4:G297A
  • seg4:G312T
  • seg4:A318G
  • seg4:A351G
  • seg4:C375T
  • seg4:C378T
  • seg4:T402C
  • seg4:A427G
  • seg4:C441T
  • seg4:T444C
  • seg4:G457A
  • seg4:A461G
  • seg4:A463G
  • seg4:A484G

    • seg5

  • seg5:C3T
  • seg5:T46C
  • seg5:A55G
  • seg5:C178T
  • seg5:A224G
  • seg5:A235G
  • seg5:C271T
  • seg5:T298C
  • seg5:C313T
  • seg5:G361A
  • seg5:A373G
  • seg5:C380T
  • seg5:A454G
  • seg5:A457G
  • seg5:A478T
  • seg5:C523T
  • seg5:C608T
  • seg5:A763G

    • seg6

  • seg6:T9C
  • seg6:C125A
  • seg6:C140T
  • seg6:A175G
  • seg6:T212C
  • seg6:A358G
  • seg6:T363C
  • seg6:C394T
  • seg6:C399T
  • seg6:A504G
  • seg6:C519T
  • seg6:C591T
  • seg6:A660C
  • seg6:T714A
  • seg6:C769A
  • seg6:C849T
  • seg6:A859G
  • seg6:T879C

    • seg8

  • seg8:G27A
  • seg8:A118G
  • seg8:T163C
  • seg8:G190A
  • seg8:T341C
  • seg8:A352C
  • seg8:T391C
  • seg8:C419T
  • seg8:C604T
  • seg8:A610T
  • seg8:C632T
  • seg8:G661A
  • seg8:T775C
  • seg8:C882T
  • seg8:A950G
  • seg8:T963C
    • Deletions
    seg4:562-570
    Insertions
    ins_seg8:1066:TAAAAATCCTCTTGTTACTAC, ins_seg8:25:A, ins_seg6:0:ATCTTCTCAAAACTGAAGCAAATAGGCCAAAAATGAACA, ins_seg6:1401:TGGGAGAATGGTTAAGTTTGTTCTAAACCCTTTGTTCCTATTTTATTTGAACAATTGTCCTTGCTAAACTTAATTGTTTCTGAAAAATCCTCTTGTTACTAC, ins_seg5:0:ATTTTCTTGTGAACTCCA, ins_seg5:1750:CGTTTGGAATATGGGTGTTTATTCTCATTAAAATAAATATAAAAAATGCTGTTGTTTCTAC

    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:E128G
  • HA1:N129D
  • HA1:K136E
  • HA1:P144L
  • HA1:N150K
  • HA1:E183K
  • HA1:G184E
  • HA1:N197E
  • HA1:A199T
  • HA1:K203R
  • HA1:R279K

    • NA

  • NA:P42Q
  • NA:A47V
  • NA:N59D
  • NA:V71A
  • NA:I120V
  • NA:K220N
  • NA:I287V
  • NA:S295R
  • NA:N340D
  • NA:K343E
  • NA:E358K
  • NA:G378E
  • NA:D384G
  • NA:A395V
  • NA:V401I

    • NEP

  • NEP:L30S
  • NEP:S93P

    • NP

  • NP:I9M
  • NP:T66A
  • NP:V453A

    • NS1

  • NS1:Y104H
  • NS1:K107N
  • NS1:L130F
  • NS1:H201Y
    • Deletions
    HA1:162-164
    Insertions
    None