GS_00DCRQR.1

Display Name: USA/GS_00DCRQR.1/2025-02-18
Steel, J.; Kirby, M.; Garten, R.; Davis, T.; Dugan, V.

Submission details

Submission ID
PV555780.1.seg4/PV555781.1.seg5/PV555782.1.seg6/PV555783.1.seg8
Submitting group
Automated Ingest from INSDC/NCBI Virus by Loculus
Date submitted
2025-04-23 17:06:54 UTC
Date released
2025-04-23 17:07:32 UTC

Authors

Author affiliations
Centers for Disease Control and Prevention, Influenza Division

INSDC

Bioproject accession
PRJNA998888
INSDC accession seg4
PV555780.1
INSDC accession seg5
PV555781.1
INSDC accession seg6
PV555782.1
INSDC accession seg8
PV555783.1
NCBI release date
2025-04-23

Clade

Clade HA
V1A.3a.2
Clade NA
B.7.3

Alignment states and QC metrics seg4

Completeness seg4
98.46%
Length seg4
1847
Total ambiguous nucs seg4
0
Total deleted nucs seg4
9
Total frame shifts seg4
0
Total inserted nucs seg4
0
Total SNPs seg4
54
Total unknown nucs seg4
0

Alignment states and QC metrics seg5

Completeness seg5
100.00%
Length seg5
1802
Total ambiguous nucs seg5
0
Total deleted nucs seg5
0
Total frame shifts seg5
0
Total inserted nucs seg5
52
Total SNPs seg5
29
Total unknown nucs seg5
0

Alignment states and QC metrics seg6

Completeness seg6
100.00%
Length seg6
1528
Total ambiguous nucs seg6
0
Total deleted nucs seg6
0
Total frame shifts seg6
0
Total inserted nucs seg6
127
Total SNPs seg6
37
Total unknown nucs seg6
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
17
Total unknown nucs seg8
0

Sample details

Collection country
USA
Collection subdivision level 1
Massachusetts
Collection date
2025-02-18
Isolate name
EPI_ISL_19790212

Host

Host name scientific
Homo sapiens
Host taxon id
9606

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: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
  • seg4:C509T

    • 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:C523T
  • seg5:C608T
  • seg5:A763G
  • seg5:C841T
  • seg5:A883G

    • seg6

  • seg6:T9C
  • seg6:C39A
  • seg6:C125A
  • seg6:C140T
  • seg6:A158G
  • seg6:G163T
  • seg6:C168T
  • seg6:T212C
  • seg6:A358G
  • seg6:T363C
  • seg6:C394T
  • seg6:C399T
  • seg6:A504G
  • seg6:C519T
  • seg6:A660C
  • seg6:T714A
  • seg6:C849T
  • seg6:T879C

    • seg8

  • seg8:G26A
  • seg8:A118G
  • seg8:T163C
  • seg8:G190A
  • seg8:T197C
  • 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:TAAA, ins_seg6:0:ATCTTCTCAAAACTGAAGCAAATAGGCCAAAAATGAACA, ins_seg6:1401:TGGGAGAATGGTTAAGTTTTTTCTAAACCCTTTGTTCCTATTTTATTTGAACAATTGTCCTTGCTAAACTTAATTGTTTCTGAAAAAT, ins_seg5:0:CTCCA, ins_seg5:1750:CGTTTGGAATATGGGTGTTTATTCTCATTAAAATAAATATAAAAAAT

    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:D53G
  • NA:A55S
  • NA:V71A
  • NA:I120V
  • NA:K220N
  • 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
  • NP:I489V

    • NS1

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