GS_00DDPEC.1

Display Name: USA/GS_00DDPEC.1/2025-03-10
Steel, J.; Kirby, M.; Garten, R.; Davis, T.; Dugan, V.

Submission details

Submission ID
PV585797.1.seg4/PV585798.1.seg5/PV585799.1.seg6/PV585800.1.seg7/PV585801.1.seg8
Submitting group
Automated Ingest from INSDC/NCBI Virus by Loculus
Date submitted
2025-05-01 10:12:40 UTC
Date released
2025-05-01 10:13:53 UTC

Authors

Author affiliations
Centers for Disease Control and Prevention, Influenza Division

INSDC

Bioproject accession
PRJNA998884
INSDC accession seg4
PV585797.1
INSDC accession seg5
PV585798.1
INSDC accession seg6
PV585799.1
INSDC accession seg7
PV585800.1
INSDC accession seg8
PV585801.1
NCBI release date
2025-04-30

Clade

Clade HA
6B.1A.5a.2a.1
Clade NA
C.5.3.1

Alignment states and QC metrics seg4

Completeness seg4
100.00%
Length seg4
1752
Total ambiguous nucs seg4
0
Total deleted nucs seg4
0
Total frame shifts seg4
0
Total inserted nucs seg4
0
Total SNPs seg4
107
Total unknown nucs seg4
0

Alignment states and QC metrics seg5

Completeness seg5
100.00%
Length seg5
1540
Total ambiguous nucs seg5
0
Total deleted nucs seg5
0
Total frame shifts seg5
0
Total inserted nucs seg5
43
Total SNPs seg5
60
Total unknown nucs seg5
0

Alignment states and QC metrics seg6

Completeness seg6
100.00%
Length seg6
1433
Total ambiguous nucs seg6
0
Total deleted nucs seg6
0
Total frame shifts seg6
0
Total inserted nucs seg6
0
Total SNPs seg6
15
Total unknown nucs seg6
0

Alignment states and QC metrics seg7

Completeness seg7
100.00%
Length seg7
1002
Total ambiguous nucs seg7
0
Total deleted nucs seg7
0
Total frame shifts seg7
0
Total inserted nucs seg7
20
Total SNPs seg7
30
Total unknown nucs seg7
0

Alignment states and QC metrics seg8

Completeness seg8
98.61%
Length seg8
865
Total ambiguous nucs seg8
0
Total deleted nucs seg8
0
Total frame shifts seg8
0
Total inserted nucs seg8
14
Total SNPs seg8
33
Total unknown nucs seg8
0

Sample details

Collection country
USA
Collection subdivision level 1
Hawaii
Collection date
2025-03-10
Isolate name
EPI_ISL_19818457

Host

Host name scientific
Homo sapiens
Host taxon id
9606

INSDC seg4

Subtype seg4
H1

INSDC seg6

Subtype seg6
N1

Nucleotide mutations

Mutations called relative to the NC_026438.1, NC_026435.1, NC_026437.1, CY121680.1, NC_026436.1, MW626056.1, NC_026431.1 & NC_026432.1 references

Substitutions

seg4

  • seg4:C42A
  • seg4:A47G
  • seg4:G57A
  • seg4:A119G
  • seg4:T161C
  • seg4:C164T
  • seg4:G188A
  • seg4:A231C
  • seg4:C281A
  • seg4:C293G
  • seg4:C318T
  • seg4:G322A
  • seg4:G360A
  • seg4:G416A
  • seg4:A429G
  • seg4:C443T
  • seg4:A456G
  • seg4:A461T

    • seg5

  • seg5:A33G
  • seg5:G42T
  • seg5:C87T
  • seg5:A97G
  • seg5:C141A
  • seg5:C171T
  • seg5:T177C
  • seg5:C180T
  • seg5:C249A
  • seg5:A288C
  • seg5:G298A
  • seg5:C303T
  • seg5:G309A
  • seg5:T314C
  • seg5:G315A
  • seg5:R341A
  • seg5:T365A
  • seg5:A390G

    • seg6

  • seg6:C301T
  • seg6:C452A
  • seg6:G607A
  • seg6:A785G
  • seg6:T799C
  • seg6:A818G
  • seg6:G914T
  • seg6:A1049G
  • seg6:C1187T
  • seg6:A1193G
  • seg6:A1208G
  • seg6:A1304G
  • seg6:G1365A
  • seg6:T1403C
  • seg6:G1415T

    • seg7

  • seg7:G48A
  • seg7:G75A
  • seg7:T123C
  • seg7:C124A
  • seg7:G238A
  • seg7:G258A
  • seg7:A293G
  • seg7:G306A
  • seg7:G339A
  • seg7:G342A
  • seg7:C375A
  • seg7:T432C
  • seg7:G441T
  • seg7:G492A
  • seg7:C507A
  • seg7:A574G
  • seg7:C622A
  • seg7:G660A

    • seg8

  • seg8:C6A
  • seg8:C42T
  • seg8:C54T
  • seg8:G60A
  • seg8:T99C
  • seg8:C108A
  • seg8:T159C
  • seg8:G163A
  • seg8:C192T
  • seg8:C204T
  • seg8:A238G
  • seg8:G250A
  • seg8:C264T
  • seg8:C268A
  • seg8:C315T
  • seg8:A367G
  • seg8:A375T
  • seg8:A391G
    • Deletions
    None
    Insertions
    ins_seg8:0:GTGACAAAAACATA, ins_seg7:982:AAAACTA, ins_seg7:0:TAGATGTTTAAAG, ins_seg5:1497:AGAAAAATAC, ins_seg5:0:GTAGATAATCACTCAATGAGTGACATCGAAGCT

    Amino acid mutations

    Mutations called relative to the NC_026438.1, NC_026435.1, NC_026437.1, CY121680.1, NC_026436.1, MW626056.1, NC_026431.1 & NC_026432.1 references

    Substitutions

    HA1

  • HA1:K54Q
  • HA1:S74R
  • HA1:P83S
  • HA1:S84N
  • HA1:D97N
  • HA1:T120A
  • HA1:N129D
  • HA1:K130N
  • HA1:P137S
  • HA1:K142R
  • HA1:N156K
  • HA1:L161I
  • HA1:S162N
  • HA1:K163Q
  • HA1:S164T
  • HA1:S183P
  • HA1:S185I
  • HA1:A186T

    • HA2

  • HA2:E29D
  • HA2:I45V
  • HA2:E47K
  • HA2:I91V
  • HA2:S124H
  • HA2:I133T
  • HA2:E172K
  • HA2:E179D
  • HA2:V193A

    • M1

  • M1:L42I
  • M1:V80I
  • M1:K98R
  • M1:M192V
  • M1:Q208K
  • M1:K230R

    • M2

  • M2:R18K
  • M2:D21G
  • M2:S23N
  • M2:I28T

    • NA

  • NA:A98V
  • NA:S200N
  • NA:I264T
  • NA:V453M
  • NA:K469N

    • NEP

  • NEP:D2E
  • NEP:N29S
  • NEP:T48A
  • NEP:M83I

    • NP

  • NP:E14D
  • NP:I33V
  • NP:V100I
  • NP:M105T
  • NP:X114E
  • NP:L122Q
  • NP:I136L
  • NP:V217I
  • NP:V425I
  • NP:S498N

    • NS1

  • NS1:D2E
  • NS1:E55K
  • NS1:T80A
  • NS1:V84I
  • NS1:L90I
  • NS1:I123V
  • NS1:E125D
  • NS1:K131E
  • NS1:A155T
  • NS1:N205S

    • SigPep

  • SigPep:L8M
  • SigPep:A13T
    • Deletions
    None
    Insertions
    None