GS_00DDLQU.1

Display Name: USA/GS_00DDLQU.1/2025-03-10
Gruner, W. E.; Muehleman, D. M.; Fries, A. C.; Hanson, J. F.; Kramer, D. L.; Demarcus, L. S.; Wasik, P. M.; Robbins, A. S.; Macias, E. A.; Garcia, J. M.; Renkas, M. C.; Hartless, T. R.; Hardy, J.

Submission details

Submission ID
PV587133.1.seg1/PV587134.1.seg2/PV587131.1.seg3/PV587123.1.seg4/PV587127.1.seg5/PV587125.1.seg7/PV587129.1.seg8
Submitting group
Automated Ingest from INSDC/NCBI Virus by Loculus
Date submitted
2025-05-01 04:10:22 UTC
Date released
2025-05-01 04:10:29 UTC

Authors

Author affiliations
United States Air Force School of Aerospace Medicine Public Health Submission Group, 711th Human Performance Wing

Clade

Clade HA
V1A.3a.2

Alignment states and QC metrics seg3

Completeness seg3
97.15%
Length seg3
2181
Total ambiguous nucs seg3
0
Total deleted nucs seg3
0
Total frame shifts seg3
0
Total inserted nucs seg3
0
Total SNPs seg3
43
Total unknown nucs seg3
0

Alignment states and QC metrics seg4

Completeness seg4
93.26%
Length seg4
1749
Total ambiguous nucs seg4
0
Total deleted nucs seg4
9
Total frame shifts seg4
0
Total inserted nucs seg4
0
Total SNPs seg4
51
Total unknown nucs seg4
0

Alignment states and QC metrics seg5

Completeness seg5
96.17%
Length seg5
1683
Total ambiguous nucs seg5
0
Total deleted nucs seg5
0
Total frame shifts seg5
0
Total inserted nucs seg5
0
Total SNPs seg5
28
Total unknown nucs seg5
0

Alignment states and QC metrics seg7

Completeness seg7
93.81%
Length seg7
1076
Total ambiguous nucs seg7
0
Total deleted nucs seg7
0
Total frame shifts seg7
0
Total inserted nucs seg7
0
Total SNPs seg7
19
Total unknown nucs seg7
0

Alignment states and QC metrics seg8

Completeness seg8
96.34%
Length seg8
1027
Total ambiguous nucs seg8
0
Total deleted nucs seg8
0
Total frame shifts seg8
0
Total inserted nucs seg8
0
Total SNPs seg8
19
Total unknown nucs seg8
0

Sample details

Collection country
USA
Collection subdivision level 1
Massachusetts
Collection date
2025-03-10
Isolate name
USAFSAM-15801

Host

Host name scientific
Homo sapiens
Host taxon id
9606

INSDC

INSDC accession seg1
PV587133.1
INSDC accession seg2
PV587134.1
INSDC accession seg3
PV587131.1
INSDC accession seg4
PV587123.1
INSDC accession seg5
PV587127.1
INSDC accession seg7
PV587125.1
INSDC accession seg8
PV587129.1
NCBI release date
2025-04-30

Alignment states and QC metrics seg1

Length seg1
2259

Alignment states and QC metrics seg2

Length seg2
2313

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:T111C
  • seg3:C117T
  • seg3:T339C
  • seg3:G414A
  • seg3:T423C
  • seg3:G549A
  • seg3:T603C
  • seg3:A618G
  • seg3:T654C
  • seg3:A771G
  • seg3:C813T
  • seg3:G867A
  • seg3:C897T
  • seg3:A935G
  • seg3:G936A
  • seg3:C1006T
  • seg3:A1054G
  • seg3:G1056A

    • seg4

  • seg4:C252A
  • seg4:G267A
  • seg4:C270T
  • seg4:G297A
  • seg4:G312T
  • seg4:A318G
  • seg4:A351G
  • seg4:C375T
  • seg4:C378T
  • seg4:A427G
  • seg4:C441T
  • seg4:T444C
  • seg4:G457A
  • seg4:G460A
  • seg4:A463G
  • seg4:A484G
  • seg4:C495T
  • seg4:C509T

    • seg5

  • seg5:T46C
  • seg5:T169C
  • seg5:C172T
  • seg5:C178T
  • seg5:A224G
  • seg5:A235G
  • seg5:T298C
  • seg5:C313T
  • seg5:G361A
  • seg5:A373G
  • seg5:C380T
  • seg5:G412A
  • seg5:A454G
  • seg5:C523T
  • seg5:C608T
  • seg5:A634G
  • seg5:A763G
  • seg5:C841T

    • seg7

  • seg7:C33T
  • seg7:C46T
  • seg7:A83G
  • seg7:T125A
  • seg7:A143G
  • seg7:G316A
  • seg7:A374C
  • seg7:A419G
  • seg7:G482A
  • seg7:G500T
  • seg7:G521A
  • seg7:A527G
  • seg7:G536A
  • seg7:A566G
  • seg7:C656T
  • seg7:C802T
  • seg7:G916A
  • seg7:A919G
  • seg7:A967G

    • seg8

  • seg8:A118G
  • seg8:T163C
  • seg8:G190A
  • seg8:T341C
  • seg8:A352C
  • seg8:T391C
  • seg8:C419T
  • seg8:G478A
  • seg8:C604T
  • seg8:A610T
  • seg8:C632T
  • seg8:A646G
  • seg8:G661A
  • seg8:C666T
  • seg8:T775C
  • seg8:G818A
  • seg8:C882T
  • seg8:A950G
  • seg8:T963C
    • Deletions
    seg4:562-570
    Insertions
    None

    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:E128K
  • HA1:N129D
  • HA1:K136E
  • HA1:P144L
  • HA1:N150K
  • HA1:E183K
  • HA1:G184E
  • HA1:N197E
  • HA1:A199T
  • HA1:K203R
  • HA1:R279K

    • M1

  • M1:T15I
  • M1:R105K

    • NEP

  • NEP:L30S
  • NEP:S93P

    • NP

  • NP:T66A
  • NP:V453A

    • NS1

  • NS1:Y104H
  • NS1:K107N
  • NS1:L130F
  • NS1:H201Y
  • NS1:A212V
  • NS1:V263M

    • PA

  • PA:K312R
  • PA:T352A
  • PA:S530T
  • PA:F709I
  • PA:N714S
  • PA:I723V
    • Deletions
    HA1:162-164
    Insertions
    None