GS_00GB2QD.2

USA/GS_00GB2QD.2/2025-10-14
E. B. Fox, J. M. Garrigues & N. M. Green

Los Angeles County Public Health Lab microbial pathogen submission group, Los Angeles County Public Health Laboratories

Submission details

Submission ID
PX568018.1.seg1/PX568019.1.seg2/PX568020.1.seg3/PX568021.1.seg4/PX568022.1.seg5/PX568023.1.seg6/PX568024.1.seg7/PX568025.1.seg8
Submitting group
Date submitted
2025-11-27 16:45:45 UTC
Date released
2025-11-27 16:51:55 UTC

Clade

Clade HA
D.3.1
Clade NA
C.5.3

Sample details

Collection country
USA
Collection subdivision level 1
California
Collection date
2025-10-14
Isolate name
A/California/LACPHL-INF02047/2025

Host

Host

INSDC

INSDC accession seg1
INSDC accession seg2
INSDC accession seg3
INSDC accession seg4
INSDC accession seg5
INSDC accession seg6
INSDC accession seg7
INSDC accession seg8
NCBI release date
2025-11-20

INSDC seg4

subtype_seg4
H1

INSDC seg6

subtype_seg6
N1

Alignment and QC

Length seg1
2280 (72.5%)
Total SNPs seg1
64
Total unknown nucs seg1
626
Length seg2
2247 (100%)
Total ambiguous nucs seg2
1
Total deleted nucs seg2
27
Total SNPs seg2
73
Length seg3
2151 (63.8%)
Total ambiguous nucs seg3
2
Total SNPs seg3
53
Total unknown nucs seg3
777
Length seg4
1701 (97.1%)
Total SNPs seg4
110
Length seg5
1497 (100%)
Total SNPs seg5
58
Length seg6
1410 (98.4%)
Total SNPs seg6
23
Length seg7
982 (100%)
Total SNPs seg7
30
Length seg8
863 (100%)
Total SNPs seg8
34

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

seg1

  • A18G
  • A90C
  • A96G
  • A108G
  • A132G
  • A138G
  • G161A
  • A174G
  • G198A
  • T201C
  • A225G
  • C242T
  • A243G
  • C285A
  • A291G
  • C309T
  • G375A
  • A441G

seg2

  • C123T
  • A129G
  • A159G
  • G168A
  • G180A
  • C192T
  • C201T
  • T207A
  • T210C
  • T222C
  • G225A
  • C297T
  • G312A
  • T324A
  • G354A
  • A366G
  • C447T
  • T450C

seg3

  • G40A
  • R53A
  • T81C
  • G84C
  • A88G
  • C90T
  • C99T
  • A114T
  • C153T
  • C162T
  • C165T
  • G187A
  • G204A
  • G298A
  • G303A
  • G423A
  • G477A
  • G498A

seg4

  • C42A
  • A47G
  • G57A
  • A119G
  • T161C
  • C164T
  • G188A
  • G209A
  • A231C
  • C281A
  • C293G
  • C318T
  • G322A
  • A328G
  • G360A
  • G380A
  • G416A
  • A429G

seg5

  • G42T
  • C87T
  • A97G
  • C141A
  • C171T
  • T177C
  • C180T
  • C249A
  • A288C
  • G298A
  • G309A
  • T314C
  • G315A
  • R341A
  • T365A
  • A390G
  • T402C
  • A406C

seg6

  • C164T
  • A291G
  • T293C
  • G350A
  • C452A
  • G607A
  • A785G
  • G788A
  • C809T
  • A818G
  • C893T
  • G914T
  • A982C
  • A1029T
  • A1049G
  • A1091G
  • A1175G
  • C1187T

seg7

  • G48A
  • G75A
  • T123C
  • C124A
  • G238A
  • G258A
  • C276T
  • A293G
  • G306A
  • G339A
  • G342A
  • C375A
  • T432C
  • G441T
  • G492A
  • C507A
  • A574G
  • C622A

seg8

  • C6A
  • C42T
  • C54T
  • G60A
  • T99C
  • C108A
  • T159C
  • G163A
  • C192T
  • C204T
  • A238G
  • G250A
  • C264T
  • C268A
  • C315T
  • G324A
  • A367G
  • A375T
Deletions

seg2

31-54, 2215-2217
Insertions
N/A

Amino acid substitutions

Substitutions 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:D86G
  • HA1:D97N
  • HA1:T120A
  • HA1:S121N
  • HA1:N129D
  • HA1:K130N
  • HA1:P137S
  • HA1:K142R
  • HA1:N156K
  • HA1:L161I
  • HA1:S162N
  • HA1:K163Q
  • HA1:S164T
  • HA1:S183P

HA2

  • HA2:E29D
  • HA2:I45V
  • HA2:E47K
  • HA2:K75R
  • 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:S95G
  • NA:S200N
  • NA:N325T
  • NA:N341Y
  • 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:Y171H
  • NS1:N205S

PA

  • PA:V14I
  • PA:X18E
  • PA:I30V
  • PA:V63I
  • PA:V100I
  • PA:S440G
  • PA:I505V

PA-X

  • PA-X:V14I
  • PA-X:X18E
  • PA-X:I30V
  • PA-X:V63I
  • PA-X:V100I

PB1

  • PB1:G154D
  • PB1:V200I
  • PB1:G216D
  • PB1:K386R
  • PB1:I397M
  • PB1:I435T
  • PB1:P454S
  • PB1:D729E
  • PB1:K757R

PB2

  • PB2:R54K
  • PB2:M66I
  • PB2:T81M
  • PB2:G388R
  • PB2:S453T
  • PB2:L475M
  • PB2:V667I
  • PB2:V731I

SigPep

  • SigPep:L8M
  • SigPep:A13T
Deletions

PB1

PB1:11-18, PB1:738
Insertions
N/A