GS_00G9Y5S.4

USA/GS_00G9Y5S.4/2025-10-23
A. P. Rothstein, G. Muir, A. Sum, A. Simas, B. Lu, B. Girinathan, H. Mammadova, P. Leeson, A. M. Plocik & D. Gratalo

Ginkgo Bioworks, Ginkgo Biosecurity

Submission details

Submission ID
PX548430.1.seg1/PX548429.1.seg2/PX548428.1.seg3/PX548423.1.seg4/PX548426.1.seg5/PX548425.1.seg6/PX548424.1.seg7/PX548427.1.seg8
Submitting group
Date submitted
2026-03-26 04:29:29 UTC
Date released
2026-03-26 04:32:01 UTC

INSDC

bioprojectAccession
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
2025-11-18

Clade

Clade HA
D.3.1
Clade NA
D.2

Sample details

Collection country
USA
Collection subdivision level 1
Virginia
Collection date
2025-10-23
Isolate name
A/Virginia/GKISBBBI21075/2025

Host

Host

INSDC seg4

subtype_seg4
H1

INSDC seg6

subtype_seg6
N1

Alignment and QC

Length seg1
2313 (100%)
Total inserted nucs seg1
33
Total SNPs seg1
84
Length seg2
2314 (96.2%)
Total inserted nucs seg2
40
Total SNPs seg2
69
Total unknown nucs seg2
87
Length seg3
2168 (92.9%)
Total inserted nucs seg3
17
Total SNPs seg3
77
Total unknown nucs seg3
152
Length seg4
1738 (99.2%)
Total SNPs seg4
112
Length seg5
1540 (100%)
Total inserted nucs seg5
43
Total SNPs seg5
60
Length seg6
1433 (100%)
Total SNPs seg6
19
Length seg7
1002 (100%)
Total inserted nucs seg7
20
Total SNPs seg7
26
Length seg8
875 (99.5%)
Total inserted nucs seg8
16
Total SNPs seg8
38

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

  • G42A
  • G168A
  • G180A
  • C192T
  • T207A
  • T210C
  • T222C
  • G225A
  • C297T
  • G312A
  • A345G
  • A366G
  • T384C
  • T397C
  • C447T
  • T450C
  • G461A
  • T474C

seg3

  • G40A
  • R53A
  • T81C
  • G84C
  • C90T
  • C99T
  • A114T
  • G126A
  • C153T
  • C162T
  • C165T
  • G187A
  • G204A
  • C209T
  • G298A
  • G423A
  • G477A
  • G498A

seg4

  • C42A
  • A47G
  • G57A
  • A119G
  • T161C
  • C164T
  • G179A
  • G188A
  • A231C
  • C293G
  • C318T
  • G322A
  • G360A
  • A408C
  • G416A
  • A429G
  • C443T
  • A456G

seg5

  • A33G
  • G42T
  • C87T
  • A97G
  • C141A
  • C171T
  • T177C
  • C180T
  • C249A
  • A288C
  • G298A
  • G309A
  • T314C
  • G315A
  • R341A
  • T365A
  • A390G
  • T402C

seg6

  • T50C
  • A144G
  • G163A
  • C452A
  • G607A
  • A629G
  • A785G
  • T799C
  • A818G
  • C893T
  • G914T
  • T1016C
  • A1049G
  • C1187T
  • A1193G
  • T1256A
  • G1365A
  • T1403C
  • G1415T

seg7

  • G75A
  • C124A
  • G238A
  • G258A
  • A293G
  • G306A
  • G339A
  • C375A
  • T432C
  • G441T
  • G492A
  • C507A
  • A574G
  • G600A
  • C622A
  • G660A
  • T663C
  • G687A

seg8

  • C6A
  • C42T
  • C54T
  • C57T
  • T99C
  • C108A
  • G123A
  • A132G
  • T150A
  • C153T
  • T159C
  • G163A
  • C192T
  • C204T
  • A238G
  • G250A
  • C264T
  • C268A
Deletions
N/A
Insertions

seg1

ins_0:AATATATTCAAT, ins_2280:TGTCGAATTGTTTAAAAACGA

seg2

ins_0:AACCATTTGA, ins_2274:TGAATTTAACTTGTCCTTCATGAAAAAATG

seg3

ins_2151:TTGTGGCAATGCTACTA

seg5

ins_0:GTAGATAATCACTCAATGAGTGACATCGAAGCC, ins_1497:AGAAAAATAC

seg7

ins_0:TAGATGTTTAAAG, ins_982:AAAACTA

seg8

ins_0:GGGTGACAAAAACATA

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: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:Q27K
  • 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:D21G
  • M2:S23N

NA

  • NA:I46V
  • NA:S52N
  • NA:S200N
  • NA:I264T
  • NA:N416K
  • 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:N377S
  • 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

PA

  • PA:V14I
  • PA:X18E
  • PA:V63I
  • PA:A70V
  • PA:V100I
  • PA:P224S
  • PA:S225C
  • PA:R262K
  • PA:N321K
  • PA:I330V
  • PA:A337T
  • PA:K339N
  • PA:R362K
  • PA:I438V
  • PA:I505V

PA-X

  • PA-X:V14I
  • PA-X:X18E
  • PA-X:V63I
  • PA-X:A70V
  • PA-X:V100I
  • PA-X:R221Q
  • PA-X:L229S

PB1

  • PB1:G154D
  • PB1:V200I
  • PB1:K386R
  • PB1:I397M
  • PB1:D398N
  • PB1:I435T
  • PB1:K757R

PB2

  • PB2:R54K
  • PB2:M66I
  • PB2:T81M
  • PB2:D195N
  • PB2:G225S
  • PB2:R293K
  • PB2:R299K
  • PB2:V344M
  • PB2:I354L
  • PB2:S453T
  • PB2:L475M
  • PB2:T524A
  • PB2:V667I
  • PB2:V731I

SigPep

  • SigPep:L8M
  • SigPep:A13T
Deletions
N/A
Insertions
N/A