PP_007N337.1

Netherlands/LUMC_case_1_Plasma/2026-05
Igor Sidorov, Dennis Heemskerk, Ali Tas, Jessika Zevenhoven-Dobbe, Marie-Astrid Hoogerwerf, Liana E. Kafetzopoulou, Stefan A. Boers & Jutte J. C. De Vries

Leiden University Medical Center (LUCID)

Sample details

Collection date
2026-05
Sampling location
Netherlands

Data use terms

Data use terms
RESTRICTED
Data use terms URL

Sampling

Sample type
EDTA Plasma

Host

Host

Sequencing

Sequencing protocol
Comprehensive Viral Research Panel (TWIST Bioscience)
Depth of coverage
139
Breadth of coverage
99

Submission details

Submission ID
LUMC_case_1_Plasma
Submitting group
Date submitted
2026-09-25 11:36:00 UTC
Date released
2026-09-25 11:36:52 UTC
Earliest release date
2026-09-25

Alignment and QC

Length L
6497 (99%)
# of SNPs L
392
Length M
3668 (99.9%)
# of SNPs M
209
Length S
1867 (99.6%)
# of SNPs S
135
# of inserted bases S
7
# of deleted bases S
3

Nucleotide mutations

Mutations called relative to the NC_003468.2, NC_003467.2 & NC_003466.1 references

Substitutions

L

  • G66T
  • T68G
  • G70T
  • G72A
  • C74T
  • C131T
  • C146T
  • C147T
  • G149A
  • C155T
  • C173T
  • T182C
  • T215C
  • A218G
  • A233C
  • T278C
  • A296G
  • T297C

M

  • G45A
  • T74C
  • T90C
  • G114A
  • C147T
  • C174T
  • C190T
  • A192G
  • C231T
  • C243T
  • A264G
  • T312C
  • C315T
  • G339C
  • T345C
  • A360G
  • T363C
  • A381G

S

  • T1C
  • T4C
  • C13T
  • T16C
  • G17A
  • A20G
  • G28A
  • G63A
  • G66A
  • G120A
  • A135G
  • T202C
  • A219G
  • T225C
  • T244C
  • T306C
  • G315A
  • A318G
Deletions

S

10, 1443, 1573
Insertions

S

ins_22:T, ins_1486:T, ins_1555:A, ins_1631:TTT, ins_1668:T

Amino acid substitutions

Substitutions called relative to the NC_003468.2, NC_003467.2 & NC_003466.1 references

Substitutions

GPC

  • GPC:V8A
  • GPC:I114V
  • GPC:H294Y
  • GPC:V346I
  • GPC:T353V
  • GPC:T516I
  • GPC:I537V
  • GPC:T1023A
  • GPC:S1055T
  • GPC:V1127I

Gc

  • Gc:T372A
  • Gc:S404T
  • Gc:V476I

Gn

  • Gn:V8A
  • Gn:I114V
  • Gn:H294Y
  • Gn:V346I
  • Gn:T353V
  • Gn:T516I
  • Gn:I537V

NSs

  • NSs:Q5R
  • NSs:E33G
  • NSs:L35S
  • NSs:I62T

RdRp

  • RdRp:V11L
  • RdRp:R12M
  • RdRp:D13N
  • RdRp:T141I
  • RdRp:L277S
  • RdRp:S338A
  • RdRp:R346K
  • RdRp:I402V
  • RdRp:A541V
  • RdRp:D780N
  • RdRp:N1033D
  • RdRp:D1303E
  • RdRp:V1665I
  • RdRp:K1750R
  • RdRp:T2113A
Deletions
N/A
Insertions
N/A

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