PP_007N41A.1

Netherlands/LUMC_case_1_Nasopharyngeal_swab/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
Nasopharyngeal swab

Host

Host

Sequencing

Sequencing instrument
Illumina NovaSeq X Plus
Sequencing protocol
Comprehensive Viral Research Panel (TWIST Bioscience)
Depth of coverage
12
Breadth of coverage
93

Submission details

Submission ID
LUMC_case_1_Nasopharyngeal_swab
Submitting group
Date submitted
2026-09-25 11:42:49 UTC
Date released
2026-09-25 11:43:52 UTC
Earliest release date
2026-09-25

Alignment and QC

Length S
1829 (97.5%)
# of SNPs S
130
# of inserted bases S
6
# of deleted bases S
2
Length L
6481 (91.1%)
# of SNPs L
353
# of unknown bases L
500
Length M
3578 (94.7%)
# of SNPs M
198
# of unknown bases M
102

Nucleotide mutations

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

Substitutions

L

  • G62A
  • T68G
  • C74T
  • C131T
  • C146T
  • C147T
  • G149A
  • C155T
  • C173T
  • T182C
  • T215C
  • A218G
  • A233C
  • T278C
  • A296G
  • T297C
  • A302G
  • A686G

M

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

S

  • G22T
  • G28A
  • G63A
  • G66A
  • G120A
  • A135G
  • T202C
  • A219G
  • T225C
  • T244C
  • T306C
  • G315A
  • A318G
  • C328T
  • C417T
  • C444A
  • G450A
  • T454C
Deletions

S

1443, 1573
Insertions

S

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:F225L
  • 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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