Netherlands/Run_1321_BC89/2026-05-22
B. B. Oude Munnink, D. F. Nieuwenhuijse, S. C. van den Boom, L. Zaeck, M. Boter, H. Cassidy, L. Schuele, R. Molenkamp, A. van der Eijk, C. GeurtsvanKessel & M. Koopmans

Department of Viroscience, Erasmus University Medical Center, Rotterdam, the Netherlands

Sample details

Collection date
2026-05-22
Sampling location
Netherlands (Rotterdam, Zuid-Holland)
City
Rotterdam

Data use terms

Data use terms
RESTRICTED

Sampling

Sample type
Serum
Purpose of sampling
Outbreak investigation

Sequencing

Purpose of sequencing
Outbreak investigation
Amplicon PCR primer scheme
modified ANDV ARTIC protocol V.4
Amplicon size
400
Sequencing instrument
GridION
Sequencing protocol
The design comprised 62 overlapping primers generating ~400 bp amplicons in two pools. A third pool contained three L-segment amplicons targeting outbreak-specific SNPs to increase sensitivity for outbreak specimens. Random priming used 65°C for 5 min followed by 2 min snap cooling at 4°C. cDNA was synthesized with SuperScript IV (Invitrogen, Carlsbad, USA) at 23°C for 10 min,...
Sequenced by - organization
Erasmus MC
Consensus sequence software name
ARTIC field bioinformatics pipeline (https://github.com/artic-network/fieldbioinformatics)

Submission details

Comment
Case 12
Submission ID
Run_1321_BC89
Submitting group
Date submitted
2026-11-02 16:45:47 UTC
Date released
2026-11-02 20:04:35 UTC
Earliest release date
2026-11-02

Files


Alignment and QC

Length L
6430 (98%)
# of SNPs L
386
Length M
3495 (95.2%)
# of SNPs M
206
Length S
1756 (93.6%)
# of SNPs S
127
# of inserted bases S
6
# of deleted bases S
2

Nucleotide mutations

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

Substitutions

L

  • T68G
  • C74T
  • C131T
  • C146T
  • C147T
  • G149A
  • C155T
  • C173T
  • T182C
  • T215C
  • A218G
  • A233C
  • T278C
  • A296G
  • T297C
  • A302G
  • T326C
  • T329C

M

  • T74C
  • T90C
  • G114A
  • C147T
  • C174T
  • C190T
  • A192G
  • C231T
  • C243T
  • A264G
  • T312C
  • C315T
  • G339C
  • T345C
  • A360G
  • T363C
  • A381G
  • T387C

S

  • G63A
  • G66A
  • G120A
  • A135G
  • T202C
  • A219G
  • T225C
  • T244C
  • T306C
  • G315A
  • A318G
  • C328T
  • C417T
  • C444A
  • G450A
  • T454C
  • C459T
  • G465A
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: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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