PP_006W8QC.1

Restricted-Use sequence

This sequence is only available under the Restricted Use Terms. This prohibits publications that use this sequence as focal data during the restricted-use period, except with the consent of the sequence submitters.
Switzerland/PP_006W8QC.1/2025-08-22
S. Cazzin, N. Liechti, D. Jandrasits, P. Hilpisch, C. Beuret, O. Engler & V. Guidi

Spiez Laboratory, Biology Department

Sample details

Collection date
2025-08-22
Sampling location
Switzerland (Ticino)

Data use terms

Data use terms
RESTRICTED

Data use terms history

ChangedUserData use terms
2026-05-11 08:40niliRESTRICTED until 2027-05-11
Data use terms URL

Lineage

Lineage
2

Sampling

Collection device
Gravid trap
Collection method
Gravid trap – FTA card

Host

Host

Sequencing

Sequencing instrument
GridION
Sequencing protocol
Amplicon
Depth of coverage
1000

Submission details

Submission ID
TI_SUPSI_157-25
Submitting group
Date submitted
2026-05-11 08:40:23 UTC
Date released
2026-05-11 08:40:50 UTC
Earliest release date
2026-05-11

Alignment and QC

Length
10395 (93.6%)
# of SNPs
2073
# of inserted bases
11
# of deleted bases
466
# of unknown bases
529
# of frame shifts
2
Frame shifts
NS4B:20-25(nt:6973-6990),NS4B:31-33(nt:7006-7014)

Nucleotide mutations

Mutations called relative to the NC_009942.1 reference

Substitutions

  • A156T
  • T167G
  • G168A
  • T180A
  • T199C
  • C204T
  • C210T
  • C216A
  • G219A
  • G222C
  • A231T
  • T234C
  • C246T
  • C255T
  • G261A
  • A267T
  • T273C
  • A285T
Deletions

6991-6998, 10409-10411, 10416, 10417, 10422-10443, 10461-10466, 10484-10490, 10499-10535, 10544-10606, 10619-10684, 10692-10712, 10718-10730, 10738-10781, 10790-10806, 10812-10828, 10842-10861, 10871-10924, 10931-10996
Insertions

ins_6972:AAGCC, ins_7005:GTTGA, ins_7014:G

Amino acid substitutions

Substitutions called relative to the NC_009942.1 reference

Substitutions

2K

  • 2K:M15L

NS1

  • NS1:S9G
  • NS1:Y34F
  • NS1:Y35H
  • NS1:K44R
  • NS1:I46V
  • NS1:K51A
  • NS1:V71I
  • NS1:E94N
  • NS1:S99A
  • NS1:T105A
  • NS1:I113M
  • NS1:L123I
  • NS1:V135I
  • NS1:K141E
  • NS1:Q146A
  • NS1:L153M
  • NS1:K170R
  • NS1:V171I

NS2A

  • NS2A:M34I
  • NS2A:L38M
  • NS2A:I39L
  • NS2A:S68A
  • NS2A:M90L
  • NS2A:N104S
  • NS2A:V112A
  • NS2A:H119Y
  • NS2A:R122K
  • NS2A:Q123N
  • NS2A:I124V
  • NS2A:L126S
  • NS2A:I129V
  • NS2A:V132I
  • NS2A:A137S
  • NS2A:T147S
  • NS2A:T150N
  • NS2A:R167K

NS2B

  • NS2B:A41V
  • NS2B:S61T
  • NS2B:M88I
  • NS2B:V103A
  • NS2B:V120I

NS3

  • NS3:K11R
  • NS3:Q92H
  • NS3:F130Y
  • NS3:D172E
  • NS3:I175A
  • NS3:R203K
  • NS3:R215K
  • NS3:A233S
  • NS3:N253S
  • NS3:V283I
  • NS3:S302A
  • NS3:S331A
  • NS3:L336M
  • NS3:S347T
  • NS3:T356V
  • NS3:V384I
  • NS3:T436E
  • NS3:E439D

NS4A

  • NS4A:I6V
  • NS4A:K11R

NS4B

  • NS4B:S11N
  • NS4B:F17L
  • NS4B:Q19H
  • NS4B:M29G
  • NS4B:T116A
  • NS4B:I168V
  • NS4B:L183M
  • NS4B:K193R
  • NS4B:I202T

NS5

  • NS5:Q18H
  • NS5:I33T
  • NS5:K45R
  • NS5:V49I
  • NS5:I78V
  • NS5:R101K
  • NS5:C139A
  • NS5:C140S
  • NS5:I162V
  • NS5:R177K
  • NS5:V181I
  • NS5:K190R
  • NS5:L197A
  • NS5:R224H
  • NS5:V229I
  • NS5:R247K
  • NS5:D312E
  • NS5:Y374C

capsid

  • capsid:V24G
  • capsid:S100T
  • capsid:K108T
  • capsid:T109A
  • capsid:I111F
  • capsid:A112T
  • capsid:V113I
  • capsid:M114L
  • capsid:I115L
  • capsid:S120C
  • capsid:V121A

env

  • env:E55D
  • env:T64S
  • env:K71R
  • env:D83E
  • env:R93K
  • env:S122T
  • env:I126T
  • env:R128W
  • env:T129I
  • env:L131Q
  • env:V159T
  • env:L167F
  • env:A172S
  • env:N199S
  • env:T205S
  • env:T208A
  • env:T210S
  • env:V232T

prM

  • prM:M44L
  • prM:D46E
  • prM:S57A
  • prM:A73S
  • prM:M112L
  • prM:V156A
  • prM:V157I
Deletions

NS4B

NS4B:26-28
Insertions

NS4B

ins_NS4B:29:V

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