PP_006WANE.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.
South_Africa/PP_006WANE.1/2026-05-02
J. Weyer, N. Moolla, A. Grobbelaar, K. Govender, J. Featherston, A. Ismail, S. Genu, M. Moodley & A. Moultrie

National Institute of Communicable Diseases

Sample details

Collection date
2026-05-02
Sample received date
2026-05-02
Sampling location
South Africa
City
Johannesburg

Data use terms

Data use terms
RESTRICTED

Data use terms history

ChangedUserData use terms
2026-05-11 13:06jonathanf@nicd.ac.zaRESTRICTED until 2027-05-11
Data use terms URL

Sampling

Anatomical material
Blood

Host

Host
Host origin country
United Kingdom

Sequencing

Purpose of sequencing
Genome reconstruction
Sequencing date
2026-05-10
Sequencing instrument
Nanopore Minion, Illumina NextSeq 2000 and Element BioSciences Aviti
Sequencing protocol
SISPA based cDNA production then Illumina DNA prep or Nanopore Rapid Kit.
Sequenced by - organization
National Institute For Communicable Disease
Sequenced by - contact name
Jonathan Featherston
Sequenced by - contact email
JonathanF@nicd.ac.za
Raw sequence data processing method
Trim-galore
Dehosting method
Map to hg38 then extract with Picard tools 3.0.0
Consensus sequence software name
Samtools
Consensus sequence software version
1.18
Depth of coverage
50

Submission details

Submission ID
SVPL_201
Submitting group
Date submitted
2026-05-11 13:06:16 UTC
Date released
2026-05-11 13:09:51 UTC
Earliest release date
2026-05-11

Alignment and QC

Length L
6463 (98.4%)
# of SNPs L
387
# of unknown bases L
5
Length S
1744 (92.8%)
# of SNPs S
124
# of inserted bases S
6
# of deleted bases S
2
# of unknown bases S
3
Length M
3595 (97.9%)
# of SNPs M
207
# of deleted bases M
1
# of unknown bases M
1
# of frame shifts M
1
Frame shifts M
GPC:861-1139(nt:2630-3468)

Nucleotide mutations

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

Substitutions

L

  • T47C
  • G62A
  • T68G
  • C74T
  • C131T
  • C146T
  • C147T
  • G149A
  • C155T
  • C173T
  • T182C
  • T215C
  • A218G
  • A233C
  • T278C
  • A296G
  • T297C
  • A302G

M

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

S

  • A18G
  • A21G
  • G28A
  • A56G
  • G63A
  • G66A
  • G120A
  • A135G
  • T202C
  • A219G
  • T225C
  • T306C
  • G315A
  • A318G
  • C328T
  • C417T
  • C444A
  • G450A
Deletions

M

2629

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

N

  • N:Q5R

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

GPC

GPC:860
Insertions
N/A

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