PP_006WDJK.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_006WDJK.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
2026-05-12 14:07jonathanf@nicd.ac.zaRESTRICTED until 2027-05-12
Data use terms URL

Sampling

Anatomical material
Blood

Host

Host
Host origin country
United Kingdom

Sequencing

Purpose of sequencing
Genome reconstruction
Sequencing date
2026-05-12
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
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
100

Submission details

Submission ID
SVPL_200
Submitting group
Date submitted
2026-05-12 14:07:54 UTC
Date released
2026-05-12 14:08:02 UTC
Earliest release date
2026-05-12

Alignment and QC

Length L
6528 (99.4%)
# of SNPs L
388
# of unknown bases L
6
Length S
1860 (98.9%)
# of SNPs S
132
# of inserted bases S
13
# of deleted bases S
6
# of unknown bases S
3
Length M
3603 (99%)
# of SNPs M
210
# of deleted bases M
39
# of unknown bases M
6

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

  • A10G
  • T74C
  • T90C
  • G114A
  • C147T
  • C174T
  • C190T
  • A192G
  • C231T
  • C243T
  • A264G
  • T312C
  • C315T
  • G339C
  • T345C
  • A360G
  • T363C
  • A381G

S

  • T7C
  • G28A
  • G63A
  • G66A
  • G120A
  • A135G
  • T202C
  • A219G
  • T225C
  • T244C
  • T306C
  • G315A
  • A318G
  • C328T
  • C417T
  • C444A
  • G450A
  • T454C
Deletions

M

14-52

S

2-5, 1443, 1573
Insertions

S

ins_0:GCTC, ins_10:TAT, 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

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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