PP_006WDJK.3

Version 3

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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.3/2026-05-02

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

Changed	User	Data use terms
2026-05-12 14:07	jonathanf@nicd.ac.za	RESTRICTED until 2027-05-12

RESTRICTED

Data use terms URL

https://pathoplexus.org/about/terms-of-use/restricted-data

Sampling

Anatomical material

Blood

Host

human (Homo sapiens)

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

NICD_SCF

Date submitted

2026-06-10 11:53:15 UTC

Date released

2026-06-10 11:53:22 UTC

Earliest release date

2026-05-12

Alignment and QC

Length L

6528 (99.4%)

# of SNPs L

388

# of unknown bases L

Length M

3594 (97.8%)

# of SNPs M

208

# of unknown bases M

Length S

1766 (94.1%)

# of SNPs S

126

# of inserted bases S

# of deleted bases S

# of unknown bases S

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

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