PP_0004CQZ.2

Display Name: Pakistan/PP_0004CQZ.2/2023-01-01
Umair, M.; Ammar, M.; Haider, S. A.; Jamal, Z.; Salman, M.

Submission details

Submission ID
OR728658.1
Submitting group
Automated Ingest from INSDC/NCBI Virus by Loculus
Date submitted
2024-09-26 15:01:22 UTC
Date released
2024-09-26 15:27:04 UTC

Data use terms

Data use terms
OPEN

Data Use Terms History

ChangedUserData Use Terms
2024-08-27 12:09insdc_ingest_userOPEN
Data use terms URL
https://pathoplexus.org/about/terms-of-use/open-data

Authors

Author affiliations
National Institute of Health, Department of Virology

Alignment states and QC metrics

Completeness
79.86%
Length
10470
Total ambiguous nucs
0
Total deleted nucs
1
Total frame shifts
0
Total inserted nucs
0
Total SNPs
329
Total stop codons
0
Total unknown nucs
1663

Sample details

Collection country
Pakistan
Collection date
2023
Collection date (lower bound)
2023-01-01
Collection date (upper bound)
2023-11-08
Isolate name
WNV/PAK-01/2023

Host

Host name scientific
Homo sapiens
Host taxon id
9606

INSDC

INSDC accession
OR728658.1
NCBI release date
2023-11-08
NCBI update date
2023-11-08

Lineage

Lineage
1A

Nucleotide mutations

Substitutions

  • G420A
  • C474T
  • T510C
  • T513C
  • T528C
  • C534T
  • T585C
  • A630G
  • T634G
  • T666C
  • C708T
  • C745T
  • G789A
  • G873A
  • G903A
  • C911A
  • A919C
  • T945C
    • Deletions
    10827
    Insertions
    None

    Amino acid mutations

    Substitutions

    NS1

  • NS1:S99P
  • NS1:L111F
  • NS1:E289D
  • NS1:T298I
  • NS1:D326G

    • NS2A

  • NS2A:H119Y
  • NS2A:V155A
  • NS2A:I183V
  • NS2A:D226N

    • NS2B

  • NS2B:A36T
  • NS2B:I107V

    • NS3

  • NS3:T356I
  • NS3:S421N

    • NS4A

  • NS4A:A85T

    • env

  • env:F90Y
  • env:I126T
  • env:I135V
  • env:V159I
  • env:L167F
  • env:V491I

    • prM

  • prM:S57A
  • prM:T149N
    • Deletions
    None
    Insertions
    None