PP_000SKQF.1

Display Name: USA/PP_000SKQF.1/2019-08-13
Feriancek, Nicole M.; Breban, Mallery I.; Bourgikos, Ellie; Bransfield, Angela; Armstrong, Philip M.; Vogels, Chantal B.F.; Grubaugh, Nathan D.

Submission details

Submission ID
Yale-WNV0599
Submitting group
Grubaugh Lab
Date submitted
2024-11-06 12:51:04 UTC
Date released
2024-11-06 12:55:45 UTC

Data use terms

Data use terms
OPEN

Data Use Terms History

ChangedUserData Use Terms
2024-11-06 12:51annaparker_curatorOPEN
Data use terms URL
https://pathoplexus.org/about/terms-of-use/open-data

Sequencing

Amplicon PCR primer scheme
WNVUS1
Amplicon size
400bp
Consensus sequence software name
iVar
Consensus sequence software version
v1.3.1
Depth of coverage
10
Quality control method name
iVar trim
Quality control method version
v1.3.1
Raw sequence data processing method
iVar v1.3.1
Sequenced by - contact name
Nicole M Feriancek
Sequenced by
Grubaugh Lab, Yale University, CT, USA
Sequencing date
2024-02-19
Sequencing protocol
COVIDSeq protocol (primers switched)

Authors

Author affiliations
Grubaugh Lab, Yale University, CT, USA

INSDC

Bioproject accession
PRJEB80643
Biosample accession
SAMEA116354794
INSDC accession
OZ201384.1

Sampling

Collection device
Mosquitos trapped using Gravid Trap
Collection method
mosquito trapping
Purpose of sampling
surveillance for arboviruses
Sample type
pooled blended mosquitoes

Alignment states and QC metrics

Completeness
97.48%
Length
11029
Total ambiguous nucs
0
Total deleted nucs
0
Total frame shifts
0
Total inserted nucs
0
Total SNPs
85
Total stop codons
0
Total unknown nucs
278

Sample details

Collection subdivision level 1
Connecticut
Collection subdivision level 2
Hartford
Collection city
Manchester
Collection country
USA
Latitude
41.7661
Longitude
-72.50121
Collection date
2019-08-13
Collection date (lower bound)
2019-08-13
Collection date (upper bound)
2019-08-13
Isolate name
MC80G-8-13-Cxp

Host

Host name scientific
Culex pipiens
Host taxon id
7175
Is lab host
False

Lineage

Lineage
1A

Specimen processing

Specimen processing details
Sample consisted of 26 whole, blended mosquitoes from a given trap pooled in groups of up to 50 by species and date

Nucleotide mutations

Substitutions

  • C93T
  • C340T
  • T375C
  • C435T
  • A630G
  • T699C
  • T1062C
  • T1442C
  • C1465T
  • G1662A
  • C1750T
  • T1998C
  • C2109T
  • C2304T
  • C2466T
  • A2517G
  • T2700C
  • C3061T
    • Deletions
    None
    Insertions
    None

    Amino acid mutations

    Substitutions

    NS2A

  • NS2A:R188K

    • NS4B

  • NS4B:I240M

    • NS5

  • NS5:M395L

    • env

  • env:V159A
  • env:L167F
    • Deletions
    None
    Insertions
    None