PP_000SKPH.1

Display Name: USA/PP_000SKPH.1/2019-08-13
Nicole M. Feriancek, Mallery I. Breban, Ellie Bourgikos, Angela Bransfield, Philip M. Armstrong, Chantal B. F. Vogels & Nathan D. Grubaugh

Sample details

Collection date
2019-08-13
Latitude
41.26405
Longitude
-72.87785
Country
USA
Admin level 1
Connecticut
Admin level 2
New Haven
City
East Haven
Isolate name
EH43G-8-13-Cxp

Data use terms

Data use terms
OPEN

Data use terms history

ChangedUserData use terms
2024-11-06 12:51annaparker_curatorOPEN
Data use terms URL

Lineage

Lineage
1A

Authors

Author affiliations
Grubaugh Lab, Yale University, CT, USA

INSDC

INSDC accession
BioProject accession
BioSample accession
GCA accession

Sampling

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

Specimen processing

Specimen processing details
Sample consisted of 9 whole, blended mosquitoes from a given trap pooled in groups of up to 50 by species and date

Host

Host taxon ID
Host name - scientific
Culex pipiens
Is lab host
False

Sequencing

Sequencing date
2024-02-19
Amplicon PCR primer scheme
WNVUS1
Amplicon size
400bp
Sequencing protocol
COVIDSeq protocol (primers switched)
Sequenced by - organization
Grubaugh Lab, Yale University, CT, USA
Sequenced by - contact name
Nicole M Feriancek
Raw sequence data processing method
iVar v1.3.1
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

Alignment and QC metrics

Length
10917
Completeness
98.98%
# of SNPs
88
# of inserted bases
0
# of deleted bases
0
# of ambiguous bases
0
# of unknown bases
0
# of frame shifts
0
# of stop codons
0

Submission details

Submission ID
Yale-WNV0598
Submitting group
Date submitted
2024-11-06 12:51:04 UTC
Date released
2024-11-06 12:55:45 UTC
Earliest release date
2024-11-06

Nucleotide mutations

Mutations called relative to the NC_009942.1 reference

Substitutions

  • C340T
  • C435T
  • C531T
  • A630G
  • T642C
  • A919C
  • T928C
  • C1170T
  • T1442C
  • C1465T
  • G1524A
  • G1662A
  • C1750T
  • T2002C
  • C2109T
  • G2257A
  • C2304T
  • C2466T
    • Deletions
    None
    Insertions
    None

    Amino acid mutations

    Mutations called relative to the NC_009942.1 reference

    Substitutions

    NS1

  • NS1:P258S

    • NS2A

  • NS2A:H119Y
  • NS2A:R188K

    • NS3

  • NS3:I352V

    • NS4B

  • NS4B:I240M

    • NS5

  • NS5:A860T

    • env

  • env:V159A
  • env:L167F
  • env:V431I

    • prM

  • prM:F155L
    • Deletions
    None
    Insertions
    None

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