PP_000SLC5.1

USA/PP_000SLC5.1/2019-08-27
Nicole M. Feriancek, Mallery I. Breban, Ellie Bourgikos, Angela Bransfield, Philip M. Armstrong, Chantal B. F. Vogels & Nathan D. Grubaugh

Grubaugh Lab, Yale University, CT, USA

Sample details

Collection date
2019-08-27
Latitude
41.3305
Longitude
-72.93995
Sampling location
USA (New Haven, Connecticut)
City
New Haven
Isolate name
NH54G-8-27-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

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 11 whole, blended mosquitoes from a given trap pooled in groups of up to 50 by species and date

Host

Host
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

Submission details

Submission ID
Yale-WNV0621
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

Alignment and QC

Length
10917 (99%)
# of SNPs
96
# of ambiguous bases
2

Nucleotide mutations

Mutations called relative to the NC_009942.1 reference

Substitutions

  • C55T
  • A630G
  • C693T
  • C762T
  • C849T
  • T1000C
  • T1368C
  • A1401G
  • T1442C
  • C1465T
  • C1878A
  • C1893T
  • A1954T
  • T1965C
  • A2097C
  • C2371T
  • C2466T
  • C2593T
Deletions
N/A
Insertions
N/A

Amino acid substitutions

Substitutions called relative to the NC_009942.1 reference

Substitutions

NS2A

  • NS2A:T52I
  • NS2A:L95F
  • NS2A:H119Y

NS3

  • NS3:S334T

NS4B

  • NS4B:S14I

NS5

  • NS5:R422K

env

  • env:V159A
  • env:L167F
  • env:T330S
Deletions
N/A
Insertions
N/A

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