Mexico/MN0053_LESPM_LANCIS_LEVE/2024-05-27
M. I. Valle-Maldonado, M. Avitia, M. T. Solano-De la Cruz, M. A. Garcia-Knight, S. I. Mora-Herrera, B. V. Rivera-Serrano & A. R. C. C. Consortium

Laboratorio Estatal de Salud Pública de Michoacán, Morelia, Michoacán, Mexico; Laboratorio Nacional de Ciencias de la Sostenibilidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico; Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico.

Sample details

Collection date
2024-05-27
Sampling location
Mexico (Michoacan)
Culture ID
Phlebotomy

Data use terms

Data use terms
RESTRICTED

Clade

Clade
Asian

Sampling

Anatomical material
Blood

Sequencing

Sequencing date
2026-06-29
Sequencing instrument
ILLUMINA
Sequencing protocol
Genomes were generated through amplicon-based sequencing using the multiplex PCR protocol described by Quick et al. (Nature Protocols, 2017). Sequencing libraries were prepared using the Illumina DNA Prep Kit, and high-throughput sequencing was performed on an Illumina MiSeq platform.
Sequencing library selection
PCR
Reference genome accession
KJ776791.2
Consensus sequence software name
iVar
Consensus sequence software version
1.4.2

Diagnostics

Diagnostic measurement - method
RT-qPCR

Submission details

Submission ID
MN0053_LESPM_LANCIS_LEVE
Submitting group
Date submitted
2026-10-07 06:31:44 UTC
Date released
2026-10-07 06:33:21 UTC
Earliest release date
2026-10-07

Files


Alignment and QC

Length
7312 (34.3%)
# of SNPs
47
# of unknown bases
3601

Nucleotide mutations

Mutations called relative to the NC_035889.1 reference

Substitutions
  • G2507A
  • T2609C
  • G2681A
  • T2724C
  • T2741C
  • T2767C
  • G2788C
  • G2852A
  • G3059A
  • A3140G
  • A3153G
  • G3186A
  • T3218A
  • G3332A
  • G3341A
  • G3350A
  • C3381T
  • G5119A
Deletions
N/A
Insertions
N/A

Amino acid substitutions

Substitutions called relative to the NC_035889.1 reference

Substitutions

NS1

  • NS1:V93A
  • NS1:G100A
  • NS1:T222A
  • NS1:A233T

NS3

  • NS3:R169K

NS4B

  • NS4B:I240T

NS5

  • NS5:C269R
  • NS5:K397R
  • NS5:R525C
Deletions
N/A
Insertions
N/A

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