Mexico/MN0054_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
MN0054_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
10611 (98.2%)
# of SNPs
102
# of ambiguous bases
1

Nucleotide mutations

Mutations called relative to the NC_035889.1 reference

Substitutions
  • T79C
  • A254G
  • G420A
  • G536A
  • T635C
  • C776T
  • C878T
  • A890G
  • C1070T
  • T1115C
  • C1196A
  • C1220T
  • C1616T
  • A1760G
  • T1814G
  • T1850C
  • G2015A
  • C2375T
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:E146K
  • NS1:T222A
  • NS1:A233T
  • NS1:V349M

NS2A

  • NS2A:I32V
  • NS2A:I34M
  • NS2A:K56R

NS3

  • NS3:R169K
  • NS3:M572L

NS4B

  • NS4B:I240T

NS5

  • NS5:C269R
  • NS5:K397R
  • NS5:R525C

ancC

  • ancC:G105S
Deletions
N/A
Insertions
N/A

Report an issue with this sequence or metadata

Create GitHub issue