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Mpox Viral Lineage Analysis and Technique Development Using Next-generation Sequencing Approach.

Farruk Kabir1, Erin Plaisance1, Alexandra Portman1

  • 1Dallas County Health and Human Services, Dallas, Texas, USA.

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Summary

Next-generation sequencing (NGS) workflows were developed to analyze mpox (monkeypox) virus. The study identified the West African clade IIb and dominant lineage B.1.2 during the 2022 mpox outbreak.

Keywords:
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Area of Science:

  • Genomics
  • Virology
  • Public Health

Background:

  • The mpox (monkeypox) virus outbreak necessitated rapid development of genomic analysis techniques.
  • The Dallas County Department of Health (DCHHS) sought to enhance mpox viral clade and lineage analysis.

Purpose of the Study:

  • To establish and validate next-generation sequencing (NGS) workflows for mpox virus surveillance.
  • To streamline the analysis of mpox viral clades and lineages.

Main Methods:

  • Adapted Illumina's COVIDSeq assay with custom primer pools for mpox DNA sequencing.
  • Utilized a comprehensive bioinformatics pipeline including BaseSpace, NextClade, and CLC Workbench for data analysis and quality control.
  • Sequenced 171 mpox samples, assessing read quality, depth, and coverage.

Main Results:

  • Confirmed West African clade IIb as the predominant mpox clade during July-October 2022.
  • Identified lineage B.1.2 as the dominant variant (77.7%) in sequenced mpox genomes, suggesting US distribution.
  • Uploaded viral sequences to GISAID EpiPox for global data sharing.

Conclusions:

  • Developed and validated NGS workflows for precise mpox viral clade and lineage detection.
  • Enhanced genomic surveillance capabilities for public health response to mpox outbreaks.