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Related Experiment Video

Updated: Feb 28, 2026

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Single-Cell Transcriptomic Profile Associated with Sub-Subtype A6 and CRF63-02A6 HIV-1 Strain Infection.

Kirill Elfimov1, Anna Khozyainova2, Ludmila Gotfrid1

  • 1State Research Centre of Virology and Biotechnology 'Vector', Koltsovo 630559, Russia.

Viruses
|February 27, 2026
PubMed
Summary

This study reveals early immune cell changes during acute HIV-1 infection in Russia and FSU countries. Single-cell analysis shows immune hyperactivation, altered cell communication, and dysregulated signaling pathways, impacting disease progression.

Keywords:
CRF63_02A6HIV-1acute HIV infectionimmune responsesub-subtype A6transcriptomics

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Area of Science:

  • Immunology
  • Virology
  • Genomics

Background:

  • The HIV-1 epidemic in Russia and Former Soviet Union (FSU) countries is predominantly driven by subtypes A6 and CRF63_02A6.
  • Understanding the early immune response to these specific HIV-1 strains is crucial for developing effective interventions.
  • Previous studies have not fully characterized the single-cell transcriptional landscape of acute HIV-1 infection in this region.

Purpose of the Study:

  • To perform single-cell transcriptomic analysis of peripheral blood mononuclear cells (PBMC) during acute HIV-1 infection.
  • To characterize the early immune responses to HIV-1 sub-subtypes A6 and CRF63_02A6.
  • To identify key immune cell populations and transcriptional pathways affected during early-stage infection.

Main Methods:

  • Single-cell RNA sequencing (scRNA-seq) using 10x Genomics technology on the Illumina NextSeq 550 platform.
  • Analysis of PBMCs from three treatment-naive patients with acute HIV-1 infection and three healthy donors.
  • Data integration (Seurat, Harmony), automated cell-type annotation (CellTypist), and Gene Ontology (GO) enrichment analysis.

Main Results:

  • Profound reorganization of transcriptional programs in memory CD4+ and CD8+ T cells, non-classical monocytes, and NK cells.
  • Observed hyperactivation of pro-inflammatory pathways (NF-kB, TNF, interferon signaling) and upregulation of migration and metabolic adaptation genes.
  • Identified dysregulation of TGF-β and mTOR signaling, disrupted intercellular communication, and altered expression of disease progression and viral control genes.

Conclusions:

  • This study provides the first single-cell transcriptional atlas of early immune responses to HIV-1 A6 and CRF63_02A6 subtypes in the FSU region.
  • The findings highlight significant immune cell hyperactivation, altered signaling, and disrupted communication networks during acute infection.
  • This detailed molecular characterization offers insights into HIV-1 pathogenesis and potential therapeutic targets in this specific epidemic context.