A novel ZIKV-targeted scRNA-seq method for precise quantification of ZIKV RNA

Area of Science:

• Virology
• Genomics
• Immunology

Background:

• Zika virus (ZIKV) poses a significant public health threat, yet precise quantitative diagnostic methods are lacking.
• Existing single-cell RNA sequencing (scRNA-seq) struggles to detect ZIKV RNA due to its lack of a poly(A) tail, hindering infected cell identification.

Purpose of the Study:

• To develop and validate a novel ZIKV-targeted scRNA-seq method for accurate ZIKV RNA quantification in individual cells.
• To compare the efficacy of the ZIKV-targeted scRNA-seq method against standard 10× Genomics scRNA-seq for ZIKV detection.
• To identify ZIKV-susceptible cell types in the brain and assess changes in cell populations post-infection.

Main Methods:

• Developed a novel ZIKV-targeted scRNA-seq method.
• Infected immunocompetent suckling mice intracerebrally with ZIKV.
• Performed comparative scRNA-seq analysis using ZIKV-targeted and 10× Genomics methods on brain samples at 10 days post-infection.
• Validated findings using immunofluorescence assay (IFA).

Main Results:

• Identified 17 distinct cell types in mouse brains, with altered distributions post-ZIKV infection.
• The ZIKV-targeted scRNA-seq method demonstrated higher efficiency in capturing exogenous cells compared to 10× Genomics scRNA-seq.
• Peripheral blood-derived monocytes/macrophages (PBDMMs), neurons, and T cells were identified as primary ZIKV RNA-expressing cell types.
• IFA confirmed ZIKV infection in neurons and microglia, with significant reductions in their numbers.

Conclusions:

• The novel ZIKV-targeted scRNA-seq method enables accurate quantification of ZIKV RNA at the single-cell level.
• This method offers advantages in detecting exogenous cells and provides insights into ZIKV pathogenesis.
• The approach is adaptable for quantifying other viral RNAs at the single-cell level, aiding therapeutic and vaccine development.