DNA sequencing of whole human cytomegalovirus genomes from formalin-fixed, paraffin-embedded tissues from congenital cytomegalovirus disease cases

Background

Congenital cytomegalovirus disease (cCMV) can be severe but is uncommon. Investigations of the role of genome sequence variation in the causative virus (human cytomegalovirus, HCMV) in clinical outcome have to date depended on small sample numbers derived from fresh tissues. Extensive formalin-fixed, paraffin-embedded (FFPE) cCMV biorepositories established worldwide potentially provide much larger sample numbers for future investigations. However, there are no published reports of sequencing whole HCMV genomes from such material.

Objective

To sequence whole HCMV genomes from cCMV FFPE material.

Study design

Sixteen FFPE samples of foetal kidney or placental tissue were processed from ten cCMV cases in foetuses or neonates. Two commercial kits for extracting DNA from FFPE material were evaluated, HCMV DNA was enriched in the extracts, and the samples were sequenced on the Illumina platform. The sequence read datasets were analysed by genotyping, genome assembly and variant calling using a published software pipeline.

Results

Whole HCMV genomes were sequenced for five cases using either DNA extraction kit.

Conclusions

Sequencing whole HCMV genomes from cCMV FFPE material is feasible. This potentially facilitates future studies of the effects of HCMV variation on the clinical outcome of cCMV.

Highlights

• Human cytomegalovirus (HCMV) causes congenital cytomegalovirus disease (cCMV).

• cCMV samples exist in formalin-fixed, paraffin-embedded (FFPE) biorepositories.

• Sequencing whole HCMV genomes from such material is feasible.

• This may aid future studies on the effect of HCMV diversity on cCMV outcomes.