Davis, C. A. et al. (2021) Hepatitis E virus: whole genome sequencing as a new tool for understanding HEV epidemiology and phenotypes. Journal of Clinical Virology, 139, 104738. (doi: 10.1016/j.jcv.2021.104738) (PMID:33933822)
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Abstract
Hepatitis E Virus (HEV) is emerging as a public health concern across Europe and tools for complete genome data to aid epidemiological and virulence analysis are needed. The high sequence heterogeneity observed amongst HEV genotypes has restricted most analyses to subgenomic regions using PCR-based methods, which can be unreliable due to poor primer homology. We designed a panel of custom-designed RNA probes complementary to all published HEV full genome NCBI sequences. A target enrichment protocol was performed according to the NimbleGen® standard protocol for Illumina® library preparation. Optimisation of this protocol was performed using 40 HEV RNA-positive serum samples and the World Health Organization International Reference Panel for Hepatitis E Virus RNA Genotypes for Nucleic Acid Amplification Technique (NAT)-Based Assays and related reference materials. Deep sequencing using this target enrichment protocol resulted in whole genome consensus sequences from samples with a viral load range of 1.25 × 104-1.17 × 107 IU/mL. Phylogenetic analysis of these sequences recapitulated and extended the partial genome results obtained from genotyping by Sanger sequencing (genotype 1, ten samples and genotype 3, 30 samples). The protocol is highly adaptable to automation and could be used to sequence full genomes of large sample numbers. A more comprehensive understanding of hepatitis E virus transmission, epidemiology and viral phenotype prediction supported by an efficient method of sequencing the whole viral genome will facilitate public health initiatives to reduce the prevalence and mitigate the harm of HEV infection in Europe.
| Item Type: | Articles |
|---|---|
| Status: | Published |
| Refereed: | Yes |
| Glasgow Author(s) Enlighten ID: | Thomson, Professor Emma and Smollett, Dr Katherine and Da Silva Filipe, Dr Ana and Vattipally, Dr Sreenu and Davis, Dr Chris |
| Authors: | Davis, C. A., Haywood, B., Vattipally, S., Da Silva Filipe, A., AlSaeed, M., Smollett, K., Baylis, S. A., Ijaz, S., Tedder, R. S., Thomson, E. C., and Abdelrahman, T. T. |
| College/School: | College of Medical Veterinary and Life Sciences > School of Infection & Immunity > Centre for Virus Research |
| Journal Name: | Journal of Clinical Virology |
| Publisher: | Elsevier |
| ISSN: | 1386-6532 |
| ISSN (Online): | 1873-5967 |
| Published Online: | 27 January 2021 |
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