Hepatitis E virus: Whole genome sequencing as a new tool for understanding HEV epidemiology and phenotypes.

Autor: Davis CA; MRC-University of Glasgow Centre for Virus Research, Glasgow, UK., Haywood B; Blood Borne Virus Unit, Virus Reference Department, National Infection Service, Public Health England, London, UK., Vattipally S; MRC-University of Glasgow Centre for Virus Research, Glasgow, UK., Da Silva Filipe A; MRC-University of Glasgow Centre for Virus Research, Glasgow, UK., AlSaeed M; Life Science & Environment Research Institute, National Center for Genome Technology, King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia., Smollet K; MRC-University of Glasgow Centre for Virus Research, Glasgow, UK., Baylis SA; Paul-Ehrlich-Institut (PEI), Langen, Germany., Ijaz S; Blood Borne Virus Unit, Virus Reference Department, National Infection Service, Public Health England, London, UK., Tedder RS; Blood Borne Virus Unit, Virus Reference Department, National Infection Service, Public Health England, London, UK; University College London, London, UK; Microbiology Services, NHS Blood and Transplant, Colindale, UK., Thomson EC; MRC-University of Glasgow Centre for Virus Research, Glasgow, UK., Abdelrahman TT; MRC-University of Glasgow Centre for Virus Research, Glasgow, UK; Microbiology Department, Laboratoire National de Sante, Dudelange, Luxembourg. Electronic address: Tamir.abdelrahman@lns.etat.lu.
Jazyk: angličtina
Zdroj: Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology [J Clin Virol] 2021 Jun; Vol. 139, pp. 104738. Date of Electronic Publication: 2021 Jan 27.
DOI: 10.1016/j.jcv.2021.104738
Abstrakt: 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 × 10 4 -1.17 × 10 7 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.
(Copyright © 2021. Published by Elsevier B.V.)
Databáze: MEDLINE
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