Genome Sequencing of Human Cytomegalovirus Strain LCW and Identification of Asia-specific Cluster

Ji Hye Kang; Jeong Hwa Yoon; Hye Rim Hwang; Chan Hee Lee

doi:10.4167/jbv.2018.48.4.147

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Kang, Yoon, Hwang, and Lee: Genome Sequencing of Human Cytomegalovirus Strain LCW and Identification of Asia-specific Cluster

Original Article

Journal of Bacteriology and Virology 2018; 48(4): 147-155.

Published online: 31 December 2018

DOI: https://doi.org/10.4167/jbv.2018.48.4.147

Genome Sequencing of Human Cytomegalovirus Strain LCW and Identification of Asia-specific Cluster

Ji Hye Kang, Jeong Hwa Yoon, Hye Rim Hwang, Chan Hee Lee

Department of Microbiology, Chungbuk National University, Cheongju, Chungbuk, Korea.

Corresponding: Chan Hee Lee, Ph.D. Department of Microbiology, Chungbuk National University, 1 Chungdae-Ro, Seowon-Gu, Cheongju, Chungbuk 28644, Korea. Phone : +82-43-261-2304, Fax : +82-43-264-9600, chlee@chungbuk.ac.kr

Received 30 October 2018 Revised 12 November 2018 Accepted 16 November 2018

The Korean Society for Microbiology and The Korean Society of Virology

(open-access):

This is an open access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/).

Abstract

Human cytomegalovirus (HCMV) is a ubiquitous human pathogen and contains double stranded DNA genome with approximately 230 kbp. Molecular genomic studies of HCMV have been attempted in order to understand the pathogenesis and evolution of HCMV. However, studies on HCMV strains of Asian origin are limited. In this study, it was attempted to understand the genomics of HCMV isolated from Korea. Clinical strain LCW isolated from Korean patient was passaged in vitro cell culture, and subjected to next-generation sequencing. Complete genome sequence was obtained and compared with other HCMV strains. The LCW genome was found to contain 170 open reading frames (ORFs) and two ORF (RL5A and RL13) of the strain LCW were found to be truncated due to early stop codon. Phylogenetic analysis suggested that the strain LCW was closely related with Asian strains such as HCMV strains JHC and HAN. Common nucleotide sequences among the 3 Asian strains distinguishable from other strains were detected at 197 sites including 104 sites in ORFs.

Keywords: Human cytomegalovirus, Genome sequence, Asian cluster

Figures and Tables

Figure 1

Genome map of the HCMV strain LCW. Nucleotide positions corresponding to the HCMV genome structure and the ORFs contained in each of the genome structure is indicated.

Figure 2

Sequence alignment of HCMV ORF RL5A and RL13. Early stops due to mutations in the strain LCW are boxed. (A) ORF RL5A due to T->A substitution at the third position of the codon, (B) RL13 due to C->A substitution at the first position of the codon.

Figure 3

Phylogenetic tree of 42 HCMV strains. Genomic DNA sequences of HCMV strains were retrieved from NCBI GenBank database and aligned with ClustalW program together with the genome sequence of the Korean strain LCW. Phylogenetic tree was constructed using neighbor-joining model in Phylip package. Cluster of HCMV strains of Asian origin is indicated as a circle.

Figure 4

Distribution of the mutations found specifically in Asian strains of HCMV. Numbers of synonymous (□) and nonsynonymous (■) mutations are shown.

Table 1

Information of 42 HCMV strains analyzed in this study

Table 2

Mutations leading to single nucleotide polymorphism specific for the HCMV strains of Asian origin

ORF: Open reading frame; NCR: Non-coding region; NonSyn: Non-synonymous mutation; NS: Nonsense mutation; Ts: Transition; Tv: Transversion; In: Insertion; Del: Deletion

ACKNOWLEDGEMENT

This study was supported in part by a grant from Green Cross Company.

Notes

No potential conflict of interest relevant to this article was reported.

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