Full genome sequencing and analysis of human cytomegalovirus strain JHC isolated from a Korean patient

Jung, Gyoo Seung; Kim, Yu Young; Kim, Jong Ik; Ji, Ga Young; Jeon, Jeong Sun; Yoon, Hyung Woo; Lee, Gyu-Cheol; Ahn, Jinhee; Lee, Keon Myung; Lee, Chan Hee

doi:10.1016/j.virusres.2011.01.005

Cited by 17 publications

(17 citation statements)

References 26 publications

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“…The set of miRNAs described in this study are conserved across different laboratory and clinical isolate strains of HCMV, despite instances of sequence variability across other genomic loci (10,15). Our smRNA-seq data did not support expression of HCMV miR-UL70, despite the recent quantitative PCR experiments by Stern-Ginossar et al using two clinical strains (35).…”

Section: Discussioncontrasting

confidence: 79%

High-Resolution Profiling and Analysis of Viral and Host Small RNAs during Human Cytomegalovirus Infection

Stark

Arnold

Spector

et al. 2012

J Virol

135

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Human cytomegalovirus (HCMV) contributes its own set of microRNAs (miRNAs) during lytic infection of cells, likely finetuning conditions important for viral replication. To enhance our understanding of this component of the HCMV-host transcriptome, we have conducted deep-sequencing analysis of small RNAs (smRNA-seq) from infected human fibroblast cells. We found that HCMV-encoded miRNAs accumulate to ϳ20% of the total smRNA population at late stages of infection, and our analysis led to improvements in viral miRNA annotations and identification of two novel HCMV miRNAs, miR-US22 and miRUS33as. Both of these miRNAs were capable of functionally repressing synthetic targets in transient transfection experiments. Additionally, through cross-linking and immunoprecipitation (CLIP) of Argonaute (Ago)-bound RNAs from infected cells, followed by high-throughput sequencing, we have obtained direct evidence for incorporation of all HCMV miRNAs into the endogenous host silencing machinery. Surprisingly, three HCMV miRNA precursors exhibited differential incorporation of their mature miRNA arms between Ago2 and Ago1 complexes. Host miRNA abundances were also affected by HCMV infection, with significant upregulation observed for an miRNA cluster containing miR-96, miR-182, and miR-183. In addition to miRNAs, we also identified novel forms of virus-derived smRNAs, revealing greater complexity within the smRNA population during HCMV infection. Human cytomegalovirus (HCMV), a member of the herpesvirus family, is prevalent in the majority of the global population and the main viral cause of birth defects (19). HCMV is capable of infecting a wide variety of human cell types in vivo and is known to establish a latent form of infection that persists throughout the life of the host. Immunocompromised patients are especially susceptible to problems associated with infection, further motivating HCMV studies.Expression of virus-encoded microRNAs (miRNAs) likely contributes to the molecular transformation necessary for productive infection in human cells. Since the initial discovery of viral miRNAs in 2004 (24), several viruses have been documented to express their own sets of miRNAs (4,5,7,11,12,23). These small RNAs (smRNAs) are highly attractive from a viral standpoint in that they require minimal space within the genome and potentially offer a robust mechanism for specific targeting of host defense genes. HCMV is known to encode at least 11 miRNA precursors that are expressed and processed into mature miRNAs during infection (12).High-throughput sequencing approaches have been instrumental in recent viral miRNA studies, acquiring a level of resolution that was previously unachievable through cloning efforts (17,27,36). Deep-sequencing approaches have not been extended to smRNA analysis of HCMV-infected cells, and previous microarray-based studies were limited in assessing only host miRNA levels (30,37). Thus, we set out to conduct a more comprehensive analysis by deep sequencing all smRNAs (smRNA-seq) from HCMV Towne-infected human f...

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Section: Discussioncontrasting

confidence: 79%

High-Resolution Profiling and Analysis of Viral and Host Small RNAs during Human Cytomegalovirus Infection

Stark

Arnold

Spector

et al. 2012

J Virol

135

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“…However, apart from two Asian strains, all isolates were collected from European and North American patients. Interestingly, Asian strains JHC (128) and HAN are neighbors in the split network (highlighted in gray in Fig. 6A), but they do not Table S1 in the supplemental material, neighbor-net split networks were constructed for HSV-1, VZV, and EBV strains.…”

Section: Resultsmentioning

confidence: 99%

High-Throughput Analysis of Human Cytomegalovirus Genome Diversity Highlights the Widespread Occurrence of Gene-Disrupting Mutations and Pervasive Recombination

Sijmons

Thys

Ngwese

et al. 2015

J Virol

159

219

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Human cytomegalovirus is a widespread pathogen of major medical importance. It causes significant morbidity and mortality in immunocompromised individuals, and congenital infections can result in severe disabilities or stillbirth. Development of a vaccine is prioritized, but no candidate is close to release. Although correlations of viral genetic variability with pathogenicity are suspected, knowledge about the strain diversity of the 235-kb genome is still limited. In this study, 96 full-length human cytomegalovirus genomes from clinical isolates were characterized, quadrupling the amount of information available for full-genome analysis. These data provide the first high-resolution map of human cytomegalovirus interhost diversity and evolution. We show that cytomegalovirus is significantly more divergent than all other human herpesviruses and highlight hot spots of diversity in the genome. Importantly, 75% of strains are not genetically intact but contain disruptive mutations in a diverse set of 26 genes, including the immunomodulatory genes UL40 and UL111A. These mutants are independent of culture passage artifacts and circulate in natural populations. Pervasive recombination, which is linked to the widespread occurrence of multiple infections, was found throughout the genome. The recombination density was significantly higher than those of other human herpesviruses and correlated with strain diversity. While the overall effects of strong purifying selection on virus evolution are apparent, evidence of diversifying selection was found in several genes encoding proteins that interact with the host immune system, including UL18, UL40, UL142, and UL147. These residues may present phylogenetic signatures of past and ongoing virus-host interactions. IMPORTANCEHuman cytomegalovirus has the largest genome of all viruses that infect humans. Currently, there is a great interest in establishing associations between genetic variants and strain pathogenicity of this herpesvirus. Since the number of publicly available full-genome sequences is limited, knowledge about strain diversity is highly fragmented and biased toward a small set of loci. Combined with our previous work, we have now contributed 101 complete genome sequences. We have used these data to conduct the first high-resolution analysis of interhost genome diversity, providing an unbiased and comprehensive overview of cytomegalovirus variability. These data are of major value to the development of novel antivirals and a vaccine and to identify potential targets for genotype-phenotype experiments. Furthermore, these data have enabled a thorough study of the evolutionary processes that have shaped cytomegalovirus diversity. Human cytomegalovirus (HCMV), the prototype member of the herpesvirus subfamily Betaherpesvirinae, is a widespread and important pathogen. Seroprevalence in the adult population ranges from 45% to 100% (1). After primary infection, HCMV establishes a lifelong, latent infection in myeloid progenitor cells (2). This virus causes mild to ...

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“…Phylogenetic analysis of gH confirmed the presence of two main genotypes in addition to a possible third group including the newly reported JHC strain that was isolated from a bone marrow transplant patient. 73 Analysis confirmed a low level of variation among the gHs (~93% identical) which may explain why anti-gH MAbs appear broadly reactive. 58,74 Due to this high level of conservation, the DNA vaccine consensus immunogen fell between gH1 and gH2, and was closest to the putative third gH group (gH3) including with the JHC clinical isolate.…”

Section: Vaccination With Synthetic Constructs Expressing Cytomegalovmentioning

confidence: 77%

“…1), 50,51,89 immunity can be further directed toward multiple circulating strains by "consensus-engineering" of the amino acid sequence of the vaccine immunogen. 63,64 Furthermore, structurally-relevant immunogens can be incorporated into the same plasmid vaccines for the co-expression of virologically-relevant macromolecular gM [gM [295][296][297][298][299][300][301][302][303][304][305][306][307][308][309] [43][44][45][46][47][48][49][50][51][52][53][54][55][56][57] ; CD8+/CD4+ (#8)], and UL131A [UL131A [61][62][63][64][65][66][67][68][69][70][71][72][73][74][75] ; CD4+ (#11)]. Two CD8-restricted immunodominant epitopes were detected follo...…”

Section: Discussionmentioning

confidence: 99%

Vaccination with synthetic constructs expressing cytomegalovirus immunogens is highly T cell immunogenic in mice

Shedlock¹,

Talbott

et al. 2012

Human Vaccines & Immunotherapeutics

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Full genome sequencing and analysis of human cytomegalovirus strain JHC isolated from a Korean patient

Cited by 17 publications

References 26 publications

High-Resolution Profiling and Analysis of Viral and Host Small RNAs during Human Cytomegalovirus Infection

High-Resolution Profiling and Analysis of Viral and Host Small RNAs during Human Cytomegalovirus Infection

High-Throughput Analysis of Human Cytomegalovirus Genome Diversity Highlights the Widespread Occurrence of Gene-Disrupting Mutations and Pervasive Recombination

Vaccination with synthetic constructs expressing cytomegalovirus immunogens is highly T cell immunogenic in mice

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