publication . Article . Other literature type . 2017

Clinical and biological insights from viral genome sequencing.

Mathew A. Beale; Mathew A. Beale; Charlotte J. Houldcroft; Charlotte J. Houldcroft; Judith Breuer;
Open Access English
  • Published: 23 Jan 2017
  • Publisher: NATURE PUBLISHING GROUP
  • Country: United Kingdom
Abstract
Whole-genome sequencing (WGS) of pathogens is becoming increasingly important not only for basic research but also for clinical science and practice. In virology, WGS is important for the development of novel treatments and vaccines, and for increasing the power of molecular epidemiology and evolutionary genomics. In this Opinion article, we suggest that WGS of viruses in a clinical setting will become increasingly important for patient care. We give an overview of different WGS methods that are used in virology and summarize their advantages and disadvantages. Although there are only partially addressed technical, financial and ethical issues in regard to the c...
Subjects
free text keywords: General Immunology and Microbiology, diagnosis, microbiology techniques, next-generation sequencing, Article, DNA sequencing, Biology, Medical research, Metagenomics, Clinical microbiology, Genomics, Bioinformatics, European union, media_common.cataloged_instance, media_common, Library science, Research centre
Funded by
EC| PATHSEEK
Project
PATHSEEK
Automated Next Generation Sequencing for Diagnostic Microbiology
  • Funder: European Commission (EC)
  • Project Code: 304875
  • Funding stream: FP7 | SP1 | HEALTH
,
WT
Project
  • Funder: Wellcome Trust (WT)
145 references, page 1 of 10

Gardner, RC. The complete nucleotide sequence of an infectious clone of cauliflower mosaic virus by M13mp7 shotgun sequencing. Nucleic Acids Res.. 1981; 9: 2871-2888 [OpenAIRE] [PubMed]

Lander, ES. Initial sequencing and analysis of the human genome. Nature. 2001; 409: 860-921 [PubMed]

Fleischmann, RD. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science. 1995; 269: 496-512 [PubMed]

Fraser, CM. The minimal gene complement of Mycoplasma genitalium. Science. 1995; 270: 397-403 [PubMed]

Hayden, EC. Technology: the $1,000 genome. Nature. 2014; 507: 294-295 [PubMed]

Turnbaugh, PJ. The human microbiome project. Nature. 2007; 449: 804-810 [OpenAIRE] [PubMed]

Grigoriev, IV. MycoCosm portal: gearing up for 1000 fungal genomes. Nucleic Acids Res.. 2014; 42: D699-D704 [OpenAIRE] [PubMed]

Worthey, EA. Making a definitive diagnosis: successful clinical application of whole exome sequencing in a child with intractable inflammatory bowel disease. Genet. Med.. 2011; 13: 255-262 [OpenAIRE] [PubMed]

Bryant, JM. Whole-genome sequencing to identify transmission of Mycobacterium abscessus between patients with cystic fibrosis: a retrospective cohort study. Lancet. 2013; 381: 1551-1560 [OpenAIRE] [PubMed]

Lamelas, A. Emergence of a new epidemic Neisseria meningitidis serogroup A clone in the African meningitis belt: high-resolution picture of genomic changes that mediate immune evasion. mBio. 2014; 5: e01974-14 [OpenAIRE] [PubMed]

Zaraket, H. Genetic makeup of amantadine-resistant and oseltamivir-resistant human influenza A/H1N1 viruses. J. Clin. Microbiol.. 2010; 48: 1085-1092 [OpenAIRE] [PubMed]

Houldcroft, CJ. Detection of low frequency multi-drug resistance and novel putative maribavir resistance in immunocompromised pediatric patients with cytomegalovirus. Front. Microbiol.. 2016; 7: 1317 [OpenAIRE] [PubMed]

Witney, AA. Clinical application of whole-genome sequencing to inform treatment for multidrug-resistant tuberculosis cases. J. Clin. Microbiol.. 2015; 53: 1473-1483 [OpenAIRE] [PubMed]

Simen, BB. Low-abundance drug-resistant viral variants in chronically HIV-infected, antiretroviral treatment-naive patients significantly impact treatment outcomes. J. Infect. Dis.. 2009; 199: 693-701 [OpenAIRE] [PubMed]

Smith, GJ. Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic. Nature. 2009; 459: 1122-1125 [PubMed]

145 references, page 1 of 10
Abstract
Whole-genome sequencing (WGS) of pathogens is becoming increasingly important not only for basic research but also for clinical science and practice. In virology, WGS is important for the development of novel treatments and vaccines, and for increasing the power of molecular epidemiology and evolutionary genomics. In this Opinion article, we suggest that WGS of viruses in a clinical setting will become increasingly important for patient care. We give an overview of different WGS methods that are used in virology and summarize their advantages and disadvantages. Although there are only partially addressed technical, financial and ethical issues in regard to the c...
Subjects
free text keywords: General Immunology and Microbiology, diagnosis, microbiology techniques, next-generation sequencing, Article, DNA sequencing, Biology, Medical research, Metagenomics, Clinical microbiology, Genomics, Bioinformatics, European union, media_common.cataloged_instance, media_common, Library science, Research centre
Funded by
EC| PATHSEEK
Project
PATHSEEK
Automated Next Generation Sequencing for Diagnostic Microbiology
  • Funder: European Commission (EC)
  • Project Code: 304875
  • Funding stream: FP7 | SP1 | HEALTH
,
WT
Project
  • Funder: Wellcome Trust (WT)
145 references, page 1 of 10

Gardner, RC. The complete nucleotide sequence of an infectious clone of cauliflower mosaic virus by M13mp7 shotgun sequencing. Nucleic Acids Res.. 1981; 9: 2871-2888 [OpenAIRE] [PubMed]

Lander, ES. Initial sequencing and analysis of the human genome. Nature. 2001; 409: 860-921 [PubMed]

Fleischmann, RD. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science. 1995; 269: 496-512 [PubMed]

Fraser, CM. The minimal gene complement of Mycoplasma genitalium. Science. 1995; 270: 397-403 [PubMed]

Hayden, EC. Technology: the $1,000 genome. Nature. 2014; 507: 294-295 [PubMed]

Turnbaugh, PJ. The human microbiome project. Nature. 2007; 449: 804-810 [OpenAIRE] [PubMed]

Grigoriev, IV. MycoCosm portal: gearing up for 1000 fungal genomes. Nucleic Acids Res.. 2014; 42: D699-D704 [OpenAIRE] [PubMed]

Worthey, EA. Making a definitive diagnosis: successful clinical application of whole exome sequencing in a child with intractable inflammatory bowel disease. Genet. Med.. 2011; 13: 255-262 [OpenAIRE] [PubMed]

Bryant, JM. Whole-genome sequencing to identify transmission of Mycobacterium abscessus between patients with cystic fibrosis: a retrospective cohort study. Lancet. 2013; 381: 1551-1560 [OpenAIRE] [PubMed]

Lamelas, A. Emergence of a new epidemic Neisseria meningitidis serogroup A clone in the African meningitis belt: high-resolution picture of genomic changes that mediate immune evasion. mBio. 2014; 5: e01974-14 [OpenAIRE] [PubMed]

Zaraket, H. Genetic makeup of amantadine-resistant and oseltamivir-resistant human influenza A/H1N1 viruses. J. Clin. Microbiol.. 2010; 48: 1085-1092 [OpenAIRE] [PubMed]

Houldcroft, CJ. Detection of low frequency multi-drug resistance and novel putative maribavir resistance in immunocompromised pediatric patients with cytomegalovirus. Front. Microbiol.. 2016; 7: 1317 [OpenAIRE] [PubMed]

Witney, AA. Clinical application of whole-genome sequencing to inform treatment for multidrug-resistant tuberculosis cases. J. Clin. Microbiol.. 2015; 53: 1473-1483 [OpenAIRE] [PubMed]

Simen, BB. Low-abundance drug-resistant viral variants in chronically HIV-infected, antiretroviral treatment-naive patients significantly impact treatment outcomes. J. Infect. Dis.. 2009; 199: 693-701 [OpenAIRE] [PubMed]

Smith, GJ. Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic. Nature. 2009; 459: 1122-1125 [PubMed]

145 references, page 1 of 10
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