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Next generation sequencing for global infectious disease control
Sequencing is getting cheaper, more accessible, and faster. With that, applications for patient care and public health work ( surveillance, outbreak detection, source tracing, virulence mapping) is becoming realistic. What does it take to bring NGS within reach of public health workers across the globe? I am interested in linking the scientific advances in the field of NGS and topics where their application may be of added value
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Divergent astrovirus associated with neurol... [Emerg Infect Dis. 2013] - PubMed - NCBI

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Direct Assessment of Viral Diversity in Soils by Random PCR Amplification of Polymorphic DNA

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important step for implementation in field and clinical work?
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A Modified RNA-Seq Approach for Whole Genome Sequen... [PLoS One. 2013] - PubMed - NCBI

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Whole-genome, deep pyrosequencing analysis... [Infect Genet Evol. 2013] - PubMed - NCBI

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Widespread infection outbreaks pose biggest detection challenge - Family Practice News Digital Network

Widespread infection outbreaks pose biggest detection challenge - Family Practice News Digital Network | Next generation sequencing for global infectious disease control | Scoop.it
Widespread infection outbreaks pose biggest detection challenge
Family Practice News Digital Network
VIENNA – Widespread foodborne infectious-disease outbreaks pose the greatest challenge for detection, according to an analysis of 101 U.S.
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Ahead of Print - Full-Genome Deep Sequencing and Phylogenetic Analysis of Novel Human Betacoronavirus - Vol. 19 No. 5 - May 2013 - Emerging Infectious Disease journal - CDC

Ahead of Print - Full-Genome Deep Sequencing and Phylogenetic Analysis of Novel Human Betacoronavirus - Vol. 19 No. 5 - May 2013 - Emerging Infectious Disease journal - CDC | Next generation sequencing for global infectious disease control | Scoop.it
A novel betacoronavirus associated with lethal respiratory and renal complications was recently identified in patients from several countries in the Middle East.
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Genomic approaches to studying the human microbiota

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preparing for a talk at the GMI eeting in Copenhagen. Fun reads...

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Evolutionary Characterization of the Pandemic H1N1/2009 Influenza Virus in Humans Based on Non-Structural Genes

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Next-generation sequencing to assess HIV ... [Curr Opin HIV AIDS. 2012] - PubMed - NCBI

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The HIV field is one of the first where next generation sequencing has made it to clinical applications

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Rescooped by Marion Koopmans from Next Gen Sequencing (NGS) and Bioinformatics at UVic
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PLoS ONE: A Practical Comparison of De Novo Genome Assembly Software Tools for Next-Generation Sequencing Technologies

PLoS ONE: A Practical Comparison of De Novo Genome Assembly Software Tools for Next-Generation Sequencing Technologies | Next generation sequencing for global infectious disease control | Scoop.it

"he advent of next-generation sequencing technologies is accompanied with the development of many whole-genome sequence assembly methods and software, especially for de novo fragment assembly. Due to the poor knowledge about the applicability and performance of these software tools, choosing a befitting assembler becomes a tough task. Here, we provide the information of adaptivity for each program, then above all, compare the performance of eight distinct tools against eight groups of simulated datasets from Solexa sequencing platform...."


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lots of comparisons needed, but hard to keep up!

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PLoS Pathogens: Routine Use of Microbial Whole Genome Sequencing in Diagnostic and Public Health Microbiology

PLoS Pathogens: Routine Use of Microbial Whole Genome Sequencing in Diagnostic and Public Health Microbiology | Next generation sequencing for global infectious disease control | Scoop.it

Whole genome sequencing (WGS) promises to be transformative for the practice of clinical microbiology, and the rapidly falling cost and turnaround time mean that this will become a viable technology in diagnostic and reference laboratories in the near future. The objective of this article is to consider at a very practical level where, in the context of a modern diagnostic microbiology laboratory, WGS might be cost-effective compared to current alternatives. We propose that molecular epidemiology performed for surveillance and outbreak investigation and genotypic antimicrobial susceptibility testing for microbes that are difficult to grow represent the most immediate areas for application of WGS, and discuss the technical and infrastructure requirements for this to be implemented.


Via Ed Rybicki
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Nice conceptual figures

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Integrating genome-based informatics to mod... [Emerg Infect Dis. 2012] - PubMed - NCBI

Integrating genome-based informatics to mod... [Emerg Infect Dis. 2012] - PubMed - NCBI | Next generation sequencing for global infectious disease control | Scoop.it
PubMed comprises more than 22 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.
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position paper on potential impact of next generation sequencing for clinical and public health labs
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Federal Agencies Get Guidance On New Data-Sharing Mandate - HPCwire (blog)

Federal Agencies Get Guidance On New Data-Sharing Mandate - HPCwire (blog) | Next generation sequencing for global infectious disease control | Scoop.it
HPCwire (blog) Federal Agencies Get Guidance On New Data-Sharing Mandate HPCwire (blog) More of that data will find its way into the hands of the public and entrepreneurs thanks to the government's new data sharing mandate, and this month, the...
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The duck genome and transcriptome provide insight ... [Nat Genet. 2013] - PubMed - NCBI

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Identification of a Pegivirus (GB Virus-Like Virus) That Infects Horses

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The Microbes You Share | The Daily Scan | GenomeWeb

The Microbes You Share | The Daily Scan | GenomeWeb | Next generation sequencing for global infectious disease control | Scoop.it
Dogs and their owners share microbiota.
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Rescooped by Marion Koopmans from Virology and Bioinformatics from Virology.ca
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PLOS Computational Biology: Viral Phylodynamics

PLOS Computational Biology: Viral Phylodynamics | Next generation sequencing for global infectious disease control | Scoop.it
PLOS Computational Biology is an open-access

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Identification of a previously undescribed divergent virus from the Flaviviridae family in an outbreak of equine serum hepatitis

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Nice study, i have come across cases during my practitioner years. NGS in action
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Next-generation sequencing technologies... [Brief Funct Genomics. 2013] - PubMed - NCBI

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Cell - Pathogenic Simian Immunodeficiency Virus Infection Is Associated with Expansion of the Enteric Virome

Cell - Pathogenic Simian Immunodeficiency Virus Infection Is Associated with Expansion of the Enteric Virome | Next generation sequencing for global infectious disease control | Scoop.it
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Fascinating work about the role of healthy gut flora, now focussing on virome

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Rescooped by Marion Koopmans from Virology and Bioinformatics from Virology.ca
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Microbial oceanography: Killers of the winners

More than 20 years ago, the discovery of billions of viruses in the oceans was big news, worthy of articles in Nature1 and on the front page of the Washington Post. A year later another Naturereport was published, this time about the most abundant bacterial group in the oceans, cryptically called SAR11. The two stories now come together in a paper published on Nature's website today. Zhao et al. describe DNA viruses that they call 'pelagiphages' and which infect laboratory-grown representatives of SAR11 bacteria. The authors use genomic-sequence data to argue that pelagiphages are among the most abundant viruses in the oceans and perhaps the entire biosphere. The report ends long-running speculation about SAR11, but prompts new questions about marine viruses and the control of microbes in the oceans.


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Ed Rybicki's curator insight, February 14, 2013 2:35 AM

GREAT field to be in!!

Ed Rybicki's curator insight, February 14, 2013 2:36 AM

Seriously big finding - there's a sea of opportunity out there!

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Towards bioinformatics assisted infectious disease control

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older paper, but nice

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Rescooped by Marion Koopmans from Next Gen Sequencing (NGS) and Bioinformatics at UVic
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Performance comparison of benchtop high-throughput sequencing platforms [Nat Biotechnol. 2012]

Loman NJ, Misra RV, Dallman TJ, Constantinidou C, Gharbia SE, Wain J, Pallen MJ.

 

Three benchtop high-throughput sequencing instruments are now available. The 454 GS Junior (Roche), MiSeq (Illumina) and Ion Torrent PGM (Life Technologies) are laser-printer sized and offer modest set-up and running costs.


Via Chris Upton + helpers
Marion Koopmans's insight:

Nice comparison. Whether differences matter depends on application/study question. 

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Catching the Cold | The Scientist Magazine®

Catching the Cold | The Scientist Magazine® | Next generation sequencing for global infectious disease control | Scoop.it
Tracking the genetic diversity and evolution of rhinoviruses can lead to a better understanding of viral evolution, the common cold, and more dangerous infections.
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