Friday, 28 January 2011

Pacific Biosciences Team Identifies Asian Origin for Haitian Cholera Bug

Rising importance of NGS for emerging infectious diseases!
excerpted from Bio-ITworld URL above

December 9, 2010 | In a dramatic piece of ultra-quick genetic detective work, next-generation sequencing company Pacific Biosciences has decoded the sequence of the strain of bacteria responsible for the deadly cholera outbreak in Haiti. The findings, which confirm the putative Asian origin for the devastating disease, are published online in the New England Journal of Medicine today. 

Each of the five strains took about one day to sequence to about 60X coverage. “They did an outstanding job in the analysis,” says Waldor. “Most of the credit for this project goes to Eric and his team.”  
“The rapidity and depth of the sequence using this 3rd-generation sequencing technology has enormous potential to transform how we can analyze outbreaks of infectious disease and even the prediction of future outbreaks because of the power of their technology.” 
According to PacBio, the five cholera genomes were sequenced on November 12 to 12-15X coverage in less than two hours. Further runs bumped up the coverage to 60X over the course of the day. Over the next three days, the sequence data were subjected to in-depth analysis, including genome assembly, annotation, and sequence comparisons, including comparisons to nearly two dozen published cholera genomes.  
From PacBio’s perspective, Schadt says that “real-time monitoring” of pathogens opens the door to using his firm’s technology as “a routine surveillance method, for public health protection in addition to pandemic prevention and response.” 

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