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Posted by cychiu98 on 20 Oct 2010 at 06:33 GMT
Metagenomics is the study of genetic material recovered directly from clinical or environmental samples. Here we explore the use of two metagenomics-based technologies, the Virochip (a DNA microarray that can detect all viruses) and deep sequencing (an unbiased method by which millions of DNA fragments are sequenced in a high-throughput fashion), for studying unknown outbreaks, using pandemic 2009 H1N1 influenza A virus as a case example. By analysis of 17 nasal swabs collected during the earliest stages of the pandemic in Mexico, Canada, and the United States, we used the Virochip to rapidly identify 2009 H1N1 as a novel virus related to pig influenza strains without a priori information. Detection of 2009 H1N1 by deep sequencing was possible even at very low virus concentrations. Deep sequencing also enabled analysis of other potential pathogens, such as bacteria, as well as the associated host response to the infection. In particular, genes related to immunity and the interferon-mediated antiviral response were found to be upregulated in 2009 H1N1 samples. In addition, we demonstrate here that even if influenza were part of a previously unknown viral family, nearly the entire genome of the virus could be recovered de novo by deep sequencing. Our study provides a blueprint for using metagenomics to investigate the cause of unexplained acute illnesses or outbreaks in clinical and public health settings.