About

Next generation sequencing (NGS) technologies have started a revolution in genomics and provided opportunities for its broad application in many other fields, including the diagnosis of human infectious diseases. However, NGS technology is still a research tool, rather than a diagnostic tool, and cannot be used in current infectious disease diagnostic laboratories due to:

• The scarcity of pathogen (especially viral) sequences in human clinical samples.
• The necessary subsequent requirement of extensive deep sequencing.
• The complexity of bioinformatics analysis required to identify pathogenic sequences.

For example, the average viral genome in a human blood sample is about 1-100 per 10 million human genome sequence reads, which usually requires deep sequencing and subsequent intensive bioinformatics analysis to identify viral sequences. Many laboratories have developed various strategies, from consensus PCR assays that use degenerate primers to computational subtraction of large sequence data in order to find possible unknown pathogens, with little success. This is like a “search for a needle in a haystack,” which has proven to be a very difficult task.