Shotgun sequencing to determine corneal infection
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A study was conducted to investigate if the shotgun-sequencing method could be useful in the detailed diagnosis of herpes simplex virus (HSV) infection and compare it with the conventional diagnostic method.

Using a sterile scraper, the infectious part of the ocular surface was scraped gently and placed on a glass slide for conventional diagnosis using PCR and histology and in RNA stabilizing reagent for shotgun sequencing respectively. The concentration of the DNA was determined using a sensitive fluorescence dye-based Qubit dsDNA HS Assay Kit. Shotgun-sequencing libraries were generated using the NEBNext DNA ultra II protocol.

Conventional diagnostic method suspected herpetic keratitis. The results indicated the presence of an amplified product of 92 bp positive HSV-DNA. The conventional diagnostic method detected the presence of Herpes Simplex Virus DNA (type 1). Shotgun sequencing confirmed the diagnosis of HSV along with the taxonomical profiling of the virus. These results were achieved using 1.9 ng/L of DNA concentration of the total sample volume.

Conclusions and importance
Shotgun sequencing is a hypothesis-free approach that identifies the full taxonomic and functional profile of an organism. This technology is advantageous as it requires a smaller sample size compared to conventional diagnostic methods.

Source: https://www.sciencedirect.com/science/article/pii/S245199362030089X
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