At the current rate of technological progress, high-throughput sequencing of nucleic acids has become a commodity. These techniques are perfectly suitable for viral small RNAs sequencing and contribute to the understanding of many aspects of virus biology in the context of host-pathogen interaction. However, the generation of high quality data is still an issue and the preparation of small RNAs libraries that accurately reflect the viral siRNAs in the sample remains a challenge. In this chapter

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... we describe how to clone and sequence libraries of viral small RNAs from infected insect samples (mosquito, drosophilidae, insectderived cell lines).