Nanopore Direct RNA Sequencing revealed the diverse defective viral genome species produced by insect-specific and arthropod-borne alphaviruses
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Defective viral genomes (DVGs) are viral replication products that cannot complete a full replication cycle without coinfection with a standard virus. Accumulating evidence demonstrates the key role played by DVGs in virus-host interactions. Historically, only one or a few DVGs were identified for specific viruses relying on a high multiplicity of infection (MOI) passaging condition. The advent of Nanopore Direct RNA Sequencing (DRS) facilitates the identification of DVGs due to its capacity to read through full-length RNAs. Here, we applied this technology to characterize the diverse defective RNA species generated by alphaviruses, a group of positive-strand RNA viruses.