DefinePK

Abstract

The global poultry industry constantly faces the threat of various bacterial and viral diseases, some of which are underreported, especially in developing countries. Even when official reports are available, the scope of the problem and its impact are unknown. Testing for individual pathogens is costly and tedious and may lead to inappropriate management, especially in the case of immunosuppressive diseases. Next-generation sequencing (NGS) provides an opportunity to discover all the events leading to clinical diseases. NGS for bacteria is well established, but this is not the case for viral agents. Because of their many variants, it is impossible to establish barcodes to detect all viruses. Therefore, we propose to establish a multi-barcode system to detect all bacteria and viruses in clinical avian specimens. The libraries can be generated with a one-step reverse transcription–PCR system for bacteria and RNA and DNA viruses, after priming with a single bacterial primer barcode and primer sets for all viruses or targeted viral genes of interest.