Metagenomic virus-screening of wild bird samples from Piano di Magadino (TI) by next generation sequencing

As part of a project by the Scuola universitaria professionale della Svizzera italiana (SUPSI), wild birds in the Magadino plain are being sampled and specifically tested for known pathogens such as West Nile virus and avian influenza. At the same time, the occurrence of mosquitoes in this area is being investigated with the aim of better understanding the dynamics and interactions between mosquitoes and birds, as well as their influence on virus transmission. The birds are caught with nets using a special permit (nature reserve) and the sample material taken (choanae and cloaca swabs, as well as blood sample) is therefore limited and very valuable. However, only a very small proportion of the potentially present viruses can be tested with specific diagnostics (PCR, ELISA). In order to use this valuable sample material as efficiently and widely as possible, we propose to test the samples nonspecifically using NGS for all known and especially potentially zoonotic / mosquito-borne viruses (virome analysis). These results would add weight to the SUPSI study and provide valuable information for early detection of "new"/unexpected viruses circulating in these birds. This knowledge could in turn be used in future studies to investigate the circulation of viruses between birds and mosquitoes (and potentially humans) using specific diagnostic methods.