An Evaluation of Avian Influenza Virus Whole-Genome Sequencing Approaches Using Nanopore Technology

As exemplified by the global response to the SARS-CoV-2 pandemic, whole-genome sequencing played an important role in monitoring the evolution of novel viral variants and provided guidance on potential antiviral treatments. The recent rapid and extensive introduction and spread of highly pathogenic avian influenza virus in Europe, North America, and elsewhere raises the need for similarly rapid sequencing to aid in appropriate response and mitigation activities. To facilitate this objective, we investigate a next-generation sequencing platform that uses a portable nanopore sequencing device to generate and present data in real time. This platform offers the potential to extend in-house sequencing capacities to laboratories that may otherwise lack resources to adopt sequencing technologies requiring large benchtop instruments. We evaluate this platform for routine use in a diagnostic laboratory. In this study, we evaluate different primer sets for the whole genome amplification of influenza A virus and evaluate five different library preparation approaches for sequencing on the nanopore platform using the MinION flow cell. A limited amplification procedure and a rapid procedure are found to be best among the approaches taken

Determining Schistosoma haematobium Population Structures in Ethiopia

Schistosomiasis, also known as bilharzia, is a Neglected Tropical Disease caused by parasitic helminths that affects over 240 million people around the world. Praziquantel has been used to treat individuals infected with schistosomiasis through Mass Drug Administration (MDA) programs but a recent reduction in its efficacy has been observed, creating concern that the parasite will evolve to become resistant to the chemotherapy drug. Monitoring changes in the population structure of Schistosoma haematobium using microsatellite markers can be a useful metric to determine praziquantel efficacy since variations in the repeat sequences of microsatellites indicate genetic diversity. Since little is known about the population structure of S. haematobium–despite urogenital schistosomiasis being a pressing issue in Ethiopia–18 microsatellite multiplex assays developed in a prior study were tested on stock DNA to validate them for use to study the effects of praziquantel on parasitic S. haematobium in Ethiopia. Through a combination of bioinformatic analysis, PCR, and Next Generation Sequencing on the MinION, 13 of the 18 microsatellite markers were validated, highlighting the importance of developing microsatellite multiplex assays not only based on length distribution, but also based on Next Generation Sequencing data.https://digitalcommons.unmc.edu/surp2023/1015/thumbnail.jp

All-sky Medium Energy Gamma-ray Observatory: Exploring the Extreme Multimessenger Universe

The All-sky Medium Energy Gamma-ray Observatory (AMEGO) is a probe class mission concept that will provide essential contributions to multimessenger astrophysics in the late 2020s and beyond. AMEGO combines high sensitivity in the 200 keV to 10 GeV energy range with a wide field of view, good spectral resolution, and polarization sensitivity. Therefore, AMEGO is key in the study of multimessenger astrophysical objects that have unique signatures in the gamma-ray regime, such as neutron star mergers, supernovae, and flaring active galactic nuclei. The order-of-magnitude improvement compared to previous MeV missions also enables discoveries of a wide range of phenomena whose energy output peaks in the relatively unexplored medium-energy gamma-ray band

An Evaluation of Avian Influenza Virus Whole-Genome Sequencing Approaches Using Nanopore Technology

As exemplified by the global response to the SARS-CoV-2 pandemic, whole-genome sequencing played an important role in monitoring the evolution of novel viral variants and provided guidance on potential antiviral treatments. The recent rapid and extensive introduction and spread of highly pathogenic avian influenza virus in Europe, North America, and elsewhere raises the need for similarly rapid sequencing to aid in appropriate response and mitigation activities. To facilitate this objective, we investigate a next-generation sequencing platform that uses a portable nanopore sequencing device to generate and present data in real time. This platform offers the potential to extend in-house sequencing capacities to laboratories that may otherwise lack resources to adopt sequencing technologies requiring large benchtop instruments. We evaluate this platform for routine use in a diagnostic laboratory. In this study, we evaluate different primer sets for the whole genome amplification of influenza A virus and evaluate five different library preparation approaches for sequencing on the nanopore platform using the MinION flow cell. A limited amplification procedure and a rapid procedure are found to be best among the approaches taken