Amplicon-Based Sequencing of Bat Coronaviruses from Ukraine

We analyzed fecal samples from bats in Ukraine using RT-PCR and amplicon-based Oxford Nanopore Technologies (ONT) sequencing. Nucleic acids were amplified via hemi-nested RT-PCR targeting the RdRp gene and sequenced with both ONT and Sanger methods. Alphacoronavirus 1 was detected, though low viral load and broad degenerate primers complicated the analysis of mixed strains.