The ongoing COVID-19 pandemic has not only globally caused a high number of causalities, but is alsoan unprecedented challenge for scientists. False-positive virus detection tests not only aggravate thesituation in the healthcare sector, but also provide ground for conspiracy theorists. Previous studies havehighlighted the importance of software choice and data interpretation in virome studies. We aimed tofurther expand theoretical and practical knowledge in virome studies by focusing on short, virus-like DNAsequences in metagenomic data.ResultsExemplarily, analyses of metagenomic data from the dried-out Aral Sea basin in Uzbekistan showed thatCoronavirus-like sequences have existed in environmental samples before the current COVID-19 crisis. Inthe analyzed environmental datasets, diverse Betacoronavirus-like sequences were detected, which alsoincluded SARS-CoV-2 matches. Moreover, the data sets harbored regions that show complementarity toPCR primers that are currently in use for virus detection and origin tracing.