Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the current COVID-19 pandemic. The 3′ untranslated region (UTR) of this β-CoV contains essential cis-acting RNA elements for the viral genome transcription and replication. These elements include an equilibrium between an extended bulged stem-loop (BSL) and a pseudoknot. The existence of such an equilibrium is supported by reverse genetic studies and phylogenetic covariation analysis and is further proposed as a molecular switch essential for the control of the viral RNA polymerase binding. Here, we report the SARS-CoV-2 3′ UTR structures in cells that transcribe the viral UTRs harbored in a minigene plasmid and isolated infectious virions using a chemical probing technique, namely dimethyl sulfate (DMS)-mutational profiling with sequencing (MaPseq). Interestingly, the putative pseudoknotted conformation was not observed, indicating that its abundance in our systems is low in the absence of the viral nonstructural proteins (nsps). Similarly, our results also suggest that another functional cis-acting element, the three-helix junction, cannot stably form. The overall architectures of the viral 3′ UTRs in the infectious virions and the minigene-transfected cells are almost identical.

We leverage two complementary Drosophila melanogaster mapping panels to genetically dissect starvation resistance, an important fitness trait. Using >1600 genotypes of the multiparental Drosophila Synthetic Population Resource (DSPR) we map numerous starvation stress QTL that collectively explain a substantial fraction of trait heritability. QTL effects further allowed us to estimate DSPR founder phenotypes, predictions that were correlated with the actual founder phenotypes. Starvation resistance has been linked to triglyceride level, and while we observe a modest phenotypic correlation between the traits in the DSPR, overlap among the QTL identified for each trait is low. Since we show that DSPR strains with extreme starvation phenotypes also differ in desiccation resistance and activity level, our data imply that multiple physiological mechanisms contribute to starvation variability. We also exploit the Drosophila Genetic Reference Panel (DGRP), identifying a number of sequence variants associated with starvation resistance. Consistent with prior work these sites rarely fall within QTL intervals mapped in the DSPR. Two other groups previously measured starvation resistance in the DGRP, offering a unique opportunity to directly compare mapping results across labs. We found strong phenotypic correlations among studies, but extremely low overlap in the sets of genomewide significant sites. Despite this, our analyses revealed that the most highly-associated variants from each study typically showed the same additive effect sign in independent studies, in contrast to otherwise equivalent sets of random variants. This consistency provides evidence for reproducible trait-associated sites in a widely-used mapping panel, and highlights the polygenic nature of starvation resistance.