43 SARS-CoV-2 pulmonary abnormalities in macaques Finch et al. 3 Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is causing an 44 exponentially increasing number of coronavirus disease 19 (COVID-19) cases 45 globally. Prioritization of medical countermeasures for evaluation in randomized 46 clinical trials is critically hindered by the lack of COVID-19 animal models that 47 enable accurate, quantifiable, and reproducible measurement of COVID-19 48 pulmonary disease free from observer bias. We first used serial computed 49 tomography (CT) to demonstrate that bilateral intrabronchial instillation of SARS-50 CoV-2 into crab-eating macaques (Macaca fascicularis) results in mild-to-moderate 51 lung abnormalities qualitatively characteristic of subclinical or mild-to-moderate 52 COVID-19 (e.g., ground-glass opacities with or without reticulation, paving, or 53 alveolar consolidation, peri-bronchial thickening, linear opacities) at typical 54 locations (peripheral>central, posterior and dependent, bilateral, multi-lobar). We 55 then used positron emission tomography (PET) analysis to demonstrate increased 56 FDG uptake in the CT-defined lung abnormalities and regional lymph nodes. 57 PET/CT imaging findings appeared in all macaques as early as 2 days post-58 exposure, variably progressed, and subsequently resolved by 6-12 days post-59 exposure. Finally, we applied operator-independent, semi-automatic quantification 60 of the volume and radiodensity of CT abnormalities as a possible primary endpoint 61 for immediate and objective efficacy testing of candidate medical countermeasures. 62 63

Summary The Long INterspersed Element-1 (LINE-1 or L1) retrotransposition assay has facilitated the discovery and characterization of active (i.e., retrotransposition-competent) LINE-1 sequences from mammalian genomes. In this assay, an engineered LINE-1 containing a retrotransposition reporter cassette is transiently transfected into a cultured cell line. Expression of the reporter cassette, which occurs only after a successful round of retrotransposition, allows the detection and quantification of the LINE-1 retrotransposition efficiency. This assay has yielded insight into the mechanism of LINE-1 retrotransposition. It also has provided a greater understanding of how the cell regulates LINE-1 retrotransposition and how LINE-1 retrotransposition impacts the structure of mammalian genomes. Below, we provide a brief introduction to LINE-1 biology and then detail how the LINE-1 retrotransposition assay is performed in cultured mammalian cells.

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This study extends the spectrum of phenotypes associated with FIG4 mutations to include cortical malformation associated with seizures and psychiatric manifestations, in addition to the previously described Charcot-Marie-Tooth disease type 4J and Yunis-Varón syndrome.