The rapid scale-up of research on coronavirus disease 2019 (COVID-19) has spawned a large number of potential vaccines and immunotherapies, accompanied by a commensurately large number of in vitro assays and in vivo models to measure their effectiveness. These assays broadly have the same end-goal — to predict the clinical efficacy of prophylactic and therapeutic interventions in humans. However, the apparent potency of different interventions can vary considerably between assays and animal models, leading to very different predictions of clinical efficacy. Complete harmonization of experimental methods may be intractable at the current pace of research. However, here we analyse a selection of existing assays for measuring antibody-mediated virus neutralization and animal models of infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and provide a framework for comparing results between studies and reconciling observed differences in the effects of interventions. Finally, we propose how we might optimize these assays for better comparison of results from in vitro and animal studies to accelerate progress.

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

SARS-CoV-2 testing is crucial to controlling the spread of this virus, yet shortages of nucleic acid extraction supplies and other key reagents have hindered the response to COVID-19 in the US. Several groups have described loop-mediated isothermal amplification (LAMP) assays for SARS-CoV-2, including testing directly from nasopharyngeal swabs and eliminating the need for reagents in short supply. Frequent surveillance of individuals attending work or school is currently unavailable to most people but will likely be necessary to reduce the ~50% of transmission that occurs when individuals are nonsymptomatic. Here we describe a fluorescence-based RT-LAMP test using direct nasopharyngeal swab samples and show consistent detection in clinically confirmed primary samples with a limit of detection (LOD) of ~625 copies/μl, approximately 100-fold lower sensitivity than qRT-PCR. While less sensitive than extraction-based molecular methods, RT-LAMP without RNA extraction is fast and inexpensive. Here we also demonstrate that adding a lysis buffer directly into the RT-LAMP reaction improves the sensitivity of some samples by approximately 10-fold. Furthermore, purified RNA in this assay achieves a similar LOD to qRT-PCR. These results indicate that high-throughput RT-LAMP testing could augment qRT-PCR in SARS-CoV-2 surveillance programs, especially while the availability of qRT-PCR testing and RNA extraction reagents is constrained.

Evidence-based public health approaches that minimize the introduction and spread of new SARS-CoV-2 transmission clusters are urgently needed in the United States and other countries struggling with expanding epidemics. Here we analyze 247 full-genome SARS-CoV-2 sequences from two nearby communities in Wisconsin, USA, and find surprisingly distinct patterns of viral spread. Dane County had the 12th known introduction of SARS-CoV-2 in the United States, but this did not lead to descendant community spread. Instead, the Dane County outbreak was seeded by multiple later introductions, followed by limited community spread. In contrast, relatively few introductions in Milwaukee County led to extensive community spread. We present evidence for reduced viral spread in both counties following the statewide “Safer at Home” order, which went into effect 25 March 2020. Our results suggest patterns of SARS-CoV-2 transmission may vary substantially even in nearby communities. Understanding these local patterns will enable better targeting of public health interventions.

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