Probing Pandemic Virus Biology: Approaches from Molecular Biology to Systems-Level Biology for Severe Acute Respiratory Syndrome Coronavirus 2 and Human Immunodeficiency Virus 1

Viral pandemics have followed humans throughout their evolutionary history. These pandemics occur when a virus to which humans have no pre-existing immunity enters the human population and impact societies on a global scale. Recent instances, such as the Human Immunodeficiency Virus 1 (HIV-1)/Acquired Immunodeficiency Syndrome (AIDS) pandemic and the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) pandemic, have demonstrated the ruinous impact of these events on both developing and developed nations. While studies of HIV-1 have been ongoing since the start of the HIV-1/AIDS pandemic in 1981, there still exists no cure to or vaccine against the virus. Likewise, the SARS-CoV-2 pandemic, which started in late 2019, will likely challenge the world for several years despite a concerted global vaccine rollout due to a lack of highly effective treatments that can be deployed in advance of local vaccination campaigns. The work completed here illustrates the value of both macroscopic and microscopic analyses in probing pandemic virus biology. As systems biology approaches to virology have become more tractable, highly studied viruses such as HIV can now be analyzed in new, unbiased ways, including spatial proteomics. Spatial proteomics is the study of the distribution of proteins across cellular organelles. We employed here a differential centrifugation protocol to fractionate an inducible model of HIV infection for proteomic analysis by mass spectrometry. Using these proteomics data, we evaluated the merits of several publicly available machine learning pipelines for classification of the spatial proteome. From these analyses we have found that the performance of different classification methods varies by organelle and with the expression of HIV. On the other hand, traditional, reductionist methods that isolate a selection of proteins from a virus can be of particular use when faced with a new viral threat such as SARS-CoV-2. Here we utilized structural nuclear magnetic resonance studies to characterize the envelope (E) protein of SARS-CoV-2. These studies highlighted a transmembrane channel formed by E that can be targeted by amiloride derivatives to significantly inhibit SARS-CoV-2 replication in cell culture. Taken together, these findings illustrate the varied approaches that can be employed in the study of pandemic viruses