RNA viruses of pandemic potential: Viral Infectivity

RNA viruses are the cause of major current and future pandemics, with few antivirals and the potential to severely strain global healthcare systems. In the past year, severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), a positive strand RNA virus that is the causative agent of COVID-19, has caused acute disruption on a global scale. While the most recent influenza pandemic (2009) had a relatively low mortality rate, the emergence of a novel influenza strain with higher mortality would place the global healthcare system under immense pressure, and remains a constant threat. In the case of SARS-CoV-2 (and likely any future coronavirus or influenza pandemic), an unparalleled demand for viral diagnostic testing resulted in global shortages of many of the required reagents. RNA extraction in particular represents a choke point, not only due to shortages of the required reagents, but also due to the cost of the extraction process, the labor and time required to perform it. While recent Emergency Use Authorizations have been approved by the US Food and Drug Administration for commercial extraction-free diagnostic tests, these are proprietary systems; protocols that work with the open-source RT-qPCR assay developed by the WHO are needed. The goal of this study is to investigate factors that correlate with and/or influence viral infectivity of SARS-CoV-2 and influenza, using clinical samples and classical virology techniques to examine what makes the particular virus, or a particular patient, infectious. An extension of a previously funded pilot project aimed at developing a streamlined SARS-CoV-2 diagnostic test, we will expand our examination to include clinical influenza samples. Additionally, we will probe a number of factors including sgRNA, negative strand RNA and SARS-CoV-2 RNA loads that considered together may be able predict the presence of infectious virus, and potentially differentiate those individuals who are simply PCR-positive from those who truly pose a risk of viral transmission. Since this work will generate a panel of clinical isolates for both SARS-CoV-2 and influenza with a range of infectivities, we will also investigate a variety of factors including RNA packaging, particle to PFU ratio, temperature stability, particle morphology and specific genetic mutations, all of which may affect viral infectivity at the molecular level.