IP24-045, SEAPREP: Seattle Pandemic Preparedness Cohort

ABSTRACT Community-based surveillance studies of respiratory viruses provide the opportunity for early viral detection and situational awareness, and may inform early public health efforts to mitigate the transmission of respiratory viruses, as was evidenced by the SARS-CoV-2 pandemic. Case-ascertained household transmission studies are an efficient and epidemiologically rich method to study respiratory virus transmission. Our team of investigators has deep expertise in community surveillance and case-ascertainment trials of respiratory viruses. Our group of collaborators include specialists in infectious diseases, epidemiology, biostatistics, virology, immunology, and infectious disease modeling. In 2018, we developed the infrastructure for a pandemic preparedness platform in Seattle, Washington, leading to the first identification of SARS-CoV-2 community transmission in the United States. We have developed innovative methods for fully remote observational studies of respiratory viruses in households, and have built a logistics and laboratory insfrastructure for rapid delivery and pickup of biospecimens, multiplex testing for a panel of respiratory pathogens, in-depth immunologic characterization, and whole genome sequencing and visualization. In this study, we propose to build on these platforms to conduct the following studies. First, we propose a prospective longitudinal cohort study of 2000 children and adults in the Seattle area, with weekly symptom screening and collection of nasal swabs for respiratory illness. We will conduct multi-pathogen testing for respiratory viruses and whole genome sequencing for RSV, SARS-CoV-2, and other respiratory viruses. We will calculate incidence, assess epidemiology and burden of respiratory viruses, measure participant knowledge, attitudes and perceptions, and measure the effectiveness of interventions in prevention of disease. We additionally propose to perform in-depth immunologic assessments by collection of serum samples longitudinally in a subset of individuals to understand antibody kinetics over the course of multiple seasons, and the effects of vaccines and infections on antibody titers across age groups. For our second study, we propose to conduct a case-ascertained household transmission study to understand transmission dynamics of SARS-CoV-2, RSV, and other viruses. Index cases will be enrolled remotely along with their household members, for serial self-swab collection for a period of two weeks after enrollment. We propose collection of environmental samples within a subset of households. Molecular testing and sequencing will be performed for SARS-CoV-2, RSV, and other viruses, as indicated, allowing for calculation of household attack rates, serial intervals, and risk factors for within household transmission for known and novel pathogens. These proposed studies will provide real-time situational awareness of community respiratory epidemiology, and our team has the experience and expertise to pivot for identification of novel pathogens and pandemic response.