Pan Coronavirus Genomic Surveillance of a Large NHP Colony

Project Summary/Abstract The novel coronavirus that emerged in late 2019, termed SARS-CoV-2, quickly spread throughout the world and has killed millions. A critical aspect of this pandemic that remains understudied is the impact of immunity to seasonal coronaviruses on COVID-19 disease. Several lines of evidence suggest there is an impact but the nature of that impact remains unclear. We have preliminary data confirming our colony of 5,000 rhesus macaques harbors a large fraction of animals with preexisting immunity to coronaviruses of unknown origin. This immunity may be important in the use of these animals for COVID-19 and other coronavirus disease. We hypothesize that our colony seasonally circulates human seasonal coronaviruses but we need to identify the actual viruses circulating. Here, we will use multiple approaches to assess the frequency of these infections and to identify the actual viruses. In Aim 1, we will use pan-coronavirus primers to quantify coronavirus infections in our colony. We will sample both nasal and rectal sites as coronaviruses are known to be shed from both. In Aim 2, we will use next generation sequencing to identify the viruses circulating. We will apply phylogenetic approaches to characterize the diversity of the virus or viruses in our colony. These data will have important implications for the use of macaques for coronavirus infections in general and may shed light on the coronavirus family.