Rapid dissemination and monopolization of viral populations in mice revealed using a panel of barcoded viruses

Abstract

17The gastrointestinal tract presents a formidable barrier for pathogens to initiate infection. 18Despite this barrier, enteroviruses, including coxsackievirus B3 (CVB3), successfully penetrate 19 the intestine to initiate infection and spread systemically prior to shedding in stool. However, the 20 effect of the gastrointestinal barrier on CVB3 population dynamics is relatively unexplored, nor 21 are the selective pressures acting on CVB3 in the intestine well-characterized. To examine viral 22 population dynamics in orally infected mice, we produced over one hundred CVB3 viruses 23 harboring unique nine nucleotide "barcodes." Using this collection of barcoded viruses, we 24 found diverse viral populations throughout each mouse within the first day post-infection, but by 25 48 hours the viral populations were dominated by less than three barcoded viruses in intestinal 26 and extra-intestinal tissues. Using light-sensitive viruses to track replication status, we found 27 diverse viruses had replicated prior to loss of diversity. Sequencing whole viral genomes from 28 samples later in infection did not reveal detectable viral adaptations. Surprisingly, orally 29 inoculated CVB3 was detectable in pancreas and liver as soon as 20 minutes post inoculation, 30indicating rapid systemic dissemination. These results suggest rapid dissemination of diverse 31 viral populations, followed by a major restriction in population diversity and monopolization in all 32 examined tissues. These results underscore a complex dynamic between dissemination and 33 clearance for an enteric virus. 35 Importance 36Enteric viruses initiate infection in the gastrointestinal tract but can disseminate to systemic 37 sites. However, the dynamics of viral dissemination are unclear. In this study, we created a 38 library of 135 barcoded coxsackieviruses to examine viral population diversity across time and 39 space following oral inoculation of mice. Overall, we found that the broad population of viruses 40 disseminates early, followed by monopolization of mouse tissues with three or fewer pool 41 members at later time points. Interestingly, we detected virus in systemic tissues such as 42 pancreas and liver just 20 minutes post-oral inoculation. These results suggest rapid 43 dissemination of diverse viral populations, followed by a major restriction in population diversity 44 and monopolization in all examined tissues. 45 46 Introduction 47 RNA virus populations are dynamic. Population diversity arises through mutations introduced by 48 the viral RNA-dependent RNA polymerases, which lack proofreading. Although many mutations 49 are detrimental, viruses can benefit from diversity within viral populations since diversity may 50 facilitate replication and dissemination within hosts (1,2). Viral diversity can be reduced through 51 selective pressures or stochastic events. Because viral diversity is a fundamental parameter in 52 viral evolution and virulence, understanding population dynamics and the factors that influence 53 viral populations is a c...