Viral coinfection is shaped by bacterial ecology and virus-virus interactions across diverse microbial taxa and environments

11 Viral coinfection is a common across taxa and environments. Coinfection can enable 12 genetic exchange, alter the dynamics of infections, and change the course of viral 13 evolution. Despite the importance of coinfection to viral ecology and evolution, the 14 factors that influence the frequency and extent of viral coinfection remain largely 15 unexplored. Here I employ an extensive data set of virus-host interactions representing 16 6,564 microbial hosts and 13,103 viruses, to test the importance of bacterial traits and 17 virus-virus interactions in shaping coinfection dynamics across a wide variety of taxa and 18 environments. Using data from phage-host infection matrices, I found that bacterial 19 ecology was the most important factor explaining variation (>28%) in the potential for 20 coinfection. Realized (actual) coinfection was affected by bacterial defense mechanisms 21 at the single-cell level. In a natural environment, the presence of CRISPR spacers in 22 marine bacteria limited coinfections with active viruses by ~50%, despite the absence of 23 spacer matches in any active infection. Analysis of viral infections mined from published 24 bacterial and archaeal sequence data (n= 5,492 hosts), showed prophages limited 25 coinfection of host cultures by other prophages, but not extrachromosomal viruses. At the 26 single-cell level, prophages virtually eliminated coinfection. Virus-virus interactions also 27 enhanced coinfection with culture coinfection by ssDNA and dsDNA viruses twice as 28 likely to occur than ssDNA-only coinfections. Collectively, these results suggest bacterial 29 ecology and virus-virus interactions are strong drivers of coinfection across different taxa 30 and environments. These findings highlight that virus-virus interactions constitute an 31 important selective pressure on viruses that is often underappreciated. 32 . CC-BY 4.0 International license peer-reviewed) is the author/funder. It is made available under a The copyright holder for this preprint (which was not . http://dx.doi.org/10.1101/038877 doi: bioRxiv preprint first posted online Feb. 7, 2016;