Irina Agarkova

Although viral life history traits—the traits that determine reproductive and survival success—are critical to understanding the population dynamics and impact of viruses, they are understudied compared to molecular traits. This discrepancy is partly due to the challenge of phenotyping viral life histories. We developed improved methods to quantify the life cycles of chloroviruses, which are lytic double-stranded DNA viruses that infect unicellular “chlorella-like” algae. We modified classical one-step growth and survival assays by including flow cytometry and kinetic modeling, and applied these to four chlorovirus strains. Together, the modified assays quantified the full life cycle, including adsorption rate, probability of depolarizing the host cell, probability of releasing progeny virions, time until lysis, burst size, specific infectivity, and mortality rate of infectious virions. We also discovered that biphasic or “tailing” decay can occur in chloroviruses, and measured the fraction of infectious virions that resisted decay. The modified assays are more efficient than existing techniques, quantify more traits, and are applicable to other lytic viruses with quantifiable virions. The modified one-step growth assay is suitable for viruses with mutual exclusion, superinfection exclusion, or superinfection immunity; the modified survival assay can be applied to any lytic virus with quantifiable virions. IMPORTANCE Viruses play a crucial role in microbial ecosystems by liberating nutrients and regulating the growth of their hosts. These effects are governed by viral life history traits, i.e., by the traits determining viral reproduction and survival. Understanding these traits is essential to predicting viral effects, but measuring them is generally labor intensive. In this study, we present efficient methods to quantify the full life cycle of lytic viruses. We developed these methods for viruses infecting unicellular Chlorella algae but expect them to be applicable to other lytic viruses that can be quantified by flow cytometry. By making viral phenotypes accessible, our methods will support research into the diversity and ecological effects of microbial viruses.