A Deterministic Model for Understanding Nonlinear Viral Dynamics in Oysters.

Contamination of oysters with a variety of viruses is one key pathway to trigger outbreaks of massive oyster mortality as well as human illnesses, including gastroenteritis and hepatitis. Much effort has gone into examining the fate of viruses in contaminated oysters, yet the current state of knowledge of nonlinear virus-oyster interactions is not comprehensive because most studies have focused on a limited number of processes under a narrow range of experimental conditions. A framework is needed for describing the complex nonlinear virus-oyster interactions. Here, we introduce a mathematical model that includes key processes for viral dynamics in oysters, such as oyster filtration, viral replication, the antiviral immune response, apoptosis, autophagy, and selective accumulation. We evaluate the model performance for two groups of viruses, those that replicate in oysters (e.g., ostreid herpesvirus) and those that do not (e.g., norovirus), and show that this model simulates well the viral dynamics in oysters for both groups. The model analytically explains experimental findings and predicts how changes in different physiological processes and environmental conditions nonlinearly affect in-host viral dynamics, for example, that oysters at higher temperatures may be more resistant to infection by ostreid herpesvirus. It also provides new insight into food treatment for controlling outbreaks, for example, that depuration for reducing norovirus levels is more effective in environments where oyster filtration rates are higher. This study provides the foundation of a modeling framework to guide future experiments and numerical modeling for better prediction and management of outbreaks. IMPORTANCE The fate of viruses in contaminated oysters has received a significant amount of attention in the fields of oyster aquaculture, food quality control, and public health. However, intensive studies through laboratory experiments and in situ observations are often conducted under a narrow range of experimental conditions and for a specific purpose in their respective fields. Given the complex interactions of various processes and nonlinear viral responses to changes in physiological and environmental conditions, a theoretical framework fully describing the viral dynamics in oysters is warranted to guide future studies from a top-down design. Here, we developed a process-based, in-host modeling framework that builds a bridge for better communications between different disciplines studying virus-oyster interactions.

Developing a 3D mechanistic model for examining factors contributing to harmful blooms of Margalefidinium polykrikoides in a temperate estuary.

Blooms of Margalefidinium (previously Cochlodinium) polykrikoides occur almost annually in summer in the lower Chesapeake Bay and its tributaries (e.g., the James and York Rivers). The Lafayette River, a sub-tributary of the lower James River, has been recognized as an initiation location for blooms in this region. The timing of bloom initiation varies interannually, ranging from late June to early August. To fully understand critical environmental factors controlling bloom initiation and interactions between physical and biological processes, a numerical module simulating M. polykrikoides blooms was developed with a focus on the bloom initiation. The module also includes life cycle and behavioral strategies such as mixotrophy, vertical migration, cyst dynamics and grazing suppression. Parameterizations for these behaviors were assigned based on published laboratory culture experiments. The module was coupled with a 3D physical-biogeochemical model for the James River that examined the contribution of each environmental factor and behavioral strategy to bloom initiation and development. Model simulation results highlight the importance of mixotrophy in maintaining high growth rates for M. polykrikoides in this region. Model results suggest that while many factors contribute to the initiation process, temperature, physical transport processes, and cyst germination are the three dominant factors controlling the interannual variability in the timing of bloom initiation.

Physical transport processes affect the origins of harmful algal blooms in estuaries.

The effects of physical transport processes on the initiation of harmful algal blooms (HABs) in estuaries were investigated through both mathematical model analysis and numerical model experiments. This study highlights the influence of the flushing effect due to physical transport processes on the location of bloom initiation, which is comparable to or even more important than local processes. The theoretical analysis suggests that the differential flushing effect at different waterbodies due to complex geometry is one of the dominant factors causing inhomogeneous distribution of algal density during HAB initiation. The ratio of residence time to volume is one of the key variables that determine the differential timing of HAB occurrence in estuary-subestuary systems with multiple interconnected waterbodies. As a result, a HAB tends to be observed first in those locations with relatively long residence time and small waterbodies, such as tributaries or areas with large eddies. Multiple unconnected originating locations can co-exist within an estuary. Two three-dimensional model experiments with realistic forcings were conducted to demonstrate the flushing effect on annual Cochlodinium polykrikoides bloom in the lower James River. The results show that while the environmental conditions that affect local processes, such as salinity and temperature, are important in determining the originating locations of HABs, the differential flushing effect is the dominant factor driving the spatial difference in the density of C. polykrikoides in this region during the bloom initiation. This explains why the occurrence of the first bloom in this region is frequently observed in the Lafayette River, a relatively small waterbody with long residence time. Because of the relatively low growth rate of C. polykrikoides and because of the high water-exchange between the mainstem and tributaries of the James River, initial cyst distribution is suggested to have a relatively small impact on originating locations of the bloom compared to flushing effect and salinity, and the HAB originating locations do not have to be in the waterbody with abundant cysts.