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A method to determine the duration of the eclipse phase for in vitro infection with a highly pathogenic SHIV strain.

Kakizoe Y, Nakaoka S, Beauchemin CA, Morita S, Mori H, Igarashi T, Aihara K, Miura T, Iwami S - Sci Rep (2015)

Bottom Line: If it is not, however, ignoring this delay affects the accuracy of the mathematical model, its parameter estimates, and predictions.Here, we introduce a new approach, consisting in a carefully designed experiment and simple analytical expressions, to determine the duration and distribution of the eclipse phase in vitro.We find that the eclipse phase of SHIV-KS661 lasts on average one day and is consistent with an Erlang distribution.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, Kyushu University, Fukuoka 812-8581, Japan.

ABSTRACT
The time elapsed between successful cell infection and the start of virus production is called the eclipse phase. Its duration is specific to each virus strain and, along with an effective virus production rate, plays a key role in infection kinetics. How the eclipse phase varies amongst cells infected with the same virus strain and therefore how best to mathematically represent its duration is not clear. Most mathematical models either neglect this phase or assume it is exponentially distributed, such that at least some if not all cells can produce virus immediately upon infection. Biologically, this is unrealistic (one must allow for the translation, transcription, export, etc. to take place), but could be appropriate if the duration of the eclipse phase is negligible on the time-scale of the infection. If it is not, however, ignoring this delay affects the accuracy of the mathematical model, its parameter estimates, and predictions. Here, we introduce a new approach, consisting in a carefully designed experiment and simple analytical expressions, to determine the duration and distribution of the eclipse phase in vitro. We find that the eclipse phase of SHIV-KS661 lasts on average one day and is consistent with an Erlang distribution.

No MeSH data available.


Related in: MedlinePlus

Fits of mathematical model to single- and multiple-cycle viral yield experiment. During the SC and MC experiments at five different MOIs (TCID50/cell), the ratio of virus-producing cells to total cells and the amount of extracellular viral RNA in the supernatant were measured. The symbols denote the ratio of virus-producing cells in (A) and viral load in (B) respectively, and the solid lines are the best fit of the mathematical model, Eqs. (7)(10)(16, 17, 18, 19), to the data.
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f4: Fits of mathematical model to single- and multiple-cycle viral yield experiment. During the SC and MC experiments at five different MOIs (TCID50/cell), the ratio of virus-producing cells to total cells and the amount of extracellular viral RNA in the supernatant were measured. The symbols denote the ratio of virus-producing cells in (A) and viral load in (B) respectively, and the solid lines are the best fit of the mathematical model, Eqs. (7)(10)(16, 17, 18, 19), to the data.

Mentions: In contrast with SC experiments, if infection is initiated with fewer infectious virus than there are cells (an MOI ≪ 1 TCID50/cell), only a few cells are infected by the inoculum, and these cells go on to infect other cells, leading to successive cycles of infection61617181929. This is called a multiple-cycle (MC) viral yield experiment and is believed to be the typical mode of infection progression for natural virus infections in humans and animals. In addition to the SC experiment introduced above and performed at a MOI of 4.2 TCID50 per cell, we have simultaneously carried out SC and MC experiments at four additional MOIs (2.1, 1.05, 0.525 and 0.2625 TCID50/cell) for the infection of HSC-F cells with SHIV-KS661, measuring both the total virus yield in the supernatant (RNA copies/ml) and the cumulative fraction of cells positive for the Nef SHIV protein (see Methods). Using model Eqs. (7)(10)(16, 17, 18, 19), we simultaneously fitted our 80 experimental data points to reproduce these SC and MC experiments and extract the remaining model parameters, namely the virus infectivity (), virus production rate (), and infectious cell lifespan (). The fits were performed as described in the Methods section, and are shown in Fig. 4, with the estimated parameters presented in Table 2, and the initial conditions in Table 3. The model Eqs.(7)(10)(16, 17, 18, 19), reproduces the infection kinetics of both the SC and MC experiments very well.


A method to determine the duration of the eclipse phase for in vitro infection with a highly pathogenic SHIV strain.

Kakizoe Y, Nakaoka S, Beauchemin CA, Morita S, Mori H, Igarashi T, Aihara K, Miura T, Iwami S - Sci Rep (2015)

Fits of mathematical model to single- and multiple-cycle viral yield experiment. During the SC and MC experiments at five different MOIs (TCID50/cell), the ratio of virus-producing cells to total cells and the amount of extracellular viral RNA in the supernatant were measured. The symbols denote the ratio of virus-producing cells in (A) and viral load in (B) respectively, and the solid lines are the best fit of the mathematical model, Eqs. (7)(10)(16, 17, 18, 19), to the data.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4440524&req=5

f4: Fits of mathematical model to single- and multiple-cycle viral yield experiment. During the SC and MC experiments at five different MOIs (TCID50/cell), the ratio of virus-producing cells to total cells and the amount of extracellular viral RNA in the supernatant were measured. The symbols denote the ratio of virus-producing cells in (A) and viral load in (B) respectively, and the solid lines are the best fit of the mathematical model, Eqs. (7)(10)(16, 17, 18, 19), to the data.
Mentions: In contrast with SC experiments, if infection is initiated with fewer infectious virus than there are cells (an MOI ≪ 1 TCID50/cell), only a few cells are infected by the inoculum, and these cells go on to infect other cells, leading to successive cycles of infection61617181929. This is called a multiple-cycle (MC) viral yield experiment and is believed to be the typical mode of infection progression for natural virus infections in humans and animals. In addition to the SC experiment introduced above and performed at a MOI of 4.2 TCID50 per cell, we have simultaneously carried out SC and MC experiments at four additional MOIs (2.1, 1.05, 0.525 and 0.2625 TCID50/cell) for the infection of HSC-F cells with SHIV-KS661, measuring both the total virus yield in the supernatant (RNA copies/ml) and the cumulative fraction of cells positive for the Nef SHIV protein (see Methods). Using model Eqs. (7)(10)(16, 17, 18, 19), we simultaneously fitted our 80 experimental data points to reproduce these SC and MC experiments and extract the remaining model parameters, namely the virus infectivity (), virus production rate (), and infectious cell lifespan (). The fits were performed as described in the Methods section, and are shown in Fig. 4, with the estimated parameters presented in Table 2, and the initial conditions in Table 3. The model Eqs.(7)(10)(16, 17, 18, 19), reproduces the infection kinetics of both the SC and MC experiments very well.

Bottom Line: If it is not, however, ignoring this delay affects the accuracy of the mathematical model, its parameter estimates, and predictions.Here, we introduce a new approach, consisting in a carefully designed experiment and simple analytical expressions, to determine the duration and distribution of the eclipse phase in vitro.We find that the eclipse phase of SHIV-KS661 lasts on average one day and is consistent with an Erlang distribution.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, Kyushu University, Fukuoka 812-8581, Japan.

ABSTRACT
The time elapsed between successful cell infection and the start of virus production is called the eclipse phase. Its duration is specific to each virus strain and, along with an effective virus production rate, plays a key role in infection kinetics. How the eclipse phase varies amongst cells infected with the same virus strain and therefore how best to mathematically represent its duration is not clear. Most mathematical models either neglect this phase or assume it is exponentially distributed, such that at least some if not all cells can produce virus immediately upon infection. Biologically, this is unrealistic (one must allow for the translation, transcription, export, etc. to take place), but could be appropriate if the duration of the eclipse phase is negligible on the time-scale of the infection. If it is not, however, ignoring this delay affects the accuracy of the mathematical model, its parameter estimates, and predictions. Here, we introduce a new approach, consisting in a carefully designed experiment and simple analytical expressions, to determine the duration and distribution of the eclipse phase in vitro. We find that the eclipse phase of SHIV-KS661 lasts on average one day and is consistent with an Erlang distribution.

No MeSH data available.


Related in: MedlinePlus