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In addition, we re-sequenced two time points for eight cultures to determine whether our sequencing method was accurately displaying the viral variation in each culture.
Viral variation was detectable prior to depletion in five of seven identified Mamu-B*08-restricted epitopes in r00078, and in four of six epitopes for which sequence was available in r98016.
To determine whether viral variation in CD8+ T cell epitopes could be associated with expression of Mamu-B*08, we first sequenced vif, rev, and nef ORFs in virus isolated from plasma of chronically infected Mamu-B*08-positive controllers and progressors.
Although we cannot yet determine which substitutions in particular Mamu-B*08-restricted CD8+ T cell epitopes can be correlated with loss of effective viremia control, we were surprised to find that Mamu-B*08-restricted CD8+ T cell responses appeared to select for viral variation in all identified epitopes in the majority of animals.
The entropy map showed that significant viral variation was observed throughout the viral genome, particularly within E2 but also in the NS regions (figure 3B).
Infection of cell cultures with cell-free virus isolated from HIV-infected patients is notoriously difficult and results in a loss of viral variation.
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We previously developed a combinatorial method for the isolation of novel sequences to cope with rapid viral variations at the G-H loop of Foot and Mouth Disease virus VP1 protein [1].
There are no rigorous measurements of viral variations within an outbreak and among different epidemic seasons.
Seasonal influenza vaccine formulation efforts struggle to keep up with viral antigenic variation.
There are few data in the literature on viral sequence variation between host generations/successive transmission events.
Therefore, initial viral genetic variation among inoculated A. thaliana plants was minimal.
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