Abstract: This invention relates to methods for predicting replication capacity of a virus based on genotype and identifying targets for antiviral therapy by identifying mutations associated with altered replication capacity. The methods are useful, for example, for identifying previously unknown interactions among viral molecules or between viral molecules and host cell molecules that are essential to viral infection and/or replication. By identifying such interactions, novel targets for antiviral therapy can be identified. In another aspect, the invention provides a method for determining that an HIV has an altered replication capacity. In certain embodiments, the method comprises detecting a mutation in a codon of gag that is selected from the group consisting of 437, 439, 441, 442, 454, 478, 479, and 484.

Abstract: The present invention provides methods and devices for predicting whether a HIV variant will be resistant to an antiviral drug based on the variant's genotype. In one aspect, methods are provided comprising determining whether a combination of protease inhibitor resistance mutations meet certain conditions, as disclosed herein, thereby assessing the effectiveness of ritonavir-boosted indinavir therapy in the HIV-infected subject. Computer implemented methods comprising determining HIV resistance are provided.

Abstract: The present invention provides a method for identifying whether a compound inhibits entry of a virus into a cell which comprises: (a) obtaining nucleic acid encoding a viral envelope protein from a patient infected by the virus; (b) co-transfecting into a first cell (i) the nucleic add of step (a), and (ii) a viral expression vector which lacks a nucleic acid encoding an envelope protein, and which comprises an indicator nucleic acid which produces a detectable signal, such that the first cell produces viral particles comprising the envelope protein encoded by the nucleic acid obtained from the patient; (c) contacting the viral particles produced in step (b) with a second cell in the presence of the compound, wherein the second cell expresses a cell surface receptor to which the virus binds; (d) measuring the amount of signal produced by the second cell in order to determine the infectivity of the viral particles; and (e) comparing the amount of signal measured in step (d) with the amount of signal produced i