In Monogram Biosciences' PhenoSense™ HIV assays, patient-derived sequences are tested as pools or libraries of sequences that capture the diversity of the viral quasi-species within a patient sample. In some instances, it may be beneficial to characterize these quasi-species to determine minor populations or changes in the viral population in the patient over time (longitudinal samples). This can be achieved by using Monogram's clonal testing assay. Patient pools generated in Monogram Biosciences' PhenoSense HIV assays are used for selecting and growing individual clones (viruses). Typically, 48 or 96 clones (viruses) are prepared per patient sample, which undergo an infectivity screen to determine clone viability. From these results, the client may select the clones (usually 12-16) that Monogram will use for subsequent testing such as genotyping, drug susceptibility and/or tropism.

Reference: Westby, M., Lewis, M., Whitcomb, J., Youle, M., Pozniak, A. L., James, I. T., Jenkins, T. M., Perros, M. & van der Ryst, E.
Emergence of CXCR4-using human immunodeficiency virus type 1 (HIV-1) variants in a minority of HIV-1-infected patients following treatment with the CCR5 antagonist maraviroc is from a pretreatment CXCR4-using virus reservoir. J Virol 80, 4909-20 (2006).

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