title: Single genome amplification and standard bulk PCR yield HIV-1 envelope products with similar genotypic and phenotypic characteristics.
abstract: Recent studies suggest that single genome amplification (SGA) as compared to standard bulk PCR and virus stocks from 293T transfection versus short term passage in peripheral blood mononuclear cells (PBMC) yield a less biased representation of HIV-1 envelope characteristics. In 9 different subjects, genetic diversity, divergence, and population structure were not significantly different among SGA or bulk PCR amplified envelope V1-V3 segments. In these subjects, 293T transfection derived virus stocks with SGA or bulk PCR amplified envelopes have similar infectivity, replication kinetics, co-receptor usage, and neutralization susceptibility. While PBMC passage as compared to the 293T derived virus stocks had similar co-receptor usage, PBMC viruses were less neutralization susceptible to some specific antibodies. Our results suggest that the method of envelope sequence amplification, either SGA or bulk PCR, does not have a significant impact on the genotypic and phenotypic properties of the virus envelope quasispecies.
authors: Department of Medicine, Boston University School of Medicine, Boston, MA, USA.
authors: Behzad
authors: B
authors: Etemad
authors: Department of Medicine, Boston University School of Medicine, Boston, MA, USA.
authors: Melissa
authors: M
authors: Ghulam-Smith
authors: Department of Medicine, Boston University School of Medicine, Boston, MA, USA.
authors: Oscar
authors: O
authors: Gonzalez
authors: Boston University School of Public Health, Boston, MA, USA.
authors: Laura F
authors: LF
authors: White
authors: Department of Medicine, Boston University School of Medicine, Boston, MA, USA. Electronic address: msagar@bu.edu.
authors: Manish
authors: M
authors: Sagar
mesh_terms: D057134:Antibodies, Neutralizing / Q000276:immunology; D002460:Cell Line; D014644:Genetic Variation; D016679:Genome, Viral; D005838:Genotype; D015483:HIV Antibodies / Q000276:immunology; D015497:HIV-1 / Q000235:genetics* / Q000276:immunology; D006801:Humans; D009500:Neutralization Tests; D010641:Phenotype; D016133:Polymerase Chain Reaction / Q000379:methods*; D054299:env Gene Products, Human Immunodeficiency Virus / Q000235:genetics*
chemical_list: D057134:Antibodies, Neutralizing; D015483:HIV Antibodies; D054299:env Gene Products, Human Immunodeficiency Virus
keywords: Diversity; Envelope; HIV-1; Neutralization; Replication; Single genome amplification