title: Comparison of standard PCR/cloning to single genome sequencing for analysis of HIV-1 populations.
abstract: To compare standard PCR/cloning and single genome sequencing (SGS) in their ability to reflect actual intra-patient polymorphism of HIV-1 populations, a total of 530 HIV-1 pro-pol sequences obtained by both sequencing techniques from a set of 17 ART naïve patient specimens was analyzed. For each specimen, 12 and 15 sequences, on average, were characterized by the two techniques. Using phylogenetic analysis, tests for panmixia and entropy, and Bland-Altman plots, no difference in population structure or genetic diversity was shown in 14 of the 17 subjects. Evidence of sampling bias by the presence of subsets of identical sequences was found by either method. Overall, the study shows that neither method was more biased than the other, and providing that an adequate number of PCR templates is analyzed, and that the bulk sequencing captures the diversity of the viral population, either method is likely to provide a similar measure of population diversity.
authors.affiliation: Tufts University School of Medicine, Tufts Medical Center, Boston, MA 02111, USA. mjordan@tuftsmedicalcenter.org
authors.forename: Michael R
authors.initials: MR
authors.lastname: Jordan
authors.forename: Mary
authors.initials: M
authors.lastname: Kearney
authors.forename: Sarah
authors.initials: S
authors.lastname: Palmer
authors.forename: Wei
authors.initials: W
authors.lastname: Shao
authors.forename: Frank
authors.initials: F
authors.lastname: Maldarelli
authors.forename: Eoin P
authors.initials: EP
authors.lastname: Coakley
authors.forename: Colombe
authors.initials: C
authors.lastname: Chappey
authors.forename: Christine
authors.initials: C
authors.lastname: Wanke
authors.forename: John M
authors.initials: JM
authors.lastname: Coffin
mesh_terms: D002648:Child; D002675:Child, Preschool; D003001:Cloning, Molecular / Q000379:methods; D016000:Cluster Analysis; D005260:Female; D016679:Genome, Viral; D015658:HIV Infections / Q000821:virology*; D015497:HIV-1 / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D006801:Humans; D007223:Infant; D008297:Male; D010802:Phylogeny; D011110:Polymorphism, Genetic; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA / Q000379:methods*; D014773:Virology / Q000379:methods*
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