Genetic Characterization of a Panel of Diverse HIV-1 Isolates at Seven International Sites.
Abstract
HIV-1 subtypes and drug resistance are routinely tested by many international surveillance
groups. However, results from different sites often vary. A systematic comparison
of results from multiple sites is needed to determine whether a standardized protocol
is required for consistent and accurate data analysis. A panel of well-characterized
HIV-1 isolates (N = 50) from the External Quality Assurance Program Oversight Laboratory
(EQAPOL) was assembled for evaluation at seven international sites. This virus panel
included seven subtypes, six circulating recombinant forms (CRFs), nine unique recombinant
forms (URFs) and three group O viruses. Seven viruses contained 10 major drug resistance
mutations (DRMs). HIV-1 isolates were prepared at a concentration of 107 copies/ml
and compiled into blinded panels. Subtypes and DRMs were determined with partial or
full pol gene sequences by conventional Sanger sequencing and/or Next Generation Sequencing
(NGS). Subtype and DRM results were reported and decoded for comparison with full-length
genome sequences generated by EQAPOL. The partial pol gene was amplified by RT-PCR
and sequenced for 89.4%-100% of group M viruses at six sites. Subtyping results of
majority of the viruses (83%-97.9%) were correctly determined for the partial pol
sequences. All 10 major DRMs in seven isolates were detected at these six sites. The
complete pol gene sequence was also obtained by NGS at one site. However, this method
missed six group M viruses and sequences contained host chromosome fragments. Three
group O viruses were only characterized with additional group O-specific RT-PCR primers
employed by one site. These results indicate that PCR protocols and subtyping tools
should be standardized to efficiently amplify diverse viruses and more consistently
assign virus genotypes, which is critical for accurate global subtype and drug resistance
surveillance. Targeted NGS analysis of partial pol sequences can serve as an alternative
approach, especially for detection of low-abundance DRMs.
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https://hdl.handle.net/10161/13343Published Version (Please cite this version)
10.1371/journal.pone.0157340Publication Info
Hora, Bhavna; Keating, Sheila M; Chen, Yue; Sanchez, Ana M; Sabino, Ester; Hunt, Gillian;
... REDS-III and EQAPOL programs (2016). Genetic Characterization of a Panel of Diverse HIV-1 Isolates at Seven International
Sites. PLoS One, 11(6). pp. e0157340. 10.1371/journal.pone.0157340. Retrieved from https://hdl.handle.net/10161/13343.This is constructed from limited available data and may be imprecise. To cite this
article, please review & use the official citation provided by the journal.
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Show full item recordScholars@Duke
Thomas Norton Denny
Professor in Medicine
Thomas N. Denny, MSc, M.Phil, is the Chief Operating Officer of the Duke Human Vaccine
Institute (DHVI), Associate Dean for Duke Research and Discovery @RTP, and a Professor
of Medicine in the Department of Medicine at Duke University Medical Center. He is
also an Affiliate Member of the Duke Global Health Institute. Previously, he served
on the Health Sector Advisory Council of the Duke University Fuquay School of Business.
Prior to joining Duke, he was an Associate Professor of Pathology, Labo
Feng Gao
Professor Emeritus in Medicine
Dr. Feng Gao is Professor of Medicine at Duke University. The Gao laboratory has a
long-standing interest in elucidating the origins and evolution of human and simian
inmmunodeficiency viruses (HIV and SIV), and in studying HIV/SIV gene function and
pathogenic mechanisms from the evolutionary perspective. These studies have led to
new strategies to better understand HIV origins, biology, pathogenesis and drug resistance,
and to design new AIDS vaccines.
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