Next Article in Journal
Structural Proteomics of Herpesviruses
Previous Article in Journal
Suppressive Effects of the Site 1 Protease (S1P) Inhibitor, PF-429242, on Dengue Virus Propagation
Article Menu

Export Article

Open AccessArticle

Genetic Variability of HIV-1 for Drug Resistance Assay Development

Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, 300 Pasteur Drive, L-134, Stanford, CA 94035, USA
HIV-1 Molecular Epidemiology Laboratory, Microbiology and Parasitology Department, Hospital Ramón y Cajal-IRYCIS and CIBER-ESP, Madrid 28034, Spain
Author to whom correspondence should be addressed.
Viruses 2016, 8(2), 48;
Received: 21 November 2015 / Revised: 2 February 2016 / Accepted: 3 February 2016 / Published: 11 February 2016
(This article belongs to the Section Antivirals & Vaccines)
PDF [1487 KB, uploaded 19 February 2016]


A hybridization-based point-of-care (POC) assay for HIV-1 drug resistance would be useful in low- and middle-income countries (LMICs) where resistance testing is not routinely available. The major obstacle in developing such an assay is the extreme genetic variability of HIV-1. We analyzed 27,203 reverse transcriptase (RT) sequences from the Stanford HIV Drug Resistance Database originating from six LMIC regions. We characterized the variability in a 27-nucleotide window surrounding six clinically important drug resistance mutations (DRMs) at positions 65, 103, 106, 181, 184, and 190. The number of distinct codons at each DRM position ranged from four at position 184 to 11 at position 190. Depending on the mutation, between 11 and 15 of the 24 flanking nucleotide positions were variable. Nonetheless, most flanking sequences differed from a core set of 10 flanking sequences by just one or two nucleotides. Flanking sequence variability was also lower in each LMIC region compared with overall variability in all regions. We also describe an online program that we developed to perform similar analyses for mutations at any position in RT, protease, or integrase. View Full-Text
Keywords: HIV-1; drug resistance mutation; variability; point-of-care HIV-1; drug resistance mutation; variability; point-of-care

Figure 1

This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited (CC BY 4.0).

Share & Cite This Article

MDPI and ACS Style

Clutter, D.S.; Sánchez, P.R.; Rhee, S.-Y.; Shafer, R.W. Genetic Variability of HIV-1 for Drug Resistance Assay Development. Viruses 2016, 8, 48.

Show more citation formats Show less citations formats

Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.

Related Articles

Article Metrics

Article Access Statistics



[Return to top]
Viruses EISSN 1999-4915 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert
Back to Top