alexa Single Base Primer Extension Assay (SNaPshot) for Rapid

Journal of Molecular Biomarkers & Diagnosis
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Research Article

Single Base Primer Extension Assay (SNaPshot) for Rapid Detection of Human Immunodeficiency Virus - 1 Drug Resistance Mutations

Arpan A1, Salil V1, Harsh P2 and Pratap NM1*
1SN GeneLab, 2nd Floor, President Plaza, Tower A, Nanpura, Ring Road, Surat, Gujarat, India
2Department of Biotechnology, JJT University, Churu Jhunjhunu Road, Vidyanagari, Chudela, Rajasthan, India
*Corresponding Author : Pratap N Mukhopadhyaya
B-604, Kapil Aasmant, Pashan-Sus Road
Pashan, Pune-411 021, Maharashtra, India
Tel: +91 98811 53425
E-mail: [email protected]
Received: December 30, 2015 Accepted: January 29, 2016 Published: January 31, 2016
Citation: Arpan A, Salil V, Harsh P, Pratap NM (2016) Single Base Primer Extension Assay (SNaPshot) for Rapid Detection of Human Immunodeficiency Virus - 1 Drug Resistance Mutations. J Mol Biomark Diagn 7:271. doi:10.4172/2155-9929.1000271
Copyright: © 2016 Arpan A, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.


The 3' primer extension assay can be employed to interrogate multiple known single nucleotide polymorphisms (SNPs) simultaneously using a multiplex approach. Over 200 Human Immunodeficiency Virus-1 (HIV-1) mutations are currently associated with drug resistance. Identifying these mutations assist in taking appropriate therapeutic decisions such that superior drug regimens can be designed for keeping the viral load below pathogenic level. Presently, reverse transcription of HIV-1 RNA followed by amplification of the pol gene and subsequent nucleotide sequencing is a popular method of HIV-1 drug resistance genotyping. However, it is still a time consuming and laborious protocol and require significant bioinformatics analysis in order to decipher the significance of mutations encountered during analysis.

In this study we analyzed 75 HIV-1 positive clinical samples for 2 representative mutations, viz., M41L and M184V using a 3' primer extension protocol popularly known as SNaPshot assay. Twenty four and 36% of the patients were found to harbor the critical M41L and M184V mutations respectively while 20% were found to contain both the mutations together. The results were 100% concordant with DNA sequencing assay which was used as a gold standard. The results substantiate the cost, speed and economy-related advantages of this technology platform for interrogating known mutations of significance within the HIV-1 genome.


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