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Emergence of Novel Unique Recombinant Forms and Multiple Subtypes in Gag-Pol Region of HIV-1 in Punjab, Pakistan

Emergence of Novel Unique Recombinant Forms and Multiple Subtypes in Gag-Pol Region of HIV-1 in Punjab, Pakistan

Amreen Zahra1*, Mushtaq A. Saleem2, Hasnain Javed3, Muhammad Azmat Ullah Khan4 and Abdul Rauf Shakoori4

1Department of Biochemistry, University of Central Punjab, Lahore 54782, Pakistan
2Ghazi National Institute of Engineering and Sciences (GNIES), Taunsa by Pass Road, Pakistan Chowk DG Khan, Pakistan
3Advanced Diagnostic Laboratory, Punjab AIDS Control Programme, Government of Punjab, Lahore 54000, Pakistan
4Department of Biochemistry and Molecular biology, University of Gujrat, Gujrat 50700, Pakistan
5School of Biological Sciences, University of the Punjab, Quaid-I-Azam Campus, Lahore 54590, Pakistan
 
* Corresponding author: amreenzara1@gmail.com

Fig. 1.

Genotypic analysis of HIV-1 Gag sequences: Boot scanning analysis of Subtype A1in HIV-1 Gag gene region. (A) isolate MBBL12 (B) isolate MBBL03 (C) isolate MBBL30 (D) isolate MBBL09. Parametrical analysis was done using the following: Window: 200 bp, step: 20 bp, gapstrip: on, reps: 100, Kimura (2-parameter), T/t: 2.0. 

Fig. 2.

Genotypic analysis of HIV-1 Gag circulating recombinant forms (CRFs): Boot scanning analysis of HIV-1 Gag gene with CRFs. (A) isolate MBBL10; (B) isolate MBBL05; (C) isolate MBBL 04. Conditions used were the following: Window: 400 bp, step size: 40 bp, gapstrip: on, reps: 100, Kimura (2-parameter), T/t: 2.0.

Fig. 3.

Genotypic analysis of Pol Unique Recombinant Forms (URFs): Boot scanning analysis of HIV-1 Pol gene with URFs. (A) isolate MBBL15; (B) isolate MBBL17; (C) isolate MBBL 24; (D) isolate MBBL18. The conditions used for this analysis were the following: Window: 400 bp, step size: 40 bp, gapstrip: on, reps: 100, Kimura (2-parameter), T/t.

Fig. 4.

Phylogenetic tree of 17 Gag isolates (A) and 13 pol isolates (B), generated via Neighbor Joining method. The distances were computed using the Kimura 2- parameter model. Evolutionary analysis were conducted in MEGA X. Sum of branch optimum length = 0.66910448. 1000 bootstrap test replicates are shown near to scale with branch lengths as those of the evolutionary distances used to infer the phylogenetic tree.

Pakistan Journal of Zoology

October

Vol. 54, Iss. 5, Pages 2003-2500

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