International Journal of Microbiology and Immunology Research Vol. 2(5), pp. 063-070, August 2014 ISSN 2327-7769 ©2014 Academe Research Journals

Full Length Research Paper

Sequence variation and co-receptor tropism prediction of V3 loop of HIV-1 from Kelantan, Malaysia

Maizan M.¹*, Nurfadhilah U.¹, Ong SM.², WNazirah WY.³, Mahiran M.⁴ and Tan SC.⁵

¹Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan, Malaysia.

²School of Health Sciences, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan, Malaysia.

³School of Medical Sciences, Universiti Sains Malaysia, 16150 KubangKerian, Kelantan, Malaysia.

⁴Hospital Raja Perempuan Zainab II, 15586 Kota Bharu, Kelantan, Malaysia.

⁵Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, 11800 USM Pulau Pinang, Malaysia.

⁶Faculty of Veterinary Medicine, Universiti Malaysia Kelantan, Locked bag 36, Pengkalan Chepa,16100 Kota Bhary, Kelantan, Malaysia

*Corresponding author. E-mail: maizan.m@umk.edu.my, Tel:+609-7717328. Fax: +609-7717132

.Accepted 19 May, 2014

Abstract

V3 loop of human HIV-1 gp120 is a major determinant for T cell and macrophage tropism by determining the co-receptor used by the virus in the cell entry. Mutations in this motif could affect the syncytium formation, virus infectivity, neutralization, replication efficiency and host cell tropism. This study was aimed to determine the sequence variation of gp120 V3 loop for the prediction of co-receptor used by HIV-1 from Kelantan, host cell tropism and prognosis of disease progression. The V3 loop tip motif sequences of 30 HIV-1 from Kelantan, Malaysia were amplified, sequenced, analyzed and predicted by their co-receptor using a co-receptor usage prediction without sequence alignments: an application of string kernels (ds)Kernel bio-informatics software. The sequences were also subjected to the phylogenetic analysis for subtyping of the virus. The result revealed that among the 30 HIV-1 from Kelantan tested, 29 viruses were predicted to use CCR5 co-receptor and one virus utilised CXCR4. Phylogenetic result showed that 29 HIV-1 from Kelantan were of the unique recombinant form (URF) derived from CRF33_01B and only one virus was clustered with CRF53_01B of Malaysian HIV-1. Hence, the variation of the V3 loop sequences could be used to predict the co-receptor used by the virus for the prognosis of disease progression of the HIV-1 patients and subtyping of the virus.

Key words: Human immunodeficiency virus type 1 (HIV-1), Kelantan, Malaysia, V3 loop, sequence variation, HIV-1 subtyping.