Background: Phosphorylation by Casein kinase 2 at two conserved seryl residues, Ser52 and Ser56 at the cytoplasmic domain of HIV-1 Viral protein U (Vpu) are essential for inducing CD4 degradation. This study is conducted to investigate the variability of HIV-1 viral protein unique particularly at amino-acid position Ser52 and Ser56 among the HIV infected individuals in the northeastern region of India. Materials and methods: Blood samples from 90 HIV-1 infected patients of Manipur have been studied by viral amplification and sequencing at vpu gene of HIV-1. For analysis of amino acid variation at Ser52 and Ser56, nucleic acid sequences were translated into amino acid and aligned with reference strain of HIV-1. Phylogenetic tree was also inferred among the studied samples. Results: The results revealed that 93% of HIV-1 infected individuals harbored virus with conserved serine at both amino acid positions 52 and 56 of vpu which were known to have the ability to induce CD4 degradation while 1% harbored viral mutation at both Ser52 and Ser56, replaced by asparagine which has been predicted to may have lost the ability to induce CD4 degradation. Moreover, 5% and 1% of HIV-1 infected individuals were found to be infected with mutated virus at ser52 and ser56 of vpu respectively. Conclusion: The overall finding of this study reveals that seryl residue of vpu at Ser52 and Ser56 was highly conserved among the HIV-1 infected individuals of the study population.