A Digital Signal Processing-Based Bioinformatics Approach to Identifying the Origins of HIV-1 Non B Subtypes Infecting US Army Personnel Serving Abroad

Abstract

Two HIV-1 non B isolates, 98US_MSC5007 and 98US_MSC5016, which have been identified amongst the US Army personnel serving abroad, are known to have originated from other nations. Notwithstanding, they are categorized as American strains. This is because their countries of origin are unknown. American isolates are basically B subtype. 98US_MSC5007 belongs to Circulating Recombinant Form (CRF02_AG) while 98US_MSC5016 is of the C clade. Both sub-groups are recognized to have originated from African and Asian continents. It has become necessary to properly determine the countries of origin of microbes and viruses. This is because diversity and cross-subtyping have been found to mitigate the designing and development of vaccine and therapeutic interventions. The aim of this study therefore is to identify the countries of origin of the two American isolates found amongst US Army personnel serving abroad. A Digital Signal Processing-based Bioinformatics technique called Informational Spectrum Method (ISM) has been engaged. ISM entails translating the amino acids sequences of the protein into numerical sequences (signals) by means of one biological parameter (Amino Acids Scale). The signals are then processed using Discrete Fourier Transform (DFT) in order to uncover and present the embedded biological information as Informational Spectra (IS). Spectral Position of Maximum Binding Interaction (SPMBI) is used. Several approaches including Phylogeny have preliminarily been employed in the determination of evolutionary trends of organisms and viruses. SPMBI has preliminarily been used to re-establish the semblance and common originality that exist between human and Chimpanzee, evolutionary roadmaps in the Influenza and HIV viruses. The results disclosed that 98US_MSC5007 shared same semblance and originality with a Nigeria isolate (92NG083) while 98US_MSC5016 with the Zairian isolates (ELI, MAL, and Z2/CDC-34). These results appear to demonstrate that the American soldiers harboring these strains may have been infected by isolates from Nigeria and Zaire, respectively. This is because 98US_MSC5007 and the Nigerian isolate share SPMBI at position 44. Additionally, 98US_MSC5016, which has SPMBI at position 148, may have come from Zaire as it has similar SPMBI with the Zairian isolates at 150. SPMBI is a demonstration of Bio-functionality arising from maximum affinity by the proteins from different sources to a common protein. To help validate the findings, the experiment was further repeated using ISM-based Phylogenetic technique. The outcome appears not to be in complete accord with the results obtained in this study. It is therefore recommended that the countries in which these US Army personnel are deployed be identified and where the findings made and the locations of the Army personnel appropriately correlate, this novel procedure be engaged in the identification of the nations of origins of all other such HIV isolates across all clades and nations.

Novel Computerized Approaches to Investigating Pharmacological Activities

“…This is catalyzed by Integrase Enzyme [7,28]. The 288 amino-acid length Integrase Enzyme is inhibited by several mechanisms.…”

“…This structural conformation brings about the CD4 perforation, and subsequently, the transfer of the viral genetic content into the host CD4. Structural re-arrangement is impossible without the formation of Six Helix Bundle (SHB) between the C-terminal of the Heptad Repeat (CHR) and the N-terminal of the Heptad Repeat (NHR) [7,28]. Both Enfuvirtide, Sifuvirtide are structural analogues of the CHR.…”

“…We have preliminarily engaged ISM and one biological parameter, Amino Acid Scale (AAS), to show how we can extract pharmacological activities from sequence information [7][8][9]. AASs are defined as the numerical values representing the level of participation of the each of the 20 essential amino acids that constitute protein in various interactions [7].…”

“…AASs are defined as the numerical values representing the level of participation of the each of the 20 essential amino acids that constitute protein in various interactions [7]. Some of the AASs are deposited at the GeomeNet Database Resources (www.genome.jp/aaindex) [10].…”

“…These preliminarily computational assessments [7][8][9]19] are therefore used to demonstrate how a computerized approach (ISM) could be engaged to assess pharmacological activities. Studies carried out on the pharmacological activities of these agents with the aim of extracting their sequence information and biological parameters are reported in section 2.1.…”