Multiple protein-domain conservation architecture as a non-deterministic confounder of linear B cell epitopes

Epitope prediction is a critical step to diagnostic and vaccine discovery. Despite existence of some parameters for epitope discovery, this area remains inconclusive and wanting-for new complementary or stand-alone tools. The phenomenon of multiple protein-domain conservation architecture (MPDCA) as used here refers to homologous motifs unveiled by multiple sequence alignments across strain-variants of the same protein aside of the conserved domains (CD) present within the same super family. Unpublished data suggests that MPDCA might be a confounder of epitope necessitating further investigation as a predictor of the same. The ease of determining MPDCA is appealing when considering protein-analysis; specifically epitope discovery. This study aimed to validate MPDCA as a predictive confounder of epitope. Using two-sets of surface viral glycoproteins of human immunodeficiency virus type I, HIV-1 (gp120) and Ebola virus, EBOV (gp1,2 preprotein) (selected because their CD-architecture has widely been studied, their sequences are available in public databases, and the same are well annotated), the MPDCAs among three different virus-strains in each-set, were compared to epitopes predicted by established tools (Bipred and DiscoTope). 4/6 (66.6%) of the linear epitopes confounded MPDCA, with 3/6 (50%) of these MPDCA’s confounding with the predicted linear epitopes (LE) at identities of > 50%, when compared to just 3/6 (50%) of the discontinuous epitopes (DE) that confounded with MPDCA at a < 50% identity. MPDCA is a non-deterministic confounder of Linear B cell epitopy. There is no causal relationship between the two, much as there is an evident co-occurrence. Therefore, MPDCA cannot accurately be used as an additional parameter to predict linear and or non-linear B cell epitopes

Proviral HIV-genome-wide and pol-gene specific Zinc Finger Nucleases: Usability for targeted HIV gene therapy

<p>Abstract</p> <p>Background</p> <p>Infection with HIV, which culminates in the establishment of a latent proviral reservoir, presents formidable challenges for ultimate cure. Building on the hypothesis that <it>ex-vivo </it>or even <it>in-vivo </it>abolition <it>or </it>disruption of HIV-gene/genome-action by target mutagenesis or excision can irreversibly abrogate HIV's innate fitness to replicate and survive, we previously identified the isoschizomeric bacteria restriction enzymes (REases) AcsI and ApoI as potent cleavers of the HIV-pol gene (11 and 9 times in HIV-1 and 2, respectively). However, both enzymes, along with others found to cleave across the entire HIV-1 genome, slice (SX) at palindromic sequences that are prevalent within the human genome and thereby pose the risk of host genome toxicity. A long-term goal in the field of R-M enzymatic therapeutics has thus been to generate synthetic restriction endonucleases with longer recognition sites limited in specificity to HIV. We aimed (i) to assemble and construct zinc finger <it>arrays </it>and <it>nucleases </it>(ZFN) with either proviral-HIV-pol gene or proviral-HIV-1 whole-genome specificity respectively, and (ii) to advance a model for pre-clinically testing lentiviral vectors (LV) that deliver and transduce either ZFN genotype.</p> <p>Methods and Results</p> <p><it>First, </it>we computationally generated the consensus sequences of (a) 114 dsDNA-binding zinc finger (Zif) <it>arrays </it>(ZFAs or Zif_HIV-pol) and (b) two zinc-finger <it>nucleases </it>(ZFNs) which, unlike the AcsI and ApoI homeodomains, possess specificity to >18 base-pair sequences uniquely present within the HIV-pol gene (Zif_HIV-polF_N). Another 15 ZFNs targeting >18 bp sequences within the complete HIV-1 proviral genome were constructed (Zif_HIV-1F_N). <it>Second, </it>a model for constructing lentiviral vectors (LVs) that deliver and transduce a diploid copy of either Zif_HIV-polF_Nor Zif_HIV-1F_Nchimeric genes (termed <b>LV- 2xZif</b>_{<b>HIV-pol</b>}<b>F</b>_{<b>N </b>}and <b>LV- 2xZif</b>_<b>HIV-1</b><b>F</b>_{<b>N, </b>}respectively) is proposed. <it>Third, </it>two preclinical models for controlled testing of the safety and efficacy of either of these LVs are described using active HIV-infected TZM-bl reporter cells (HeLa-derived JC53-BL cells) and latent HIV-infected cell lines.</p> <p>Conclusion</p> <p><b>LV-2xZif</b>_{<b>HIV-pol</b>}<b>F</b>_{<b>N </b>}and <b>LV- 2xZif</b>_<b>HIV-1</b><b>F</b>_{<b>N </b>}may offer the <it>ex-vivo </it>or even <it>in-vivo </it>experimental opportunity to halt HIV replication functionally by directly abrogating HIV-pol-gene-action <it>or </it>disrupting/excising over 80% of the proviral HIV DNA from latently infected cells.</p

On the general theory of the origins of retroviruses

<p>Abstract</p> <p>Background</p> <p>The order retroviridae comprises viruses based on ribonucleic acids (RNA). Some, such as HIV and HTLV, are human pathogens. Newly emerged human retroviruses have zoonotic origins. As far as has been established, both repeated infections (themselves possibly responsible for the evolution of viral mutations <b>(Vm) </b>and host adaptability <b>(Ha)</b>); along with interplay between <it>inhibitors </it>and <it>promoters </it>of cell tropism, are needed to effect retroviral cross-species transmissions. However, the exact <it>modus operadi </it>of intertwine between these factors at molecular level remains to be established. Knowledge of such intertwine could lead to a better understanding of retrovirology and possibly other infectious processes. This study was conducted to derive the mathematical equation of a general theory of the origins of retroviruses.</p> <p>Methods and results</p> <p>On the basis of an arbitrarily non-Euclidian geometrical "thought experiment" involving the cross-species transmission of simian foamy virus (sfv) from a non-primate species <it>Xy </it>to <it>Homo sapiens </it>(<it>Hs</it>), initially excluding all social factors, the following was derived. At the port of exit from <it>Xy </it>(where the species barrier, SB, is defined by the <it>Index of Origin</it>, IO), sfv shedding is (1) enhanced by two transmitting tensors <b>(Tt)</b>, (i) virus-specific immunity (VSI) and (ii) evolutionary defenses such as APOBEC, RNA interference pathways, and (when present) expedited therapeutics (denoted e²D); and (2) opposed by the five accepting scalars <b>(At)</b>: (a) genomic integration hot spots, gIHS, (b) nuclear envelope transit <b>(</b>NMt) vectors, (c) virus-specific cellular biochemistry, VSCB, (d) virus-specific cellular receptor repertoire, VSCR, and (e) pH-mediated cell membrane transit, (↓_pHCMat). Assuming <b>As </b>and <b>Tt </b>to be independent variables, <b>IO = Tt/As</b>. The same forces acting in an opposing manner determine SB at the port of sfv entry (defined here by the <it>Index of Entry</it>, <b>IE = As/Tt</b>). Overall, If sfv encounters no unforeseen effects on transit between X<it>y </it>and <it>Hs</it>, then the square root of the combined index of sfv transmissibility (√<b>|RTI|) </b>is proportional to the product IO* IE (or ~Vm* Ha* ∑Tt*∑As*<b>Ω</b>), where <b>Ω </b>is the retrovirological constant and ∑ is a function of the ratio Tt/As or As/Tt for sfv transmission from <it>Xy </it>to <it>Hs</it>.</p> <p>Conclusions</p> <p>I present a mathematical formalism encapsulating the general theory of the origins of retroviruses. It summarizes the choreography for the intertwined interplay of factors influencing the probability of retroviral cross-species transmission: <b>Vm, Ha, Tt, As, </b>and <b>Ω</b>.</p

Identification of restriction endonuclease with potential ability to cleave the HSV-2 genome: Inherent potential for biosynthetic versus live recombinant microbicides

<p>Abstract</p> <p>Background</p> <p>Herpes Simplex virus types 1 and 2 are enveloped viruses with a linear dsDNA genome of ~120–200 kb. Genital infection with HSV-2 has been denoted as a major risk factor for acquisition and transmission of HIV-1. Developing biomedical strategies for HSV-2 prevention is thus a central strategy in reducing global HIV-1 prevalence. This paper details the protocol for the isolation of restriction endunucleases (REases) with potent activity against the HSV-2 genome and models two biomedical interventions for preventing HSV-2.</p> <p>Methods and Results</p> <p>Using the whole genome of HSV-2, 289 REases and the bioinformatics software Webcutter2; we searched for potential recognition sites by way of genome wide palindromics. REase application in HSV-2 biomedical therapy was modeled concomitantly. Of the 289 enzymes analyzed; 77(26.6%) had potential to cleave the HSV-2 genome in > 100 but < 400 sites; 69(23.9%) in > 400 but < 700 sites; and the 9(3.1%) enzymes: BmyI, Bsp1286I, Bst2UI, BstNI, BstOI, EcoRII, HgaI, MvaI, and SduI cleaved in more than 700 sites. But for the 4: PacI, PmeI, SmiI, SwaI that had no sign of activity on HSV-2 genomic DNA, all 130(45%) other enzymes cleaved < 100 times. In silico palindromics has a PPV of 99.5% for in situ REase activity (2) Two models detailing how the REase EcoRII may be applied in developing interventions against HSV-2 are presented: a nanoparticle for microbicide development and a "recombinant lactobacillus" expressing cell wall anchored receptor (truncated nectin-1) for HSV-2 plus EcoRII.</p> <p>Conclusion</p> <p>Viral genome slicing by way of these bacterially- derived R-M enzymatic peptides may have therapeutic potential in HSV-2 infection; a cofactor for HIV-1 acquisition and transmission.</p

Theoretical basis for reducing time-lines to the determination of positive Mycobacterium tuberculosis cultures using thymidylate kinase (TMK) assays

<p>Abstract</p> <p>Background</p> <p><it>In vitro </it>culture of pathogens on growth media forms a "pillar" for both infectious disease diagnosis and drug sensitivity profiling. Conventional cultures of <it>Mycobacterium tuberculosis </it>(M.<it>tb</it>) on Lowenstein Jensen (LJ) medium, however, take over two months to yield observable growth, thereby delaying diagnosis and appropriate intervention. Since DNA duplication during interphase precedes microbial division, "para-DNA synthesis assays" could be used to predict impending microbial growth. Mycobacterial thymidylate kinase (TMKmyc) is a phosphotransferase critical for the synthesis of the thymidine triphosphate precursor necessary for M.<it>tb </it>DNA synthesis. Assays based on high-affinity detection of secretory TMKmyc levels in culture using specific antibodies are considered. The aim of this study was to define algorithms for predicting positive TB cultures using antibody-based assays of TMKmyc levels <it>in vitro</it>.</p> <p>Methods and results</p> <p>Systems and chemical biology were used to derive parallel correlation of "M.<it>tb </it>growth curves" with "TMKmyc curves" theoretically in four different scenarios, showing that changes in TMKmyc levels in culture would in each case be predictive of M.<it>tb </it>growth through a simple quadratic curvature, |tmk| = at²+ bt + c, consistent with the "S" pattern of microbial growth curves. Two drug resistance profiling scenarios are offered: isoniazid (INH) resistance and sensitivity. In the INH resistance scenario, it is shown that despite the presence of optimal doses of INH in LJ to stop M.<it>tb </it>proliferation, bacilli grow and the resulting phenotypic growth changes in colonies/units are predictable through the TMKmyc assay. According to our current model, the areas under TMKmyc curves (AUC, calculated as the integral ∫(at²+ bt + c)dt or ~1/3 at³+ 1/2 bt²+ct) could directly reveal the extent of prevailing drug resistance and thereby aid decisions about the usefulness of a resisted drug in devising "salvage combinations" within resource-limited settings, where second line TB chemotherapy options are limited.</p> <p>Conclusion</p> <p>TMKmyc assays may be useful for reducing the time-lines to positive identification of <it>Mycobacterium tuberculosis </it>(M.<it>tb</it>) cultures, thereby accelerating disease diagnosis and drug resistance profiling. Incorporating "chemiluminiscent or fluorescent" strategies may enable "photo-detection of TMKmyc changes" and hence automation of the entire assay.</p

An up-date on the prevalence of sickle cell trait in Eastern and Western Uganda

<p>Abstract</p> <p>Background</p> <p>The first survey on sickle cell disease (SCD) done in Uganda in 1949, reported the district of Bundibugyo in Western Uganda to have the highest sickle cell trait (SCT) prevalence (45%). This is believed to be the highest in the whole world. According to the same survey, the prevalence of SCT in the districts of Mbale and Sironko in the East was 20-28%, whilst the districts of Mbarara and Ntungamo in the West had 1-5%. No follow-up surveys have been conducted over the past 60 years. SCA accounts for approximately 16.2% of all pediatric deaths in Uganda. The pattern of SCT inheritance, however, predicts likely changes in the prevalence and distribution of the SCT. The objective of the study therefore was to establish the current prevalence of the SCT in Uganda.</p> <p>Methods</p> <p>This study was a cross sectional survey which was carried out in the districts of Mbale and Sironko in the Eastern, Mbarara/Ntungamo and Bundibugyo in Western Uganda. The participants were children (6 months-5 yrs). Blood was collected from each subject and analyzed for hemoglobin S using cellulose acetate Hb electrophoresis.</p> <p>Results</p> <p>The established prevalence of the SCT (As) in Eastern Uganda was 17.5% compared to 13.4% and 3% in Bundibugyo and Mbarara/Ntungamo respectively. 1.7% of the children in Eastern Uganda tested positive for haemoglobin ss relative to 3% in Bundibugyo, giving gene frequencies of 0.105 and 0.097 for the recessive gene respectively. No ss was detected in Mbarara/Ntungamo.</p> <p>Conclusions</p> <p>A shift in the prevalence of the SCT and ss in Uganda is notable and may be explained by several biological and social factors. This study offers some evidence for the possible outcome of intermarriages in reducing the incidence of the SCT.</p

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Slow progression of paediatric HIV disease: Selective adaptation or a chance phenomenon?

Background: Disease progression in human immunodeficiency virus/Acquired immunodeficiency syndrome (HIV/AIDS) is affected by several factors both external and internal to the human hosts. In the European Caucasian populations, the chemokine-cell receptor variant CCR5 \"Delta 32\" is a the genetic determinant of HIV disease progression that is believed to have been selected for in the general population by exposure to antigens closely interlinked to HIV like Yersinia pestis or small pox virus. Among African populations, it is possible that this selection will be induced by HIV over time. Aim: To present two cases of mother-to-child transmitted HIV highlighting the possible increasing prevalence of slow disease progression. Methods: Clinical case reports of slow progression of pediatric HIV Results: Both patients were female, had lost one parent >10yrs earlier but had the other surviving parent exhibiting slow HIV disease progression. We question the possible inheritance of the genetic factors associated with slow disease progression in a recessive X-linked Mendellian pattern and the role of the high prevalence of HIV within the sub-Saharan setting as the selective pressure favoring the establishment of the currently known immunologic and genetic factors influencing HIV diseases progression. Conclusion: A more in-depth immunologic and genetic approach is called for to further examine the baseline prevalence and possibility of adaptive selection for immunogenetic protectors of HIV disease progression within the sub-Saharan setting. Keywords: Paediatric HIV, Slow progression, Selective adaptation, Chance phenomenon Port Harcourt Medical Journal Vol. 2 (1) 2007: pp. 83-8

Predicted role of small non-coding Ribonucleic acids (ncRNAs) and Ribonucleoproteins (RNPs) in Influenza genetic shifts and drifts

ABSTRACT Objective: Influenza disease has been observed to be severe in animal hosts in associations with coinfection with H.Influenza species. This phenomenon is widely related to H.Influenza associated inflammation, but may as well be due to emergence of new virus strains. If the later is true, then H. Influenza may be releasing modulators of Influenza genomic variation aside of innate virus&apos; error prone polymerase. Group II Retroposon elements (RTE) are a mobile class of small noncoding RNAs (snRNA) with both RNA and DNA catalytic potential found distributed across organella genomes, eubacteria and archeabacteria. To aimed to investigate if H. Influenza RTE derived snRNA may be exogenous mediators of Influenza genomic splicing Methodology and Results: we employed Insilco palindromics to search for potential cleavage sites in 8 Influenza genomic RNA segments using 14 H. Influenza derived REases; AND a search for ORF encoding RT, X and En domains in 16 H. influenza species genome databases by BLASTP with query H.s.I1. Palindromes were found distributed in order of polymerase acidic protein gene PA 14 (100%), S2 13 (93%); HA;7 (50%), NA;7 (50%), PB1;8 (57%), PB2;7 (50%), M1&amp;2;10 (71%), S1;8 (57%), S3;9 (64%), S4;7 (50%), S5;7 (50%), S6;7 (50%), S7;6 (43%), S8;6 (43%), NP;4 (29%), and the NS1&amp;2;3 (21%). 15 low score blast hits were found, 7 of which were MTase-subunits of putative type I R-M systems, but no ortholog of the H.s.I1 ORF except in the query source genome H.somnus. Conclusions: While the distribution of Palindromes supports the existence of HNHc/HHVR cleavage sites in Influenza RNA, the role of Group II RTE snRNA in drifts and shifts is limited by lack of conclusive homologs of RT ORF. Key words: Group II Retroelements; Haemophilus Influenza species; Influenza antigenic drifts and reassortments; Restriction Endonuclease (REases). Abbreviations: DNA-Deoxyribonucleic acid; RNA-Ribonucleic acids; NA-Neuraminidase; HA-Haemagglutinin; PAPolymerase acidic protein; PB1&amp;2-Polymerase basic proteins 1&amp;2; M1,2-Matrix proteins 1,2; S1-8-genomic RNA segments 1-8; NP-Nucleoprotein; NS1&amp;2-Non-structural proteins 1&amp;2, RM -Restriction modification: This paper has supplementary files that can be accessed on a separate link provided next to the paper title at the journal website