Genomic analysis of SARS-CoV-2 omicron sublineage BA.5.2.1 in Erbil/Iraq.

Due to several mutations in its genomic sequence, particularly in the spike protein region, the recently-discovered SARS-CoV-2 variant B.5.2.1 has alarmed health policy authorities worldwide. The World Health Organization (WHO) has labelled it "Omicron" and classified it as a worldwide variant of concern (VOC). Following the appearance of Omicron in Iraq, new cases were also detected and analyzed in Kurdistan regions. Two hundred patients were recruited in this study from Erbil/Iraq. The RNA genome samples were extracted,  the qRT-PCR performed, and 10 samples were sequenced. The sample sequence was published (EPI ISL 15921492) in the GISAID international gene bank for COVID-19. When compared to the BA.1 Omicron sublineage, 17 new mutations and five deletions in the  Omicron subvariant BA.5.2.1 sequence were detected. The spike region includes eight of these variations and one deletion. Overall, 30 substitutions were shared between those previously seen in the BA.1 sublineage and the newly-detected BA.5.2.1 Omicron subvariant. We detected eight new substitutions in our BA.5.2.1 subvariants (T112I, A27S, V213G, T376F, D405N, R408S, L452R, F486V), which were not mentioned previously, should be cause for concern and may be related to immune escape or viral oligomerization. Omicron might be more immune-escape-capable than the current VOCs/VOIs. However, the predicted mutational research shows no conclusive evidence that the Omicron variant may be more virulent or fatal than other variations, including Delta. The greater capacity for immunological evasion may cause the current increase in Omicron cases in Erbil/Iraq.

Isolation and characterization of lactic acid bacteria with probiotic potential from traditional fermented special Kurdish cheese (Zhazhi) in Kurdistan Region, Iraq.

 Zhazhi cheese is a unique farmhouse traditional fermented dairy of the Kurdistan Region in Iraq for its desired aroma and flavor. Undoubtedly, the lactic acid bacteria (LAB) are the critical factors in developing the aroma, flavor, and texture of Zhazhi cheese but it has not been studied or characterised. LAB has many important nutritional benefits, including increasing the nutritional value of food. Therefore, this research was performed to isolate and identify the potential probiotic LAB from traditional homemade Kurdish cheese. Then, the identified strains were tested to determine their probiotics traits, which include acid resistance, bile-salt tolerance, haemolytic, DNase, hydrophobic, autoaggregation, antimicrobial and antibiotic activities. The isolated five LAB strains comprised Lactobacillus casei, Lactobacillus rhamnosus, Enterococcus faecium, Pediococcus pentocaseus and Lactobacillus helvaticum were recognized as promising and the most potential probiotics for further applications. This is the first report on the direct selection of potentially probiotic LAB from Kurdish special cheese (Zhazhi).

SARS-CoV-2 Omicron Variant Genomic and Phylogenetic Analysis in Iraqi Kurdistan Region.

Omicron variants have been classified as Variants of Concern (VOC) by the World Health Organization (WHO) ever since they first emerged as a result of a significant mutation in this variant, which showed to have an impact on transmissibility and virulence of the virus, as evidenced by the ongoing modifications in the SARS-CoV-2 virus. As a global pandemic, the Omicron variant also spread among the Kurdish population. This study aimed to analyze different strains from different cities of the Kurdistan region of Iraq to show the risk of infection and the impact of the various mutations on immune responses and vaccination. A total of 175 nasopharyngeal/oropharyngeal specimens were collected at West Erbil Emergency Hospital and confirmed for SARS-CoV-2 infection by RT-PCR. The genomes of the samples were sequenced using the Illumina COVID-Seq Method. The genome analysis was established based on previously published data in the GISAID database and compared to previously detected mutations in the Omicron variants, and that they belong to the BA.1 lineage and include most variations determined in other studies related to transmissibility, high infectivity and immune escape. Most of the mutations were found in the RBD (receptor binding domain), the region related to the escape from humoral immunity. Remarkably, these point mutations (G339D, S371L, S373P, S375F, T547K, D614G, H655Y, N679K and N969K) were also determined in this study, which were unique, and their impact should be addressed more. Overall, the Omicron variants were more contagious than other variants. However, the mortality rate was low, and most infectious cases were asymptomatic. The next step should address the potential of Omicron variants to develop the next-generation COVID-19 vaccine.

SNPs at 3'UTR of APOL1 and miR-6741-3p target sites associated with kidney diseases more susceptible to SARS-COV-2 infection: in silco and in vitro studies.

Acute Kidney Injury (AKI) is a common manifestation of COVID-19 and several cases have been reported in the setting of the high-risk APOL1 genotype (common genetic variants). This increases the likelihood that African American people with the high-risk genotype APOL1 are at increased risk for kidney disease in the COVID-19 environment. Single-nucleotide polymorphisms (SNPs) are found in various microRNAs (miRNAs) and target genes change the miRNA activity that leads to different diseases. Evidence has shown that SNPs increase/decrease the effectiveness of the interaction between miRNAs and disease-related target genes. The aim of this study is not only to identify miRSNPs on the APOL1 gene and SNPs in miRNA genes targeting 3'UTR but also to evaluate the effect of these gene variations in kidney patients and their association with SARS-COV-2 infection. In 3'UTR of the APOL1 gene, we detected 96 miRNA binding sites and 35 different SNPs with 10 different online software in the binding sites of the miRNA (in silico). Also we studied gene expression of patients and control samples by using qRT-PCR (in vitro). In silico study, the binding site of miR-6741-3p on APOL1 has two SNPs (rs1288875001, G > C; rs1452517383, A > C) on APOL1 3'UTR, and its genomic sequence is the same nucleotide as rs1288875001. Similarly, two other SNPs (rs1142591, T > A; rs376326225, G > A) were identified in the binding sites of miR-6741-3p at the first position. Here, the miRSNP (rs1288875001) in APOL1 3'UTR and SNP (rs376326225) in the miR-6741-3p genomic sequence are cross-matched in the same binding region. In vitro study, the relative expression levels were calculated by the 2-ΔΔCt method & Mann-Whitney U test. The expression of APOL1 gene was different in chronic kidney patients along with COVID-19. By these results, APOL1 expression was found lower in patients than healthy (p < 0.05) in kidney patients along with COVID-19. In addition, miR-6741-3p targets many APOL1-related genes (TLR7, SLC6A19, IL-6,10,18, chemokine (C-C motif) ligand 5, SWT1, NFYB, BRF1, HES2, NFYB, MED12L, MAFG, GTF2H5, TRAF3, angiotensin II receptor-associated protein, PRSS23) by evaluating online software in the binding sites of the miR-6741-3p. miR-6741-3p has not previously shown any association with kidney diseases and SARS-COV-2 infection. It assures that APOL1 can have a significant consequence in kidney-associated diseases by different pathways. Henceforth, this study represents and demonstrates an effective association between miR-6741-3p and kidney diseases, i.e., collapsing glomerulopathy, chronic kidney disease (CKD), acute kidney injury (AKI), and tubulointerstitial lesions susceptibility to SARS-COV-2 infection via in silico and in vitro exploration and recommended to have better insight.

Analysis of cytokines in SARS-CoV-2 or COVID-19 patients in Erbil city, Kurdistan Region of Iraq.

The emergence of the novel coronavirus and then pandemic outbreak was coined 2019- nCoV or COVID-19 (or SARS-CoV-2 disease 2019). This disease has a mortality rate of about 3·7 percent, and successful therapy is desperately needed to combat it. The exact cellular mechanisms of COVID-19 need to be illustrated in detail. This study aimed to evaluate serum cytokines in COVID-19 patients. In this study, serum was collected from volunteer individuals, moderate COVID-19 patients, severe cases of COVID-19 patients, and patients who recovered from COVID-19 (n = 122). The serum concentrations of interleukins such as IL-1, IL-4, IL-6, IL-8, IL-10, and tumor necrosis factor-alpha (TNF-α), were measured by enzyme-linked immunosorbent assays (ELISA). The concentrations of IL-1 and TNF-α were did not differ significantly among groups. However, the concentration of IL-6 was significantly higher in moderate COVID-19 and severe cases of COVID-19 groups compared to control and recovered groups indicating it to be an independent predictor in the coronavirus disease. The levels of IFN-γ and IL-4 were significantly lower in the recovery group than the severe case of the COVID-19 group. In contrast, the level of IL-10 in recovered COVID-19 patients was significantly higher in compare to severe cases, COVID-19 patients. Varying levels of cytokines were detected in COVID-19 group than control group suggesting distinct immunoregulatory mechanisms involved in COVID-19 pathogenesis. However, additional investigations are needed to be to be performed to understand the exact cellular mechanism of this disease.

Strategies of enzyme immobilization on nanomatrix supports and their intracellular delivery.

Enzymes are one of the foundations and regulators for all major biological activities in living bodies. Hence, enormous efforts have been made for enhancing the efficiency of enzymes under different conditions. The use of nanomaterials as novel carriers for enzyme delivery and regulating the activities of enzymes has stimulated significant interests in the field of nano-biotechnology for biomedical applications. Since, all types of nanoparticles (NPs) offer large surface to volume ratios, the use of NPs as enzyme carriers affect the structure, performance, loading efficiency, and the reaction kinetics of enzymes. Hence, the immobilization of enzymes on nanomatrices can be used as a useful approach for direct delivery of therapeutic enzymes to the targeted sites. In other words, NPs can be used as advanced enzyme delivery nanocarriers. In this paper, we present an overview of different binding of enzymes to the nanomaterials as well as different types of nanomatrix supports for immobilization of enzymes. Afterwards, the enzyme immobilization on nanomaterials as a potential system for enzyme delivery has been discussed. Finally, the challenges associated with the enzyme delivery using nano matrices and their future perspective have been discussed.Communicated by Ramasamy H. Sarma.

Enzyme immobilization onto the nanomaterials: Application in enzyme stability and prodrug-activated cancer therapy.

Nanoparticles (NPs) have been widely used for immobilization of wide ranges of enzymes. However, the stabilization of enzymes on NPs is a major challenge, crucial for regulating enzymatic activity and their medical applications. To overcome these challenges, it is necessary to explore how enzymes attach to nanomaterials and their properties are affected by such interactions. In this review we present an overview on the different strategies of the enzyme immobilization into the NPs and their corresponding stability against temperature and pH. The effects of surface charge, particle size, morphology, and aggregation of NPs on the stability of immobilized enzymes were summarized. The activity of immobilized enzyme into the NPs was reviewed to disclose more detail regarding the interaction of biomolecules with NPs. The combination of enzyme immobilization with prodrugs was also reviewed as a promising approach for biomedical application of enzyme in cancer therapy. Finally, the current challenges and future applications of NPs in enzyme immobilization and the utilization of immobilized enzyme toward prodrug activation in cytoplasm of cancer cells were presented. In conclusion, this review may pave the way for providing a perspective on development to the industrial and clinical translation of immobilized enzymes.