Gene Reports最新文献

{"title":"Genetic expression in cancer research: Challenges and complexity","authors":"","doi":"10.1016/j.genrep.2024.102042","DOIUrl":"10.1016/j.genrep.2024.102042","url":null,"abstract":"<div><div>Cancer research is profoundly influenced by the complex interplay of gene expression, yet conventional studies often emphasize genes with high expression levels, potentially overlooking those that contribute subtly to tumorigenesis. This review challenges the standard paradigms by questioning the direct causality often attributed to high gene expression in cancer progression and underscores the importance of distinguishing correlation from causation. It highlights how traditional bulk data analysis might mask crucial cell-specific gene activities, a limitation increasingly addressed by emerging single-cell and spatial transcriptomics, albeit with their own inherent challenges. Additionally, the review delves into the critical roles of both oncogenes and tumor driver genes, advocating for a precise differentiation in research and therapy. Furthermore, it discusses the revolutionary impact of CRISPR technology in identifying essential genes for cancer cell survival, which, while crucial, may not necessarily drive cancer. The complexities of epigenetic regulation and the discrepancies between mRNA and protein expression levels are also explored, emphasizing the necessity for integrated approaches that combine transcriptomics, proteomics, and computational models. This integrated perspective is vital for developing targeted therapies that address the multifaceted nature of gene expression and its regulation in cancer, aiming to refine therapeutic strategies and enhance clinical outcomes.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2024-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142314809","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"miR-16-5p may modulate migration and proliferation through TP53 and LncRNA-NEAT1 in triple-negative breast cancer","authors":"","doi":"10.1016/j.genrep.2024.102038","DOIUrl":"10.1016/j.genrep.2024.102038","url":null,"abstract":"<div><h3>Introduction</h3><div>MicroRNAs (miRNAs) are potential candidate clinical biomarkers for many diseases. This study explored the role and potential mechanisms of miR-16-5p in triple-negative breast cancer (TNBC).</div></div><div><h3>Results</h3><div>The expression of miR-16-5p was lower in wax block sections obtained from 47 TNBC patient samples. Overexpression of miR-16-5p decreased the migratory abilities and the cell proliferation in MDA-MB-231 cells. We found miR-16-5p modulated TP53 and LncRNA-NEAT1 in bioinformatics analysis. In transfection experiments, the higher expression of lncRNA-NEAT1 and TP53 were observed in miR-16-5p inhibitor group.</div></div><div><h3>Conclusion</h3><div>Our data demonstrated that miR-16-5p was lowly expressed and acted as a tumor suppressor in TNBC. Moreover, miR-16-5p regulated TNBC cell proliferation and migratory capacity by modulating TP53 and lncRNA-NEAT1 in vitro.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2024-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142310856","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"miR-98 and miR-629 can be used as a potential biomarker on relapsing-remitting multiple sclerosis patients","authors":"","doi":"10.1016/j.genrep.2024.102041","DOIUrl":"10.1016/j.genrep.2024.102041","url":null,"abstract":"<div><h3>Introduction</h3><div>Multiple Sclerosis (MS) is an autoimmune disease that affects the central nervous system (CNS), characterized by chronic inflammation, demyelination, and neurodegeneration. In recent years, among non-coding RNAs miRNA have emerged as key regulators of different biological processes and it has been suggested that they play an important role in the mechanisms underlying MS pathogenesis. Through in silico methods, miR-629-5p and miR-98-5p were identified as significant factors in MS pathology. The aim of this study was to examine the levels of expression of miR-629-5p and miR-98-5p in blood samples obtained from patients with relapsing–remitting MS. Methods: Total blood were recruited from RRMS and control group and qPCR analysis was used for evaluating of target miRNAs expression. The mirDIP database was utilized to identify the target genes. Hub genes were identified with the Cytoscape and target pathways were identified using the STRING. Results: Expression analysis revealed a significant upregulation of miR-629-5p and miR-98-5p (FC ≥ 1.5 and <em>p</em> &lt; 0.05) in patients with RRMS. PI3K-Akt, Rap1, MAPK and FoxO signaling pathways were found as target. Discussion: The discovery of these miRNAs suggests that they may have a notable impact on MS patients by intervening on pathways involved in both the immune and nervous systems.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142314810","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Missense variant rs75603675 within TMPRSS2 gene is associated with the increased risk of severe form of COVID-19","authors":"","doi":"10.1016/j.genrep.2024.102039","DOIUrl":"10.1016/j.genrep.2024.102039","url":null,"abstract":"<div><div>Host genetics among other factors play an important role in COVID-19 disease severity. TMPRSS2, a serine protease, facilitates the priming of the SARS-CoV-2 spike protein, which is essential for the virus to enter the host cell. Several studies had targeted the TMPRSS2 polymorphisms with respect to SARS-CoV-2 infection and COVID-19 disease severity. Initially, the Whole Exome Sequencing (WES) of 7 healthy individuals and 22 COVID-19 patients with different degrees of disease severity was conducted to find the mutational landscape in different genes. A total of 26 single nucleotide polymorphisms (SNPs) were identified of which six were within the exons of TMPRSS2 (four synonymous and two nonsynonymous variants) while the rest of the 20 SNPs were recognized within the flanking intronic regions of TMPRSS2 gene. The nonsynonymous SNPs, rs75603675 and rs12329760, were further evaluated for association with disease severity in a larger sample size of 120 individuals by PCR followed by Sanger sequencing. Neither allelic nor genotypic distributions of rs12329760 were significantly associated with COVID-19 disease severity. However, individuals harboring the A allele of rs75603675 was found to have higher risk of severe COVID-19 compared to the C allele [OR (95%CI): 1.95 (1.11–3.39), <em>p</em> = 0.019]. Also, the genotype A/A [OR (95%CI): 5.13 (1.00–26.38), <em>p</em> = 0.033] of rs75603675 was associated with increased risk of severe COVID-19 under the recessive genetic inheritance model. Although the impact of COVID-19 pandemic has waned due to vaccination and public health measures, continued research on the association of COVID-19 disease severity and infection susceptibility with host genetics is required to shed valuable insights on the future long-term health effects of COVID-19 and impact of new variants on different populations and enable implication of proper informed healthcare strategies during future public health crises.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142310865","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Modulatory effects of sub-MIC concentrations silver nanoparticles on virulence factor gene expression in Staphylococcus aureus","authors":"","doi":"10.1016/j.genrep.2024.102034","DOIUrl":"10.1016/j.genrep.2024.102034","url":null,"abstract":"<div><h3>Background</h3><p>Silver nanoparticles (AgNPs) exhibit a dose-dependent anti-bacterial effect, and it was aimed in this study to investigate the impact of sub-minimum inhibitory concentration (MIC) doses of AgNPs on the expression of virulence genes in <em>Staphylococcus aureus</em> (<em>S. aureus</em>).</p></div><div><h3>Methods</h3><p>Minimum inhibitory concentration (MIC) values for AgNPs were determined for 183 <em>S. aureus</em> isolates. Gene expression was assessed in 14 isolates with <em>sea</em> and <em>seb</em> genes treated with AgNPs at a sub-MIC dose of 1 μg/ml. Accordingly, these strains were exposed to 1 μg/ml doses of AgNPs, and gene expression levels of <em>sea</em>, <em>seb</em>, and <em>agr</em> were assessed using quantitative RT-PCR after 4- and 12-hour post-AgNPs inoculation at 37 °C. The impact of AgNPs on the virulence factors of <em>S. aureus</em> was investigated over different time points, focusing on methicillin-sensitive <em>S. aureus</em> (MSSA) and methicillin-resistant <em>S. aureus</em> (MRSA) isolates.</p></div><div><h3>Results</h3><p>Analysis revealed significant reductions in gene expression levels of <em>seb</em> and <em>agr</em> after 4 h post-AgNPs treatment in the MSSA group (<em>p</em> &lt; 0.05), with further decreases observed at 12 h for <em>sea</em>, <em>seb</em>, and <em>agr</em> genes (<em>p</em> &lt; 0.0001). MRSA isolates exhibited significant declines in <em>sea</em> and <em>agr</em> gene expression levels at both time points (<em>p</em> &lt; 0.0001). However, no significant changes were observed in <em>seb</em> gene expression among MRSA isolates. Fold-change analysis indicated time-dependent effects of AgNP treatment on gene expression, highlighting substantial alterations in gene expression levels over time, particularly in <em>seb</em> and <em>agr</em> genes.</p></div><div><h3>Conclusion</h3><p>These results show that sub-MIC levels of AgNPs greatly decrease the gene expression of important virulence factors in MSSA and MRSA strains, indicating their promise as treatments for <em>S. aureus</em> infections, particularly at 12 h post-treatment. The differential response between MSSA and MRSA isolates highlights the importance of strain variation in antimicrobial strategies.</p></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142242679","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Inhibitory effect of dendrosomal-nanocurcumin on Burkitt's lymphoma cells by reducing EBV lytic gene expression","authors":"","doi":"10.1016/j.genrep.2024.102035","DOIUrl":"10.1016/j.genrep.2024.102035","url":null,"abstract":"<div><h3>Introduction</h3><div>Epstein-Barr virus (EBV) is a human oncogenic virus that targets B lymphocytes and is associated with some malignancies, such as Burkitt's lymphoma. Curcumin, as a natural product, has anticancer, antiproliferative, and antiviral properties. The combination of curcumin with some nanoparticles, such as dendrosom, can increase its solubility and anti-cancer effects. The present research aims to investigate the antiviral effect of Dendrosomal NanoCurcumin (DNC) on Burkitt's lymphoma cells (Daudi cell line) and the expression of EBV lytic genes and apoptosis.</div></div><div><h3>Materials and methods</h3><div>The cytotoxicity of curcumin, DNC, and dendrosome on Daudi cells and Peripheral Blood Mononuclear Cells (PBMC) as a control was assessed using a (3-(4, 5-dimethyl thiazolyl-2)-2, 5-diphenyltetrazolium bromide) MTT assay. Cell apoptosis was evaluated by Annexin/PI flow cytometry. RNA expression of <em>BZLF1</em>, <em>BHRF1</em>, and <em>BRLF1</em> was assessed by quantitative real-time reverse transcription-polymerase chain reaction (qRT-PCR) assay. The <em>t</em>-test was used for statistical analysis.</div></div><div><h3>Results</h3><div>The half-minimum concentration of cytotoxicity (CC50) for nanocurcumin was 30 μg/ml, for curcumin 50 μg/ml, and for dendrosome 987 μg/ml. DNC caused time and dose-dependent death in Daudi cancer cells compared to curcumin and showed no toxicity in control cells. Quantitative RT-PCR evaluation showed a significant decrease in <em>BZLF1</em>, <em>BHRF1</em>, and <em>BRLF1</em> mRNA expression at 30 μg/ml concentration of DNC compared to the control. The data obtained from the relative measurement of gene expression showed a decrease in the expression of viral lytic genes (<em>P</em> &lt; 0.001).</div></div><div><h3>Conclusion</h3><div>In this study, it is noted that carriers, such as dendrosome, enhance the bioavailability of curcumin, thereby increasing its antitumor properties and cell apoptosis. Noteworthy, DNC nanoparticles can serve as a promising drug candidate and supplement in the treatment of Burkitt's lymphoma and in improving patient survival by reducing the expression of EBV lytic phase viral genes.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142310968","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bioevaluation, pharmacokinetics and molecular docking study of terpenoid-rich rhizome essential oil of Zingiber officinale","authors":"","doi":"10.1016/j.genrep.2024.102027","DOIUrl":"10.1016/j.genrep.2024.102027","url":null,"abstract":"<div><div>The study focuses on the phytochemical composition, <em>in vitro</em> and <em>in silico</em> antioxidant and NO reduction potential of <em>Zingiber Officinale</em> rhizome essential oil (ZOREO). The GC–MS analysis has revealed the presence of 47 volatile constituents representing 94.35 % of the total area of EO. The major compounds identified were α-zingiberene (20.58 %), geranial (10 %), β-sesquiphellandrene (7.39 %), and neral (7.23 %). The EO was rich in sesquiterpene hydrocarbons (45.93 %) followed by monoterpene hydrocarbons (29.29 %). The EO showed moderate antioxidant activity compared to the standard (IC₅₀ = 5.16 ± 0.4 mg/mL for DPPH assay and EC₅₀ = 0.52 ± 0.6 mg/mL for FRAP assay). The cytotoxic analysis showed significant viability towards RAW 264.7 cell lines. Treatment with ginger EO at a concentration of 100 μg/mL showed significant anti-inflammatory activity by the significant reduction of LPS-induced nitric oxide (NO) production to 31.35 %, in comparison with the LPS-treated group. Further, the EO components were screened in order to provide mechanistic insights into Xanthine oxidase (XO) and iNOS inhibition. The docking results showed that the volatile constituents of ginger EO have substantial binding affinity with the active site residues of the receptor. The simulation conducted for the top compounds- geranyl acetate and β-eudesmol having the highest binding affinity towards both the proteins XO and iNOS respectively. Both the results showed the compounds steadily interacted with both of the proteins active site residues throughout the simulation. The current analysis showed the phytoconstituents showed better antioxidant activity than the EO. Hence these compounds could be further considered for <em>in vitro</em> and <em>in vivo</em> evaluation for the development of efficient phytopharmaceuticals.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2024-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142314808","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic predisposition to vitamin D deficiency in Indian athletes: Role of CYP2R1 rs10741657 variant","authors":"","doi":"10.1016/j.genrep.2024.102033","DOIUrl":"10.1016/j.genrep.2024.102033","url":null,"abstract":"<div><div>Vitamin D deficiency can negatively impact the health and training efficiency of athletes. The rs10741657(G) allele in CYP2R1 gene has been associated with lower vitamin D status, potentially contributing to vitamin D deficiency observed across various populations, including Indians. This study aimed to investigate whether the CYP2R1 (rs10741657) polymorphism is contributing to the vitamin D status among Indian athletes. Blood samples were collected from 92 Indian elite and sub-elite athletes participating in weightlifting (29), badminton (32), athletics (14), and rowing (17) for laboratory analysis. PCR-RFLP of the CYP2R1 (rs10741657) SNP was performed, and vitamin D levels were measured. Statistical analysis was done to assess the association between genotype and vitamin D status. Vitamin D levels were comparable between genders but differed across sports, with indoor athletes, especially badminton players having higher levels. The AA genotype was associated with higher vitamin D levels compared to the GG and AG genotypes. Vitamin D deficiency is highly prevalent among the athletes studied. This deficiency may be due to the higher prevalence of the alternate allele (G) of CYP2R1 polymorphism, suggesting that genetic predisposition plays a key role in determining the vitamin D status of athletes.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2024-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142310966","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Exploring herbal preconditioning strategies to improve adipose tissue stem cell therapy efficacy","authors":"","doi":"10.1016/j.genrep.2024.102030","DOIUrl":"10.1016/j.genrep.2024.102030","url":null,"abstract":"&lt;div&gt;&lt;div&gt;The application of mesenchymal stem cells (MSCs), specifically those sourced from adipose tissue, has become a focal point in regenerative medicine, showing potential for effective cell therapy. Adipose-derived stem cells (ASCs) offer hope in treating various conditions, yet their viability and integration rates are hindered by the harsh post-transplantation environment marked by inflammation and oxidative stress at the injury site. &lt;em&gt;Lawsonia inermis&lt;/em&gt; (henna), &lt;em&gt;Zizyphus spina-christ&lt;/em&gt;i (Christ's Thorn), and &lt;em&gt;Glycyrrhiza glabra&lt;/em&gt; (licorice) are three plants known for their potent antioxidant properties primarily due to their rich content of phenolic compounds and flavonoids. Their potential health benefits make them valuable in both traditional medicine and modern therapeutic applications.&lt;/div&gt;&lt;div&gt;This research delves into investigating and contrasting the effects of hydroalcoholic extracts from &lt;em&gt;Lawsonia inermis&lt;/em&gt;, &lt;em&gt;Zizyphus spina-christi&lt;/em&gt;, and &lt;em&gt;Glycyrrhiza glabra&lt;/em&gt; on human adipose tissue stem cells as a pre-conditioning method to alleviate oxidative stress in cell therapy. ASCs were isolated from the pelvic cavity and abdomen, characterized using flow cytometry, and prompted to differentiate into adipogenic and osteogenic lineages. They were then subjected to different concentrations of the aforementioned herbal extracts at varying time frames, followed by MIC and MTT analysis. The MTT (3-[4,5-dimethylthiazol-2-yl]-2,5-diphenyltetrazolium bromide) assay and the Minimum Inhibitory Concentration (MIC) assay are both used to evaluate the effects of substances on cell viability and cell growth receptively. RNA extraction from ASCs and evaluation of antioxidant gene expression were conducted via Real-time PCR. Flow cytometry data confirmed the presence of MSC markers in the isolated cells from ASCs. Analysis of the herbal extract concentrations revealed that 50 ng/ml had a toxic effect on ASCs, establishing a toxicity reference point for adipose-derived MSCs. Real-time PCR results showcased a notable increase in the expression of antioxidant genes post-preconditioning with hydroalcoholic extracts. This study underscores, for the first time, the safety and lack of toxicity of preconditioning with these extracts for h.ASCs, enhancing their resilience and acclimatization under oxidative stress conditions, potentially boosting the therapeutic potential of h.ASCs. The antioxidant properties of &lt;em&gt;Lawsonia inermis&lt;/em&gt;, &lt;em&gt;Zizyphus spina-christi&lt;/em&gt;, and &lt;em&gt;Glycyrrhiza glabra&lt;/em&gt; may enhance the expression of antioxidant genes (Sod, Gpx and Cata) through several mechanisms, including the activation of transcription factors like Nrf2 (Nuclear factor erythroid 2-related factor 2), which regulates antioxidant gene expression; modulation of signaling pathways such as MAPK (Mitogen-Activated Protein Kinase) and PI3K/Akt (Phosphoinositide 3-kinase/Protein Kinase B); and influencing epigenetic modifications ","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142310967","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A retrospective whole genome sequencing of SARS-CoV-2 isolate from respiratory sample of an individual from Ota – Ogun State, Nigeria","authors":"","doi":"10.1016/j.genrep.2024.102032","DOIUrl":"10.1016/j.genrep.2024.102032","url":null,"abstract":"<div><p>Severe acute respiratory syndrome coronavirus – 2 (SARS-CoV-2) which was responsible for the COVID-19 pandemic has now been considered an endemic virus, that will continually produce sporadic outbreaks in different communities around the globe. Although, there are several surveillance studies on SARS-CoV-2 globally, including Nigeria, there is still an important need to understand the uniqueness of the strains of the virus that was circulating immediately after the pandemic, to add to the global database of information that will aid vaccine production and future preparedness against another SARS - related CoV pandemic.</p><p>Towards the end of the pandemic, between February – August 2022, SARS-CoV-2 was detected in a surveillance project in Ota – Ogun State Nigeria. We carried out a retrospective whole genome sequencing (WGS) analysis of SARS-CoV-2 in the previously reported positive sample, at Inqaba biotech in South Africa. RNA extraction was carried out using the Quick – RNA viral kit (Zymo) and library preparation was done by NEBNext ARTIC SARS-CoV-2 FS Library Prep kit (Illumina) according to the manufacturer's instruction. The WGS was carried out on the NextSeq500 platform by Illumina. The fastq file containing the unassembled raw sequence reads were submitted to NCBI SARS-CoV-2 resources, and a BioProject accession number PRJNA1076330 was issued. The DRAGEN Targeted Microbial, GISAID-CoVsurver mutation, BLAST and MAFFT applications were used for analysis.</p><p>The spike (s) gene of the study sequence possessed seven mutations (G142D, A163V, V213G, D614G, H655Y, N679K, P681H) and shared 99.4 % identity with those of the Wuhan reference sequence WIV04. The non-structural proteins (NSP) – 7,8,9,10 and 16 shared 100 % identity with bat/Yunnan/RaTG13 (a SARS- related CoV found in bats) sequence on GISAID. Although, the study sequence was obtained from an asymptomatic individual, the S mutations observed are known to be related to virulence, antigenic shift, enhanced transmissibility and host change. Thus, upon successful exploitation of this asymptomatic variant, it may possibly be transformed to a potential candidate for SARS-CoV-2 vaccine in future.</p></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142232927","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}