Advances in Virology最新文献

{"title":"Evaluation of Immune Characteristics and Factors Associated with Immune Response following Hepatitis B Vaccination among Ghanaian Adolescents.","authors":"Samuel Asamoah Sakyi, Joseph Badu Gyapong, Ebenezer Krampah Aidoo, Alfred Effah, Simon Koffie, Oscar Simon Olympio Mensah, Isaac Arddey, Godwin Boakye, Stephen Opoku, Benjamin Amoani, Robert Amadu Ngala","doi":"10.1155/2024/9502939","DOIUrl":"10.1155/2024/9502939","url":null,"abstract":"<p><strong>Background: </strong>WHO recommends HBV-negative babies in high-prevalence (8%) countries receive anti-HBV vaccination. Ghana initiated mass immunization in 2002, but concerns remain about vaccine effectiveness and long-term protection. We evaluated immune characteristics and factors following hepatitis B vaccination among Ghanaian adolescents who received HBV vaccines.</p><p><strong>Methods: </strong>In this longitudinal cross-sectional study, 74 participants were enrolled from the Kumasi Metropolis, Ghana. Sociodemographic and lifestyle characteristics of participants were obtained using a questionnaire. Blood samples were obtained before and after booster administration for anti-HBsAg, IL-6, and IL-10 estimations using ELISA kit (Shanghai Chemical Ltd., China). Anti-HBsAg titers ≥10 mIU/ml were considered protective. Statistical analyses were done using SPSS version 26.0 and R programming language, <i>p</i> < 0.05 was considered statistically significant.</p><p><strong>Results: </strong>We found 100% seroconversion rate, with 25.7% seroprotection rate (anti-HBsAg >10 mIU/ml). Gender (<i>p</i>=0.009), age (<i>p</i>=0.001), and exercising (<i>p</i>=0.044) were significantly associated with seroprotection. Following booster administration, 59.4% were hyporesponders (10 ≤ anti-HBsAg titre ≤99 mIU/ml) whilst 40.6% were good responders (anti-HBsAg titre ≥100 mIU/ml). Exercise (<i>p</i>=0.034) was significantly associated with immune response after booster administration. Moreover, we reported significant positive correlation between cytokines [IL-6 (<i>r</i> = 0.817, <i>p</i> < 0.001) and IL-10 (<i>r</i> = 0.928, <i>p</i> < 0.001)] and anti-HBsAg titre.</p><p><strong>Conclusion: </strong>Approximately two thirds of adolescents vaccinated at birth lack protective levels of antibodies against hepatitis B virus. Booster vaccines could aid in mounting protective levels of anti-HBsAg. Physical exercise was negatively associated with immune response to hepatitis B vaccinations.</p>","PeriodicalId":7473,"journal":{"name":"Advances in Virology","volume":"2024 ","pages":"9502939"},"PeriodicalIF":2.2,"publicationDate":"2024-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11142859/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141199273","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"High Transmission Rates of Early Omicron Subvariant BA.2 in Bangkok, Thailand","authors":"Sininat Petcharat, Ananporn Supataragul, Piyapha Hirunpatrawong, P. Torvorapanit, C. Klungthong, P. Chinnawirotpisan, Sasiprapa Ninwattana, N. Thippamom, L. Paitoonpong, G. Suwanpimolkul, W. Jantarabenjakul, R. Buathong, K. Joonlasak, W. Manasatienkij, Khwankamon Rattanatumhi, N. Chantasrisawad, Nuntana Chumpa, Thomas S. Cotrone, S. Fernandez, S. Sriswasdi, S. Wacharapluesadee, O. Putcharoen","doi":"10.1155/2023/4940767","DOIUrl":"https://doi.org/10.1155/2023/4940767","url":null,"abstract":"The emergence of Omicron as the fifth variant of concern within the SARS-CoV-2 pandemic in late 2021, characterized by its rapid transmission and distinct spike gene mutations, underscored the pressing need for cost-effective and efficient methods to detect viral variants, especially given their evolving nature. This study sought to address this need by assessing the effectiveness of two SARS-CoV-2 variant classification platforms based on RT-PCR and mass spectrometry. The primary aim was to differentiate between Delta, Omicron BA.1, and Omicron BA.2 variants using 618 COVID-19-positive samples collected from Bangkok patients between November 2011 and March 2022. The analysis revealed that both BA.1 and BA.2 variants exhibited significantly higher transmission rates, up to 2-3 times, when compared to the Delta variant. This research presents a cost-efficient approach to virus surveillance, enabling a quantitative evaluation of variant-specific public health implications, crucial for informing and adapting public health strategies.","PeriodicalId":7473,"journal":{"name":"Advances in Virology","volume":"4 9","pages":""},"PeriodicalIF":2.2,"publicationDate":"2023-12-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138596781","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":"Fraxin in Combination with Dexamethasone Attenuates LPS-Induced Liver and Heart Injury and Their Anticytokine Activity in Mice.","authors":"Nada Sahib Shaker,&nbsp;Hayder Bahaa Sahib","doi":"10.1155/2023/5536933","DOIUrl":"10.1155/2023/5536933","url":null,"abstract":"<p><strong>Background: </strong>Cytokine storm syndrome (CSS) is a major cause of morbidity and mortality in people suffering from hyperinflammatory status, which diverse etiological factors, including pathogens, therapeutic interventions, malignancies, and autoimmune disorders, can instigate. Since there is limited research on the antioxidant properties of fraxin and no studies have investigated its potential as an anticytokine storm agent, it is important to note that most studies have primarily focused on proinflammatory cytokines such as IL-1<i>β</i>, IL-6, and TNF<i>α</i> during cytokine storm. However, little research discusses the role of chemokines, particularly IL-8, during cytokine storms. Therefore, further investigation is warranted into the role of fraxin as an anticytokine storm agent and the involvement of IL-8 in cytokine storms. The present study examines the preventive efficacy of fraxin and the combination of fraxin and dexamethasone (FD) in mitigating lipopolysaccharide-induced systemic inflammation in mice caused by <i>Escherichia coli</i>, 055: B5.</p><p><strong>Methods: </strong>Five groups of ten mice were randomly assigned: LPS only group (5 mg/kg, intraperitoneally i.p.), control (normal saline N.S. 1 ml/kg, i.p.), concentrations were selected based on previous literature, fraxin (120 mg/kg, i.p.), dexamethasone (5 mg/kg, i.p.), fraxin + dexamethasone (FD) (60 mg/kg + 2.5 mg/kg, i.p.), administered one hour before LPS injection (5 mg/kg,i.p.), animals were euthanized next day, and interleukin-8 (IL-8) was quantified in serum using an enzyme-linked immunosorbent assay. The liver and heart tissues underwent histopathological analysis to assess morphological changes. For data analysis using ANOVA and Tukey post hoc tests, the Kruskal-Wallis and Mann-Whitney <i>U</i> tests were employed to analyze the histological results.</p><p><strong>Results: </strong>A significant decline in IL-8 levels was recorded in the treatment groups almost to the same degree (<i>p</i> < 0.001), and the percentage of inhibition of IL-8 for fraxin, dexamethasone, and FD was 93%.92.4%, and 93%, respectively, compared to the LPS-only group. Histopathological scores were significantly reduced in liver and heart tissue (<i>P</i> < 0.05).</p><p><strong>Conclusions: </strong>All interventions used in this study significantly reduced interleukin-8 (IL-8) levels and reduced LPS-induced liver and cardiac damage. The combination (FD) did not result in an evident superiority of either agent. More research is required to identify the possible usefulness of these agents in treating hyperinflammatory diseases, such as cytokine storms, in future clinical practice.</p>","PeriodicalId":7473,"journal":{"name":"Advances in Virology","volume":"2023 ","pages":"5536933"},"PeriodicalIF":2.2,"publicationDate":"2023-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10506875/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41094914","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Development and Validation of Rapid Colorimetric Reverse Transcription Loop-Mediated Isothermal Amplification for Detection of Rift Valley Fever Virus.","authors":"Francis Wekesa,&nbsp;Mark Wamalwa,&nbsp;Richard Oduor,&nbsp;Yatinder Binepal,&nbsp;Leonard Ateya,&nbsp;Noah Okumu,&nbsp;Angela M'kwenda,&nbsp;Christopher Masaba,&nbsp;Eugine Mukhaye","doi":"10.1155/2023/1863980","DOIUrl":"https://doi.org/10.1155/2023/1863980","url":null,"abstract":"<p><p>Rift Valley fever virus (RVFV) is a high-priority zoonotic pathogen with the ability to cause massive loss during its outbreak within a very short period of time. Lack of a highly sensitive, instant reading diagnostic method for RVFV, which is more suitable for on-site testing, is a big gap that needs to be addressed. The aim of this study was to develop a novel one-step reverse transcription loop-mediated isothermal amplification (RT-LAMP) method for the rapid detection of RVFV. To achieve this, the selected RVFV <i>M</i> segment nucleotide sequences were aligned using Multiple Sequence Comparison by Log-Expectation (MUSCLE) software in MEGA11 version 11.0.11 program to identify conserved regions. A 211 pb sequence was identified and six different primers to amplify it were designed using NEB LAMP Primer design tool version 1.1.0. The specificity of the designed primers was tested using primer BLAST, and a primer set, specific to RVFV and able to form a loop, was selected. In this study, we developed a single-tube test based on calorimetric RT-LAMP that enabled the visual detection of RVFV within 30 minutes at 65°C. Diagnostic sensitivity and specificity of the newly developed kit were compared with RVFV qRT-PCR, using total RNA samples extracted from 118 blood samples. The colorimetric RT-LAMP assay had a sensitivity of 98.36% and a specificity of 96.49%. The developed RT-LAMP was found to be tenfold more sensitive compared to the RVFV qRT-PCR assay commonly used in the confirmatory diagnosis of RVFV.</p>","PeriodicalId":7473,"journal":{"name":"Advances in Virology","volume":"2023 ","pages":"1863980"},"PeriodicalIF":2.2,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9902148/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10684332","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Ethyl Gallate: Promising Cytoprotective against HIV-1-Induced Cytopathy and Antiretroviral-Induced Cytotoxicity.","authors":"C Muddu Krishna,&nbsp;J N Kolla,&nbsp;Hari Babu Bollikolla,&nbsp;T Sravan Kumar Reddy,&nbsp;S Asha","doi":"10.1155/2023/6727762","DOIUrl":"https://doi.org/10.1155/2023/6727762","url":null,"abstract":"<p><strong>Introduction: </strong>HIV-1 infection in cell culture is typically characterized by certain cytopathic effects such as vacuolization of cells and development of syncytia, which further lead to cell death. In addition, the majority of drugs during HIV treatment exhibit serious adverse effects in patients, apart from their beneficial role. During the screening of cytoprotective agents to protect the cells from HIV-1-associated cell death and also drug-associated toxicity, antioxidants from a natural source are assumed to be a choice. A well-known antioxidant, ethyl gallate (EG), was selected for cytoprotection studies which have already been proven as an anti-HIV agent.</p><p><strong>Objective: </strong>The main objective of the study was to explore the cytoprotective potential of EG against HIV-1-induced cytopathic effect and antiretroviral drug toxicity.</p><p><strong>Methods: </strong>DPPH free radical scavenging assay was performed with EG to find the effective concentration for antioxidant activity. HIV-1infection-associated cytopathic effects and further rescue by EG were studied in MT-2 lymphocytes by the microscopic method and XTT cytopathic assays. The cellular toxicity of different antiretroviral drugs in different cell lines and the consequent cytoprotective effectiveness of EG were investigated using an MTT cell viability assay.</p><p><strong>Results: </strong>Like ascorbic acid, EG exhibited promising antioxidant activity. HIV-1 infection of MT2 cells induces cell death often referred to as the cytopathic effect. In addition, the usage of antiretroviral drugs also causes severe adverse effects like cytotoxicity. In this context, EG was tested for its cytoprotective properties against HIV-1-induced cytopathic effect and drug-mediated cellular toxicity. EG reclaimed back the MT2 cells from HIV-1-induced cell death. Antiretroviral drugs, such as ritonavir, efavirinz, AZT, and nevirapine, were tested for their toxicity and induced more cell death at higher concentrations in different tissue models such as the liver (THLE-3), lung (AEpiCM), colorectal (HT-29), and brain (U87 MG). Pretreated cells with EG were rescued from the toxic doses of ART.</p><p><strong>Conclusion: </strong>EG was found to be exhibited cytoprotection not only from HIV-1-linked cell death but also from the chemotoxicity of antiretroviral drugs. Evidently, EG could be a cytoprotective supplement in the management of AIDS along with its enormous antioxidant benefits.</p>","PeriodicalId":7473,"journal":{"name":"Advances in Virology","volume":"2023 ","pages":"6727762"},"PeriodicalIF":2.2,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10356543/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9849833","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Whole-Genome Comparison of Representatives of All Variants of SARS-CoV-2, Including Subvariant BA.2 and the GKA Clade.","authors":"Ida B K Suardana,&nbsp;Bayu K Mahardika,&nbsp;Made Pharmawati,&nbsp;Putu H Sudipa,&nbsp;Tri K Sari,&nbsp;Nyoman B Mahendra,&nbsp;Gusti N Mahardika","doi":"10.1155/2023/6476626","DOIUrl":"https://doi.org/10.1155/2023/6476626","url":null,"abstract":"<p><p>Since its discovery at the end of 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has rapidly evolved into many variants, including the subvariant BA.2 and the GKA clade. Genomic clarification is needed for better management of the current pandemic as well as the possible reemergence of novel variants. The sequence of the reference genome Wuhan-Hu-1 and approximately 20 representatives of each variant were downloaded from GenBank and GISAID. Two representatives with no track of in-definitive nucleotides were selected. The sequences were aligned using muscle. The location of insertion/deletion (indel) in the genome was mapped following the open reading frame (ORF) of Wuhan-Hu-1. The phylogeny of the spike protein coding region was constructed using the maximum likelihood method. Amino acid substitutions in all ORFs were analyzed separately. There are two indel sites in ORF1AB, eight in spike, and one each in ORF3A, matrix (MA), nucleoprotein (NP), and the 3'-untranslated regions (3'UTR). Some indel sites and residues/substitutions are not unique, and some are variant-specific. The phylogeny shows that Omicron, Deltacron, and BA2 are clustered together and separated from other variants with 100% bootstrap support. In conclusion, whole-genome comparison of representatives of all variants revealed indel patterns that are specific to SARS-CoV-2 variants or subvariants. Polymorphic amino acid comparison across all coding regions also showed amino acid residues shared by specific groups of variants. Finally, the higher transmissibility of BA.2 might be due at least in part to the 48 nucleotide deletions in the 3'UTR, while the seem-to-be extinction of GKA clade is due to the lack of genetic advantages as a consequence of amino acid substitutions in various genes.</p>","PeriodicalId":7473,"journal":{"name":"Advances in Virology","volume":"2023 ","pages":"6476626"},"PeriodicalIF":2.2,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10019969/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9153508","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evaluation of the MAScIR SARS-CoV-2 M Kit 2.0 on the SARS-CoV-2 Infection.","authors":"Amal Zouaki,&nbsp;Hakima Kabbaj,&nbsp;Ghizlane El Amin,&nbsp;Mouna Ouadghiri,&nbsp;Bouchra Belefquih,&nbsp;Azeddine Ibrahimi,&nbsp;Myriam Seffar","doi":"10.1155/2023/9313666","DOIUrl":"https://doi.org/10.1155/2023/9313666","url":null,"abstract":"<p><p>SARS-CoV-2 is a major public health problem worldwide. Since its emergence, several diagnostic kits have been developed to ensure rapid patient management. The aim of our study is to check the performance of the new Moroccan SARS-CoV-2 detection kit: MAScIR SARS-CoV-2 M 2.0. The following parameters were studied: repeatability, reproducibility, analytical specificity, analytical sensitivity, and comparison with the GeneFinder™ COVID-19 Plus RealAmp Kit. In addition, an external quality evaluation comprising five specimens was carried out as part of an international program for the external quality evaluation of sublaboratories of the WHO and the Laboratory Office of the National Institute of Hygiene of Morocco. The results of all parameters studied showed an analytical performance that complied with the requirements of the method verification/validation protocol adopted by the Central Laboratory of Virology and met the recommendations of COFRAC (French Accreditation Committee). During the current study, the sequencing of some randomly selected positive samples was performed, among which the carriers of the Alpha variant, the Delta variant, and the Omicron variant were detected. These results allowed us to deduce that this kit was valid for detecting these three variants.</p>","PeriodicalId":7473,"journal":{"name":"Advances in Virology","volume":"2023 ","pages":"9313666"},"PeriodicalIF":2.2,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9929027/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10824641","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Hepatitis B Virus Immunity Gap: A Six-Year Laboratory Data Review of Hepatitis B Serological Profiles in Gauteng Province, South Africa.","authors":"Nonhlanhla Mbenenge,&nbsp;Kathleen Subramoney,&nbsp;Clement Gascua Adu-Gyamfi,&nbsp;Florette K Treurnicht","doi":"10.1155/2023/6374874","DOIUrl":"https://doi.org/10.1155/2023/6374874","url":null,"abstract":"<p><strong>Background: </strong>In 1995, the hepatitis B vaccine in South Africa was incorporated into the childhood expanded programme of immunization. We report on immunity gaps of laboratory-based hepatitis B virus (HBV) among patients in public facilities in Gauteng Province from 1st January 2014 to 31st December 2019. <i>Methodology</i>. We analyzed HBV serological data extracted from the National Health Laboratory Services Central Data Warehouse (NHLS CDW). A descriptive analysis was performed for hepatitis B surface antigen (HBsAg), antibodies to HBV core (anti-HBc) total, anti-HBc IgM, and antibodies to HBV surface antigen (anti-HBs) according to annual distribution, age groups, and sex.</p><p><strong>Results: </strong>The HBsAg positivity rate was 7.0% (75,596/1,095,561; <i>p</i>=0.001): 7.4% (96,532/944,077) in the 25 years and over age group and 4.0% (358/9,268 and 325/10,864) in the under 5 and 13-24 year age groups. The positivity rates of the other HBV serological markers were as follows: anti-HBc total was 37.0% (34,377/93,711; <i>p</i>  <  0.001), anti-HBc IgM was 2.4% (5,661/239,237; <i>p</i>=0.05), and anti-HBs was 37.0% (76,302/206,138; <i>p</i> ≤ 0.001). Naturally acquired HBV immunity was detected in 25.7% (11,188/43,536) of patients in the 25 years and over age group, and 9.7% and 8.2% (113/1,158 and 541/6,522) among those under 5 years and 13-24 year age group, respectively (<i>p</i>  <  0.001). Vaccine-induced immunity was 56.6% (656/1,158) in children under 5 years and 10.2% (4,425/43,536) among those 25 years and above (<i>p</i>  <  0.001). Fifty-six percent (29,404/52,581) of patients were HBV seronegative; predominantly among patients in the 13-24 year age group (60.6%; (3,952/6,522)) and 25 years and over (56.3% (24,524/43,536)) (<i>p</i>=<0.001).</p><p><strong>Conclusion: </strong>The HBV infection seroprevalence remains high in South Africa, with Gauteng province having high intermediate endemicity. However, the HBV immunity gap has shifted from younger children to older children and adults.</p>","PeriodicalId":7473,"journal":{"name":"Advances in Virology","volume":"2023 ","pages":"6374874"},"PeriodicalIF":2.2,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10208757/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9579774","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Single-Nucleotide Polymorphism (SNP) Validity to Detect Omicron Variants.","authors":"Lia Gardenia Partakusuma,&nbsp;Luhung Budiailmiawan,&nbsp;Budiman,&nbsp;Ida Parwati,&nbsp;Aryati,&nbsp;Basti Andriyoko,&nbsp;Louisa Markus,&nbsp;Corine Niswara,&nbsp;Cut Nur Cinthia Alamanda","doi":"10.1155/2023/6618710","DOIUrl":"https://doi.org/10.1155/2023/6618710","url":null,"abstract":"<p><strong>Introduction: </strong>Mutation of SARS-CoV-2 has generated several variants of concern (VOC) which spread promptly worldwide. These emerging variants affected global strategies to overcome COVID-19. Variants of SARS-CoV-2 are determined by the whole genome sequencing (WGS) assay, which is time-consuming, with limited availability (only in several laboratories). Hence, a faster and more accessible examination is needed. The single-nucleotide polymorphism (SNP) method is one of the options for genomic variation surveillance that can help provide an answer to this challenge. This study aims to determine the validity of the SNP method with PCR to detect omicron variants of SARS-CoV-2 compared with the gold standard, WGS.</p><p><strong>Methods: </strong>This is a diagnostic analysis of 140 confirmed COVID-19 nasopharyngeal samples taken from the Kemayoran COVID Emergency Hospital Laboratory and the West Java Provincial Health Laboratory from April to October 2022. Data analysis was carried out to determine conformity and validity values.</p><p><strong>Results: </strong>Analysis using Cohen's kappa coefficient test showed high conformity between SNP and WGS (<i>p</i> value <0.001; kappa coefficient = 0.948). SNP showed great validity values on omicron BA.1 (90% sensitivity; 100% specificity), omicron BA.2 (100% sensitivity; 99% specificity), and omicron BA.4/5 (99.2% sensitivity; 100% specificity).</p><p><strong>Conclusion: </strong>The SNP method can be a more time-efficient alternative to detect omicron variants of SARS-CoV-2 and distinguish their sublineages (BA.1, BA.2, and BA.4/5) by two different specific gene mutations in combination analysis (ΔH69/V70 and Q493R mutations).</p>","PeriodicalId":7473,"journal":{"name":"Advances in Virology","volume":"2023 ","pages":"6618710"},"PeriodicalIF":2.2,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10501844/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10311090","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The SARS-CoV-2 UTR's Intrudes Host RBP's and Modulates Cellular Splicing.","authors":"Anjali Singh,&nbsp;Kush Kumar Pandey,&nbsp;Shubham Kumar Agrawal,&nbsp;Rupesh K Srivastava,&nbsp;Sankar Bhattacharyya,&nbsp;Bhupendra Verma","doi":"10.1155/2023/2995443","DOIUrl":"https://doi.org/10.1155/2023/2995443","url":null,"abstract":"<p><p>SARS-CoV-2 is a novel coronavirus that causes a potentially fatal respiratory disease known as coronavirus disease (COVID-19) and is responsible for the ongoing pandemic with increasing mortality. Understanding the host-virus interaction involved in SARS-CoV-2 pathophysiology will enhance our understanding of the mechanistic basis of COVID-19 infection. The characterization of post-transcriptional gene regulatory networks, particularly pre-mRNA splicing, and the identification and characterization of host proteins interacting with the 5' and 3'UTRs of SARS-CoV-2 will improve our understanding of post-transcriptional gene regulation during SARS-CoV-2 pathogenesis. Here, we demonstrate that either SARS-CoV-2 infection or exogenous overexpression of the 5' and 3'UTRs of the viral genomic RNAs, results in reduced mRNA levels possibly due to modulation of host cell pre-mRNA splicing. Further, we have investigated the potential RNA-binding proteins interacting with the 5' and 3'UTRs, using <i>in-silico</i> approaches. Our results suggest that 5' and 3'UTRs indeed interact with many RNA-binding proteins. Our results provide a primer for further investigations into the UTR-mediated regulation of splicing and related molecular mechanisms in host cells.</p>","PeriodicalId":7473,"journal":{"name":"Advances in Virology","volume":"2023 ","pages":"2995443"},"PeriodicalIF":2.2,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10098413/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9318480","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}