Advances in Virology最新文献

{"title":"Predictive Assessment of the Antiviral Properties of <i>Imperata cylindrica</i> against SARS-CoV-2.","authors":"Frank Eric Tatsing Foka, Hazel Tumelo Mufhandu","doi":"10.1155/2024/8598708","DOIUrl":"10.1155/2024/8598708","url":null,"abstract":"<p><p>The omicron variant and its sublineages are highly contagious, and they still constitute a global source of concern despite vaccinations. Hospitalizations and mortality rates resulting from infections by these variants of concern are still common. The existing therapeutic alternatives have presented various setbacks such as low potency, poor pharmacokinetic profiles, and drug resistance. The need for alternative therapeutic options cannot be overemphasized. Plants and their phytochemicals present interesting characteristics that make them suitable candidates for the development of antiviral therapeutic agents. This study aimed to investigate the antiviral potential of <i>Imperata cylindrica</i> (<i>I. cylindrica</i>). Specifically, the objective of this study was to identify <i>I. cylindrica</i> phytochemicals that display inhibitory effects against SARS-CoV-2 main protease (M^pro), a highly conserved protein among coronaviruses. Molecular docking and <i>in silico</i> pharmacokinetic assays were used to assess 72 phytocompounds that are found in <i>I. cylindrica</i> as ligands and M^pro (6LU7) as the target. Only eight phytochemicals (bifendate, cylindrene, tabanone, siderin, 5-hydroxy-2-[2-(2-hydroxyphenyl)ethyl]-4H-1-benzopyran-4-one, maritimin, 5-methoxyflavone, and flavone) displayed high binding affinities with M^pro with docking scores ranging from -5.6 kcal/mol to -9.1 kcal/mol. The <i>in silico</i> pharmacokinetic and toxicological assays revealed that tabanone was the best and safest phytochemical for the development of an inhibitory agent against coronavirus main protease. Thus, the study served as a baseline for further <i>in vitro</i> and <i>in vivo</i> assessment of this phytochemical against M^pro of SARS-CoV-2 variants of concern to validate these <i>in silico</i> findings.</p>","PeriodicalId":7473,"journal":{"name":"Advances in Virology","volume":"2024 ","pages":"8598708"},"PeriodicalIF":1.1,"publicationDate":"2024-08-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11317227/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141970405","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":"Corrigendum to \"Influenza Virus Aerosols in the Air and Their Infectiousness\".","authors":"Nikolai Nikitin, Ekaterina Petrova, Ekaterina Trifonova, Olga Karpova","doi":"10.1155/2024/9762961","DOIUrl":"10.1155/2024/9762961","url":null,"abstract":"<p><p>[This corrects the article DOI: 10.1155/2014/859090.].</p>","PeriodicalId":7473,"journal":{"name":"Advances in Virology","volume":"2024 ","pages":"9762961"},"PeriodicalIF":1.1,"publicationDate":"2024-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11300107/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141892649","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":"Genotyping and Molecular Characterization of VP6 and NSP4 Genes of Unusual Rotavirus Group A Isolated from Children with Acute Gastroenteritis.","authors":"Charilaos Dellis, Elizabeth-Barbara Tatsi, Dimitra-Maria Koukou, Filippos Filippatos, Evangelia-Eirini Vetouli, Emmanouil Zoumakis, Athanasios Michos, Vasiliki Syriopoulou","doi":"10.1155/2024/3263228","DOIUrl":"10.1155/2024/3263228","url":null,"abstract":"<p><p>Group A rotavirus (RVA), which causes acute gastroenteritis (AGE) in children worldwide, is categorized mainly based on VP7 (genotype G) and VP4 (genotype P) genes. Genotypes that circulate at <1% are considered unusual. Important genes also include VP6 (genotype I) and NSP4 (genotype E). VP6 establishes the group and affects immunogenicity, while NSP4, as an enterotoxin, is responsible for the clinical symptoms. The aim of this study was to genotype the VP6 and NSP4 genes and molecularly characterize the NSP4 and VP6 genes of unusual RVA. Unusual RVA strains extracted from fecal samples of children ≤16 years with AGE were genotyped in VP6 and NSP4 genes with Sanger sequencing. In a 15-year period (2007-2021), 54.8% (34/62) of unusual RVA were successfully I and E genotyped. Three different I and E genotypes were identified; I2 (73.5%, 25/34) and E2 (35.3%, 12/34) were the most common. E3 genotype was detected from 2017 onwards. The uncommon combination of I2-E3 was found in 26.5% (9/34) of the strains and G3-P[9]-I2-E3 remained the most frequent G-P-I-E combination (20.6%, 7/34). Children infected with RVA E2 strains had a statistically higher frequency of dehydration (50%) than those infected with RVA E3 strains (<i>p</i> = 0.019). Multiple substitutions were detected in NSP4, but their functional effect remains unknown. The result indicates the genetic diversity of RVA strains. Continuous surveillance of the RVA based on the whole genome will provide better knowledge of its evolution.</p>","PeriodicalId":7473,"journal":{"name":"Advances in Virology","volume":"2024 ","pages":"3263228"},"PeriodicalIF":1.1,"publicationDate":"2024-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11239230/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141589439","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":"Molecular Epidemiology of Human Norovirus Variants from Outbreaks in Zhejiang Province, China, during 2021.","authors":"Yi Sun, Yongjuan Yuan, Haiyan Mao, Lingxuan Su, Qiong Ge, Jian Gao, Changping Xu, Liming Gong","doi":"10.1155/2024/7972494","DOIUrl":"10.1155/2024/7972494","url":null,"abstract":"<p><strong>Background: </strong>Noroviruses are the most frequent cause of epidemic acute viral gastroenteritis in China.</p><p><strong>Objectives: </strong>The aim of this study was to determine the molecular epidemiological characteristics of norovirus outbreaks and the molecular genetic features of norovirus in Zhejiang Province during 2021.</p><p><strong>Methods: </strong>First, the local Centers for Disease Control and Prevention in the outbreak area conducted on-site epidemiologic investigations and collected samples from ill patients for initial testing. The general epidemiologic characteristics of the demographic information are presented through descriptive analysis. Positive samples were sent to the Microbiology Laboratory of Zhejiang Provincial Center for Disease Control and Prevention for further verification. The presence of norovirus genogroups I (GI) and II (GII), along with sapovirus, was detected. Subsequently, the specimens positive for norovirus were sequenced for genotyping purposes. Furthermore, the whole genomes of positive samples were sequenced, enabling the characterization of both nucleotide and amino acid differences within the virus. Finally, phylogenetic trees were constructed to further analyze and understand the genetic relationships among the detected viruses.</p><p><strong>Result: </strong>227 norovirus outbreaks were reported in Zhejiang Province, China, during 2021. Schools were the main setting while January was the peak month for outbreaks. A total of 17 diverse genotypes of norovirus were identified in 2021, and GII.P16-GII.2 was the most frequent genotype (30.19%). Seven genomes (five GI.P4-GI.5 and two GII.P16-GII.2) were obtained. Although GI.P4-GI.5 is considered to be a rare genotype of norovirus, the prevalence might have been underestimated. Capsid microvariation of GII.2 displayed histo-blood group antigen binding patterns compared to the GII.2 prototype, although VP1 sequences were considered to have a minimal impact on antigenicity.</p><p><strong>Conclusion: </strong>This study revealed the diversity of norovirus strains' genotypes circulating in Zhejiang Province in 2021. Continued molecular surveillance of noroviruses should be strengthened in our further efforts to the development of vaccines.</p>","PeriodicalId":7473,"journal":{"name":"Advances in Virology","volume":"2024 ","pages":"7972494"},"PeriodicalIF":2.2,"publicationDate":"2024-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11156503/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141282700","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 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}