Advances in Virology最新文献

{"title":"Measles Outbreaks in the Republic of Congo: Epidemiology of Laboratory-Confirmed Cases Between 2019 and 2022.","authors":"Yanne Vanessa Thiécesse Mavoungou, Fabien Roch Niama, Léa Gwladys Gangoué, Felix Koukouikila-Koussounda, Marianne Bouanga Bayonne, Cynthia Nkoua Badzi, Leblanc Albert Gandza Gampouo, Pathou Christelle Kiminou, Paule Biyama-Kimia, Princesse Mahoukou, Nadia Claricelle Bongolo Loukabou, Jean Medard Kankou, Pembe Issamou Mayengue, Gabriel Ahombo","doi":"10.1155/2024/8501027","DOIUrl":"10.1155/2024/8501027","url":null,"abstract":"<p><p>In Africa, measles epidemics are frequently reported, despite numerous preventive measures, such as vaccination, which targets children under 5 years of age. Unfortunately, the Republic of the Congo is not an exception to this major health concern. Indeed, many cases are reported annually. Here, we provide an overview of the epidemiological characteristics of laboratory-confirmed measles cases from January 2019 to October 2022 as well as the risk factors associated with the occurrence of measles outbreak. Samples from suspected measles cases were collected across the country and sent to the National Laboratory of Public Health for confirmation. Specific IgM was tested using the enzyme-linked immunosorbent assay (ELISA). Data were analyzed using descriptive and analytic statistics (<i>p</i> < 0.05 was statistically significant). A total of 1330 samples were collected and analyzed. Over those 4 years, 537 samples were confirmed to be positive (40.3%) but with important disparities between years. A relatively low frequency of cases was reported in 2020. Overall, a progressive and significant evolution of positive cases was observed between 2019 and 2022, increasing from 16.8% in 2019 to 65.9% in 2022 (<i>p</i> < 0.0001). We report a low vaccination rate among children (44.8%) and a significantly high positivity rate in this group (46.6%) (<i>p</i> < 0.0008). No difference was reported according to the completeness of the vaccination scheme (<i>p</i>=0.094). Females were slightly more exposed to this infection than males (<i>p</i>=0.04; adjusted odds ratio [aOR]: 1.25 [1.01-1.6]), with an increased risk of exposure in rural areas (<i>p</i>=0.0001; aOR: 0.41 [0.32-0.53]). The department of Pointe-Noire had the highest positivity rate, while three other departments were considered high-risk areas: Likouala (<i>p</i> = 0.0001; aOR: 3.18 [1.80-5.61]), Pool (<i>p</i>=0.0001; aOR: 2.90 [1.70-4.95]), and Brazzaville (<i>p</i>=0.0005; aOR: 0.52 [0.36-0.75]). This study calls for strengthening the epidemiological surveillance system and vaccination strategy in the country. It remains important to research factors that induce a high positive rate among vaccinated children by biological verification of the immunization.</p>","PeriodicalId":7473,"journal":{"name":"Advances in Virology","volume":"2024 ","pages":"8501027"},"PeriodicalIF":1.1,"publicationDate":"2024-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11535416/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142581422","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":"In Silico Design of a Trans-Amplifying RNA-Based Vaccine against SARS-CoV-2 Structural Proteins.","authors":"Fatemeh Nafian, Ghazal Soleymani, Zahra Pourmanouchehri, Mahnaz Kiyanjam, Simin Nafian, Sayed Mohammad Mohammadi, Hanie Jeyroudi, Sharareh Berenji Jalaei, Fatemeh Sabzpoushan","doi":"10.1155/2024/3418062","DOIUrl":"https://doi.org/10.1155/2024/3418062","url":null,"abstract":"<p><p>Nucleic acid-based vaccines allow scalable, rapid, and cell-free vaccine production in response to an emerging disease such as the current COVID-19 pandemic. Here, we objected to the design of a multiepitope mRNA vaccine against the structural proteins of SARS-CoV-2. Through an immunoinformatic approach, promising epitopes were predicted for the spike (S), envelope (E), membrane (M), and nucleocapsid (N) proteins. Fragments rich in overlapping epitopes were selected based on binding affinities with HLA classes I and II for the specific presentation to B and T lymphocytes. Two constructs were designed by fusing the fragments in different arrangements via GG linkers. Construct 1 showed better structural properties and interactions with toll-like receptor 2 (TLR-2), TLR-3, and TLR-4 during molecular docking and dynamic simulation. A 50S ribosomal L7/L12 adjuvant was added to its N-terminus to improve stability and immunogenicity. The final RNA sequence was used to design a trans-amplifying RNA (taRNA) vaccine in a split-vector system. It consists of two molecules: a nonreplicating RNA encoding a trans-acting replicase to amplify the second one, a trans-replicon (TR) RNA encoding the vaccine protein. Overall, the immune response simulation detected that activated B and T lymphocytes and increased memory cell formation. Macrophages and dendritic cells proliferated continuously, and IFN-<i>γ</i> and cytokines like IL-2 were released highly.</p>","PeriodicalId":7473,"journal":{"name":"Advances in Virology","volume":"2024 ","pages":"3418062"},"PeriodicalIF":1.1,"publicationDate":"2024-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11459942/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142387243","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":"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":"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":"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}