Acta virologica最新文献

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Study of anti-S1-protein IgG antibody levels as potential correlates of protection against breakthrough infection with SARS-CoV-2 Omicron BA.1 and BA.2 variants 抗S1-蛋白IgG抗体水平作为预防严重急性呼吸系统综合征冠状病毒2型奥密克戎BA.1和BA.2变异株突破性感染的潜在相关性的研究
IF 1.7 4区 医学
Acta virologica Pub Date : 2023-06-22 DOI: 10.3389/av.2023.11652
I. Kajanová, Z. Radiková, Ľ. Lukáčiková, L. Jelenska, Katarina Grossmannova, Martina Belisova, J. Kopáček, S. Pastoreková
{"title":"Study of anti-S1-protein IgG antibody levels as potential correlates of protection against breakthrough infection with SARS-CoV-2 Omicron BA.1 and BA.2 variants","authors":"I. Kajanová, Z. Radiková, Ľ. Lukáčiková, L. Jelenska, Katarina Grossmannova, Martina Belisova, J. Kopáček, S. Pastoreková","doi":"10.3389/av.2023.11652","DOIUrl":"https://doi.org/10.3389/av.2023.11652","url":null,"abstract":"Despite considerable efforts, the scientific community has not yet succeeded to define uniform correlate of protection (CoP) against SARS-CoV-2 infections based on the level of specific (receptor-binding domain (RBD)-targeting or neutralizing) antibodies (Perry et al., 2022). Obviously, this is because of the high complexity and great interindividual variability of the immune response. Although the share of cellular immunity in the response to SARS-CoV-2 infection is considerable, it would not be appropriate to underestimate the protective function of specific antibodies. Increase in their level generally correlates with a decrease in the probability of infection as well as the probability of a more severe course of the disease (Khoury et al., 2021). Determining the quantity of specific antibodies providing CoP is, however, challenging precisely in view of the individual characteristics of the T-cell branch of the immune system. However, that does not diminish the significance of studying the protective function of antibodies generated after vaccination or infection with different variants of SARS-CoV-2 against breakthrough infections with new variants of the virus. Antibodies against the RBD domain of the S1 subunit of the Spike protein have the greatest importance in the neutralization of viral particles (Dolscheid-Pommerich et al., 2022). At the same time, the OPEN ACCESS","PeriodicalId":7205,"journal":{"name":"Acta virologica","volume":" ","pages":""},"PeriodicalIF":1.7,"publicationDate":"2023-06-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47497620","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
Comparison of microbial diversity of respiratory tract between COVID-19 patients and healthy population COVID-19患者与健康人群呼吸道微生物多样性比较
IF 1.7 4区 医学
Acta virologica Pub Date : 2023-06-22 DOI: 10.3389/av.2023.11664
Klaudia Babišová, Patrik Krumpolec, Dominik Hadžega, P. Sabaka, P. Jackuliak, G. Minárik, M. Hyblová
{"title":"Comparison of microbial diversity of respiratory tract between COVID-19 patients and healthy population","authors":"Klaudia Babišová, Patrik Krumpolec, Dominik Hadžega, P. Sabaka, P. Jackuliak, G. Minárik, M. Hyblová","doi":"10.3389/av.2023.11664","DOIUrl":"https://doi.org/10.3389/av.2023.11664","url":null,"abstract":"Since its outbreak in late 2019, the SARS-CoV-2 virus has been the main subject of interest for a number of studies. Clinical manifestations are ranging from asymptomatic to mild and severe. Major risk factors for developing severe COVID-19 are age and comorbidities, although younger people suffer from severe COVID-19 as well. One of the explanations for why can be the composition of respiratory tract microbiota. In this article, we review studies linking respiratory tract microbiome and its changes during COVID-19 infection. The respiratory tract microbiome helps shape immunity and it is assumed that it can affect the outcome of several viral infections. Several studies show differences in the microbial composition of the respiratory tract between COVID-19 patients and healthy individuals. The diversity of the respiratory tract microbiome is reduced with increasing severity of COVID-19.","PeriodicalId":7205,"journal":{"name":"Acta virologica","volume":" ","pages":""},"PeriodicalIF":1.7,"publicationDate":"2023-06-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44830063","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Phaseolus vulgaris alphaendornavirus-1 is frequent in bean germplasm in Slovakia and shows low molecular variability 菜豆αendornavirus-1在斯洛伐克的大豆种质中很常见,并且表现出低分子变异性
IF 1.7 4区 医学
Acta virologica Pub Date : 2023-06-05 DOI: 10.3389/av.2023.11484
M. Mrkvová, Adam Achs, P. Alaxin, Z. Šubr, L. Predajňa, E. Zetochova, P. Hauptvogel, Katarína Šoltýs, T. Candresse, M. Glasa
{"title":"Phaseolus vulgaris alphaendornavirus-1 is frequent in bean germplasm in Slovakia and shows low molecular variability","authors":"M. Mrkvová, Adam Achs, P. Alaxin, Z. Šubr, L. Predajňa, E. Zetochova, P. Hauptvogel, Katarína Šoltýs, T. Candresse, M. Glasa","doi":"10.3389/av.2023.11484","DOIUrl":"https://doi.org/10.3389/av.2023.11484","url":null,"abstract":"Phaseolus vulgaris alphaendornavirus-1 (PvEV-1, family Endornaviridae) was identified by ribodepleted total RNA high-throughput sequencing in the virome of two bean plants (Phaseouls vulgaris L.) grown in a garden in western Slovakia. Two nearly complete PvEV-1 genomes (ca. 14.06 kb, named PV1 and PV2) were assembled, showing 99.9% nucleotide identity, while their nucleotide identity with the reference PvEV-1 genome (NC_039217) reached 98.4%. Two primer pairs spanning the viral helicase encoding region and sequence upstream of the RNA-dependent RNA polymerase were designed and used to confirm the presence of the virus in the original bean samples by RT-PCR. A subsequent search for PvEV-1 presence in Slovakia was focused on two groups of samples: 1) bean plants grown under open field conditions and sampled during the vegetation period and 2) bean accessions grown from seeds obtained from a Slovak and French bean germplasm collection. Based on RT-PCR results, 4 out of 15 bean samples from open fields and 12 out of 21 bean accessions from the curated germplasm collection tested PvEV-1-positive. Interestingly, sequencing of RT-PCR products revealed that all amplified isolates are identical in the two amplified genomic portion which is also identical to those of the PV1 and PV2 isolates. These results suggest a relatively high incidence of PvEV-1 in bean in Slovakia. This is the first evidence and characterization of PvEV-1 from bean plants in Europe.","PeriodicalId":7205,"journal":{"name":"Acta virologica","volume":" ","pages":""},"PeriodicalIF":1.7,"publicationDate":"2023-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46768028","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
A novel deltacryptic virus identified in Allium cepa from Brazil. 一种在巴西葱属植物中发现的新型deltacrypa病毒。
IF 1.7 4区 医学
Acta virologica Pub Date : 2023-01-01 DOI: 10.4149/av_2023_111
José Ailton Cruz, Adriano Márcio Freire, Júlio Carlos Polimeni, Rosana Blawid
{"title":"A novel deltacryptic virus identified in Allium cepa from Brazil.","authors":"José Ailton Cruz,&nbsp;Adriano Márcio Freire,&nbsp;Júlio Carlos Polimeni,&nbsp;Rosana Blawid","doi":"10.4149/av_2023_111","DOIUrl":"https://doi.org/10.4149/av_2023_111","url":null,"abstract":"<p><p> This work describes a novel partitivirus genome assembled from RNA-seq data generated from onion tissue from fields in Brazil. A new partitivirus genome composed of three dsRNAs, which was closely related to arhar cryptic virus 1, was assembled from Allium cepa samples from Brazil. The genomic sequences were also identified from available transcriptomic datasets of onion samples from China, Czech Republic, India, South Korea and USA. According to the species demarcation in the Partitiviridae family, the new virus was classified into the genus Deltapartitivirus with the suggested name of allium deltapartitivirus. This is the first report of the occurrence of a cryptic virus in plants of the genus Allium, and therefore, this work contributes to the understanding of the genetic diversity of partitiviruses  that infect the genus Allium. Keywords: Allium sp.; high-throughput sequencing; partitiviruses.</p>","PeriodicalId":7205,"journal":{"name":"Acta virologica","volume":"67 1","pages":"109-113"},"PeriodicalIF":1.7,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9159734","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
Notoginsenoside R1 inhibits hepatitis B virus replication by modulating SIRT1 activity. 三七皂苷R1通过调节SIRT1活性抑制乙型肝炎病毒复制。
IF 1.7 4区 医学
Acta virologica Pub Date : 2023-01-01 DOI: 10.4149/av_2023_105
Wujing Zhang, Jingjing Cui, Lichun Li, Lijuan Chai, Qingling Hou, Huaqi Yu
{"title":"Notoginsenoside R1 inhibits hepatitis B virus replication by modulating SIRT1 activity.","authors":"Wujing Zhang,&nbsp;Jingjing Cui,&nbsp;Lichun Li,&nbsp;Lijuan Chai,&nbsp;Qingling Hou,&nbsp;Huaqi Yu","doi":"10.4149/av_2023_105","DOIUrl":"https://doi.org/10.4149/av_2023_105","url":null,"abstract":"<p><p>The hepatitis B virus (HBV) infection remains highly prevalent globally. The present study aimed to explore the possible therapeutic effect of notoginsenoside R1, which has attracted considerable attention due to its diverse pharmacological effects, on HBV infection. The HBV-containing hepatocellular carcinoma cell lines, HepG2 and MHCC97H, were used in this study. We first treated the two cell lines with different concentrations of notoginsenoside R1 and subsequently measured the relative levels of HBV DNA, HBV surface antigen, HBV core antigen, and sirtuin 1 (SIRT1) using reverse transcription-quantitative polymerase chain reaction and western blotting. Finally, an HBV hemodynamic replication model was created to test the effect of notoginsenoside R1 on HBV replication. Notoginsenoside R1 inhibited the replication of HBV. This inhibitory effect was mediated through the downregulation of SIRT1 activity. Additionally, the inhibition of SIRT1 activity by silencing its expression or treatment with the SIRT1 inhibitor, selisistat, suppressed HBV replication. Furthermore, our animal experiments demonstrated that notoginsenoside R1 was effective at suppressing HBV replication in vivo. Thus, notoginsenoside R1 suppresses HBV replication by downregulating SIRT1 activity in vitro and in vivo. Keywords: notoginsenoside R1; hepatitis B virus; SIRT1.</p>","PeriodicalId":7205,"journal":{"name":"Acta virologica","volume":"67 1","pages":"51-58"},"PeriodicalIF":1.7,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9159735","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Effects of LEF-11 acetylation modification on the regulation of baculovirus infection. LEF-11乙酰化修饰对杆状病毒感染的调控作用。
IF 1.7 4区 医学
Acta virologica Pub Date : 2023-01-01 DOI: 10.4149/av_2023_104
Jiannan Wu, Shuli Shen, Xu Gao, Meng Miao, Yanping Quan, Wei Yu
{"title":"Effects of LEF-11 acetylation modification on the regulation of baculovirus infection.","authors":"Jiannan Wu,&nbsp;Shuli Shen,&nbsp;Xu Gao,&nbsp;Meng Miao,&nbsp;Yanping Quan,&nbsp;Wei Yu","doi":"10.4149/av_2023_104","DOIUrl":"https://doi.org/10.4149/av_2023_104","url":null,"abstract":"<p><p>Late expression factor 11 (LEF-11) is an essential protein in the regulation of Bombyx mori nucleopolyhedrovirus (BmNPV) DNA replication and late gene expression. Our recent quantitative analysis of protein acetylome revealed for the first time that LEF-11 can be acetylated at one lysine residue (K83) during viral infection, but the underlying mechanism is unclear. The acetylation level for K83 was down-regulated after 36 h post-infection by approximately 30%. To clarify the regulatory function of this modification, overlap PCR was used for site-specific mutagenesis for acetylated (K83Q) or deacetylated (K83R) mimic mutants of LEF-11. The results of viral titration and quantitative polymerase chain reaction showed that after K83 acetylation, budding virion production and the viral genome replication level were significantly upregulated. Meanwhile, the results of yeast two-hybrid (Y2H) system confirmed that K83 deacetylation modification inhibited the interaction between LEF-11 and immediate early gene 1 (IE-1). In conclusion, the acetylation of LEF-11 at K83 might enhance the interaction with IE-1 in the host cell nucleus to promote viral DNA replication, and might be one of the antiviral strategies of the silkworm host. The host inhibits virus proliferation by deacetylating LEF-11. Keywords: BmNPV; LEF-11; acetylation; virus replication; protein interaction.</p>","PeriodicalId":7205,"journal":{"name":"Acta virologica","volume":"67 1","pages":"42-50"},"PeriodicalIF":1.7,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9167035","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Structural and functional characterization of SARS-CoV-2 nucleocapsid protein mutations identified in Turkey by using in silico approaches. 利用计算机方法在土耳其鉴定出的SARS-CoV-2核衣壳蛋白突变的结构和功能特征
IF 1.7 4区 医学
Acta virologica Pub Date : 2023-01-01 DOI: 10.4149/av_2023_106
Betul Akcesme, Burcin Erkal, Zehra Yaren Donmez
{"title":"Structural and functional characterization of SARS-CoV-2 nucleocapsid protein mutations identified in Turkey by using in silico approaches.","authors":"Betul Akcesme,&nbsp;Burcin Erkal,&nbsp;Zehra Yaren Donmez","doi":"10.4149/av_2023_106","DOIUrl":"https://doi.org/10.4149/av_2023_106","url":null,"abstract":"<p><p>Missense mutations in the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus may cause changes in the structure of proteins. The nucleocapsid (N) protein is an important target for drugs and vaccines. The main purpose of this study is to detect missense mutations in the SARS-CoV-2 N protein and to reveal the effects of these mutations on protein structure by using in silico approaches. 161 missense mutations of the N protein were determined in 2286 SARS-CoV-2 genomes derived from the GISAID EpiCoV database in the Turkish population. Identified 161 missense mutations were analyzed by using sequence and structure-based methods to predict effects of mutation on function and structure of SARS-CoV-2 N protein. These analyzes revealed that some mutations showed deleterious effects and change of stability and flexibility of nucleocapsid protein. D3L, S194L, S235F, and P13L (Omicron variant) mutations were further analyzed in our study due to their importance in the literature and in our results. Even though, our findings are essential for research of SARS-CoV-2 virus, in vitro and in vivo validations are necessary. Keywords: nucleocapsid protein; SARS-CoV-2; missense mutations; protein stability; protein flexibility.</p>","PeriodicalId":7205,"journal":{"name":"Acta virologica","volume":"67 1","pages":"59-68"},"PeriodicalIF":1.7,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9592356","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Sensitive SARS-CoV-2 detection, air travel Covid-19 testing, variant determination and fast direct PCR detection, using ddPCR and RT-qPCR methods. 采用ddPCR和RT-qPCR方法对SARS-CoV-2进行灵敏检测、航空旅行Covid-19检测、变异检测和快速直接PCR检测。
IF 1.7 4区 医学
Acta virologica Pub Date : 2023-01-01 DOI: 10.4149/av_2023_101
Tatiana Burjanivova, Eva Lukacova, Vincent Lucansky, Marek Samec, Petar Podlesniy, Zuzana Kolkova, Lenka Reizigova, Marian Grendar, Eva Turyova, Veronika Holubekova, Bibiana Malicherova, Vladimir Nosal, Ivana Kasubova, Robert Dusenka, Denisa Osinova, Jana Hosalova Matisova, Dana Dvorska, Dusan Brany, Zuzana Dankova, Elena Novakova, Andrea Calkovska, Erika Halasova
{"title":"Sensitive SARS-CoV-2 detection, air travel Covid-19 testing, variant determination and fast direct PCR detection, using ddPCR and RT-qPCR methods.","authors":"Tatiana Burjanivova,&nbsp;Eva Lukacova,&nbsp;Vincent Lucansky,&nbsp;Marek Samec,&nbsp;Petar Podlesniy,&nbsp;Zuzana Kolkova,&nbsp;Lenka Reizigova,&nbsp;Marian Grendar,&nbsp;Eva Turyova,&nbsp;Veronika Holubekova,&nbsp;Bibiana Malicherova,&nbsp;Vladimir Nosal,&nbsp;Ivana Kasubova,&nbsp;Robert Dusenka,&nbsp;Denisa Osinova,&nbsp;Jana Hosalova Matisova,&nbsp;Dana Dvorska,&nbsp;Dusan Brany,&nbsp;Zuzana Dankova,&nbsp;Elena Novakova,&nbsp;Andrea Calkovska,&nbsp;Erika Halasova","doi":"10.4149/av_2023_101","DOIUrl":"https://doi.org/10.4149/av_2023_101","url":null,"abstract":"<p><p>Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) monitoring in air traffic is important in the prevention of the virus spreading from abroad. The gold standard for SARS-CoV-2 detection is RT-qPCR; however, for early and low viral load detection, a much more sensitive method, such as droplet digital PCR (ddPCR), is required. Our first step was to developed both, ddPCR and RT-qPCR methods, for sensitive SARS-CoV-2 detection. Analysis of ten swab/saliva samples of five Covid-19 patients in different stages of disease showed positivity in 6/10 samples with RT-qPCR and 9/10 with ddPCR. We also used our RT-qPCR method for SARS-CoV-2 detection without the need of RNA extraction, obtaining results in 90-120 minutes. We analyzed 116 self-collected saliva samples from passengers and airport staff arriving from abroad. All samples were negative by RT-qPCR, while 1 was positive, using ddPCR. Lastly, we developed ddPCR assays for SARS-CoV-2 variants identification (alpha, beta, gamma, delta/kappa) that are more economically advantageous when compared to NGS. Our findings demonstrated that saliva samples can be stored at ambient temperature, as we did not observe any significant difference between a fresh sample and the same sample after 24 hours (p = 0.23), hence, saliva collection is the optimal route for sampling airplane passengers. Our results also showed that droplet digital PCR is a more suitable method for detecting virus from saliva, compared to RT-qPCR. Keywords: COVID-19; RT-PCR; ddPCR; SARS-CoV-2; nasopharyngeal swab; saliva.</p>","PeriodicalId":7205,"journal":{"name":"Acta virologica","volume":"67 1","pages":"3-12"},"PeriodicalIF":1.7,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9164591","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 2
Instrument-free, visual and direct detection of porcine reproductive and respiratory syndrome viruses in resource-limited settings. 在资源有限的环境中无仪器、目视和直接检测猪繁殖和呼吸综合征病毒。
IF 1.7 4区 医学
Acta virologica Pub Date : 2023-01-01 DOI: 10.4149/av_2023_107
Diem Hong Tran, Ngan Anh Ngoc, Hau Thi Tran, Trang Nguyen Minh, Thi Bich Ngoc, Van Tam Nguyen, Van Phan Le, Huong Thi Thu
{"title":"Instrument-free, visual and direct detection of porcine reproductive and respiratory syndrome viruses in resource-limited settings.","authors":"Diem Hong Tran,&nbsp;Ngan Anh Ngoc,&nbsp;Hau Thi Tran,&nbsp;Trang Nguyen Minh,&nbsp;Thi Bich Ngoc,&nbsp;Van Tam Nguyen,&nbsp;Van Phan Le,&nbsp;Huong Thi Thu","doi":"10.4149/av_2023_107","DOIUrl":"https://doi.org/10.4149/av_2023_107","url":null,"abstract":"<p><p>Porcine reproductive and respiratory syndrome (PRRS) caused by PRRS virus (PRRSV) is one of the most complicated and dangerous diseases in pigs with high mortality since it modulates the immune system of the lungs and has been closely associated with secondary infection of other lethal bacteria and viruses. The gold standard of molecular diagnosis for PRRSV, reverse transcription (RT)-PCR, is time-consuming, expensive and requires transportation of samples to a specialized laboratory. In this study, a direct colorimetric RT-loop-mediated isothermal amplification (RT-LAMP) method was developed to specifically and rapidly detect PRRSV. The RT-LAMP outcomes can be visualized by the naked eye after 45 min of incubation at 65˚C without any cross-reactivity recorded with the bacteria and other viruses tested. In particular, the mobile, non-instrumented, commercial pocket hand warmers were demonstrated to su-ccessfully provide constant temperature for consistent nucleic acid amplification throughout the RT-LAMP reactions. The limit of detection of the assay was defined as the genomic RNA concentration extracted from a known viral titer of 10-2.5 TCID50/ml. The direct use of clinical serum samples required a simple dilution to maintain the performance of the colorimetric RT-LAMP assay. Therefore, the direct colorimetric RT-LAMP assay developed is well-qualified for producing a ready-to-use kit for PRRSV diagnosis in the field. Keywords: porcine reproductive and respiratory syndrome; rapid testing; RT-LAMP; colorimetric; direct detection; instrument-free.</p>","PeriodicalId":7205,"journal":{"name":"Acta virologica","volume":"67 1","pages":"69-78"},"PeriodicalIF":1.7,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9159733","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 2
High resolution melting curve analysis for rapid detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants. 高分辨率融化曲线分析快速检测严重急性呼吸综合征冠状病毒2 (SARS-CoV-2)变异。
IF 1.7 4区 医学
Acta virologica Pub Date : 2023-01-01 DOI: 10.4149/av_2023_109
Seyed Jalal Kiani, Mehdi Ramshini, Farah Bokharaei-Salim, Tahereh Donyavi, Babak Eshrati, Majid Khoshmirsafa, Saied Ghorbani, Ahmad Tavakoli, Seyed Hamidreza Monavari, Zohreh Yousefi Ghalejoogh, Mohammad Abbasi-Kolli
{"title":"High resolution melting curve analysis for rapid detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants.","authors":"Seyed Jalal Kiani,&nbsp;Mehdi Ramshini,&nbsp;Farah Bokharaei-Salim,&nbsp;Tahereh Donyavi,&nbsp;Babak Eshrati,&nbsp;Majid Khoshmirsafa,&nbsp;Saied Ghorbani,&nbsp;Ahmad Tavakoli,&nbsp;Seyed Hamidreza Monavari,&nbsp;Zohreh Yousefi Ghalejoogh,&nbsp;Mohammad Abbasi-Kolli","doi":"10.4149/av_2023_109","DOIUrl":"https://doi.org/10.4149/av_2023_109","url":null,"abstract":"<p><p>Since the emergence of the original Wuhan SARS-CoV-2 strain, several new variants of the virus have emerged. Alpha, Beta, Gamma, Delta and the most recent Omicron variants have been introduced during this pandemic. Several methods including, but not restricted to, allele-specific PCR, ligation with rolling circle amplification and real-time PCR with allele-specific probes are able to detect mutations as low as a single nucleotide polymorphism. High-resolution melting curve analysis is ano-ther technique to assess any mutations in a nucleic acid chain. Confirmed samples with SARS-CoV-2 infection were subjected to variant identification using a de novo-designed HRM assay. In order to select for mutations with the highest effect on Tm of the amplicon, deletion mutations of NSP6 (Del 3675-3677), and S1 (Del 144) were chosen for HRM analysis. HRM analysis for the amplicon of the primer set-1 (NSP6) resulted in Tm differences of -0.39°C, +0.4°C, and -0.6°C between Alpha, Delta, and Omicron variants, respectively, in comparison to the original Wuhan strain. Moreover, HRM analysis of the amplification performed by primer set-2 (S1) led to Tm differences of +0.32°C, -0.26°C, and +0.24°C between Alpha, Delta, and Omicron variants, respectively, in comparison to original Wuhan strain. The test was able to specify each sample to its variant group with more than 90 percent of confidence. The results obtained in this study demonstrate that using a single closed-tube strategy with a HRM-equipped machine, screening new variants of the virus is possible in a fast and reliable way. Keywords: high resolution melting; SARS coronavirus 2; mutation; variant; genotyping.</p>","PeriodicalId":7205,"journal":{"name":"Acta virologica","volume":"67 1","pages":"91-98"},"PeriodicalIF":1.7,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9167036","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
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