Pub Date : 2024-11-21DOI: 10.1016/j.jviromet.2024.115070
Crystal M. Gigante , Vaughn Wicker , Kimberly Wilkins , Melanie Seiders , Hui Zhao , Puja Patel , Lillian Orciari , Rene Edgar Condori , Lisa Dettinger , Pamela Yager , Dongxiang Xia , Yu Li
Reliable, validated diagnostic tests are critical for rabies control in animals and prevention in people. We present a performance assessment and updates to the LN34 real-time RT-PCR assay for rabies diagnosis in postmortem animal brain samples. In two U.S. laboratories during 2017–2022, routine used of the LN34 assay produced excellent diagnostic sensitivity (99.72–100 %) and specificity (99.99–100 %) compared to the direct fluorescence antibody test (DFA). Almost all (>90 %) DFA indeterminate results caused by non-specific or atypical fluorescence were negative by LN34 testing, representing up to 111 cases where unnecessary post-exposure prophylaxis could be avoided. LN34 assay original primer sequences showed low sensitivity for some rare lyssaviruses. Increased primer concentration combined with new primer formulation showed improved performance for impacted lyssaviruses with no loss in performance across diverse rabies virus variants from clinical samples. The updated LN34 and internal control assays were combined into a single-well LN34 multiplexed (LN34M) format, run at half reagent volumes. The LN34M assay showed similar detection of rabies virus to the singleplexed assay with simplified assay set-up, lower cost, and improved quality controls.
{"title":"Optimization of pan-lyssavirus LN34 assay for streamlined rabies diagnostics by real-time RT-PCR","authors":"Crystal M. Gigante , Vaughn Wicker , Kimberly Wilkins , Melanie Seiders , Hui Zhao , Puja Patel , Lillian Orciari , Rene Edgar Condori , Lisa Dettinger , Pamela Yager , Dongxiang Xia , Yu Li","doi":"10.1016/j.jviromet.2024.115070","DOIUrl":"10.1016/j.jviromet.2024.115070","url":null,"abstract":"<div><div>Reliable, validated diagnostic tests are critical for rabies control in animals and prevention in people. We present a performance assessment and updates to the LN34 real-time RT-PCR assay for rabies diagnosis in postmortem animal brain samples. In two U.S. laboratories during 2017–2022, routine used of the LN34 assay produced excellent diagnostic sensitivity (99.72–100 %) and specificity (99.99–100 %) compared to the direct fluorescence antibody test (DFA). Almost all (>90 %) DFA indeterminate results caused by non-specific or atypical fluorescence were negative by LN34 testing, representing up to 111 cases where unnecessary post-exposure prophylaxis could be avoided. LN34 assay original primer sequences showed low sensitivity for some rare lyssaviruses. Increased primer concentration combined with new primer formulation showed improved performance for impacted lyssaviruses with no loss in performance across diverse rabies virus variants from clinical samples. The updated LN34 and internal control assays were combined into a single-well LN34 multiplexed (LN34M) format, run at half reagent volumes. The LN34M assay showed similar detection of rabies virus to the singleplexed assay with simplified assay set-up, lower cost, and improved quality controls.</div></div>","PeriodicalId":17663,"journal":{"name":"Journal of virological methods","volume":"333 ","pages":"Article 115070"},"PeriodicalIF":2.2,"publicationDate":"2024-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142695431","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}
Gammaretroviral vectors are widely used in cellular and gene therapy products because of the availability of stable vector producer cells. Accurately assessing vector copy number (VCN) is critical for selecting appropriate clones to avoid the risks of homologous recombination and complications in mutation detection. Traditional methods such as quantitative polymerase chain reaction (PCR) and Southern blotting have limitations in accuracy and throughput. This study presents a triplex droplet digital PCR (ddPCR) method for analyzing the VCN in gammaretroviral vector producer cells. We designed a universal primer– probe set targeting the packaging signal sequence common to murine leukemia virus– and murine stem cell virus– based gammaretroviral vectors. Two reference genes were selected after karyotyping the PG13 gammaretroviral vector packaging cell line to identify stable chromosomes. The triplex ddPCR assay was optimized and verified using PG13 cells transduced with constructs of different transgene and vector backbones. The assay showed high concordance with Southern blot. Using multiple reference genes ensures accurate and robust VCN assessment, especially in cell lines with chromosomal instability. This method improves the clone selection process for gammaretroviral vector producer cells, accelerates the development of novel cellular and gene therapy products, and ensures their rapid delivery to patients.
{"title":"Accurate vector copy number determination in gammaretroviral vector producer cell clones using triplex digital droplet PCR","authors":"Tomomine Iida , Yoshiki Nakamura , Katsuhiko Yamamoto , Eiki Maeda , Yukihiro Ikeda","doi":"10.1016/j.jviromet.2024.115075","DOIUrl":"10.1016/j.jviromet.2024.115075","url":null,"abstract":"<div><div>Gammaretroviral vectors are widely used in cellular and gene therapy products because of the availability of stable vector producer cells. Accurately assessing vector copy number (VCN) is critical for selecting appropriate clones to avoid the risks of homologous recombination and complications in mutation detection. Traditional methods such as quantitative polymerase chain reaction (PCR) and Southern blotting have limitations in accuracy and throughput. This study presents a triplex droplet digital PCR (ddPCR) method for analyzing the VCN in gammaretroviral vector producer cells. We designed a universal primer– probe set targeting the packaging signal sequence common to murine leukemia virus– and murine stem cell virus– based gammaretroviral vectors. Two reference genes were selected after karyotyping the PG13 gammaretroviral vector packaging cell line to identify stable chromosomes. The triplex ddPCR assay was optimized and verified using PG13 cells transduced with constructs of different transgene and vector backbones. The assay showed high concordance with Southern blot. Using multiple reference genes ensures accurate and robust VCN assessment, especially in cell lines with chromosomal instability. This method improves the clone selection process for gammaretroviral vector producer cells, accelerates the development of novel cellular and gene therapy products, and ensures their rapid delivery to patients.</div></div>","PeriodicalId":17663,"journal":{"name":"Journal of virological methods","volume":"332 ","pages":"Article 115075"},"PeriodicalIF":2.2,"publicationDate":"2024-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142682056","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-19DOI: 10.1016/j.jviromet.2024.115069
Anaïs Scohy , Maria A. Argudín , Florence Kabera , Nathalie Olive , Benoît Kabamba Mukadi
CMV infection remains a well-recognized threat in immunocompromised patients and is a major cause of congenital infection. If plasma and whole blood are routinely used as clinical samples for detection of CMV infection and disease, CMV laboratory testing in non-blood samples is becoming more and more relevant to support the diagnosis, prognosis and management of CMV infection. Accurate CMV viral load assessment in various body fluids is therefore essential. We evaluated the performance of the Alinity m CMV assay for detecting and quantifying CMV in plasma, amniotic fluid, bronchoalveolar lavage, cerebrospinal fluid, saliva and urine. Using a commercially available CMV reference panel and CMV culture supernatant, we assessed the linearity and accuracy of the Alinity m CMV assay across the different sample types. Excellent linear correlations (r values > 0.98) and a good accuracy (bias < ± 0.50 Log10 IU/mL and SD < 0.23) were observed. In conclusion, the Alinity m CMV assay is suitable to detect and quantify CMV DNA in plasma but also in all non-plasma samples tested. Random and continuous access capabilities of the Alinity m enable rapid and efficient laboratory detection and quantification of CMV DNA.
CMV 感染在免疫力低下的患者中仍是一个公认的威胁,也是先天性感染的一个主要原因。如果说血浆和全血是检测 CMV 感染和疾病的常规临床样本,那么非血液样本中的 CMV 实验室检测对于支持 CMV 感染的诊断、预后和管理则变得越来越重要。因此,准确评估各种体液中的 CMV 病毒载量至关重要。我们评估了 Alinity m CMV 检测试剂盒检测和定量血浆、羊水、支气管肺泡灌洗液、脑脊液、唾液和尿液中 CMV 的性能。我们使用市售的 CMV 参考面板和 CMV 培养上清,评估了 Alinity m CMV 检测法在不同样本类型中的线性和准确性。我们观察到了极好的线性相关性(r 值 > 0.98)和良好的准确性(偏差 < ± 0.50 Log10 IU/mL,SD < 0.23)。总之,Alinity m CMV 检测试剂盒不仅适用于检测血浆中的 CMV DNA,也适用于检测所有非血浆样本中的 CMV DNA。Alinity m 的随机和连续访问功能可实现快速、高效的 CMV DNA 实验室检测和定量。
{"title":"Evaluation of the Alinity m CMV assay for detecting and quantifying cytomegalovirus DNA in non-plasma samples","authors":"Anaïs Scohy , Maria A. Argudín , Florence Kabera , Nathalie Olive , Benoît Kabamba Mukadi","doi":"10.1016/j.jviromet.2024.115069","DOIUrl":"10.1016/j.jviromet.2024.115069","url":null,"abstract":"<div><div>CMV infection remains a well-recognized threat in immunocompromised patients and is a major cause of congenital infection. If plasma and whole blood are routinely used as clinical samples for detection of CMV infection and disease, CMV laboratory testing in non-blood samples is becoming more and more relevant to support the diagnosis, prognosis and management of CMV infection. Accurate CMV viral load assessment in various body fluids is therefore essential. We evaluated the performance of the Alinity m CMV assay for detecting and quantifying CMV in plasma, amniotic fluid, bronchoalveolar lavage, cerebrospinal fluid, saliva and urine. Using a commercially available CMV reference panel and CMV culture supernatant, we assessed the linearity and accuracy of the Alinity m CMV assay across the different sample types. Excellent linear correlations (r values > 0.98) and a good accuracy (bias < ± 0.50 Log<sub>10</sub> IU/mL and SD < 0.23) were observed. In conclusion, the Alinity m CMV assay is suitable to detect and quantify CMV DNA in plasma but also in all non-plasma samples tested. Random and continuous access capabilities of the Alinity m enable rapid and efficient laboratory detection and quantification of CMV DNA.</div></div>","PeriodicalId":17663,"journal":{"name":"Journal of virological methods","volume":"332 ","pages":"Article 115069"},"PeriodicalIF":2.2,"publicationDate":"2024-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142687357","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}
Pub Date : 2024-11-17DOI: 10.1016/j.jviromet.2024.115062
Azzania Fibriani, Katerina Naisanu, Nicholas Yamahoki, Denti Rizki Kinanti
Severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) is the primary cause of the Coronavirus disease 2019 (COVID-19) pandemic, which affects millions of people worldwide with high levels of infectivity and mortality. However, the antibodies developed for COVID-19 research and diagnostics are still limited. Therefore, in this study, we developed polyclonal immunoglobulin (IgY) antibodies from chicken egg yolk targeting multi-epitope antigen of SARS-CoV-2. After immunizing hens with a SARS-CoV-2 multi-epitope peptide, IgY antibodies were isolated from chicken eggs and further characterized using SDS-PAGE and ELISA. The results showed that the IgY antibodies were successfully isolated from egg yolks. The sandwich ELISA results demonstrated that the isolated IgYs could bind to SARS-CoV-2 antigens, both the multi-epitope peptide and the trimeric Spike. Furthermore, the developed polyclonal antibodies could recognize SARS-CoV-2 in human nasopharyngeal swab samples, even at the lowest concentration (dilution at 1:10000). Thus, it can be concluded that the developed polyclonal IgYs were successfully produced and have the potential to be applied in the development of COVID-19 diagnostics.
{"title":"Development of polyclonal chicken egg yolk immunoglobulin Y (IgY) antibodies targeting SARS-CoV-2 multi-epitope antigen","authors":"Azzania Fibriani, Katerina Naisanu, Nicholas Yamahoki, Denti Rizki Kinanti","doi":"10.1016/j.jviromet.2024.115062","DOIUrl":"10.1016/j.jviromet.2024.115062","url":null,"abstract":"<div><div>Severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) is the primary cause of the Coronavirus disease 2019 (COVID-19) pandemic, which affects millions of people worldwide with high levels of infectivity and mortality. However, the antibodies developed for COVID-19 research and diagnostics are still limited. Therefore, in this study, we developed polyclonal immunoglobulin (IgY) antibodies from chicken egg yolk targeting multi-epitope antigen of SARS-CoV-2. After immunizing hens with a SARS-CoV-2 multi-epitope peptide, IgY antibodies were isolated from chicken eggs and further characterized using SDS-PAGE and ELISA. The results showed that the IgY antibodies were successfully isolated from egg yolks. The sandwich ELISA results demonstrated that the isolated IgYs could bind to SARS-CoV-2 antigens, both the multi-epitope peptide and the trimeric Spike. Furthermore, the developed polyclonal antibodies could recognize SARS-CoV-2 in human nasopharyngeal swab samples, even at the lowest concentration (dilution at 1:10000). Thus, it can be concluded that the developed polyclonal IgYs were successfully produced and have the potential to be applied in the development of COVID-19 diagnostics.</div></div>","PeriodicalId":17663,"journal":{"name":"Journal of virological methods","volume":"331 ","pages":"Article 115062"},"PeriodicalIF":2.2,"publicationDate":"2024-11-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142647708","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}
Pub Date : 2024-11-16DOI: 10.1016/j.jviromet.2024.115073
Caroline L. Ashley , Malik Bloul , Sibel Alca , Lachlan Smith , Wang Jin , David Khoury , Claudio Counoupas , Miles Davenport , James A. Triccas , Megan Steain
A multiplexed, lentivirus-based pseudovirus neutralisation assay (pVNT) was developed for high-throughput measurement of neutralising antibodies (nAbs) against three distinct SARS-CoV-2 spike variants. Intra-assay variability was minimised by optimising the plate layout and determining an optimal percentage transduction for the pseudovirus inoculum. Comparison of EC50 titres between single and multiplexed pVNT assays showed no significant differences, indicating reliability of the multiplexed assay. Evaluation of convalescent human sera confirmed assay robustness, with consistent EC50 titres for variant pseudoviruses relative to the ancestral strain observed across single and multiplexed assays. This multiplexed pVNT provides a reliable tool for assessing nAb responses against SARS-CoV-2 variants and could be used to accelerate preclinical vaccine assessment in preparation for the next coronavirus pandemic.
{"title":"Optimisation of a multiplexed, high throughput assay to measure neutralising antibodies against SARS-CoV-2 variants","authors":"Caroline L. Ashley , Malik Bloul , Sibel Alca , Lachlan Smith , Wang Jin , David Khoury , Claudio Counoupas , Miles Davenport , James A. Triccas , Megan Steain","doi":"10.1016/j.jviromet.2024.115073","DOIUrl":"10.1016/j.jviromet.2024.115073","url":null,"abstract":"<div><div>A multiplexed, lentivirus-based pseudovirus neutralisation assay (pVNT) was developed for high-throughput measurement of neutralising antibodies (nAbs) against three distinct SARS-CoV-2 spike variants. Intra-assay variability was minimised by optimising the plate layout and determining an optimal percentage transduction for the pseudovirus inoculum. Comparison of EC<sub>50</sub> titres between single and multiplexed pVNT assays showed no significant differences, indicating reliability of the multiplexed assay. Evaluation of convalescent human sera confirmed assay robustness, with consistent EC<sub>50</sub> titres for variant pseudoviruses relative to the ancestral strain observed across single and multiplexed assays. This multiplexed pVNT provides a reliable tool for assessing nAb responses against SARS-CoV-2 variants and could be used to accelerate preclinical vaccine assessment in preparation for the next coronavirus pandemic.</div></div>","PeriodicalId":17663,"journal":{"name":"Journal of virological methods","volume":"332 ","pages":"Article 115073"},"PeriodicalIF":2.2,"publicationDate":"2024-11-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142668436","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}
Cytomegalovirus (CMV) can cause symptomatic CMV syndrome or tissue-invasive CMV disease in immunocompromised individuals, including solid-organ transplant and hematopoietic stem cell transplant recipients. In these populations, monitoring of CMV load is essential, assessing both risk of disease and response to antiviral therapy. High throughput commercial assays are currently available for CMV quantitation, but they are often evaluated independently, with few studies comparing these assays. This study evaluated CMV quantitative assays for use with the Roche cobas 6800, Abbott Alinity m and Hologic Panther platforms using stored patient plasma.
Methods
Analytical evaluation was performed using the 1st WHO international standard for human CMV for Nucleic Acid Amplification Techniques (cobas and Alinity m) or the Hologic CMV QC Calibrator 6 (Aptima). Parallel testing of 136 clinical plasma samples was performed across the three platforms.
Results
Linearity for each assay ranged from 98.6 % to 99.96 % and precision and limit of quantitation were as expected with little variation between platforms. 136 clinical plasma samples were evaluated with similar agreement observed between each assay. The greatest positive agreement was between the Aptima Quant and Alinity m assays (95.6 %, 95 % CI 89–98.6 %) and the lowest between the Aptima Quant and cobas assays (94.1 %, 87.4–97.5 %).
Conclusions
All assays were sensitive and accurate when quantifying CMV, and performance across all 3 assays was comparable for monitoring CMV viral loads in patient plasma.
{"title":"Evaluation and comparison of three high throughput assays (Alinity m CMV, Aptima CMV Quant and cobas CMV) for quantifying CMV DNA in plasma samples","authors":"Jodie D’Costa, Doris Chibo, Katherine Soloczynskyj, Mitchell Batty, Rizmina Sameer, Elaine Lee, Thomas Tran, Dimi Mavroulis, Megan Gooey, Eloise Williams, Kathy Jackson","doi":"10.1016/j.jviromet.2024.115068","DOIUrl":"10.1016/j.jviromet.2024.115068","url":null,"abstract":"<div><h3>Background</h3><div>Cytomegalovirus (CMV) can cause symptomatic CMV syndrome or tissue-invasive CMV disease in immunocompromised individuals, including solid-organ transplant and hematopoietic stem cell transplant recipients. In these populations, monitoring of CMV load is essential, assessing both risk of disease and response to antiviral therapy. High throughput commercial assays are currently available for CMV quantitation, but they are often evaluated independently, with few studies comparing these assays. This study evaluated CMV quantitative assays for use with the Roche cobas 6800, Abbott Alinity m and Hologic Panther platforms using stored patient plasma.</div></div><div><h3>Methods</h3><div>Analytical evaluation was performed using the 1st WHO international standard for human CMV for Nucleic Acid Amplification Techniques (cobas and Alinity m) or the Hologic CMV QC Calibrator 6 (Aptima). Parallel testing of 136 clinical plasma samples was performed across the three platforms.</div></div><div><h3>Results</h3><div>Linearity for each assay ranged from 98.6 % to 99.96 % and precision and limit of quantitation were as expected with little variation between platforms. 136 clinical plasma samples were evaluated with similar agreement observed between each assay. The greatest positive agreement was between the Aptima Quant and Alinity m assays (95.6 %, 95 % CI 89–98.6 %) and the lowest between the Aptima Quant and cobas assays (94.1 %, 87.4–97.5 %).</div></div><div><h3>Conclusions</h3><div>All assays were sensitive and accurate when quantifying CMV, and performance across all 3 assays was comparable for monitoring CMV viral loads in patient plasma.</div></div>","PeriodicalId":17663,"journal":{"name":"Journal of virological methods","volume":"332 ","pages":"Article 115068"},"PeriodicalIF":2.2,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142647720","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}
Pub Date : 2024-11-15DOI: 10.1016/j.jviromet.2024.115067
Júlia Gomes da Silva , Viviana Galimberti Arruk , Glaucia Raquel Luciano da Veiga , Luiz Vinícius de Alcantara Sousa , Beatriz da Costa Aguiar Alves , Fernando Luiz Affonso Fonseca , Inneke Marie van der Heijden Natário
A descriptive study was carried out with health professionals in Sao Paulo city. Were included individuals vaccinated with 2 doses of the inactivated vaccine. Demographic, clinical and vaccination information was obtained from professionals with or without comorbidities. Two serological assays were used to identify the presence and quantity of anti-Spike IgG in serum samples. 433 healthy healthcare professionals were included and 58.9 % completed the 4 clinical stages of serological assessment. Among adults and elderly people, 25.2 % had chronic diseases (hypertension 50.5 %, diabetes 10 % and obesity 6.5 %). Most individuals have 95 % protection in the first 3 months after the second dose, and 67.68 % protection after 6 months. Total antibodies ranged from 3 to 10 on the reactivity index, and the anti-RBD IgG levels were high. CoronaVac has a 94 % seroconversion rate after 2 doses and can prevent serious cases and outbreaks of the disease, if used on a large scale.
{"title":"Quantitative and qualitative analysis of seroconversion after one year of vaccination with inactivated SARS-CoV-2 vaccine (CoronaVac®) in healthcare workers: Cross-sectional analytical study","authors":"Júlia Gomes da Silva , Viviana Galimberti Arruk , Glaucia Raquel Luciano da Veiga , Luiz Vinícius de Alcantara Sousa , Beatriz da Costa Aguiar Alves , Fernando Luiz Affonso Fonseca , Inneke Marie van der Heijden Natário","doi":"10.1016/j.jviromet.2024.115067","DOIUrl":"10.1016/j.jviromet.2024.115067","url":null,"abstract":"<div><div>A descriptive study was carried out with health professionals in Sao Paulo city. Were included individuals vaccinated with 2 doses of the inactivated vaccine. Demographic, clinical and vaccination information was obtained from professionals with or without comorbidities. Two serological assays were used to identify the presence and quantity of anti-Spike IgG in serum samples. 433 healthy healthcare professionals were included and 58.9 % completed the 4 clinical stages of serological assessment. Among adults and elderly people, 25.2 % had chronic diseases (hypertension 50.5 %, diabetes 10 % and obesity 6.5 %). Most individuals have 95 % protection in the first 3 months after the second dose, and 67.68 % protection after 6 months. Total antibodies ranged from 3 to 10 on the reactivity index, and the anti-RBD IgG levels were high. CoronaVac has a 94 % seroconversion rate after 2 doses and can prevent serious cases and outbreaks of the disease, if used on a large scale.</div></div>","PeriodicalId":17663,"journal":{"name":"Journal of virological methods","volume":"332 ","pages":"Article 115067"},"PeriodicalIF":2.2,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142647543","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}
Pub Date : 2024-11-15DOI: 10.1016/j.jviromet.2024.115066
Pinky Dutta, Kristiina Mäkinen
Potato virus A belongs to the genus Potyvirus, a group of single-stranded positive sense RNA viruses infecting crops worldwide. To initiate infection in a host, its genome takes part in different activities, viz., translation, replication, encapsidation during the infection cycle. Extensive research has been carried out to scrutinize the stages of potyviral infection cycle and decipher the strategies it employs to cause disease. Nonetheless, the amount of viral RNA taking part in translation and virion formation, at a given time point, is missing. In this study, we quantified the percentage of viral RNA that exists as virions and those that associates with host polysome, relative to total viral RNA in infected plant tissue. We employed a revised version of immuno-capture reverse transcription PCR and polysome profiling to address our queries. We tested three different coating antibody concentrations and further optimized the immuno-capture reverse transcription PCR protocol to address its limitation of binding and retaining viral particles. Our results indicate that most of the viral RNA (69 %) exists as encapsidated genomes, while 3 % of total viral RNA associates with host polysomes. These findings are crucial for correct interpretation of quantitative translational studies in which correlation must be made between the number of polysome-associated transcripts and the amount of protein synthesized.
{"title":"Mapping and quantification of potato virus A RNA genomes within viral particles and polysomes in infected plant cells","authors":"Pinky Dutta, Kristiina Mäkinen","doi":"10.1016/j.jviromet.2024.115066","DOIUrl":"10.1016/j.jviromet.2024.115066","url":null,"abstract":"<div><div>Potato virus A belongs to the genus <em>Potyvirus,</em> a group of single-stranded positive sense RNA viruses infecting crops worldwide. To initiate infection in a host, its genome takes part in different activities, <em>viz.</em>, translation, replication, encapsidation during the infection cycle. Extensive research has been carried out to scrutinize the stages of potyviral infection cycle and decipher the strategies it employs to cause disease. Nonetheless, the amount of viral RNA taking part in translation and virion formation, at a given time point, is missing. In this study, we quantified the percentage of viral RNA that exists as virions and those that associates with host polysome, relative to total viral RNA in infected plant tissue. We employed a revised version of immuno-capture reverse transcription PCR and polysome profiling to address our queries. We tested three different coating antibody concentrations and further optimized the immuno-capture reverse transcription PCR protocol to address its limitation of binding and retaining viral particles. Our results indicate that most of the viral RNA (69 %) exists as encapsidated genomes, while 3 % of total viral RNA associates with host polysomes. These findings are crucial for correct interpretation of quantitative translational studies in which correlation must be made between the number of polysome-associated transcripts and the amount of protein synthesized.</div></div>","PeriodicalId":17663,"journal":{"name":"Journal of virological methods","volume":"332 ","pages":"Article 115066"},"PeriodicalIF":2.2,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142644280","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-14DOI: 10.1016/j.jviromet.2024.115063
Gordon Webster , Shrinivas Nivrutti Dighe , William B. Perry , Ewan H. Stenhouse , Davey L. Jones , Peter Kille , Andrew J. Weightman
Wastewater-based epidemiology (WBE) is a crucial tool for health and environmental monitoring, providing real-time data on public health indicators by analysis of sewage samples. Ensuring the integrity of these samples from collection to analysis is paramount. This study investigates the effects of different cold-storage conditions on the integrity of wastewater samples, focusing on both microbiological markers (such as extractable nucleic acids, SARS-CoV-2, and crAssphage) and physicochemical parameters (including ammonium, orthophosphate, pH, conductivity, and turbidity). Composite samples from the raw wastewater influent from five wastewater treatment works in South Wales, UK, were stored at 4°C, -20°C, and -80°C, and subjected to up to six freeze-thaw cycles over one year. The study found significant effects of storage temperature on the preservation of certain WBE markers, with the best yield most frequently seen in samples stored at -80°C. However, the majority of WBE markers showed no significant difference between storage at -80°C or at 4°C, demonstrating that it may not always be necessary to archive wastewater samples at ultra-low temperatures, thus reducing CO2 emissions and laboratory energy costs. These findings underscore the importance of optimized storage conditions to maintain sample integrity, while ensuring accurate and reliable WBE data for public health and environmental monitoring.
{"title":"Wastewater sample storage for physicochemical and microbiological analysis","authors":"Gordon Webster , Shrinivas Nivrutti Dighe , William B. Perry , Ewan H. Stenhouse , Davey L. Jones , Peter Kille , Andrew J. Weightman","doi":"10.1016/j.jviromet.2024.115063","DOIUrl":"10.1016/j.jviromet.2024.115063","url":null,"abstract":"<div><div>Wastewater-based epidemiology (WBE) is a crucial tool for health and environmental monitoring, providing real-time data on public health indicators by analysis of sewage samples. Ensuring the integrity of these samples from collection to analysis is paramount. This study investigates the effects of different cold-storage conditions on the integrity of wastewater samples, focusing on both microbiological markers (such as extractable nucleic acids, SARS-CoV-2, and crAssphage) and physicochemical parameters (including ammonium, orthophosphate, pH, conductivity, and turbidity). Composite samples from the raw wastewater influent from five wastewater treatment works in South Wales, UK, were stored at 4°C, -20°C, and -80°C, and subjected to up to six freeze-thaw cycles over one year. The study found significant effects of storage temperature on the preservation of certain WBE markers, with the best yield most frequently seen in samples stored at -80°C. However, the majority of WBE markers showed no significant difference between storage at -80°C or at 4°C, demonstrating that it may not always be necessary to archive wastewater samples at ultra-low temperatures, thus reducing CO<sub>2</sub> emissions and laboratory energy costs. These findings underscore the importance of optimized storage conditions to maintain sample integrity, while ensuring accurate and reliable WBE data for public health and environmental monitoring.</div></div>","PeriodicalId":17663,"journal":{"name":"Journal of virological methods","volume":"332 ","pages":"Article 115063"},"PeriodicalIF":2.2,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142639191","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-14DOI: 10.1016/j.jviromet.2024.115065
Shinsuke Higuchi , Tatsuki Satou , Yuki Uchida
Virus concentration using hollow fibers is widely used for vaccine production to maintain viral infectivity with low shear stress and to allow for easier scale-up of production. However, research laboratories often have limited available viral materials at the early stage of vaccine development, making it difficult to find an optimal hollow-fiber. In addition, few research articles have reported on optimizing hollow fiber pore size and membrane structure for virus concentration. In this study, the previously established handheld hollow fiber virus concentration method was modified to reduce the sample volume required and to enable simple and easy hollow fiber screening. The handheld hollow fiber screening method for virus concentration was confirmed to be effective using Zika as a model virus.
{"title":"Evaluation of the impact of hollow fiber pore size and membrane material on virus concentration using a handheld hollow fiber method","authors":"Shinsuke Higuchi , Tatsuki Satou , Yuki Uchida","doi":"10.1016/j.jviromet.2024.115065","DOIUrl":"10.1016/j.jviromet.2024.115065","url":null,"abstract":"<div><div>Virus concentration using hollow fibers is widely used for vaccine production to maintain viral infectivity with low shear stress and to allow for easier scale-up of production. However, research laboratories often have limited available viral materials at the early stage of vaccine development, making it difficult to find an optimal hollow-fiber. In addition, few research articles have reported on optimizing hollow fiber pore size and membrane structure for virus concentration. In this study, the previously established handheld hollow fiber virus concentration method was modified to reduce the sample volume required and to enable simple and easy hollow fiber screening. The handheld hollow fiber screening method for virus concentration was confirmed to be effective using Zika as a model virus.</div></div>","PeriodicalId":17663,"journal":{"name":"Journal of virological methods","volume":"332 ","pages":"Article 115065"},"PeriodicalIF":2.2,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142639174","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}