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Yamamoto H, Tamura T, Ichikawa T, Taguchi Y, Mori K, Oguri S, Suzuki R, Suzuki S, Teshima T, Fukuhara T. Generation of recombinant viruses directly from clinical specimens of COVID-19 patients. J Clin Microbiol 2024; 62:e0004224. [PMID: 38874339 PMCID: PMC11250110 DOI: 10.1128/jcm.00042-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 05/17/2024] [Indexed: 06/15/2024] Open
Abstract
Rapid characterization of the causative agent(s) during a disease outbreak can aid in the implementation of effective control measures. However, isolation of the agent(s) from crude clinical samples can be challenging and time-consuming, hindering the establishment of countermeasures. In the present study, we used saliva specimens collected for the diagnosis of SARS-CoV-2-a good example of a practical target-and attempted to characterize the virus within the specimens without virus isolation. Thirty-four saliva samples from coronavirus disease 2019 patients were used to extract RNA and synthesize DNA amplicons by PCR. New primer sets were designed to generate DNA amplicons of the full-length spike (S) gene for subsequent use in a circular polymerase extension reaction (CPER), a simple method for deriving recombinant viral genomes. According to the S sequence, four clinical specimens were classified as BA. 1, BA.2, BA.5, and XBB.1 and were used for the de novo generation of recombinant viruses carrying the entire S gene. Additionally, chimeric viruses carrying the gene encoding GFP were generated to evaluate viral propagation using a plate reader. We successfully used the RNA purified directly from clinical saliva samples to generate chimeric viruses carrying the entire S gene by our updated CPER method. The chimeric viruses exhibited robust replication in cell cultures with similar properties. Using the recombinant GFP viruses, we also successfully characterized the efficacy of the licensed antiviral AZD7442. Our proof-of-concept demonstrates the novel utility of CPER to allow rapid characterization of viruses from clinical specimens. IMPORTANCE Characterization of the causative agent(s) for infectious diseases helps in implementing effective control measurements, especially in outbreaks. However, the isolation of the agent(s) from clinical specimens is often challenging and time-consuming. In this study, saliva samples from coronavirus disease 2019 patients were directly subjected to purifying viral RNA, synthesizing DNA amplicons for sequencing, and generating recombinant viruses. Utilizing an updated circular polymerase extension reaction method, we successfully generated chimeric SARS-CoV-2 viruses with sufficient in vitro replication capacity and antigenicity. Thus, the recombinant viruses generated in this study were applicable for evaluating the antivirals. Collectively, our developed method facilitates rapid characterization of specimens circulating in hosts, aiding in the establishment of control measurements. Additionally, this approach offers an advanced strategy for controlling other (re-)emerging viral infectious diseases.
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Affiliation(s)
- Hirotaka Yamamoto
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
| | - Tomokazu Tamura
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (IVReD), Hokkaido University, Sapporo, Japan
- One Health Research Center, Hokkaido University, Sapporo, Japan
| | - Takaya Ichikawa
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Department of Hematology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Department of Hematology, Sapporo City General Hospital, Sapporo, Japan
| | - Yudai Taguchi
- Department of Clinical Laboratory Testing, Sapporo City General Hospital, Sapporo, Japan
| | - Kento Mori
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
| | - Satoshi Oguri
- Division of Laboratory and Transfusion Medicine, Hokkaido University Hospital, Sapporo, Japan
| | - Rigel Suzuki
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (IVReD), Hokkaido University, Sapporo, Japan
| | - Saori Suzuki
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (IVReD), Hokkaido University, Sapporo, Japan
| | - Takanori Teshima
- Department of Hematology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Division of Laboratory and Transfusion Medicine, Hokkaido University Hospital, Sapporo, Japan
| | - Takasuke Fukuhara
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (IVReD), Hokkaido University, Sapporo, Japan
- One Health Research Center, Hokkaido University, Sapporo, Japan
- Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
- AMED-CREST, Japan Agency for Medical Research and Development (AMED), Tokyo, Japan
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Kawashiro K, Suzuki R, Nogimori T, Tsujino S, Iwahara N, Hirose T, Okada K, Yamamoto T, Fukuhara T, Hotta K, Shinohara N. Neutralizing antibody responses and cellular responses against SARS-CoV-2 Omicron subvariants after mRNA SARS-CoV-2 vaccination in kidney transplant recipients. Sci Rep 2024; 14:12176. [PMID: 38806644 PMCID: PMC11133393 DOI: 10.1038/s41598-024-63147-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 05/24/2024] [Indexed: 05/30/2024] Open
Abstract
Although the mRNA SARS-CoV-2 vaccine has improved the mortality rate in the general population, its efficacy against rapidly mutating virus strains, especially in kidney transplant recipients, remains unclear. We examined the anti-SARS-CoV-2 spike protein IgG antibody and neutralizing antibody titers and cellular immunity against B.1.1, BA.1, and BA.5 antigens in 73 uninfected kidney recipients and 16 uninfected healthy controls who received three doses of an mRNA SARS-CoV-2 vaccine. The IgG antibody titers were significantly lower in recipients than in healthy controls. Similarly, neutralizing antibody titers against three viral variants were significantly lower in recipients. When the virus was mutated, the neutralizing antibody titers decreased significantly in both groups. In cellular immunity analysis, the number of spike-specific CD8 + non-naïve T cells against three variants significantly decreased in recipients. Conversely, the frequency of spike-specific Th2 CD4 + T-cells in recipients was higher than that in healthy controls. Nineteen recipients and six healthy controls also received a bivalent omicron-containing booster vaccine, leading to increase IgG and neutralizing antibody titers in both groups. After that, eleven recipients and five healthy controls received XBB.1.5 monovalent vaccines, increasing the neutralizing antibody titers against not only XBB.1.5, but also EG.5.1 and BA.2.86 antigens in kidney recipients. Although kidney recipients did not gain sufficient immunity against Omicron BA.5 with the third dose of vaccine, humoral response against mutant SARS-CoV-2 lineages significantly increased after bivalent Omicron-containing booster vaccine and the XBB.1.5 monovalent vaccine. Therefore, it is important for kidney recipients to continue to administer updated vaccines.
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Affiliation(s)
- Keita Kawashiro
- Department of Urology, Hokkaido University Hospital, Sapporo, Japan
| | - Rigel Suzuki
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development: HU-IVReD, Hokkaido University, Sapporo, Japan
| | - Takuto Nogimori
- Laboratory of Precision Immunology, Center for Intractable Diseases and ImmunoGenomics, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Japan
| | - Shuhei Tsujino
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
| | - Naoya Iwahara
- Department of Urology, Hokkaido University Hospital, Sapporo, Japan
| | - Takayuki Hirose
- Department of Urology, Hokkaido University Hospital, Sapporo, Japan
| | - Kazufumi Okada
- Data Science Center, Promotion Unit, Institute of Health Science Innovation for Medical Care, Hokkaido University Hospital, Sapporo, Japan
| | - Takuya Yamamoto
- Laboratory of Precision Immunology, Center for Intractable Diseases and ImmunoGenomics, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Japan.
- Laboratory of Aging and Immune Regulation, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Japan.
- Department of Virology and Immunology, Graduate School of Medicine, Osaka University, Suita, Japan.
| | - Takasuke Fukuhara
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan.
- Institute for Vaccine Research and Development: HU-IVReD, Hokkaido University, Sapporo, Japan.
- Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Suita, Japan.
- AMED-CREST, Japan Agency for Medical Research and Development (AMED), Tokyo, Japan.
| | - Kiyohiko Hotta
- Department of Urology, Hokkaido University Hospital, Sapporo, Japan.
| | - Nobuo Shinohara
- Department of Urology, Hokkaido University Hospital, Sapporo, Japan
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Suzuki R, Kamiyama A, Ito H, Kawashiro K, Tomiyama T, Tamura T, Suzuki S, Yoshizumi T, Hotta K, Fukuhara T. The development of a rapid, high-throughput neutralization assay using a SARS-CoV-2 reporter. J Virol Methods 2024; 326:114894. [PMID: 38360268 DOI: 10.1016/j.jviromet.2024.114894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 02/10/2024] [Accepted: 02/12/2024] [Indexed: 02/17/2024]
Abstract
Many methods have been developed to measure the neutralizing capacity of antibodies to SARS-CoV-2. However, these methods are low throughput and can be difficult to quickly modify in response to emerging variants. Therefore, an experimental system for rapid and easy measurement of the neutralizing capacity of antibodies against various variants is needed. In this study, we developed an experimental system that can efficiently measure the neutralizing capacity of sera by using a GFP-carrying recombinant SARS-CoV-2 with spike proteins of multiple variants (B.1.1, BA.5, or XBB.1.5). For all 3 recombinant chimeric genomes generated, neutralizing antibody titers determined by measuring GFP fluorescence intensity correlated significantly with those calculated from viral RNA levels measured by RT-qPCR in the supernatant of infected cells. Furthermore, neutralizing antibody titers determined by visually assessing GFP fluorescence using microscopy were also significantly correlated with those determined by RT-qPCR. By using this high-throughput method, it is now possible to quickly and easily determine the neutralizing capacity of antibodies against SARS-CoV-2 variants.
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Affiliation(s)
- Rigel Suzuki
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo 060-8638, Japan; Institute for Vaccine Research and Development: Hu-IVReD, Hokkaido University, Sapporo 060-8638, Japan
| | - Akifumi Kamiyama
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo 060-8638, Japan
| | - Hayato Ito
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo 060-8638, Japan
| | - Keita Kawashiro
- Department of Urology, Hokkaido University Hospital, Sapporo 060-8638, Japan
| | - Takahiro Tomiyama
- Department of Surgery and Sciences, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Tomokazu Tamura
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo 060-8638, Japan; Institute for Vaccine Research and Development: Hu-IVReD, Hokkaido University, Sapporo 060-8638, Japan
| | - Saori Suzuki
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo 060-8638, Japan; Institute for Vaccine Research and Development: Hu-IVReD, Hokkaido University, Sapporo 060-8638, Japan
| | - Tomoharu Yoshizumi
- Department of Surgery and Sciences, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Kiyohiko Hotta
- Department of Urology, Hokkaido University Hospital, Sapporo 060-8638, Japan
| | - Takasuke Fukuhara
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo 060-8638, Japan; Institute for Vaccine Research and Development: Hu-IVReD, Hokkaido University, Sapporo 060-8638, Japan; Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Suita 565-0871, Japan; AMED-CREST, Japan Agency for Medical Research and Development (AMED), Tokyo 100-004, Japan.
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Murali TM, Shunmuganathan B, Trueman ELL, Gupta R, Tan RSW, Sran HK, D’Costa MR, Wong ETY, Gu Y, Cui J, Wee Kun K, Lim AQH, Qian X, Purushotorman K, Chen J, MacAry PA, Vathsala A. Analyzing COVID-19 Vaccine Responses in Transplant Recipients. Immunohorizons 2023; 7:708-717. [PMID: 37889158 PMCID: PMC10615654 DOI: 10.4049/immunohorizons.2300071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 09/29/2023] [Indexed: 10/28/2023] Open
Abstract
COVID-19 vaccination has significantly impacted the global pandemic by reducing the severity of infection, lowering rates of hospitalization, and reducing morbidity/mortality in healthy individuals. However, the degree of vaccine-induced protection afforded to renal transplant recipients who receive forms of maintenance immunosuppression remains poorly defined. This is particularly important when we factor in the emergence of SARS-CoV-2 variants of concern (VOCs) that have defined mutations that reduce the effectiveness of Ab responses targeting the Spike Ags from the ancestral Wuhan-Hu-1 variants employed in the most widely used vaccine formats. In this study, we describe a qualitative, longitudinal analysis of neutralizing Ab responses against multiple SARS-CoV-2 VOCs in 129 renal transplant recipients who have received three doses of the Pfizer-BioNTech COVID-19 vaccine (BNT162b2). Our results reveal a qualitative and quantitative reduction in the vaccine-induced serological response in transplant recipients versus healthy controls where only 51.9% (67 of 129) made a measurable vaccine-induced IgG response and 41.1% (53 of 129) exhibited a significant neutralizing Ab titer (based on a pseudovirus neutralization test value >50%). Analysis on the VOCs revealed strongest binding toward the wild-type Wuhan-Hu-1 and Delta variants but none with both of the Omicron variants tested (BA1 and BA2). Moreover, older transplant recipients and those who are on mycophenolic acid as part of their maintenance therapy exhibited a profound reduction in all of the analyzed vaccine-induced immune correlates. These data have important implications for how we monitor and manage transplant patients in the future as COVID-19 becomes endemic in our populations.
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Affiliation(s)
- Tanusya Murali Murali
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- NUS-Cambridge Immune Phenotyping Centre, Life Sciences Institute, National University of Singapore, Singapore
| | - Bhuvaneshwari Shunmuganathan
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Antibody Engineering Programme, Life Sciences Institute, National University of Singapore, Singapore
| | - Emma Li-Lin Trueman
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Rashi Gupta
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Rebecca See Weng Tan
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Hersharan Kaur Sran
- National University Centre for Organ Transplantation, National University Hospital, Singapore
| | - Matthew Ross D’Costa
- National University Centre for Organ Transplantation, National University Hospital, Singapore
| | - Emmett Tsz-Yeung Wong
- National University Centre for Organ Transplantation, National University Hospital, Singapore
| | - Yue Gu
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Jianzhou Cui
- Immunology Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Koh Wee Kun
- National University Centre for Organ Transplantation, National University Hospital, Singapore
| | - Amy Qiao Hui Lim
- National University Centre for Organ Transplantation, National University Hospital, Singapore
| | - Xinlei Qian
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Antibody Engineering Programme, Life Sciences Institute, National University of Singapore, Singapore
| | - Kiren Purushotorman
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- NUS-Cambridge Immune Phenotyping Centre, Life Sciences Institute, National University of Singapore, Singapore
- Antibody Engineering Programme, Life Sciences Institute, National University of Singapore, Singapore
| | - Jinmiao Chen
- Immunology Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore
| | - Paul Anthony MacAry
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- NUS-Cambridge Immune Phenotyping Centre, Life Sciences Institute, National University of Singapore, Singapore
- Antibody Engineering Programme, Life Sciences Institute, National University of Singapore, Singapore
- Immunology Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Anantharaman Vathsala
- National University Centre for Organ Transplantation, National University Hospital, Singapore
- Department of Medicine, National University of Singapore, Singapore
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