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de Vries M, Ciabattoni GO, Rodriguez-Rodriguez BA, Crosse KM, Papandrea D, Samanovic MI, Dimartino D, Marier C, Mulligan MJ, Heguy A, Desvignes L, Duerr R, Dittmann M. Generation of quality-controlled SARS-CoV-2 variant stocks. Nat Protoc 2023; 18:3821-3855. [PMID: 37833423 DOI: 10.1038/s41596-023-00897-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 07/28/2023] [Indexed: 10/15/2023]
Abstract
One of the main challenges in the fight against coronavirus disease 2019 (COVID-19) stems from the ongoing evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) into multiple variants. To address this hurdle, research groups around the world have independently developed protocols to isolate these variants from clinical samples. These isolates are then used in translational and basic research-for example, in vaccine development, drug screening or characterizing SARS-CoV-2 biology and pathogenesis. However, over the course of the COVID-19 pandemic, we have learned that the introduction of artefacts during both in vitro isolation and subsequent propagation to virus stocks can lessen the validity and reproducibility of data. We propose a rigorous pipeline for the generation of high-quality SARS-CoV-2 variant clonal isolates that minimizes the acquisition of mutations and introduces stringent controls to detect them. Overall, the process includes eight stages: (i) cell maintenance, (ii) isolation of SARS-CoV-2 from clinical specimens, (iii) determination of infectious virus titers by plaque assay, (iv) clonal isolation by plaque purification, (v) whole-virus-genome deep-sequencing, (vi and vii) amplification of selected virus clones to master and working stocks and (viii) sucrose purification. This comprehensive protocol will enable researchers to generate reliable SARS-CoV-2 variant inoculates for in vitro and in vivo experimentation and will facilitate comparisons and collaborative work. Quality-controlled working stocks for most applications can be generated from acquired biorepository virus within 1 month. An additional 5-8 d are required when virus is isolated from clinical swab material, and another 6-7 d is needed for sucrose-purifying the stocks.
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Affiliation(s)
- Maren de Vries
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY, USA
| | - Grace O Ciabattoni
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY, USA
| | | | - Keaton M Crosse
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY, USA
| | - Dominick Papandrea
- High Containment Laboratories-Office of Science and Research, NYU Langone Health, New York, NY, USA
| | - Marie I Samanovic
- Department of Medicine, NYU Grossman School of Medicine, New York, NY, USA
- NYU Langone Vaccine Center, NYU Grossman School of Medicine, New York, NY, USA
| | - Dacia Dimartino
- Genome Technology Center, Office of Science and Research, NYU Langone Health, New York, NY, USA
| | - Christian Marier
- Genome Technology Center, Office of Science and Research, NYU Langone Health, New York, NY, USA
| | - Mark J Mulligan
- Department of Medicine, NYU Grossman School of Medicine, New York, NY, USA
- NYU Langone Vaccine Center, NYU Grossman School of Medicine, New York, NY, USA
| | - Adriana Heguy
- Genome Technology Center, Office of Science and Research, NYU Langone Health, New York, NY, USA
- Department of Pathology, NYU Grossman School of Medicine, New York, NY, USA
| | - Ludovic Desvignes
- High Containment Laboratories-Office of Science and Research, NYU Langone Health, New York, NY, USA
- Department of Medicine, NYU Grossman School of Medicine, New York, NY, USA
| | - Ralf Duerr
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY, USA
- Department of Medicine, NYU Grossman School of Medicine, New York, NY, USA
- NYU Langone Vaccine Center, NYU Grossman School of Medicine, New York, NY, USA
| | - Meike Dittmann
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY, USA.
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Sung A, Bailey AL, Stewart HB, McDonald D, Wallace MA, Peacock K, Miller C, Reske KA, O’Neil CA, Fraser VJ, Diamond MS, Burnham CAD, Babcock HM, Kwon JH. Isolation of SARS-CoV-2 in Viral Cell Culture in Immunocompromised Patients With Persistently Positive RT-PCR Results. Front Cell Infect Microbiol 2022; 12:804175. [PMID: 35186791 PMCID: PMC8847756 DOI: 10.3389/fcimb.2022.804175] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 01/04/2022] [Indexed: 12/16/2022] Open
Abstract
Immunocompromised adults can have prolonged acute respiratory syndrome coronavirus 2 (SARS-CoV-2) positive RT-PCR results, long after the initial diagnosis of coronavirus disease 2019 (COVID-19). This study aimed to determine if SARS-CoV-2 virus can be recovered in viral cell culture from immunocompromised adults with persistently positive SARS-CoV-2 RT-PCR tests. We obtained 20 remnant SARS-CoV-2 PCR positive nasopharyngeal swabs from 20 immunocompromised adults with a positive RT-PCR test ≥14 days after the initial positive test. The patients' 2nd test samples underwent SARS-CoV-2 antigen testing, and culture with Vero-hACE2-TMPRSS2 cells. Viral RNA and cultivable virus were recovered from the cultured cells after qRT-PCR and plaque assays. Of 20 patients, 10 (50%) had a solid organ transplant and 5 (25%) had a hematologic malignancy. For most patients, RT-PCR Ct values increased over time. There were 2 patients with positive viral cell cultures; one patient had chronic lymphocytic leukemia treated with venetoclax and obinutuzumab who had a low viral titer of 27 PFU/mL. The second patient had marginal zone lymphoma treated with bendamustine and rituximab who had a high viral titer of 2 x 106 PFU/mL. Most samples collected ≥7 days after an initial positive SARS-CoV-2 RT-PCR had negative viral cell cultures. The 2 patients with positive viral cell cultures had hematologic malignancies treated with chemotherapy and B cell depleting therapy. One patient had a high concentration titer of cultivable virus. Further data are needed to determine risk factors for persistent viral shedding and methods to prevent SARS-CoV-2 transmission from immunocompromised hosts.
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Affiliation(s)
- Abby Sung
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine in St. Louis, St. Louis, MO, United States
| | - Adam L. Bailey
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine in St. Louis, St. Louis, MO, United States
| | - Henry B. Stewart
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine in St. Louis, St. Louis, MO, United States
| | - David McDonald
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine in St. Louis, St. Louis, MO, United States
| | - Meghan A. Wallace
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, United States
| | - Kate Peacock
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine in St. Louis, St. Louis, MO, United States
| | - Candace Miller
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine in St. Louis, St. Louis, MO, United States
| | - Kimberly A. Reske
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine in St. Louis, St. Louis, MO, United States
| | - Caroline A. O’Neil
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine in St. Louis, St. Louis, MO, United States
| | - Victoria J. Fraser
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine in St. Louis, St. Louis, MO, United States
| | - Michael S. Diamond
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine in St. Louis, St. Louis, MO, United States
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, United States
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, MO, United States
| | - Carey-Ann D. Burnham
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, United States
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, MO, United States
- Departments of Medicine and Pediatrics, Washington University School of Medicine in St. Louis, St. Louis, MO, United States
| | - Hilary M. Babcock
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine in St. Louis, St. Louis, MO, United States
| | - Jennie H. Kwon
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine in St. Louis, St. Louis, MO, United States
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