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Strizki JM, Grobler JA, Murgolo N, Fridman A, Johnson MG, Du J, Carmelitano P, Brown ML, Paschke A, De Anda C. Virologic Outcomes with Molnupiravir in Non-hospitalized Adult Patients with COVID-19 from the Randomized, Placebo-Controlled MOVe-OUT Trial. Infect Dis Ther 2023; 12:2725-2743. [PMID: 37995070 PMCID: PMC10746688 DOI: 10.1007/s40121-023-00891-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 10/31/2023] [Indexed: 11/24/2023] Open
Abstract
INTRODUCTION The randomized, placebo-controlled, double-blind MOVe-OUT trial demonstrated molnupiravir (800 mg every 12 h for 5 days) as safe and effective for outpatient treatment of mild-to-moderate COVID-19, significantly reducing the risk of hospitalization/death in high-risk adults. At the time of that report, virologic assessments from the trial were partially incomplete as a result of their time-intensive nature. Here we present final results from all prespecified virology endpoints in MOVe-OUT based on the full trial dataset. METHODS Nasopharyngeal swabs were collected at baseline (day 1, prior to first dose) and days 3, 5 (end-of-treatment visit), 10, 15, and 29. From these samples, change from baseline in SARS-CoV-2 RNA titers (determined by quantitative PCR), detection of infectious SARS-CoV-2 (by plaque assay), and SARS-CoV-2 viral error induction (determined by whole genome next-generation sequencing) were assessed as exploratory endpoints. RESULTS Molnupiravir was associated with greater mean reductions from baseline in SARS-CoV-2 RNA than placebo (including 50% relative reduction at end-of-treatment) through day 10. Among participants with infectious virus detected at baseline (n = 96 molnupiravir, n = 97 placebo) and evaluable post-baseline samples, no molnupiravir-treated participant had infectious SARS-CoV-2 by day 3, whereas infectious virus was recovered from 21% of placebo-arm participants on day 3 and 2% at end-of-treatment. Consistent with molnupiravir's mechanism of action, sequence analysis demonstrated that molnupiravir was associated with an increased number of low-frequency transition errors randomly distributed across the SARS-CoV-2 RNA genome compared with placebo (median 143.5 molnupiravir, 15 placebo), while transversion errors were infrequent overall (median 2 in both arms). Outcomes were consistent regardless of baseline SARS-CoV-2 clade, presence of SARS-CoV-2-specific immune response, or viral load. CONCLUSIONS A 5-day course of orally administered molnupiravir demonstrated a consistently greater virologic effect than placebo, including rapidly eliminating infectious SARS-CoV-2, in high-risk outpatients with mild-to-moderate COVID-19. TRIAL REGISTRATION ClinicalTrials.gov, NCT04575597.
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Affiliation(s)
| | - Jay A Grobler
- Merck & Co., Inc., 90 E Scott Ave, Rahway, NJ, 07065, USA
| | | | - Arthur Fridman
- Merck & Co., Inc., 90 E Scott Ave, Rahway, NJ, 07065, USA
| | | | - Jiejun Du
- Merck & Co., Inc., 90 E Scott Ave, Rahway, NJ, 07065, USA
| | | | | | - Amanda Paschke
- Merck & Co., Inc., 90 E Scott Ave, Rahway, NJ, 07065, USA
| | - Carisa De Anda
- Merck & Co., Inc., 90 E Scott Ave, Rahway, NJ, 07065, USA
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2
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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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Farfour E, Yung T, Baudoin R, Vasse M. Evaluation of Four Fully Integrated Molecular Assays for the Detection of Respiratory Viruses during the Co-Circulation of SARS-CoV-2, Influenza and RSV. J Clin Med 2022; 11:jcm11143942. [PMID: 35887705 PMCID: PMC9317686 DOI: 10.3390/jcm11143942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 06/27/2022] [Accepted: 07/05/2022] [Indexed: 11/30/2022] Open
Abstract
Background: The clinical presentation of viral respiratory infections is unspecific. We assessed the performances of two new RT-PCR, the Idylla™ SARS-CoV-2 and the Idylla™ SARS-CoV2/Flu/RSV, and two isothermal amplification assays, the ID NOW COVID and the ID NOW influenza A & B 2. Methods: The study was conducted in two parts: (i) the Idylla™ assays were assessed using a collection of nasopharyngeal swabs which were positive for various respiratory viruses. (ii) The performances of the four assays were assessed prospectively: all of the symptomatic patients admitted to the emergency department from 10 to 21 December were enrolled. Results: (i) All of the SARS-CoV-2 false negatives with the Idylla™ assays had a Ct value greater than 30 with the reference RT-PCR. No cross-reactivity was identified. (ii) Overall, 218 patients were enrolled. The respective prevalences of SARS-CoV-2, influenza A, and RSV were 19.8%, 4.8%, and 3.2%. All of the assays were 100% specific. The sensitivity of SARS-CoV-2 detection was 97.7%, 82.5%, and 86.3% for the Idylla™ SARS-CoV2, the Idylla™ SARS-CoV2/Flu/RSV, and the ID NOW COVID-19, respectively. For influenza A, it was 90.0% for the Idylla™ SARS-CoV2/Flu/RSV and 80.0% for the ID NOW Influenza. Discussion. All of the assays are suitable for testing patients with respiratory symptoms. False negatives should be considered, and the test should be repeated regarding the context.
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Affiliation(s)
- Eric Farfour
- Service de Biologie Clinique, Hôpital Foch, 92150 Suresnes, France; (T.Y.); (M.V.)
- Correspondence: or ; Tel.: +33-1-46-25-75-51
| | - Thomas Yung
- Service de Biologie Clinique, Hôpital Foch, 92150 Suresnes, France; (T.Y.); (M.V.)
| | - Robin Baudoin
- Service d’Otho-Rhino-Laryngologie, Hôpital Foch, 92150 Suresnes, France;
| | - Marc Vasse
- Service de Biologie Clinique, Hôpital Foch, 92150 Suresnes, France; (T.Y.); (M.V.)
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Sonnleitner ST, Prelog M, Sonnleitner S, Hinterbichler E, Halbfurter H, Kopecky DBC, Almanzar G, Koblmüller S, Sturmbauer C, Feist L, Horres R, Posch W, Walder G. Cumulative SARS-CoV-2 mutations and corresponding changes in immunity in an immunocompromised patient indicate viral evolution within the host. Nat Commun 2022; 13:2560. [PMID: 35538074 PMCID: PMC9090742 DOI: 10.1038/s41467-022-30163-4] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 04/19/2022] [Indexed: 01/07/2023] Open
Abstract
Different scenarios explaining the emergence of novel variants of concern (VOC) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been reported, including their evolution in scarcely monitored populations, in animals as alternative hosts, or in immunocompromised individuals. Here we report SARS-CoV-2 immune escape mutations over a period of seven months in an immunocompromised patient with prolonged viral shedding. Signs of infection, viral shedding and mutation events are periodically analyzed using RT-PCR and next-generation sequencing based on naso-pharyngeal swabs, with the results complemented by immunological diagnostics to determine humoral and T cell immune responses. Throughout the infection course, 17 non-synonymous intra-host mutations are noted, with 15 (88.2%) having been previously described as prominent immune escape mutations (S:E484K, S:D950N, S:P681H, S:N501Y, S:del(9), N:S235F and S:H655Y) in VOCs. The high frequency of these non-synonymous mutations is consistent with multiple events of convergent evolution. Thus, our results suggest that specific mutations in the SARS-CoV-2 genome may represent positions with a fitness advantage, and may serve as targets in future vaccine and therapeutics development for COVID-19. Variants of concerns arise from SARS-CoV-2 mutations poise as severe public health threats. Here the authors chronicle SARS-CoV-2 mutations onset and immune parameters in an immunocompromised patient with continuous virus-shedding, thereby hinting potential intra-host viral evolution and escape facilitated by ineffective T cell immunity.
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Affiliation(s)
- Sissy Therese Sonnleitner
- Infektiologie Tirol, Department of Virology, 9931, Unterwalden 30, Außervillgraten, Austria. .,Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, 6020, Innsbruck, Austria.
| | - Martina Prelog
- Pediatric Rheumatology/Special Immunology, Department of Pediatrics, University Hospital Wuerzburg, Josef-Schneider-Str. 2, Wuerzburg, Germany
| | - Stefanie Sonnleitner
- Infektiologie Tirol, Department of Virology, 9931, Unterwalden 30, Außervillgraten, Austria
| | - Eva Hinterbichler
- Infektiologie Tirol, Department of Virology, 9931, Unterwalden 30, Außervillgraten, Austria
| | - Hannah Halbfurter
- Infektiologie Tirol, Department of Virology, 9931, Unterwalden 30, Außervillgraten, Austria
| | - Dominik B C Kopecky
- Infektiologie Tirol, Department of Virology, 9931, Unterwalden 30, Außervillgraten, Austria
| | - Giovanni Almanzar
- Pediatric Rheumatology/Special Immunology, Department of Pediatrics, University Hospital Wuerzburg, Josef-Schneider-Str. 2, Wuerzburg, Germany
| | - Stephan Koblmüller
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010, Graz, Austria
| | - Christian Sturmbauer
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010, Graz, Austria
| | - Leonard Feist
- GenXPro GmbH, Altenhoeferallee 3, 60438, Frankfurt am Main, Germany
| | - Ralf Horres
- GenXPro GmbH, Altenhoeferallee 3, 60438, Frankfurt am Main, Germany
| | - Wilfried Posch
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, 6020, Innsbruck, Austria
| | - Gernot Walder
- Infektiologie Tirol, Department of Virology, 9931, Unterwalden 30, Außervillgraten, Austria
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5
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Baselga M, Güemes A, Alba JJ, Schuhmacher AJ. SARS-CoV-2 Droplet and Airborne Transmission Heterogeneity. J Clin Med 2022; 11:2607. [PMID: 35566733 PMCID: PMC9099777 DOI: 10.3390/jcm11092607] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 04/21/2022] [Accepted: 05/03/2022] [Indexed: 12/13/2022] Open
Abstract
The spread dynamics of the SARS-CoV-2 virus have not yet been fully understood after two years of the pandemic. The virus's global spread represented a unique scenario for advancing infectious disease research. Consequently, mechanistic epidemiological theories were quickly dismissed, and more attention was paid to other approaches that considered heterogeneity in the spread. One of the most critical advances in aerial pathogens transmission was the global acceptance of the airborne model, where the airway is presented as the epicenter of the spread of the disease. Although the aerodynamics and persistence of the SARS-CoV-2 virus in the air have been extensively studied, the actual probability of contagion is still unknown. In this work, the individual heterogeneity in the transmission of 22 patients infected with COVID-19 was analyzed by close contact (cough samples) and air (environmental samples). Viral RNA was detected in 2/19 cough samples from patient subgroups, with a mean Ct (Cycle Threshold in Quantitative Polymerase Chain Reaction analysis) of 25.7 ± 7.0. Nevertheless, viral RNA was only detected in air samples from 1/8 patients, with an average Ct of 25.0 ± 4.0. Viral load in cough samples ranged from 7.3 × 105 to 8.7 × 108 copies/mL among patients, while concentrations between 1.1-4.8 copies/m3 were found in air, consistent with other reports in the literature. In patients undergoing follow-up, no viral load was found (neither in coughs nor in the air) after the third day of symptoms, which could help define quarantine periods in infected individuals. In addition, it was found that the patient's Ct should not be considered an indicator of infectiousness, since it could not be correlated with the viral load disseminated. The results of this work are in line with proposed hypotheses of superspreaders, which can attribute part of the heterogeneity of the spread to the oversized emission of a small percentage of infected people.
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Affiliation(s)
- Marta Baselga
- Institute for Health Research Aragon (IIS Aragón), 50009 Zaragoza, Spain; (M.B.); (A.G.); (J.J.A.)
| | - Antonio Güemes
- Institute for Health Research Aragon (IIS Aragón), 50009 Zaragoza, Spain; (M.B.); (A.G.); (J.J.A.)
- Department of Surgery, University of Zaragoza, 50009 Zaragoza, Spain
| | - Juan J. Alba
- Institute for Health Research Aragon (IIS Aragón), 50009 Zaragoza, Spain; (M.B.); (A.G.); (J.J.A.)
- Department of Mechanical Engineering, University of Zaragoza, 50018 Zaragoza, Spain
| | - Alberto J. Schuhmacher
- Institute for Health Research Aragon (IIS Aragón), 50009 Zaragoza, Spain; (M.B.); (A.G.); (J.J.A.)
- Fundación Agencia Aragonesa para la Investigación y el Desarrollo (ARAID), 50018 Zaragoza, Spain
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6
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Fomenko A, Weibel S, Moezi H, Menger K, Schmucker C, Metzendorf MI, Motschall E, Falcone V, Huzly D, Panning M, Rücker G, Hengel H. Assessing severe acute respiratory syndrome coronavirus 2 infectivity by reverse-transcription polymerase chain reaction: A systematic review and meta-analysis. Rev Med Virol 2022; 32:e2342. [PMID: 35366033 PMCID: PMC9111068 DOI: 10.1002/rmv.2342] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 02/21/2022] [Accepted: 02/23/2022] [Indexed: 12/19/2022]
Abstract
The cornerstone of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) detection is reverse‐transcription polymerase chain reaction (RT‐PCR) of viral RNA. As a surrogate assay SARS‐CoV‐2 RNA detection does not necessarily imply infectivity. Only virus isolation in permissive cell culture systems can indicate infectivity. Here, we review the evidence on RT‐PCR performance in detecting infectious SARS‐CoV‐2. We searched for any studies that used RT‐PCR and cell culture to determine infectious SARS‐CoV‐2 in respiratory samples. We assessed (i) diagnostic accuracy of RT‐PCR compared to cell culture as reference test, (ii) performed meta‐analysis of positive predictive values (PPV) and (iii) determined the virus isolation probabilities depending on cycle threshold (Ct) or log10 genome copies/ml using logistic regression. We included 55 studies. There is substantial statistical and clinical heterogeneity. Seven studies were included for diagnostic accuracy. Sensitivity ranged from 90% to 99% and specificity from 29% to 92%. In meta‐analysis, the PPVs varied across subgroups with different sampling times after symptom onset, with 1% (95% confidence interval [CI], 0%–7%) in sampling beyond 10 days and 27% (CI, 19%–36%) to 46% (CI, 33%–60%) in subgroups that also included earlier samples. Estimates of virus isolation probability varied between 6% (CI, 0%–100%) and 50% (CI, 0%–100%) at a Ct value of 30 and between 0% (CI, 0%–22%) and 63% (CI, 0%–100%) at 5 log10 genome copies/ml. Evidence on RT‐PCR performance in detecting infectious SARS‐CoV‐2 in respiratory samples was limited. Major limitations were heterogeneity and poor reporting. RT‐PCR and cell culture protocols need further standardisation.
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Affiliation(s)
- Alexey Fomenko
- Institute of Virology, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Stephanie Weibel
- Department of Anaesthesiology, Intensive Care, Emergency and Pain Medicine, University Hospital Wuerzburg, Wuerzburg, Germany
| | - Helia Moezi
- Department of Anaesthesiology, Intensive Care, Emergency and Pain Medicine, University Hospital Wuerzburg, Wuerzburg, Germany
| | - Kristina Menger
- Department of Anaesthesiology, Intensive Care, Emergency and Pain Medicine, University Hospital Wuerzburg, Wuerzburg, Germany
| | - Christine Schmucker
- Institute for Evidence in Medicine, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Maria-Inti Metzendorf
- Cochrane Metabolic and Endocrine Disorders Group, Institute of General Practice, Medical Faculty, Heinrich-Heine-University Duesseldorf, Duesseldorf, Germany
| | - Edith Motschall
- Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Valeria Falcone
- Institute of Virology, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Daniela Huzly
- Institute of Virology, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Marcus Panning
- Institute of Virology, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Gerta Rücker
- Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Hartmut Hengel
- Institute of Virology, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
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7
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Sonnleitner ST, Sonnleitner S, Hinterbichler E, Halbfurter H, Kopecky DB, Koblmüller S, Sturmbauer C, Posch W, Walder G. The mutational dynamics of the SARS-CoV-2 virus in serial passages in vitro. Virol Sin 2022; 37:198-207. [PMID: 35277373 PMCID: PMC8800542 DOI: 10.1016/j.virs.2022.01.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 01/21/2022] [Indexed: 11/04/2022] Open
Abstract
Since its outbreak in 2019, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) keeps surprising the medical community by evolving diverse immune escape mutations in a rapid and effective manner. To gain deeper insight into mutation frequency and dynamics, we isolated ten ancestral strains of SARS-CoV-2 and performed consecutive serial incubation in ten replications in a suitable and common cell line and subsequently analysed them using RT-qPCR and whole genome sequencing. Along those lines we hoped to gain fundamental insights into the evolutionary capacity of SARS-CoV-2 in vitro. Our results identified a series of adaptive genetic changes, ranging from unique convergent substitutional mutations and hitherto undescribed insertions. The region coding for spike proved to be a mutational hotspot, evolving a number of mutational changes including the already known substitutions at positions S:484 and S:501. We discussed the evolution of all specific adaptations as well as possible reasons for the seemingly inhomogeneous potential of SARS-CoV-2 in the adaptation to cell culture. The combination of serial passage in vitro with whole genome sequencing uncovers the immense mutational potential of some SARS-CoV-2 strains. The observed genetic changes of SARS-CoV-2 in vitro could not be explained solely by selectively neutral mutations but possibly resulted from the action of directional selection accumulating favourable genetic changes in the evolving variants, along the path of increasing potency of the strain. Competition among a high number of quasi-species in the SARS-CoV-2 in vitro population gene pool may reinforce directional selection and boost the speed of evolutionary change. Ten genetically similar strains evolved very differently in serial passage in vitro. Observed mutations included substitutions at important spike positions. The three strains with the highest replication rates developed two convergent mutations. Via directional selection favourable genetic changes are accumulated. Competition among many quasi-species boosts the speed of evolutionary change.
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8
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Porter WT, Kelley EJ, Bowers JR, Engelthaler DM. Normalization of SARS-CoV-2 viral load via RT-qPCR provides higher-resolution data for comparison across time and between patients. Virus Res 2021; 306:198604. [PMID: 34662682 PMCID: PMC8519666 DOI: 10.1016/j.virusres.2021.198604] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 10/08/2021] [Indexed: 12/15/2022]
Abstract
The 2020 pandemic has transformed the world and elicited thousands of studies to better understand the SARS-CoV-2 virus. Viral load has been a common measure to monitor treatment therapies and associate viral dynamics with patient outcomes; however, methods associated with viral load have varied across studies. These variations have the potential to sacrifice the accuracy of findings as they often do not account for inter-assay variation or variation across samples. In a retrospective study of nasopharyngeal samples, we found a significant amount of variation within the DNA and RNA targets; for example, across time within a single patient, there was an average of a 32-fold change. Further, we explore the impacts of host normalization on 94 clinical samples using the TGen Quantitative SARS-CoV-2 assay, finding that without host normalization samples with the same viral concentration can have up to 100-fold variation in the viral load.
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Affiliation(s)
- W Tanner Porter
- Translational Genomics Research Institute, 3051 W. Shamrell Blvd. Ste. 106, Flagstaff, AZ 86005, USA.
| | - Erin J Kelley
- Translational Genomics Research Institute, 3051 W. Shamrell Blvd. Ste. 106, Flagstaff, AZ 86005, USA.
| | - Jolene R Bowers
- Translational Genomics Research Institute, 3051 W. Shamrell Blvd. Ste. 106, Flagstaff, AZ 86005, USA.
| | - David M Engelthaler
- Translational Genomics Research Institute, 3051 W. Shamrell Blvd. Ste. 106, Flagstaff, AZ 86005, USA.
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9
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Young RM, Solis CJ, Barriga-Fehrman A, Abogabir C, Thadani AR, Labarca M, Bustamante E, Tapia CV, Sarda AG, Sepulveda F, Pozas N, Cerpa LC, Lavanderos MA, Varela NM, Santibañez A, Sandino AM, Reyes-Lopez F, Dixon G, Quiñones LA. Smartphone screen testing, a novel pre-diagnostic method to identify SARS-CoV-2 infectious individuals. eLife 2021; 10:e70333. [PMID: 34155970 PMCID: PMC8275127 DOI: 10.7554/elife.70333] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 06/21/2021] [Indexed: 11/25/2022] Open
Abstract
The COVID-19 pandemic will likely take years to control globally, and constant epidemic surveillance will be required to limit the spread of SARS-CoV-2, especially considering the emergence of new variants that could hamper the effect of vaccination efforts. We developed a simple and robust - Phone Screen Testing (PoST) - method to detect SARS-CoV-2-positive individuals by RT-PCR testing of smartphone screen swab samples. We show that 81.3-100% of individuals with high-viral-load SARS-CoV-2 nasopharyngeal-positive samples also test positive for PoST, suggesting this method is effective in identifying COVID-19 contagious individuals. Furthermore, we successfully identified polymorphisms associated with SARS-CoV-2 Alpha, Beta, and Gamma variants, in SARS-CoV-2-positive PoST samples. Overall, we report that PoST is a new non-invasive, cost-effective, and easy-to-implement smartphone-based smart alternative for SARS-CoV-2 testing, which could help to contain COVID-19 outbreaks and identification of variants of concern in the years to come.
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Affiliation(s)
- Rodrigo M Young
- Diagnosis BiotechSantiagoChile
- Institute of Ophthalmology, University College LondonLondonUnited Kingdom
| | | | | | | | | | | | - Eva Bustamante
- Grupo Oncológico Cooperativo Chileno de InvestigaciónSantiagoChile
| | | | | | | | - Nadia Pozas
- Laboratorio de Especialidad, Clínica DávilaSantiagoChile
| | - Leslie C Cerpa
- Laboratory of Chemical Carcinogenesis and Pharmacogenetics (Chilean Health Council Diagnostic Covid19 Laboratory), Department of Basic and Clinical Oncology, Faculty of Medicine, University of ChileSantiagoChile
| | - María A Lavanderos
- Laboratory of Chemical Carcinogenesis and Pharmacogenetics (Chilean Health Council Diagnostic Covid19 Laboratory), Department of Basic and Clinical Oncology, Faculty of Medicine, University of ChileSantiagoChile
| | - Nelson M Varela
- Laboratory of Chemical Carcinogenesis and Pharmacogenetics (Chilean Health Council Diagnostic Covid19 Laboratory), Department of Basic and Clinical Oncology, Faculty of Medicine, University of ChileSantiagoChile
| | - Alvaro Santibañez
- Centro de Biotecnología Acuícola, Facultad de Química y BiologíaSantiagoChile
- Programa Disciplinario de Inmunología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de ChileSantiagoChile
| | - Ana M Sandino
- Centro de Biotecnología Acuícola, Facultad de Química y BiologíaSantiagoChile
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de ChileSantiagoChile
| | - Felipe Reyes-Lopez
- Centro de Biotecnología Acuícola, Facultad de Química y BiologíaSantiagoChile
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de ChileSantiagoChile
- Department of Cell Biology, Physiology and Immunology, Universitat Autònoma de BarcelonaBellaterraSpain
- Facultad de Medicina Veterinaria y Agronomía, Universidad de Las AméricasProvidenciaChile
| | - Garth Dixon
- Department of Cell Biology, Physiology and Immunology, Universitat Autònoma de BarcelonaBellaterraSpain
- Department of Microbiology, Virology and Infection Control, Hospital National Health Service Foundation TrustLondonUnited Kingdom
- National Institute for Health Research Biomedical Research Centre at Great Ormond Hospital for Children National Health Service Foundation Trust and University CollegeLondonUnited Kingdom
| | - Luis A Quiñones
- Laboratory of Chemical Carcinogenesis and Pharmacogenetics (Chilean Health Council Diagnostic Covid19 Laboratory), Department of Basic and Clinical Oncology, Faculty of Medicine, University of ChileSantiagoChile
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10
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Brukner I, Resendes A, Eintracht S, Papadakis AI, Oughton M. Sample Adequacy Control (SAC) Lowers False Negatives and Increases the Quality of Screening: Introduction of "Non-Competitive" SAC for qPCR Assays. Diagnostics (Basel) 2021; 11:diagnostics11071133. [PMID: 34206413 PMCID: PMC8305439 DOI: 10.3390/diagnostics11071133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 06/15/2021] [Accepted: 06/20/2021] [Indexed: 01/15/2023] Open
Abstract
Sample Adequacy Control (SAC) has critical analytical, clinical and epidemiological value that increases confidence in a negative test result. The SAC is an integral qPCR assay control, which ensures that all pre-analytical and analytical steps are adequate for accurate testing and reporting. As such, a negative SAC with a negative result on pathogen screen specifies that the result should be reported as inconclusive instead of negative. Despite this, many regulatory approved tests do not incorporate SAC into their assay design. Herein, we emphasize the universal value of SAC and offer for the first time, a simple technical strategy to introduce non-competitive SAC which does not interfere with the limit of detection for the screened pathogen. Integration of SAC can provide key benefits towards identifying, isolating, quarantining and contact tracing infected individuals and in turn can improve worldwide efforts in infection control.
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Affiliation(s)
- Ivan Brukner
- Lady Davis Institute for Medical Research, Montréal, QC H3T 1E2, Canada; (A.R.); (A.I.P.)
- Faculty of Medicine, McGill University, Montreal, QC H3A 0G4, Canada;
- Correspondence: (I.B.); (M.O.); Tel.: +1-514-8038782 (I.B.); +1-514-3408222 (ext. 22662) (M.O.)
| | - Alex Resendes
- Lady Davis Institute for Medical Research, Montréal, QC H3T 1E2, Canada; (A.R.); (A.I.P.)
| | - Shaun Eintracht
- Faculty of Medicine, McGill University, Montreal, QC H3A 0G4, Canada;
| | - Andreas I. Papadakis
- Lady Davis Institute for Medical Research, Montréal, QC H3T 1E2, Canada; (A.R.); (A.I.P.)
| | - Matthew Oughton
- Faculty of Medicine, McGill University, Montreal, QC H3A 0G4, Canada;
- Correspondence: (I.B.); (M.O.); Tel.: +1-514-8038782 (I.B.); +1-514-3408222 (ext. 22662) (M.O.)
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11
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Sonnleitner ST, Dorighi J, Jansen B, Schönegger C, Gietl S, Koblmüller S, Sturmbauer C, Posch W, Walder G. Correction to: An in vitro model for assessment of SARS‑CoV‑2 infectivity by defining the correlation between virus isolation and quantitative PCR value: isolation success of SARS‑CoV‑2 from oropharyngeal swabs correlates negatively with Cq value. Virol J 2021; 18:82. [PMID: 33879217 PMCID: PMC8056994 DOI: 10.1186/s12985-021-01558-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
An amendment to this paper has been published and can be accessed via the original article.
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Affiliation(s)
- Sissy Therese Sonnleitner
- Medical Laboratory, Department of Virology, Dr. Gernot Walder GmbH, 9931, Außervillgraten 30, Austria. .,Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, 6020, Innsbruck, Austria.
| | - Julian Dorighi
- Medical Laboratory, Department of Virology, Dr. Gernot Walder GmbH, 9931, Außervillgraten 30, Austria
| | - Bianca Jansen
- Medical Laboratory, Department of Virology, Dr. Gernot Walder GmbH, 9931, Außervillgraten 30, Austria
| | - Carmen Schönegger
- Medical Laboratory, Department of Virology, Dr. Gernot Walder GmbH, 9931, Außervillgraten 30, Austria
| | - Sarah Gietl
- Medical Laboratory, Department of Virology, Dr. Gernot Walder GmbH, 9931, Außervillgraten 30, Austria
| | - Stephan Koblmüller
- Institute of Biology, University of Graz, Universitaetsplatz 2, 8010, Graz, Austria
| | - Christian Sturmbauer
- Institute of Biology, University of Graz, Universitaetsplatz 2, 8010, Graz, Austria
| | - Wilfried Posch
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, 6020, Innsbruck, Austria
| | - Gernot Walder
- Medical Laboratory, Department of Virology, Dr. Gernot Walder GmbH, 9931, Außervillgraten 30, Austria
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