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Chen R, Bao J, Huang X, Chen Q, Huang M, Gao M, Yu F, Chen J, Zou W, Shi L, Chen X, Feng B, Wang R, Feng B, Zheng S, Yu F. Comparison of "hock-a-loogie" saliva versus nasopharyngeal and oropharyngeal swabs for detecting common respiratory pathogens. Heliyon 2023; 9:e20965. [PMID: 37867842 PMCID: PMC10587520 DOI: 10.1016/j.heliyon.2023.e20965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 10/10/2023] [Accepted: 10/12/2023] [Indexed: 10/24/2023] Open
Abstract
Self-collection of saliva samples has attracted considerable attention in recent years, particularly during the coronavirus disease 2019 pandemic. However, studies investigating the detection of other common respiratory pathogens in saliva samples are limited. In this study, nasopharyngeal swabs (NPS), oropharyngeal swabs (OPS), and "hock-a-loogie" saliva (HLS) were collected from 469 patients to detect 13 common respiratory pathogens. Overall positivity rates for NPS (66.1 %), HLS (63.5 %), and OPS (57.8 %) were statistically different (P = 0.028), with an overall concordance of 72.7 %. Additionally, detection rates for NPS (85.9 %) and HLS (83.2 %) for all pathogens were much higher than for OPS (73.3 %). Coronavirus and human rhinovirus were most frequently detected pathogens in NPS (P < 0.001). Mycoplasma pneumoniae was significantly more prevalent in the HLS group (P = 0.008). In conclusion, NPS was a reliable sample type for detecting common respiratory pathogens. HLS was more easily collected and can be used in emergencies or specific conditions. Mixed NPS/OPS and NPS/HLS specimens have the potential to improve detection rates, although OPS testing alone has a relatively high risk for missed detection.
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Affiliation(s)
- Renke Chen
- The First Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, China
| | - Jiaqi Bao
- Department of Laboratory Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Clinical In Vitro Diagnostic Techniques of Zhejiang Province, Hangzhou, China
- Institute of Laboratory Medicine, Zhejiang University, Hangzhou, China
| | - Xiaojuan Huang
- Department of Laboratory Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Qianna Chen
- Department of Laboratory Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Maowen Huang
- Center of Clinical Laboratory, Ningbo Beilun People's Hospital, Ningbo, China
| | - Min Gao
- Department of Clinical Laboratory, Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, Huzhou, China
| | - Fanghao Yu
- Department of Clinical Laboratory, Yiwu Central Hospital, Yiwu, China
| | - Jiayao Chen
- Department of Clinical Laboratory, Zhoushan Hospital of Zhejiang Province, Zhoushan, China
| | - Weihua Zou
- Department of Clinical Laboratory, Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, Huzhou, China
| | - Lumei Shi
- Center of Clinical Laboratory, Ningbo Beilun People's Hospital, Ningbo, China
| | - Xiao Chen
- Department of Laboratory Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Clinical In Vitro Diagnostic Techniques of Zhejiang Province, Hangzhou, China
- Institute of Laboratory Medicine, Zhejiang University, Hangzhou, China
| | - Bo Feng
- Department of Nephrology, Jiaxing Hospital of Traditional Chinese Medicine, Jiaxing, China
| | - Ruonan Wang
- Department of Laboratory Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Clinical In Vitro Diagnostic Techniques of Zhejiang Province, Hangzhou, China
- Institute of Laboratory Medicine, Zhejiang University, Hangzhou, China
| | - Baihuan Feng
- Department of Laboratory Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Clinical In Vitro Diagnostic Techniques of Zhejiang Province, Hangzhou, China
- Institute of Laboratory Medicine, Zhejiang University, Hangzhou, China
| | - Shufa Zheng
- Department of Laboratory Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Clinical In Vitro Diagnostic Techniques of Zhejiang Province, Hangzhou, China
- Institute of Laboratory Medicine, Zhejiang University, Hangzhou, China
| | - Fei Yu
- Department of Laboratory Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Clinical In Vitro Diagnostic Techniques of Zhejiang Province, Hangzhou, China
- Institute of Laboratory Medicine, Zhejiang University, Hangzhou, China
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Silva LM, Riani LR, Leite JB, de Assis Chagas JM, Fernandes LS, Fochat RC, Perches CGP, Nascimento TC, Jaeger LH, Silvério MS, dos Santos Pereira-Júnior O, Pittella F. The Influence of the Omicron Variant on RNA Extraction and RT-qPCR Detection of SARS-CoV-2 in a Laboratory in Brazil. Viruses 2023; 15:1690. [PMID: 37632032 PMCID: PMC10458054 DOI: 10.3390/v15081690] [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: 06/28/2023] [Revised: 07/19/2023] [Accepted: 07/30/2023] [Indexed: 08/27/2023] Open
Abstract
The emergence of SARS-CoV-2 variants can affect their detection via RT-qPCR. The Omicron variant has a greater affinity for the upper respiratory system and causes clinical conditions similar to bronchitis, as opposed to the pneumonitis-like conditions caused by other SARS-CoV-2 variants. This characteristic increases the viscosity of clinical samples collected for diagnosis. Coinciding with the arrival of the Omicron variant, we observed a failure in control gene expression in our laboratory. In this report, we have optimized a rapid nucleic acid extraction step to restore gene expression and detect the presence of the SARS-CoV-2 virus. We reevaluated 3000 samples, compared variant types occurring in different time periods, and confirmed that the presence of the Omicron variant was responsible for changes observed in the characteristics of these clinical samples. For samples with large amounts of mucus, such as those containing the Omicron variant, a modification to the nucleic acid extraction step was sufficient to restore the quality of RT-qPCR results.
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Affiliation(s)
- Lívia Mara Silva
- Faculdade de Farmácia, Universidade Federal de Juiz de Fora, Rua José Lourenço Kelmer, s/n–Campus Universitário, Juiz de Fora 36036-900, MG, Brazil; (L.M.S.); (L.R.R.); (J.B.L.); (J.M.d.A.C.); (L.S.F.); (R.C.F.); (L.H.J.); (M.S.S.); (O.d.S.P.-J.)
| | - Lorena Rodrigues Riani
- Faculdade de Farmácia, Universidade Federal de Juiz de Fora, Rua José Lourenço Kelmer, s/n–Campus Universitário, Juiz de Fora 36036-900, MG, Brazil; (L.M.S.); (L.R.R.); (J.B.L.); (J.M.d.A.C.); (L.S.F.); (R.C.F.); (L.H.J.); (M.S.S.); (O.d.S.P.-J.)
| | - Juliana Brovini Leite
- Faculdade de Farmácia, Universidade Federal de Juiz de Fora, Rua José Lourenço Kelmer, s/n–Campus Universitário, Juiz de Fora 36036-900, MG, Brazil; (L.M.S.); (L.R.R.); (J.B.L.); (J.M.d.A.C.); (L.S.F.); (R.C.F.); (L.H.J.); (M.S.S.); (O.d.S.P.-J.)
| | - Jessica Mara de Assis Chagas
- Faculdade de Farmácia, Universidade Federal de Juiz de Fora, Rua José Lourenço Kelmer, s/n–Campus Universitário, Juiz de Fora 36036-900, MG, Brazil; (L.M.S.); (L.R.R.); (J.B.L.); (J.M.d.A.C.); (L.S.F.); (R.C.F.); (L.H.J.); (M.S.S.); (O.d.S.P.-J.)
| | - Laura Silva Fernandes
- Faculdade de Farmácia, Universidade Federal de Juiz de Fora, Rua José Lourenço Kelmer, s/n–Campus Universitário, Juiz de Fora 36036-900, MG, Brazil; (L.M.S.); (L.R.R.); (J.B.L.); (J.M.d.A.C.); (L.S.F.); (R.C.F.); (L.H.J.); (M.S.S.); (O.d.S.P.-J.)
| | - Romário Costa Fochat
- Faculdade de Farmácia, Universidade Federal de Juiz de Fora, Rua José Lourenço Kelmer, s/n–Campus Universitário, Juiz de Fora 36036-900, MG, Brazil; (L.M.S.); (L.R.R.); (J.B.L.); (J.M.d.A.C.); (L.S.F.); (R.C.F.); (L.H.J.); (M.S.S.); (O.d.S.P.-J.)
| | - Carmen Gomide Pinto Perches
- Hospital Universitário, Universidade Federal de Juiz de Fora, Av. Eugênio do Nascimento, s/n, Juiz de Fora 36038-330, MG, Brazil;
| | - Thiago César Nascimento
- Faculdade de Enfermagem, Universidade Federal de Juiz de Fora, Rua José Lourenço Kelmer, s/n–Campus Universitário, Juiz de Fora 36036-900, MG, Brazil;
| | - Lauren Hubert Jaeger
- Faculdade de Farmácia, Universidade Federal de Juiz de Fora, Rua José Lourenço Kelmer, s/n–Campus Universitário, Juiz de Fora 36036-900, MG, Brazil; (L.M.S.); (L.R.R.); (J.B.L.); (J.M.d.A.C.); (L.S.F.); (R.C.F.); (L.H.J.); (M.S.S.); (O.d.S.P.-J.)
| | - Marcelo Silva Silvério
- Faculdade de Farmácia, Universidade Federal de Juiz de Fora, Rua José Lourenço Kelmer, s/n–Campus Universitário, Juiz de Fora 36036-900, MG, Brazil; (L.M.S.); (L.R.R.); (J.B.L.); (J.M.d.A.C.); (L.S.F.); (R.C.F.); (L.H.J.); (M.S.S.); (O.d.S.P.-J.)
| | - Olavo dos Santos Pereira-Júnior
- Faculdade de Farmácia, Universidade Federal de Juiz de Fora, Rua José Lourenço Kelmer, s/n–Campus Universitário, Juiz de Fora 36036-900, MG, Brazil; (L.M.S.); (L.R.R.); (J.B.L.); (J.M.d.A.C.); (L.S.F.); (R.C.F.); (L.H.J.); (M.S.S.); (O.d.S.P.-J.)
| | - Frederico Pittella
- Faculdade de Farmácia, Universidade Federal de Juiz de Fora, Rua José Lourenço Kelmer, s/n–Campus Universitário, Juiz de Fora 36036-900, MG, Brazil; (L.M.S.); (L.R.R.); (J.B.L.); (J.M.d.A.C.); (L.S.F.); (R.C.F.); (L.H.J.); (M.S.S.); (O.d.S.P.-J.)
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Drago L, Romanò CL. Commentary: Dithiothreitol (DTT), When Used as Biofilm Detaching Method to Diagnose Implant-Associated Infections, Does Not Affect Microorganisms' Viability, According to the Current Literature. Front Microbiol 2022; 12:814945. [PMID: 35345543 PMCID: PMC8957080 DOI: 10.3389/fmicb.2021.814945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 12/27/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
- Lorenzo Drago
- Clinical Microbiology Unit, Department of Biomedical Sciences for Health, Faculty of Medicine and Surgery, University of Milan, Milan, Italy
| | - Carlo Luca Romanò
- Orthopaedic Department, Monza Polyclinic-San Gaudenzio Hospital, Novara, Italy
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4
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Shukla A, Gangwar M, Sharma G, Prakash P, Nath G. Vitality of Proteinase K in rRTPCR Detection of SARS-CoV2 Bypassing RNA Extraction. Front Cell Infect Microbiol 2021; 11:717068. [PMID: 34804989 PMCID: PMC8595283 DOI: 10.3389/fcimb.2021.717068] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 09/27/2021] [Indexed: 11/23/2022] Open
Abstract
This study aimed to detect the SARS-COV2 viral component directly from inoculated VTM without RNA extraction. Inoculated VTMs of already tested 50 positive and 50 negative samples were divided into three groups. Group I was treated with Proteinase K (PK) followed by 3-step-heat treatment at different temperatures (25°C, 60°C, and 98°C) and stored at 4°C. Group II was directly subjected to 3-step-heat treatment without PK exposure and stored at 4°C. And group III was set-up as standard group; it was processed using Qiagen's column based QIAamp Nucleic Acid kit and the obtained nucleic acids were stored at 4°C. These stored samples were used as a template to execute real-time polymerase chain reaction, and results were noted. Group I demonstrated 96% and 88% sensitivity for N and ORF1ab genes respectively, whereas group II demonstrated 78% and 60% when compared to the results of standard group III. Overall group I showed better results than group II when compared to group III. Thus, in situations where gold-standard reagents are not available, PK exposure and heat treatment can be employed to carry out molecular detection of SARS-CoV2 viral component.
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Affiliation(s)
- Alka Shukla
- Viral Research and Diagnostic Laboratory, Department of Microbiology, Faculty of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Mayank Gangwar
- Viral Research and Diagnostic Laboratory, Department of Microbiology, Faculty of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Gaurav Sharma
- Department of Public Health Dentistry, SriRama Chandra Bhanj Dental College & Hospital, Cuttack, India
| | - Pradyot Prakash
- Viral Research and Diagnostic Laboratory, Department of Microbiology, Faculty of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Gopal Nath
- Viral Research and Diagnostic Laboratory, Department of Microbiology, Faculty of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
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Evaluation of sample treatments in a safe and straightforward procedure for the detection of SARS-CoV-2 in saliva. Int J Infect Dis 2021; 108:413-418. [PMID: 34044144 PMCID: PMC8142814 DOI: 10.1016/j.ijid.2021.05.053] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 05/19/2021] [Accepted: 05/21/2021] [Indexed: 01/23/2023] Open
Abstract
Objectives To evaluate four sample treatments in a safe and straightforward procedure to detect SARS-CoV-2 in saliva. Methods Four sample treatments were evaluated in a 3-step procedure to detect SARS-CoV-2 in saliva: 1) heating at 95 °C for 5 min for sample inactivation; 2) sample treatment; 3) analysis by reverse-transcription loop-mediated isothermal amplification (LAMP). Saliva samples used were from infected individuals or were spiked with known quantities of viral particles. Results Three treatments had a limit of detection (LOD) of 500.000 viral particles per ml of saliva and could be used to detect individuals with potential to transmit the disease. The treatment of phosphate buffer, dithiothreitol, ethylenediaminetetraacetic acid and proteinase K, with an additional 95 °C heating step, yielded a lower LOD of 95; its sensitivity ranged from 100% in patients with nasopharyngeal swab reverse-transcriptase polymerase chain reaction cycle threshold values <20 to 47.8% for values >30. Conclusions This report highlights the importance of an adequate sample treatment for saliva to detect SARS-CoV-2 and describes a flexible procedure that can be adapted to point-of-care. Although its sensitivity when LAMP is used is lower than reverse-transcriptase polymerase chain reaction, this procedure can contribute to COVID-19 control by detecting individuals able to transmit the disease.
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6
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Ko SH, Bayat Mokhtari E, Mudvari P, Stein S, Stringham CD, Wagner D, Ramelli S, Ramos-Benitez MJ, Strich JR, Davey RT, Zhou T, Misasi J, Kwong PD, Chertow DS, Sullivan NJ, Boritz EA. High-throughput, single-copy sequencing reveals SARS-CoV-2 spike variants coincident with mounting humoral immunity during acute COVID-19. PLoS Pathog 2021; 17:e1009431. [PMID: 33831133 PMCID: PMC8031304 DOI: 10.1371/journal.ppat.1009431] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 02/28/2021] [Indexed: 12/23/2022] Open
Abstract
Tracking evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) within infected individuals will help elucidate coronavirus disease 2019 (COVID-19) pathogenesis and inform use of antiviral interventions. In this study, we developed an approach for sequencing the region encoding the SARS-CoV-2 virion surface proteins from large numbers of individual virus RNA genomes per sample. We applied this approach to the WA-1 reference clinical isolate of SARS-CoV-2 passaged in vitro and to upper respiratory samples from 7 study participants with COVID-19. SARS-CoV-2 genomes from cell culture were diverse, including 18 haplotypes with non-synonymous mutations clustered in the spike NH2-terminal domain (NTD) and furin cleavage site regions. By contrast, cross-sectional analysis of samples from participants with COVID-19 showed fewer virus variants, without structural clustering of mutations. However, longitudinal analysis in one individual revealed 4 virus haplotypes bearing 3 independent mutations in a spike NTD epitope targeted by autologous antibodies. These mutations arose coincident with a 6.2-fold rise in serum binding to spike and a transient increase in virus burden. We conclude that SARS-CoV-2 exhibits a capacity for rapid genetic adaptation that becomes detectable in vivo with the onset of humoral immunity, with the potential to contribute to delayed virologic clearance in the acute setting.
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Affiliation(s)
- Sung Hee Ko
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Elham Bayat Mokhtari
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Prakriti Mudvari
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Sydney Stein
- Emerging Pathogens Section, Critical Care Medicine Department, National Institutes of Health Clinical Center, Bethesda, Maryland, United States of America
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Christopher D. Stringham
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Danielle Wagner
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Sabrina Ramelli
- Emerging Pathogens Section, Critical Care Medicine Department, National Institutes of Health Clinical Center, Bethesda, Maryland, United States of America
| | - Marcos J. Ramos-Benitez
- Emerging Pathogens Section, Critical Care Medicine Department, National Institutes of Health Clinical Center, Bethesda, Maryland, United States of America
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Jeffrey R. Strich
- Emerging Pathogens Section, Critical Care Medicine Department, National Institutes of Health Clinical Center, Bethesda, Maryland, United States of America
| | - Richard T. Davey
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Tongqing Zhou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - John Misasi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Peter D. Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Daniel S. Chertow
- Emerging Pathogens Section, Critical Care Medicine Department, National Institutes of Health Clinical Center, Bethesda, Maryland, United States of America
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Nancy J. Sullivan
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Eli A. Boritz
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
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7
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Ko SH, Mokhtari EB, Mudvari P, Stein S, Stringham CD, Wagner D, Ramelli S, Ramos-Benitez MJ, Strich JR, Davey RT, Zhou T, Misasi J, Kwong PD, Chertow DS, Sullivan NJ, Boritz EA. High-Throughput, Single-Copy Sequencing Reveals SARS-CoV-2 Spike Variants Coincident with Mounting Humoral Immunity during Acute COVID-19. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.02.21.432184. [PMID: 33655255 PMCID: PMC7924285 DOI: 10.1101/2021.02.21.432184] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Tracking evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) within infected individuals will help elucidate coronavirus disease 2019 (COVID-19) pathogenesis and inform use of antiviral interventions. In this study, we developed an approach for sequencing the region encoding the SARS-CoV-2 virion surface proteins from large numbers of individual virus RNA genomes per sample. We applied this approach to the WA-1 reference clinical isolate of SARS-CoV-2 passaged in vitro and to upper respiratory samples from 7 study participants with COVID-19. SARS-CoV-2 genomes from cell culture were diverse, including 18 haplotypes with non-synonymous mutations clustered in the spike NH 2 -terminal domain (NTD) and furin cleavage site regions. By contrast, cross-sectional analysis of samples from participants with COVID-19 showed fewer virus variants, without structural clustering of mutations. However, longitudinal analysis in one individual revealed 4 virus haplotypes bearing 3 independent mutations in a spike NTD epitope targeted by autologous antibodies. These mutations arose coincident with a 6.2-fold rise in serum binding to spike and a transient increase in virus burden. We conclude that SARS-CoV-2 exhibits a capacity for rapid genetic adaptation that becomes detectable in vivo with the onset of humoral immunity, with the potential to contribute to delayed virologic clearance in the acute setting. AUTHOR SUMMARY Mutant sequences of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) arising during any individual case of coronavirus disease 2019 (COVID-19) could theoretically enable the virus to evade immune responses or antiviral therapies that target the predominant infecting virus sequence. However, commonly used sequencing technologies are not optimally designed to detect variant virus sequences within each sample. To address this issue, we developed novel technology for sequencing large numbers of individual SARS-CoV-2 genomic RNA molecules across the region encoding the virus surface proteins. This technology revealed extensive genetic diversity in cultured viruses from a clinical isolate of SARS-CoV-2, but lower diversity in samples from 7 individuals with COVID-19. Importantly, concurrent analysis of paired serum samples in selected individuals revealed relatively low levels of antibody binding to the SARS-CoV-2 spike protein at the time of initial sequencing. With increased serum binding to spike protein, we detected multiple SARS-CoV-2 variants bearing independent mutations in a single epitope, as well as a transient increase in virus burden. These findings suggest that SARS-CoV-2 replication creates sufficient virus genetic diversity to allow immune-mediated selection of variants within the time frame of acute COVID-19. Large-scale studies of SARS-CoV-2 variation and specific immune responses will help define the contributions of intra-individual SARS-CoV-2 evolution to COVID-19 clinical outcomes and antiviral drug susceptibility.
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Affiliation(s)
- Sung Hee Ko
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Elham Bayat Mokhtari
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Prakriti Mudvari
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sydney Stein
- Emerging Pathogens Section, Critical Care Medicine Department, National Institutes of Health Clinical Center, Bethesda, MD 20892, USA
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Christopher D. Stringham
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Danielle Wagner
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sabrina Ramelli
- Emerging Pathogens Section, Critical Care Medicine Department, National Institutes of Health Clinical Center, Bethesda, MD 20892, USA
| | - Marcos J. Ramos-Benitez
- Emerging Pathogens Section, Critical Care Medicine Department, National Institutes of Health Clinical Center, Bethesda, MD 20892, USA
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jeffrey R. Strich
- Emerging Pathogens Section, Critical Care Medicine Department, National Institutes of Health Clinical Center, Bethesda, MD 20892, USA
| | - Richard T. Davey
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tongqing Zhou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - John Misasi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Peter D. Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Daniel S. Chertow
- Emerging Pathogens Section, Critical Care Medicine Department, National Institutes of Health Clinical Center, Bethesda, MD 20892, USA
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nancy J. Sullivan
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Eli A. Boritz
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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8
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Matic N, Lawson T, Ritchie G, Stefanovic A, Leung V, Champagne S, Romney MG, Lowe CF. Automated molecular testing of saliva for SARS-CoV-2 detection. Diagn Microbiol Infect Dis 2021; 100:115324. [PMID: 33529938 PMCID: PMC7826079 DOI: 10.1016/j.diagmicrobio.2021.115324] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 01/17/2021] [Accepted: 01/18/2021] [Indexed: 01/12/2023]
Abstract
With surging global demand for SARS-CoV-2 testing capacity, laboratories seek automated, high-throughput molecular solutions, particularly for specimens not requiring specialized collection devices or viral transport media. Saliva specimens submitted from patients under investigation for COVID-19 from March to July 2020 were processed in the laboratory with sterile phosphate-buffered saline in a 1:2 dilution and tested using manual extraction and a commercial assay for detection of the SARS-CoV-2 E gene (LightMix®) in comparison to the Roche cobas® SARS-CoV-2 Test on the cobas® 6800 instrument. 34.4% (22/64) of saliva samples were positive for SARS-CoV-2. Positive and negative concordance between the LightMix® and cobas® assays were 100%. The overall invalid rate for saliva on the cobas® 6800 (1/128, 0.78%) was similar to the baseline invalid rate observed for nasopharyngeal swabs/viral transport media. Saliva is a feasible specimen type for SARS-CoV-2 testing on the cobas® 6800 platform, with potential to improve turnaround time and enhance testing capacity.
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Affiliation(s)
- Nancy Matic
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada.
| | - Tanya Lawson
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada
| | - Gordon Ritchie
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Aleksandra Stefanovic
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Victor Leung
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Sylvie Champagne
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Marc G Romney
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Christopher F Lowe
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
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9
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Premraj A, Aleyas AG, Nautiyal B, Rasool TJ. Nucleic Acid and Immunological Diagnostics for SARS-CoV-2: Processes, Platforms and Pitfalls. Diagnostics (Basel) 2020; 10:E866. [PMID: 33114057 PMCID: PMC7690661 DOI: 10.3390/diagnostics10110866] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 10/12/2020] [Accepted: 10/20/2020] [Indexed: 12/26/2022] Open
Abstract
Accurate diagnosis at an early stage of infection is essential for the successful management of any contagious disease. The coronavirus disease 2019 (COVID-19), caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) virus is a pandemic that has affected 214 countries affecting more than 37.4 million people causing 1.07 million deaths as of the second week of October 2020. The primary diagnosis of the infection is done either by the molecular technique of RT-qPCR by detecting portions of the RNA of the viral genome or through immunodiagnostic tests by detecting the viral proteins or the antibodies produced by the host. As the demand for the test increased rapidly many naive manufacturers entered the market with novel kits and more and more laboratories also entered the diagnostic arena making the test result more error-prone. There are serious debates globally and regionally on the sensitivity and specificity of these tests and about the overall accuracy and reliability of the tests for decision making on control strategies. The significance of the test is also complexed by the presence of asymptomatic carriers, re-occurrence of infection in cured patients as well as by the varied incubation periods of the infection and shifting of the viral location in the host tissues. In this paper, we review the techniques available for SARS-CoV-2 diagnosis and probable factors that can reduce the sensitivity and specificity of the different test methods currently in vogue. We also provide a checklist of factors to be considered to avoid fallacious practices to reduce false positive and false negative results by the clinical laboratories.
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Affiliation(s)
| | | | | | - Thaha J Rasool
- Camel Biotechnology Center, Presidential Camels and Camel Racing Affairs Centre, Department of the President’s Affairs, P.O. Box 17292, Al Ain 17292, UAE; (A.P.); (A.G.A.); (B.N.)
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10
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Goldenberger D, Leuzinger K, Sogaard KK, Gosert R, Roloff T, Naegele K, Cuénod A, Mari A, Seth-Smith H, Rentsch K, Hinić V, Hirsch HH, Egli A. Brief validation of the novel GeneXpert Xpress SARS-CoV-2 PCR assay. J Virol Methods 2020; 284:113925. [PMID: 32659240 PMCID: PMC7351036 DOI: 10.1016/j.jviromet.2020.113925] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 06/08/2020] [Accepted: 06/30/2020] [Indexed: 02/02/2023]
Abstract
The clinical and epidemiologic management of the SARS-CoV-2 pandemic is critically dependent on molecular assays with short turn-around time. We validated the novel Xpert Xpress SARS-CoV-2 assay using a commercial nucleic acid testing (Roche Cobas 6800). We found an excellent concordance over a range of SARS-CoV-2 loads and across established human coronaviruses.
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Affiliation(s)
- Daniel Goldenberger
- Clinical Bacteriology and Mycology, Laboratory Medicine, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Karoline Leuzinger
- Clinical Virology, Laboratory Medicine, University Hospital Basel, Basel, Switzerland
| | - Kirstine K Sogaard
- Clinical Bacteriology and Mycology, Laboratory Medicine, University Hospital Basel and University of Basel, Basel, Switzerland; Applied Microbiology Research, Laboratory Medicine, Department Biomedicine, University of Basel, Basel, Switzerland
| | - Rainer Gosert
- Clinical Virology, Laboratory Medicine, University Hospital Basel, Basel, Switzerland
| | - Tim Roloff
- Clinical Bacteriology and Mycology, Laboratory Medicine, University Hospital Basel and University of Basel, Basel, Switzerland; Applied Microbiology Research, Laboratory Medicine, Department Biomedicine, University of Basel, Basel, Switzerland
| | - Klaudia Naegele
- Clinical Virology, Laboratory Medicine, University Hospital Basel, Basel, Switzerland
| | - Aline Cuénod
- Applied Microbiology Research, Laboratory Medicine, Department Biomedicine, University of Basel, Basel, Switzerland
| | - Alfredo Mari
- Applied Microbiology Research, Laboratory Medicine, Department Biomedicine, University of Basel, Basel, Switzerland
| | - Helena Seth-Smith
- Clinical Bacteriology and Mycology, Laboratory Medicine, University Hospital Basel and University of Basel, Basel, Switzerland; Applied Microbiology Research, Laboratory Medicine, Department Biomedicine, University of Basel, Basel, Switzerland
| | | | - Vladimira Hinić
- Clinical Bacteriology and Mycology, Laboratory Medicine, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Hans H Hirsch
- Clinical Virology, Laboratory Medicine, University Hospital Basel, Basel, Switzerland; Infectious Diseases & Hospital Epidemiology, University Hospital Basel, Basel, Switzerland; Transplantation & Clinical Virology, Department Biomedicine, University of Basel, Basel, Switzerland
| | - Adrian Egli
- Clinical Bacteriology and Mycology, Laboratory Medicine, University Hospital Basel and University of Basel, Basel, Switzerland; Applied Microbiology Research, Laboratory Medicine, Department Biomedicine, University of Basel, Basel, Switzerland.
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11
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Peng J, Lu Y, Song J, Vallance BA, Jacobson K, Yu HB, Sun Z. Direct Clinical Evidence Recommending the Use of Proteinase K or Dithiothreitol to Pretreat Sputum for Detection of SARS-CoV-2. Front Med (Lausanne) 2020; 7:549860. [PMID: 33043036 PMCID: PMC7530184 DOI: 10.3389/fmed.2020.549860] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 08/27/2020] [Indexed: 01/08/2023] Open
Abstract
One of the primary tools for diagnosing COVID-19 is the nucleic acid-based real-time reverse transcriptase-polymerase chain reaction (RT-PCR) test performed on respiratory specimens. The detection rate of SARS-CoV-2 in lower respiratory specimens (such as sputum) is higher than that for upper respiratory specimens (such as nasal and pharyngeal swabs). However, sputum specimens are usually quite viscous, requiring a homogenization process prior to nucleic acid (NA) extraction for RT-PCR. Sputum specimens from COVID-19 and non-COVID-19 patients were treated with four commonly used reagents—saline, N-acetyl-L-cysteine (NALC), proteinase K (PK), and dithiothreitol (DTT), prior to NA extraction. These reagents were then compared for their performance in diagnosing COVID-19 in real clinical practice. The detection rate of SARS-CoV-2 in PK- or DTT-treated sputum was comparable, and higher than that in sputum treated with NALC or saline. While there was a 4.8% (1/21) false negative rate for the PK- and DTT-treated sputum, neither treatment showed any false positive cases among patients with non-COVID diseases. Moreover, sputum pretreated with saline, NALC, PK or DTT showed higher detection rates of SARS-CoV-2 as compared to pharyngeal swabs. Taken together, we provide direct evidence recommending the use of PK or DTT to pretreat sputum samples to facilitate SARS-CoV-2 detection by clinical laboratories. Moreover, our methods should help to standardize the procedure of processing sputum specimens and improve the ability to detect SARS-CoV-2 in these samples.
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Affiliation(s)
- Jing Peng
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yanjun Lu
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Juan Song
- Department of Gastroenterology & Endocrinology, Wuhan No. 9 Hospital, Wuhan, China
| | - Bruce A Vallance
- Department of Pediatrics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Kevan Jacobson
- Department of Pediatrics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Hong Bing Yu
- Department of Pediatrics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Ziyong Sun
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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