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Ganesan SM, Peter TK, Withanage MHH, Boksa F, Zeng E, Martinez A, Dabdoub SM, Dhingra K, Hernandez-Kapila Y. COVID-19 associated oral and oropharyngeal microbiome: Systematic review and meta-analysis. Periodontol 2000 2024; 94:603-626. [PMID: 37277934 DOI: 10.1111/prd.12489] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 04/01/2023] [Indexed: 06/07/2023]
Abstract
Three years into the coronavirus disease 2019 (COVID-19) pandemic, there are still growing concerns with the emergence of different variants, unknown long- and short-term effects of the virus, and potential biological mechanisms underlying etiopathogenesis and increased risk for morbidity and mortality. The role of the microbiome in human physiology and the initiation and progression of several oral and systemic diseases have been actively studied in the past decade. With the proof of viral transmission, carriage, and a potential role in etiopathogenesis, saliva and the oral environment have been a focus of COVID-19 research beyond diagnostic purposes. The oral environment hosts diverse microbial communities and contributes to human oral and systemic health. Several investigations have identified disruptions in the oral microbiome in COVID-19 patients. However, all these studies are cross-sectional in nature and present heterogeneity in study design, techniques, and analysis. Therefore, in this undertaking, we (a) systematically reviewed the current literature associating COVID-19 with changes in the microbiome; (b) performed a re-analysis of publicly available data as a means to standardize the analysis, and (c) reported alterations in the microbial characteristics in COVID-19 patients compared to negative controls. Overall, we identified that COVID-19 is associated with oral microbial dysbiosis with significant reduction in diversity. However, alterations in specific bacterial members differed across the study. Re-analysis from our pipeline shed light on Neisseria as the potential key microbial member associated with COVID-19.
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Affiliation(s)
- Sukirth M Ganesan
- Department of Periodontics, The University of Iowa College of Dentistry and Dental Clinics, Iowa, USA
- Iowa Institute for Oral Health Research, The University of Iowa College of Dentistry and Dental Clinics, Iowa City, Iowa, USA
| | - Tabitha K Peter
- Division of Biostatistics and Computational Biology, The University of Iowa College of Dentistry and Dental Clinics, Iowa City, Iowa, USA
| | - Miyuraj H H Withanage
- Division of Biostatistics and Computational Biology, The University of Iowa College of Dentistry and Dental Clinics, Iowa City, Iowa, USA
| | - Frank Boksa
- Department of Periodontics, The University of Iowa College of Dentistry and Dental Clinics, Iowa, USA
| | - Erliang Zeng
- Iowa Institute for Oral Health Research, The University of Iowa College of Dentistry and Dental Clinics, Iowa City, Iowa, USA
- Division of Biostatistics and Computational Biology, The University of Iowa College of Dentistry and Dental Clinics, Iowa City, Iowa, USA
- Department of Preventive and Community Dentistry, The University of Iowa College of Dentistry and Dental Clinics, Iowa City, Iowa, USA
| | - April Martinez
- Division of Periodontology, University of California at San Francisco School of Dentistry, San Francisco, California, USA
| | - Shareef M Dabdoub
- Department of Periodontics, The University of Iowa College of Dentistry and Dental Clinics, Iowa, USA
- Iowa Institute for Oral Health Research, The University of Iowa College of Dentistry and Dental Clinics, Iowa City, Iowa, USA
- Division of Biostatistics and Computational Biology, The University of Iowa College of Dentistry and Dental Clinics, Iowa City, Iowa, USA
| | - Kunaal Dhingra
- Periodontology Division, Centre for Dental Education and Research, All India Institute of Medical Sciences, New Delhi, India
| | - Yvonne Hernandez-Kapila
- Section of Biosystems and Function Periodontics, University of California at Los Angeles School of Dentistry, Los Angeles, California, USA
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Suh IB, Lim J, Kim HS, Rhim G, Kim H, Kim H, Lee SM, Park HS, Song HJ, Hong M, Shin GS, Kim MJ. Development and Evaluation of AccuPower COVID-19 Multiplex Real-Time RT-PCR Kit and AccuPower SARS-CoV-2 Multiplex Real-Time RT-PCR Kit for SARS-CoV-2 Detection in Sputum, NPS/OPS, Saliva and Pooled Samples. PLoS One 2022; 17:e0263341. [PMID: 35143538 PMCID: PMC8830688 DOI: 10.1371/journal.pone.0263341] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 01/17/2022] [Indexed: 11/19/2022] Open
Abstract
Rapid and accurate detection of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is essential for the successful control of the current global COVID-19 pandemic. The real-time reverse transcription polymerase chain reaction (Real-time RT-PCR) is the most widely used detection technique. This research describes the development of two novel multiplex real-time RT-PCR kits, AccuPower® COVID-19 Multiplex Real-Time RT-PCR Kit (NCVM) specifically designed for use with the ExiStation™48 system (comprised of ExiPrep™48 Dx and Exicycler™96 by BIONEER, Korea) for sample RNA extraction and PCR detection, and AccuPower® SARS-CoV-2 Multiplex Real-Time RT-PCR Kit (SCVM) designed to be compatible with manufacturers’ on-market PCR instruments. The limit of detection (LoD) of NCVM was 120 copies/mL and the LoD of the SCVM was 2 copies/μL for both the Pan-sarbecovirus gene and the SARS-CoV-2 gene. The AccuPower® kits demonstrated high precision with no cross reactivity to other respiratory-related microorganisms. The clinical performance of AccuPower® kits was evaluated using the following clinical samples: sputum and nasopharyngeal/oropharyngeal swab (NPS/OPS) samples. Overall agreement of the AccuPower® kits with a Food and Drug Administration (FDA) approved emergency use authorized commercial kit (STANDARD™ M nCoV Real-Time Detection kit, SD BIOSENSOR, Korea) was above 95% (Cohen’s kappa coefficient ≥ 0.95), with a sensitivity of over 95%. The NPS/OPS specimen pooling experiment was conducted to verify the usability of AccuPower® kits on pooled samples and the results showed greater than 90% agreement with individual NPS/OPS samples. The clinical performance of AccuPower® kits with saliva samples was also compared with NPS/OPS samples and demonstrated over 95% agreement (Cohen’s kappa coefficient > 0.95). This study shows the BIONEER NCVM and SCVM assays are comparable with the current standard confirmation assay and are suitable for effective clinical management and control of SARS-CoV-2.
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Affiliation(s)
- In Bum Suh
- Department of Laboratory Medicine, College of Medicine, Kangwon National University, Chuncheon, Korea
| | - Jaegyun Lim
- Department of Laboratory Medicine, Myongji Hospital, Hanyang University College of Medicine, Goyang, Korea
| | - Hyo Seon Kim
- Research Administration Team, Institute of Clinical Medicine, Myongji Hospital, Hanyang University College of Medicine, Goyang, Korea
| | - Guil Rhim
- Department of General Affairs, Korean Association of Otorhinolaryngologists, Seoul, Korea
| | - Heebum Kim
- Department of Laboratory Medicine, College of Medicine, Kangwon National University, Chuncheon, Korea
| | - Hana Kim
- Department of Laboratory Medicine, College of Medicine, Kangwon National University, Chuncheon, Korea
| | - Sae-Mi Lee
- Department of Laboratory Medicine, College of Medicine, Kangwon National University, Chuncheon, Korea
| | - Hyun-sang Park
- Department of Laboratory Medicine, College of Medicine, Kangwon National University, Chuncheon, Korea
| | - Hyun Ju Song
- Department of Laboratory Medicine, College of Medicine, Kangwon National University, Chuncheon, Korea
| | - MyungKook Hong
- Department of Laboratory Medicine, College of Medicine, Kangwon National University, Chuncheon, Korea
| | - Gyung Sook Shin
- Department of Laboratory Medicine, College of Medicine, Kangwon National University, Chuncheon, Korea
| | - Moon Jung Kim
- Department of Laboratory Medicine, Myongji Hospital, Hanyang University College of Medicine, Goyang, Korea
- * E-mail:
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Alghounaim M, Caya C, Alothman K, Alhasawi A, Papenburg J. SARS-CoV-2 Clinical Characteristics and Viral Shedding in Kuwait. Med Princ Pract 2022; 31:93-97. [PMID: 34883487 PMCID: PMC8805077 DOI: 10.1159/000521408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 12/02/2021] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVES We aimed to describe the clinical characteristics of SARS-CoV-2 infection and estimate viral shedding duration in respiratory specimens. METHODS A retrospective cohort study was performed from February 25 to March 25, 2020. In Kuwait, all suspected coronavirus disease 2019 (COVID-19) cases, contacts of cases, and returning travelers were systematically tested for SARS-CoV-2 by RT-PCR. All infected persons, regardless of symptoms, were hospitalized and serially tested until they had two negative results. Descriptive statistics and regression analyses were performed. RESULTS Two hundred seven cases of SARS-CoV-2 infection were included in this study. About half of the cases were asymptomatic and 1.9% died. The median time to negative RT-PCR was 22 days. Increasing age, ARDS, and low peripheral white blood cell count were associated with prolonged PCR positivity. CONCLUSION Predictors for prolonged RT-PCR positivity included increasing age, ARDS, and low white blood cell count. The findings of this study may aid in better understanding of the epidemiology of SARS-CoV-2 infection and molecular testing dynamics.
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Affiliation(s)
- Mohammad Alghounaim
- Department of Pediatrics, Amiri Hospital, Ministry of Health, Kuwait, Kuwait
- *Mohammad Alghounaim,
| | - Chelsea Caya
- McGill University Health Centre Research Institute, Montreal, Québec, Canada
| | - Khalid Alothman
- Department of Pediatrics, Jaber Alahmad Hospital, Ministry of Health, Kuwait, Kuwait
| | - Almonther Alhasawi
- Department of Medicine, Infectious Diseases Hospital, Ministry of Health, Kuwait, Kuwait
| | - Jesse Papenburg
- Division of Pediatric Infectious Diseases, The Montreal Children's Hospital, McGill University Health Centre, Montreal, Québec, Canada
- Division of Microbiology, Department of Laboratory Medicine, McGill University Health Centre, Montreal, Québec, Canada
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Morán-Torres A, Pazos-Salazar NG, Téllez-Lorenzo S, Jiménez-Lima R, Lizano M, Reyes-Hernández DO, Marin-Aquino JDJ, Manzo-Merino J. HPV oral and oropharynx infection dynamics in young population. Braz J Microbiol 2021; 52:1991-2000. [PMID: 34482527 PMCID: PMC8578222 DOI: 10.1007/s42770-021-00602-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Accepted: 08/27/2021] [Indexed: 12/24/2022] Open
Abstract
The incidence of human papillomavirus (HPV)-associated cancers, especially those from the head and neck region, has increased. The relatively early age of presentation of HPV-positive head and neck cancer (HNC) indicates that viral infection might be acquired early in life. Persistent HPV infection has been recognized as the main risk factor for cancer development, but most studies have focused on evaluating HPV persistence in the genital region. Thus, in this work, we aimed to evaluate the prevalence of HPV in oral cavity and oropharynx in a young population, as well as the possible persistence of the infection after 12 months. Our results indicate that almost half (46.8%) of the analyzed population harbors an HPV infection either in the oral cavity or in the oropharynx. Furthermore, after 1 year of initial identification, half of them eliminated the infection, and only one person (5.26%) exhibited persistence. Interestingly, 50% of the individuals who successfully eliminated the infection acquired a new viral type, indicating that even when the primary infection is effectively eliminated by the immune system, there is a dynamic circulation of HR-HPV types that produce reinfection. This dynamic HPV infection among young individuals could influence the future establishment of cancer in some proportion of the cases.
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Affiliation(s)
- Adriana Morán-Torres
- Departamento de Microbiología, Facultad de Ciencias Químicas, Benemérita Universidad Autónoma de Puebla, Av. San Claudio, Edificio FCQ1, Ciudad Universitaria, 72570, Puebla, Mexico
- Instituto Nacional de Cancerología, Av. San Fernando No. 22, Col. Sección XVI, Tlalpan, 14080, Mexico City, Mexico
| | - Nidia G Pazos-Salazar
- Departamento de Microbiología, Facultad de Ciencias Químicas, Benemérita Universidad Autónoma de Puebla, Av. San Claudio, Edificio FCQ1, Ciudad Universitaria, 72570, Puebla, Mexico
| | - Susana Téllez-Lorenzo
- Departamento de Microbiología, Facultad de Ciencias Químicas, Benemérita Universidad Autónoma de Puebla, Av. San Claudio, Edificio FCQ1, Ciudad Universitaria, 72570, Puebla, Mexico
| | - Roberto Jiménez-Lima
- Instituto Nacional de Cancerología, Av. San Fernando No. 22, Col. Sección XVI, Tlalpan, 14080, Mexico City, Mexico
| | - Marcela Lizano
- Instituto Nacional de Cancerología, Av. San Fernando No. 22, Col. Sección XVI, Tlalpan, 14080, Mexico City, Mexico
- Departamento de Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Diego O Reyes-Hernández
- Instituto Nacional de Cancerología, Av. San Fernando No. 22, Col. Sección XVI, Tlalpan, 14080, Mexico City, Mexico
| | - José de J Marin-Aquino
- Departamento de Patologia, Hospital General "Dr. Manuel Gea Gonzalez", Calzada de Tlalpan 4800, Belisario Dominguez secc 1, Tlalpan, 14080, Mexico City, , Mexico
| | - Joaquín Manzo-Merino
- Instituto Nacional de Cancerología, Av. San Fernando No. 22, Col. Sección XVI, Tlalpan, 14080, Mexico City, Mexico.
- Cátedras CONACyT-Instituto Nacional de Cancerología, San Fernando No. 22, Col. Sección XVI, Tlalpan, 14080, Mexico City, Mexico.
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Bahadur S, Kalonia T, Kamini K, Gupta B, Kalhan S, Jain M. Changes in peripheral blood in SARS CoV-2 patients and its clinico-pathological correlation: A prospective cross-sectional study. Int J Lab Hematol 2021; 43:1334-1340. [PMID: 34596329 PMCID: PMC8653337 DOI: 10.1111/ijlh.13720] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 08/19/2021] [Accepted: 09/09/2021] [Indexed: 01/08/2023]
Abstract
INTRODUCTION Coronavirus disease 2019 (COVID-19) caused by SARS-CoV2 can present from mild flu-like symptoms to acute respiratory distress syndrome. There is multi-organ involvement; particularly, hematopoietic system can be associated with morphological changes in blood cells of COVID-19 patients. METHOD We conducted a cross-sectional study on a cohort of 50 COVID-19 patients, confirmed on RT-PCR with documented cycle threshold (Ct) value. Peripheral blood sample of these patients was collected and examined for complete blood counts (CBC) on automated haematological analyser as well as Leishman-stained blood smears to look for morphological changes in blood cells. Morphological changes were evaluated with reference to clinical severity and Ct value. Additionally, association between Ct value and clinical severity was also performed. Statistical tests were performed, and P value <.05 was considered significant. RESULTS Mean age of our study group was 42.16 ± 15.55 years, with male preponderance. Most commonly observed peripheral blood changes were hypolobation (P value = .002) and toxic granules (P value = .005) in neutrophils, atypical granules with nucleolar prominence in lymphocytes, cytoplasmic granulation with clumped nuclear chromatin in monocytes, giant platelets and thrombocytopenia and normocytic normochromic anaemia. CONCLUSION No association was found between clinical severity and Ct value as well as peripheral blood morphological changes with Ct value. We conclude that examination of peripheral smear coupled with complete blood count (CBC) is only partially supportive of disease pathogenesis and to assess the viral load other parameters should be utilised instead of relying solely on Ct value.
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Affiliation(s)
- Shalini Bahadur
- Department of PathologyGovernment Institute of Medical SciencesGreater NoidaIndia
| | - Tushar Kalonia
- Department of PathologyGovernment Institute of Medical SciencesGreater NoidaIndia
| | - Kanchan Kamini
- Department of PathologyNational Institute of Medical SciencesJaipurIndia
| | - Bhumika Gupta
- Department of PathologyGovernment Institute of Medical SciencesGreater NoidaIndia
| | - Shivani Kalhan
- Department of PathologyGovernment Institute of Medical SciencesGreater NoidaIndia
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Luyt CE, Hajage D, Burrel S, Hraiech S, Diallo MH, Papazian L, Boutolleau D. Efficacy of Acyclovir to Suppress Herpes Simplex Virus Oropharyngeal Reactivation in Patients Who Are Mechanically Ventilated: An Ancillary Study of the Preemptive Treatment for Herpesviridae (PTH) Trial. JAMA Netw Open 2021; 4:e2139825. [PMID: 34928361 PMCID: PMC8689380 DOI: 10.1001/jamanetworkopen.2021.39825] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
This analysis of a randomized clinical trial examines the efficacy of acyclovir for preventing oropharyngeal HSV reactivation among patients who were mechanically ventilated.
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Affiliation(s)
- Charles-Edouard Luyt
- Service de Médecine Intensive Réanimation, Sorbonne Université, Hôpitaux Universitaires Pitié Salpêtrière-Charles Foix, Assistance Publique-Hôpitaux de Paris, Paris, France
- Institut national de la Santé et de la Recherche Médicale Unité Mixte de Recherche S 1166-Institute of Cardiometabolism and Nutrition, Paris, France
| | - David Hajage
- Sorbonne Université, Institut national de la Santé et de la Recherche Médicale, Institut Pierre Louis d’Epidémiologie et de Santé Publique, Assistance Publique-Hôpitaux de Paris, Hôpitaux Universitaires Pitié Salpêtrière-Charles Foix, Département de Santé Publique, Centre de Pharmacoépidémiologie, Centre d'Investigation Clinique-1421, Paris, France
| | - Sonia Burrel
- Centre National de Référence Herpèsvirus, Département de Virologie, Sorbonne Université, Hôpitaux Universitaires Pitié Salpêtrière-Charles Foix, Assistance Publique-Hôpitaux de Paris
- Institut National de la Santé et de la Recherche Médicale U1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Paris, France
| | - Sami Hraiech
- Médecine Intensive Réanimation, Aix-Marseille Université, Hôpital Nord, Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Mamadou Hassimiou Diallo
- Sorbonne Université, Institut national de la Santé et de la Recherche Médicale, Institut Pierre Louis d’Epidémiologie et de Santé Publique, Assistance Publique-Hôpitaux de Paris, Hôpitaux Universitaires Pitié Salpêtrière-Charles Foix, Département de Santé Publique, Centre de Pharmacoépidémiologie, Centre d'Investigation Clinique-1421, Paris, France
| | - Laurent Papazian
- Médecine Intensive Réanimation, Aix-Marseille Université, Hôpital Nord, Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - David Boutolleau
- Centre National de Référence Herpèsvirus, Département de Virologie, Sorbonne Université, Hôpitaux Universitaires Pitié Salpêtrière-Charles Foix, Assistance Publique-Hôpitaux de Paris
- Institut National de la Santé et de la Recherche Médicale U1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Paris, France
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Pryce TM, Boan PA, Kay ID, Flexman JP. Qualitative and quantitative effects of thermal treatment of naso-oropharyngeal samples before cobas SARS-CoV-2 testing. Diagn Microbiol Infect Dis 2021; 101:115519. [PMID: 34571354 PMCID: PMC8382495 DOI: 10.1016/j.diagmicrobio.2021.115519] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 08/08/2021] [Accepted: 08/11/2021] [Indexed: 02/08/2023]
Abstract
To improve laboratory safety we thermally treated naso-oropharyngeal samples before testing with the cobas SARS-CoV-2 assay. This study aimed to determine if thermal treatment significantly affects the qualitative detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the quantitative measurement of cobas SARS-CoV-2 ORF1a and E-gene target copy number using an in-house quantitative method. A collection of positive (n = 238) and negative samples (n = 196) was tested in parallel comparing thermal treatment (75 °C for 15 minutes) to room-temperature. There were no significant differences in the final qualitative outcomes for thermal treatment versus room-temperature (99.8% agreement) despite a statistically significant reduction (P < 0.05) in target copy number following thermal treatment. The median ORF1a and E-gene reduction in target copy number was 0.07 (1.6%) and 0.22 (4.2%) log10 copies/mL respectively. The standard curves for both ORF1a and E-gene targets were highly linear (r2 = 0.99). Good correlation was observed for ORF1a (r2 = 0.96) and E-gene (r2 = 0.98) comparing thermal treatment to room-temperature control.
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Affiliation(s)
- Todd M Pryce
- Department of Clinical Microbiology, PathWest Laboratory Medicine WA, Fiona Stanley Hospital, Murdoch, Western Australia, Australia.
| | - Peter A Boan
- Department of Clinical Microbiology, PathWest Laboratory Medicine WA, Fiona Stanley Hospital, Murdoch, Western Australia, Australia; Department of Infectious Diseases, Fiona Stanley Fremantle Hospital Group, Murdoch, Western Australia, Australia
| | - Ian D Kay
- Department of Clinical Microbiology, PathWest Laboratory Medicine WA, Fiona Stanley Hospital, Murdoch, Western Australia, Australia
| | - James P Flexman
- Department of Clinical Microbiology, PathWest Laboratory Medicine WA, Fiona Stanley Hospital, Murdoch, Western Australia, Australia
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Tsang NNY, So HC, Ng KY, Cowling BJ, Leung GM, Ip DKM. Diagnostic performance of different sampling approaches for SARS-CoV-2 RT-PCR testing: a systematic review and meta-analysis. Lancet Infect Dis 2021; 21:1233-1245. [PMID: 33857405 PMCID: PMC8041361 DOI: 10.1016/s1473-3099(21)00146-8] [Citation(s) in RCA: 157] [Impact Index Per Article: 52.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 02/24/2021] [Accepted: 03/03/2021] [Indexed: 12/11/2022]
Abstract
BACKGROUND The comparative performance of different clinical sampling methods for diagnosis of SARS-CoV-2 infection by RT-PCR among populations with suspected infection remains unclear. This meta-analysis aims to systematically compare the diagnostic performance of different clinical specimen collection methods. METHODS In this systematic review and meta-analysis, we systematically searched PubMed, Embase, MEDLINE, Web of Science, medRxiv, bioRxiv, SSRN, and Research Square from Jan 1, 2000, to Nov 16, 2020. We included original clinical studies that examined the performance of nasopharyngeal swabs and any additional respiratory specimens for the diagnosis of SARS-CoV-2 infection among individuals presenting in ambulatory care. Studies without data on paired samples, or those that only examined different samples from confirmed SARS-CoV-2 cases were not useful for examining diagnostic performance of a test and were excluded. Diagnostic performance, including sensitivity, specificity, positive predictive value, and negative predictive value, was examined using random effects models and double arcsine transformation. FINDINGS Of the 5577 studies identified in our search, 23 studies including 7973 participants with 16 762 respiratory samples were included. Respiratory specimens examined in these studies included 7973 nasopharyngeal swabs, 1622 nasal swabs, 6110 saliva samples, 338 throat swabs, and 719 pooled nasal and throat swabs. Using nasopharyngeal swabs as the gold standard, pooled nasal and throat swabs gave the highest sensitivity of 97% (95% CI 93-100), whereas lower sensitivities were achieved by saliva (85%, 75-93) and nasal swabs (86%, 77-93) and a much lower sensitivity by throat swabs (68%, 35-94). A comparably high positive predictive value was obtained by pooled nasal and throat (97%, 90-100) and nasal swabs (96%, 87-100) and a slightly lower positive predictive value by saliva (93%, 88-97). Throat swabs have the lowest positive predictive value of 75% (95% CI 45-96). Comparably high specificities (range 97-99%) and negative predictive value (range 95-99%) were observed among different clinical specimens. Comparison between health-care-worker collection and self-collection for pooled nasal and throat swabs and nasal swabs showed comparable diagnostic performance. No significant heterogeneity was observed in the analysis of pooled nasal and throat swabs and throat swabs, whereas moderate to substantial heterogeneity (I2 ≥30%) was observed in studies on saliva and nasal swabs. INTERPRETATION Our review suggests that, compared with the gold standard of nasopharyngeal swabs, pooled nasal and throat swabs offered the best diagnostic performance of the alternative sampling approaches for diagnosis of SARS-CoV-2 infection in ambulatory care. Saliva and nasal swabs gave comparable and very good diagnostic performance and are clinically acceptable alternative specimen collection methods. Throat swabs gave a much lower sensitivity and positive predictive value and should not be recommended. Self-collection for pooled nasal and throat swabs and nasal swabs was not associated with any significant impairment of diagnostic accuracy. Our results also provide a useful reference framework for the proper interpretation of SARS-CoV-2 testing results using different clinical specimens. FUNDING Hong Kong Research Grants Council.
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Affiliation(s)
- Nicole Ngai Yung Tsang
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Hau Chi So
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Ka Yan Ng
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Benjamin J Cowling
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Gabriel M Leung
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Dennis Kai Ming Ip
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China.
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Tsang NNY, So HC, Ng KY, Cowling BJ, Leung GM, Ip DKM. Diagnostic performance of different sampling approaches for SARS-CoV-2 RT-PCR testing: a systematic review and meta-analysis. Lancet Infect Dis 2021. [PMID: 33857405 DOI: 10.1016/s1473-3099(1021)00146-00148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
BACKGROUND The comparative performance of different clinical sampling methods for diagnosis of SARS-CoV-2 infection by RT-PCR among populations with suspected infection remains unclear. This meta-analysis aims to systematically compare the diagnostic performance of different clinical specimen collection methods. METHODS In this systematic review and meta-analysis, we systematically searched PubMed, Embase, MEDLINE, Web of Science, medRxiv, bioRxiv, SSRN, and Research Square from Jan 1, 2000, to Nov 16, 2020. We included original clinical studies that examined the performance of nasopharyngeal swabs and any additional respiratory specimens for the diagnosis of SARS-CoV-2 infection among individuals presenting in ambulatory care. Studies without data on paired samples, or those that only examined different samples from confirmed SARS-CoV-2 cases were not useful for examining diagnostic performance of a test and were excluded. Diagnostic performance, including sensitivity, specificity, positive predictive value, and negative predictive value, was examined using random effects models and double arcsine transformation. FINDINGS Of the 5577 studies identified in our search, 23 studies including 7973 participants with 16 762 respiratory samples were included. Respiratory specimens examined in these studies included 7973 nasopharyngeal swabs, 1622 nasal swabs, 6110 saliva samples, 338 throat swabs, and 719 pooled nasal and throat swabs. Using nasopharyngeal swabs as the gold standard, pooled nasal and throat swabs gave the highest sensitivity of 97% (95% CI 93-100), whereas lower sensitivities were achieved by saliva (85%, 75-93) and nasal swabs (86%, 77-93) and a much lower sensitivity by throat swabs (68%, 35-94). A comparably high positive predictive value was obtained by pooled nasal and throat (97%, 90-100) and nasal swabs (96%, 87-100) and a slightly lower positive predictive value by saliva (93%, 88-97). Throat swabs have the lowest positive predictive value of 75% (95% CI 45-96). Comparably high specificities (range 97-99%) and negative predictive value (range 95-99%) were observed among different clinical specimens. Comparison between health-care-worker collection and self-collection for pooled nasal and throat swabs and nasal swabs showed comparable diagnostic performance. No significant heterogeneity was observed in the analysis of pooled nasal and throat swabs and throat swabs, whereas moderate to substantial heterogeneity (I2 ≥30%) was observed in studies on saliva and nasal swabs. INTERPRETATION Our review suggests that, compared with the gold standard of nasopharyngeal swabs, pooled nasal and throat swabs offered the best diagnostic performance of the alternative sampling approaches for diagnosis of SARS-CoV-2 infection in ambulatory care. Saliva and nasal swabs gave comparable and very good diagnostic performance and are clinically acceptable alternative specimen collection methods. Throat swabs gave a much lower sensitivity and positive predictive value and should not be recommended. Self-collection for pooled nasal and throat swabs and nasal swabs was not associated with any significant impairment of diagnostic accuracy. Our results also provide a useful reference framework for the proper interpretation of SARS-CoV-2 testing results using different clinical specimens. FUNDING Hong Kong Research Grants Council.
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Affiliation(s)
- Nicole Ngai Yung Tsang
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Hau Chi So
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Ka Yan Ng
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Benjamin J Cowling
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Gabriel M Leung
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Dennis Kai Ming Ip
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China.
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10
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de Koff EM, Euser SM, Badoux P, Sluiter-Post J, Eggink D, Sanders EAM, van Houten MA. Respiratory Pathogen Detection in Children: Saliva as a Diagnostic Specimen. Pediatr Infect Dis J 2021; 40:e351-e353. [PMID: 34260500 DOI: 10.1097/inf.0000000000003191] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
We compared pathogen detection between saliva, nasopharyngeal and oropharyngeal swabs in children with respiratory symptoms. The sensitivity in nasopharyngeal swabs was 93% (95% confidence interval [CI]: 78%-98%), in oropharyngeal swabs 79% (95% CI: 60%-90%), in saliva overall 76% (95% CI: 58%-88%) and in 18 saliva samples collected with drooling or sponges, 94% (95% CI: 74%-99%). Saliva could be a relevant specimen alternative.
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Affiliation(s)
- Emma M de Koff
- From the Spaarne Academy, Spaarne Gasthuis, Hoofddorp and Haarlem, The Netherlands
- Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Sjoerd M Euser
- Regional Public Health Laboratory Kennemerland, Haarlem, The Netherlands
| | - Paul Badoux
- Regional Public Health Laboratory Kennemerland, Haarlem, The Netherlands
| | - Judith Sluiter-Post
- From the Spaarne Academy, Spaarne Gasthuis, Hoofddorp and Haarlem, The Netherlands
| | - Dirk Eggink
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Elisabeth A M Sanders
- Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Marlies A van Houten
- From the Spaarne Academy, Spaarne Gasthuis, Hoofddorp and Haarlem, The Netherlands
- Department of Pediatrics, Spaarne Gasthuis, Hoofddorp and Haarlem, The Netherlands
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11
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Morehouse ZP, Samikwa L, Proctor CM, Meleke H, Kamdolozi M, Ryan GL, Chaima D, Ho A, Nash RJ, Nyirenda TS. Validation of a direct-to-PCR COVID-19 detection protocol utilizing mechanical homogenization: A model for reducing resources needed for accurate testing. PLoS One 2021; 16:e0256316. [PMID: 34407126 PMCID: PMC8372900 DOI: 10.1371/journal.pone.0256316] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 08/03/2021] [Indexed: 12/18/2022] Open
Abstract
Efficient and effective viral detection methodologies are a critical piece in the global response to COVID-19, with PCR-based nasopharyngeal and oropharyngeal swab testing serving as the current gold standard. With over 100 million confirmed cases globally, the supply chains supporting these PCR testing efforts are under a tremendous amount of stress, driving the need for innovative and accurate diagnostic solutions. Herein, the utility of a direct-to-PCR method of SARS-CoV-2 detection grounded in mechanical homogenization is examined for reducing resources needed for testing while maintaining a comparable sensitivity to the current gold standard workflow of nasopharyngeal and oropharyngeal swab testing. In a head-to-head comparison of 30 patient samples, this initial clinical validation study of the proposed homogenization-based workflow demonstrated significant agreeability with the current extraction-based method utilized while cutting the total resources needed in half.
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Affiliation(s)
- Zachary P. Morehouse
- Michigan State University College of Osteopathic Medicine, East Lansing, Michigan, United States of America
- Omni International Inc, A PerkinElmer Company, Kennesaw, Georgia, United States of America
- Jeevan BioSciences, Tucker, Georgia, United States of America
| | - Lyson Samikwa
- Department of Pathology, College of Medicine, University of Malawi, Blantyre, Malawi
| | - Caleb M. Proctor
- Omni International Inc, A PerkinElmer Company, Kennesaw, Georgia, United States of America
| | - Harry Meleke
- Department of Pathology, College of Medicine, University of Malawi, Blantyre, Malawi
| | - Mercy Kamdolozi
- Department of Pathology, College of Medicine, University of Malawi, Blantyre, Malawi
| | - Gabriella L. Ryan
- Omni International Inc, A PerkinElmer Company, Kennesaw, Georgia, United States of America
| | - David Chaima
- Department of Pathology, College of Medicine, University of Malawi, Blantyre, Malawi
| | - Antonia Ho
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Rodney J. Nash
- Omni International Inc, A PerkinElmer Company, Kennesaw, Georgia, United States of America
- Jeevan BioSciences, Tucker, Georgia, United States of America
- Department of Biology, Georgia State University, Atlanta, Georgia, United States of America
| | - Tonney S. Nyirenda
- Department of Pathology, College of Medicine, University of Malawi, Blantyre, Malawi
- * E-mail:
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12
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Syrjänen S, Syrjänen K. HPV-Associated Benign Squamous Cell Papillomas in the Upper Aero-Digestive Tract and Their Malignant Potential. Viruses 2021; 13:v13081624. [PMID: 34452488 PMCID: PMC8402864 DOI: 10.3390/v13081624] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 08/11/2021] [Accepted: 08/13/2021] [Indexed: 12/18/2022] Open
Abstract
Squamous cell papilloma (SCP) in the upper aero-digestive tract is a rare disease entity with bimodal age presentation both at childhood and in adults. It originates from stratified squamous and/or respiratory epithelium. Traditionally, SCPs have been linked to chemical or mechanical irritation but, since the 1980s, they have also been associated with human papillomavirus (HPV) infection. Approximately 30% of the head and neck SCPs are associated with HPV infection, with this association being highest for laryngeal papillomas (76–94%), followed by oral (27–48%), sinonasal (25–40%), and oropharyngeal papillomas (6–7%). There is, however, a wide variation in HPV prevalence, the highest being in esophageal SCPs (11–57%). HPV6 and HPV11 are the two main HPV genotypes present, but these are also high-risk HPVs as they are infrequently detected. Some 20% of the oral and oropharyngeal papillomas also contain cutaneous HPV genotypes. Despite their benign morphology, some SCPs tend to recur and even undergo malignant transformation. The highest malignant potential is associated with sinonasal inverted papillomas (7–11%). This review discusses the evidence regarding HPV etiology of benign SCPs in the upper aero-digestive tract and their HPV-related malignant transformation. In addition, studies on HPV exposure at an early age are discussed, as are the animal models shedding light on HPV transmission, viral latency, and its reactivation.
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Affiliation(s)
- Stina Syrjänen
- Department of Oral Pathology and Oral Radiology, Institute of Dentistry, Faculty of Medicine, University of Turku, 20520 Turku, Finland
- Department of Pathology, Turku University Hospital, 20521 Turku, Finland
- Correspondence:
| | - Kari Syrjänen
- Department of Clinical Research, Biohit Oyj, 00880 Helsinki, Finland;
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13
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Bergevin MA, Freppel W, Robert G, Ambaraghassi G, Aubry D, Haeck O, Saint-Jean M, Carignan A. Validation of saliva sampling as an alternative to oro-nasopharyngeal swab for detection of SARS-CoV-2 using unextracted rRT-PCR with the Allplex 2019-nCoV assay. J Med Microbiol 2021; 70:001404. [PMID: 34369860 PMCID: PMC8513629 DOI: 10.1099/jmm.0.001404] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 06/10/2021] [Indexed: 12/23/2022] Open
Abstract
Introduction. The current severe acute respiratory syndrome-associated coronavirus-2 (SARS-CoV-2) pandemic has stressed the global supply chain for specialized equipment, including flocked swabs.Hypothesis. Saliva could be a potential alternative specimen source for diagnosis of SARS-CoV-2 infection by reverse-transcriptase PCR (RT-PCR).Aim. To compare the detection efficiency of SARS-CoV-2 RNA in saliva and oro-nasopharyngeal swab (ONPS) specimens.Methodology. Patients recruited from hospital provided paired saliva and ONPS specimens. We performed manual or automated RT-PCR with prior proteinase K treatment without RNA extraction using the Seegene Allplex 2019 nCoV assay.Results. Of the 773 specimen pairs, 165 (21.3 %) had at least one positive sample. Additionally, 138 specimens tested positive by both sampling methods. Fifteen and 12 cases were detected only by nasopharyngeal swab and saliva, respectively. The sensitivity of ONPS (153/165; 92.7 %; 95 % CI: 88.8-96.7) was similar to that of saliva (150/165; 90.9 %; 95 % CI: 86.5-95.3; P=0.5). In patients with symptoms for ≤ 10 days, the sensitivity of ONPS (118/126; 93.7 %; 95 % CI: 89.4-97.9) was similar to that of saliva (122/126; 96.8 %; 95 % CI: 93.8-99.9 %; P=0.9). However, the sensitivity of ONPS (20/22; 95.2 %; 95 % CI: 86.1-100) was higher than that of saliva (16/22; 71.4 %; 95 % CI: 52.1-90.8) in patients with symptoms for more than 10 days.Conclusions. Saliva sampling is an acceptable alternative to ONPS for diagnosing SARS-CoV-2 infection in symptomatic individuals displaying symptoms for ≤ 10 days. These results reinforce the need to expand the use of saliva samples, which are self-collected and do not require swabs.
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Affiliation(s)
| | - Wesley Freppel
- Institut National de la Recherche Scientifique, Centre Armand-Frappier Santé Biotechnologie, Laval, Quebec, Canada
| | - Guylaine Robert
- Department of Medical Biology, Hôpital Cité-de-la-Santé, Laval, QC H7M 3L9, Canada
| | - Georges Ambaraghassi
- Department of Microbiology, Immunology and Infectious Diseases, Faculty of Medicine, Université de Montréal, Montreal, Quebec, Canada
| | - Dany Aubry
- Optilab Laval-Laurentides-Lanaudière, Quebec, Canada
| | - Olivier Haeck
- Department of Medical Biology, Hôpital Cité-de-la-Santé, Laval, QC H7M 3L9, Canada
| | - Maude Saint-Jean
- Department of Medical Biology, Hôpital Cité-de-la-Santé, Laval, QC H7M 3L9, Canada
| | - Alex Carignan
- Department of Microbiology and Infectious Diseases, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Quebec, Canada
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14
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Klaus J, Zini E, Hartmann K, Egberink H, Kipar A, Bergmann M, Palizzotto C, Zhao S, Rossi F, Franco V, Porporato F, Hofmann-Lehmann R, Meli ML. SARS-CoV-2 Infection in Dogs and Cats from Southern Germany and Northern Italy during the First Wave of the COVID-19 Pandemic. Viruses 2021; 13:1453. [PMID: 34452319 PMCID: PMC8402904 DOI: 10.3390/v13081453] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/22/2021] [Accepted: 07/23/2021] [Indexed: 12/29/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has affected millions of people globally since its first detection in late 2019. Besides humans, cats and, to some extent, dogs were shown to be susceptible to SARS-CoV-2, highlighting the need for surveillance in a One Health context. Seven veterinary clinics from regions with high incidences of coronavirus disease (COVID-19) were recruited during the early pandemic (March to July 2020) for the screening of patients. A total of 2257 oropharyngeal and nasal swab specimen from 877 dogs and 260 cats (including 18 animals from COVID-19-affected households and 92 animals with signs of respiratory disease) were analyzed for the presence of SARS-CoV-2 RNA using reverse transcriptase real-time polymerase chain reaction (RT-qPCR) targeting the viral envelope (E) and RNA dependent RNA polymerase (RdRp) genes. One oropharyngeal swab from an Italian cat, living in a COVID-19-affected household in Piedmont, tested positive in RT-qPCR (1/260; 0.38%, 95% CI: 0.01-2.1%), and SARS-CoV-2 infection of the animal was serologically confirmed six months later. One oropharyngeal swab from a dog was potentially positive (1/877; 0.1%, 95% CI: 0.002-0.63%), but the result was not confirmed in a reference laboratory. Analyses of convenience sera from 118 animals identified one dog (1/94; 1.1%; 95% CI: 0.02-5.7%) from Lombardy, but no cats (0/24), as positive for anti-SARS-CoV-2 receptor binding domain (RBD) antibodies and neutralizing activity. These findings support the hypothesis that the prevalence of SARS-CoV-2 infection in pet cat and dog populations, and hence, the risk of zoonotic transmission to veterinary staff, was low during the first wave of the pandemic, even in hotspot areas.
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Affiliation(s)
- Julia Klaus
- Clinical Laboratory, Department of Clinical Diagnostics and Services, and Center for Clinical Studies, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 260, 8057 Zurich, Switzerland; (R.H.-L.); (M.L.M.)
| | - Eric Zini
- AniCura Istituto Veterinario Novara, Strada Provinciale 9, 28060 Granozzo con Monticello, Novara, Italy; (E.Z.); (C.P.); (F.R.); (V.F.); (F.P.)
- Clinic for Small Animal Internal Medicine, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 260, 8057 Zurich, Switzerland
- Department of Animal Medicine, Production and Health, University of Padova, Viale dell′Università 16, 35020 Legnaro, Padova, Italy
| | - Katrin Hartmann
- Centre for Clinical Veterinary Medicine, Clinic of Small Animal Medicine, LMU Munich, 80539 Munich, Germany; (K.H.); (M.B.)
| | - Herman Egberink
- Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, University of Utrecht, 3584 CL Utrecht, The Netherlands; (H.E.); (S.Z.)
| | - Anja Kipar
- Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 268, 8057 Zurich, Switzerland;
| | - Michèle Bergmann
- Centre for Clinical Veterinary Medicine, Clinic of Small Animal Medicine, LMU Munich, 80539 Munich, Germany; (K.H.); (M.B.)
| | - Carlo Palizzotto
- AniCura Istituto Veterinario Novara, Strada Provinciale 9, 28060 Granozzo con Monticello, Novara, Italy; (E.Z.); (C.P.); (F.R.); (V.F.); (F.P.)
| | - Shan Zhao
- Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, University of Utrecht, 3584 CL Utrecht, The Netherlands; (H.E.); (S.Z.)
- Research Center of Swine Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
| | - Francesco Rossi
- AniCura Istituto Veterinario Novara, Strada Provinciale 9, 28060 Granozzo con Monticello, Novara, Italy; (E.Z.); (C.P.); (F.R.); (V.F.); (F.P.)
| | - Vittoria Franco
- AniCura Istituto Veterinario Novara, Strada Provinciale 9, 28060 Granozzo con Monticello, Novara, Italy; (E.Z.); (C.P.); (F.R.); (V.F.); (F.P.)
| | - Federico Porporato
- AniCura Istituto Veterinario Novara, Strada Provinciale 9, 28060 Granozzo con Monticello, Novara, Italy; (E.Z.); (C.P.); (F.R.); (V.F.); (F.P.)
| | - Regina Hofmann-Lehmann
- Clinical Laboratory, Department of Clinical Diagnostics and Services, and Center for Clinical Studies, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 260, 8057 Zurich, Switzerland; (R.H.-L.); (M.L.M.)
| | - Marina L. Meli
- Clinical Laboratory, Department of Clinical Diagnostics and Services, and Center for Clinical Studies, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 260, 8057 Zurich, Switzerland; (R.H.-L.); (M.L.M.)
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15
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Song Y, Chen C, Wang Y, Zhang J, Chen M, Gao G, Wang S, Yang D, Song R, Wang L, Xie W, Yu F, Yan L, Wang Y, Zeng H, Zhang F. Early and consecutive RT-PCR tests with both oropharyngeal swabs and sputum could improve testing yield for patients with COVID-19: An observation cohort study in China. Int J Infect Dis 2021; 107:242-246. [PMID: 33930545 PMCID: PMC8079261 DOI: 10.1016/j.ijid.2021.04.076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 04/20/2021] [Accepted: 04/23/2021] [Indexed: 11/30/2022] Open
Abstract
Objective The real-time polymerase chain reaction (RT-PCR) test is recommended for the diagnosis of COVID-19 and provides a powerful tool to identify new infections and facilitate contact tracing. In fact, as the prevalence of COVID-19 decreases, this RT-PCR testing remains as the main preventive measure to avoid rebound. However, inconsistent results can lead to misdiagnoses in the clinic. These inconsistencies are due to the variability in (1) the collection times of biological samples post infection, and (2) sampling procedures. Methods We applied the Kaplan–Meier method and multivariate logistic regression on RT-PCR results from 258 confirmed patients with COVID-19 to evaluate the factors associated with negative conversion. We also estimated the proportion (%) of negative conversion among patients who had tested twice or more, and compared the proportions arising from oropharyngeal swabs, sputum, and combined double testing, respectively. Main results The proportion of negative conversion was 6.7% on day 4, 16.4% on day 7, 41.0% at 2 weeks, and 61.0% at 3 weeks post-admission. We also found that 34.1% and 60.3% of subjects had at least one negative RT-PCR result on days 7 and 14 after the onset of symptoms, respectively. The proportion of negative conversions following sputum testing was higher than that from oropharyngeal swabs in the early stages but this declined after the onset of symptoms. Conclusion In the absence of effective treatments or vaccines, efficient testing strategies are critical if we are to control the COVID-19 epidemic. According to this study, early, consecutive and combined double testing, will be the key to identify infected patients, particularly for asymptomatic and mild symptomatic cases. These strategies will minimize misdiagnosis and the ineffective isolation of infected patients.
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Affiliation(s)
- Yangzi Song
- Beijing Ditan Hospital, Capital Medical University, Beijing 100102, China; Beijing Key Laboratory of Emerging Infectious Diseases, Beijing 100102, China.
| | - Chen Chen
- Beijing Ditan Hospital, Capital Medical University, Beijing 100102, China; Beijing Key Laboratory of Emerging Infectious Diseases, Beijing 100102, China.
| | - Yu Wang
- Beijing Ditan Hospital, Capital Medical University, Beijing 100102, China.
| | - Ju Zhang
- Beijing Ditan Hospital, Capital Medical University, Beijing 100102, China; Beijing Key Laboratory of Emerging Infectious Diseases, Beijing 100102, China.
| | - Meiling Chen
- Beijing Ditan Hospital, Capital Medical University, Beijing 100102, China.
| | - Guiju Gao
- Beijing Ditan Hospital, Capital Medical University, Beijing 100102, China.
| | - Sa Wang
- Beijing Ditan Hospital, Capital Medical University, Beijing 100102, China.
| | - Di Yang
- Beijing Ditan Hospital, Capital Medical University, Beijing 100102, China.
| | - Rui Song
- Beijing Ditan Hospital, Capital Medical University, Beijing 100102, China.
| | - Linghang Wang
- Beijing Ditan Hospital, Capital Medical University, Beijing 100102, China.
| | - Wen Xie
- Beijing Ditan Hospital, Capital Medical University, Beijing 100102, China.
| | - Fengting Yu
- Beijing Ditan Hospital, Capital Medical University, Beijing 100102, China.
| | - Liting Yan
- Beijing Ditan Hospital, Capital Medical University, Beijing 100102, China.
| | - Yajie Wang
- Beijing Ditan Hospital, Capital Medical University, Beijing 100102, China.
| | - Hui Zeng
- Beijing Ditan Hospital, Capital Medical University, Beijing 100102, China; Beijing Key Laboratory of Emerging Infectious Diseases, Beijing 100102, China.
| | - Fujie Zhang
- Beijing Ditan Hospital, Capital Medical University, Beijing 100102, China; Beijing Key Laboratory of Emerging Infectious Diseases, Beijing 100102, China.
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16
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Lee RA, Herigon JC, Benedetti A, Pollock NR, Denkinger CM. Performance of Saliva, Oropharyngeal Swabs, and Nasal Swabs for SARS-CoV-2 Molecular Detection: a Systematic Review and Meta-analysis. J Clin Microbiol 2021; 59:JCM.02881-20. [PMID: 33504593 DOI: 10.1101/2020.11.12.20230748] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2023] Open
Abstract
Nasopharyngeal (NP) swabs are considered the highest-yield sample for diagnostic testing for respiratory viruses, including SARS-CoV-2. The need to increase capacity for SARS-CoV-2 testing in a variety of settings, combined with shortages of sample collection supplies, have motivated a search for alternative sample types with high sensitivity. We systematically reviewed the literature to understand the performance of alternative sample types compared to NP swabs. We systematically searched PubMed, Google Scholar, medRxiv, and bioRxiv (last retrieval 1 October 2020) for comparative studies of alternative specimen types (saliva, oropharyngeal [OP], and nasal [NS] swabs) versus NP swabs for SARS-CoV-2 diagnosis using nucleic acid amplification testing (NAAT). A logistic-normal random-effects meta-analysis was performed to calculate % positive alternative-specimen, % positive NP, and % dual positives overall and in subgroups. The QUADAS 2 tool was used to assess bias. From 1,253 unique citations, we identified 25 saliva, 11 NS, 6 OP, and 4 OP/NS studies meeting inclusion criteria. Three specimen types captured lower % positives (NS [82%, 95% CI: 73 to 90%], OP [84%, 95% CI: 57 to 100%], and saliva [88%, 95% CI: 81 to 93%]) than NP swabs, while combined OP/NS matched NP performance (97%, 95% CI: 90 to 100%). Absence of RNA extraction (saliva) and utilization of a more sensitive NAAT (NS) substantially decreased alternative-specimen yield of positive samples. NP swabs remain the gold standard for diagnosis of SARS-CoV-2, although alternative specimens are promising. Much remains unknown about the impact of variations in specimen collection, processing protocols, and population (pediatric versus adult, late versus early in disease course), such that head-to head studies of sampling strategies are urgently needed.
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Affiliation(s)
- Rose A Lee
- Division of Infectious Diseases, Department of Pediatrics, Boston Children's Hospital, Boston, Massachusetts, USA
- Division of Infectious Diseases, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Joshua C Herigon
- Division of Infectious Diseases, Department of Pediatrics, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Andrea Benedetti
- Department of Medicine and of Epidemiology, Biostatistics & Occupational Health, McGill University, Montreal, Quebec, Canada
| | - Nira R Pollock
- Division of Infectious Diseases, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
- Department of Laboratory Medicine, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Claudia M Denkinger
- Division of Clinical Tropical Medicine, Center of Infectious Diseases, Heidelberg University Hospital, Heidelberg, Germany
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17
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Lee RA, Herigon JC, Benedetti A, Pollock NR, Denkinger CM. Performance of Saliva, Oropharyngeal Swabs, and Nasal Swabs for SARS-CoV-2 Molecular Detection: a Systematic Review and Meta-analysis. J Clin Microbiol 2021; 59:e02881-20. [PMID: 33504593 PMCID: PMC8091856 DOI: 10.1128/jcm.02881-20] [Citation(s) in RCA: 181] [Impact Index Per Article: 60.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Nasopharyngeal (NP) swabs are considered the highest-yield sample for diagnostic testing for respiratory viruses, including SARS-CoV-2. The need to increase capacity for SARS-CoV-2 testing in a variety of settings, combined with shortages of sample collection supplies, have motivated a search for alternative sample types with high sensitivity. We systematically reviewed the literature to understand the performance of alternative sample types compared to NP swabs. We systematically searched PubMed, Google Scholar, medRxiv, and bioRxiv (last retrieval 1 October 2020) for comparative studies of alternative specimen types (saliva, oropharyngeal [OP], and nasal [NS] swabs) versus NP swabs for SARS-CoV-2 diagnosis using nucleic acid amplification testing (NAAT). A logistic-normal random-effects meta-analysis was performed to calculate % positive alternative-specimen, % positive NP, and % dual positives overall and in subgroups. The QUADAS 2 tool was used to assess bias. From 1,253 unique citations, we identified 25 saliva, 11 NS, 6 OP, and 4 OP/NS studies meeting inclusion criteria. Three specimen types captured lower % positives (NS [82%, 95% CI: 73 to 90%], OP [84%, 95% CI: 57 to 100%], and saliva [88%, 95% CI: 81 to 93%]) than NP swabs, while combined OP/NS matched NP performance (97%, 95% CI: 90 to 100%). Absence of RNA extraction (saliva) and utilization of a more sensitive NAAT (NS) substantially decreased alternative-specimen yield of positive samples. NP swabs remain the gold standard for diagnosis of SARS-CoV-2, although alternative specimens are promising. Much remains unknown about the impact of variations in specimen collection, processing protocols, and population (pediatric versus adult, late versus early in disease course), such that head-to head studies of sampling strategies are urgently needed.
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Affiliation(s)
- Rose A Lee
- Division of Infectious Diseases, Department of Pediatrics, Boston Children's Hospital, Boston, Massachusetts, USA
- Division of Infectious Diseases, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Joshua C Herigon
- Division of Infectious Diseases, Department of Pediatrics, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Andrea Benedetti
- Department of Medicine and of Epidemiology, Biostatistics & Occupational Health, McGill University, Montreal, Quebec, Canada
| | - Nira R Pollock
- Division of Infectious Diseases, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
- Department of Laboratory Medicine, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Claudia M Denkinger
- Division of Clinical Tropical Medicine, Center of Infectious Diseases, Heidelberg University Hospital, Heidelberg, Germany
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Sonnleitner ST, Dorighi J, Jansen B, Schönegger C, Gietl S, Koblmüller S, Sturmbauer C, Posch W, Walder G. 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; 18:71. [PMID: 33827618 PMCID: PMC8025900 DOI: 10.1186/s12985-021-01542-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Accepted: 03/31/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND At the beginning of the pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), little was known about its actual rate of infectivity and any COVID-19 patient positive in laboratory testing was supposed to be highly infective and a public health risk factor. METHODS One hundred oropharyngeal samples were obtained during routine work flow of testing symptomatic persons by quantitative polymerase chain reaction (qPCR) and were inoculated onto cell culture of VeroB4 cells to study the degree of infectivity of SARS-CoV-2 in vitro. Quantification by virus titration and an external standard using synthetic RNA gave the breaking point of infectivity in SARS-CoV-2 in vitro. RESULTS A clear negative correlation (r = - 0.76; p < 0.05) could be asserted between the viral load in quantitative polymerase chain reaction (qPCR) and the probability of a successful isolation in serial isolation experiments of specific oropharyngeal samples positive in qPCR. Quantification by virus titration and an external standard using synthetic RNA indicate a Cq between 27 and 30 in E-gene screening PCR as a breaking point in vitro, where infectivity decreases significantly and isolations become less probable. CONCLUSIONS This study showed that only the 21% of samples with the highest viral load were infectious enough to transmit the virus in vitro and determined that the dispersion rate in vitro is surprisingly close to those calculated in large retrospective epidemiological studies for SARS-CoV-2. This raises the question of whether this simple in vitro model is suitable to give first insights in dispersion characters of novel or neglected viral pathogens. The statement that SARS-CoV-2 needs at least 40,000 copies to reliably induce infection in vitro is an indication of its transmissibility in Public Health decisions. Applying quantitative PCR systems in diagnosis of SARS-CoV2 can distinguish between patients providing a high risk of transmission and those, where the risk of transmission is probably limited to close and long-lasting contacts.
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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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19
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Todsen T, Tolsgaard M, Folke F, Jakobsen KK, Ersbøll AK, Benfield T, von Buchwald C, Kirkby N. SARS-CoV-2 in saliva, oropharyngeal and nasopharyngeal specimens. Dan Med J 2021; 68:A01210087. [PMID: 33832565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
INTRODUCTION The reference test to evaluate patients with suspected respiratory virus infection is a real-time reverse transcription-polymerase chain reaction (RT-PCR) from a nasopharyngeal swab (NPS). However, other specimen collection methods such as an oropharyngeal swab (OPS) or saliva specimen are also used for SARS-CoV-2 testing during the ongoing COVID-19 pandemic. However, it remains unclear if rates of SARS-CoV-2 detection differ between sampling methods. This study will compare the rates of SARS-CoV-2 detection by saliva, OPS, and NPS sampling in a public setting. METHODS Individuals referred for outpatient SARS-CoV-2 testing will be invited to participate in a prospective clinical study. They will have saliva, OPS and NPS specimens collected that will be analysed separately for SARS-CoV-2 RNA by RT-PCR. The rate of SARS-CoV-2 detection in saliva, OPS and NPS will be compared using a logistic regression mixed-effect model analysis. A sample of 19,110 participants is required at an expected 1.5% test-positive rate in order to detect a 25.6% difference. The total sample size will be adjusted as the test-positive rate changes. CONCLUSIONS This study will provide evidence for the optimal site of specimen collection to detect SARS-CoV-2. The results may help guide the health authorities. FUNDING This is an investigator-initiated trial based on an unrestricted grant from the Novo Nordisk Foundation and the Aage og Johanne Louis-Hansens Fond. The foundations have had no say in the decisions on study design or reporting. TRIAL REGISTRATION ClinicalTrials.gov (ID: NCT04715607).
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20
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Sharma K, Aggarwala P, Gandhi D, Mathias A, Singh P, Sharma S, Negi SS, Bhargava A, Das P, Gaikwad U, Wankhede A, Behra A, Nagarkar NM. Comparative analysis of various clinical specimens in detection of SARS-CoV-2 using rRT-PCR in new and follow up cases of COVID-19 infection: Quest for the best choice. PLoS One 2021; 16:e0249408. [PMID: 33819290 PMCID: PMC8021168 DOI: 10.1371/journal.pone.0249408] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 03/18/2021] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND An appropriate specimen is of paramount importance in Real Time reverse transcription-polymerase chain reaction (rRT-PCR) based diagnosis of novel coronavirus (nCoV) disease (COVID-19). Thus, it's pertinent to evaluate various diversified clinical specimens' diagnostic utility in both diagnosis and follow-up of COVID-19. METHODS A total of 924 initial specimens from 130 COVID-19 symptomatic cases before initiation of treatment and 665 follow up specimens from 15 randomly selected cases comprising of equal number of nasopharyngeal swab (NPS), oropharyngeal swab (OPS), combined NPS and OPS (Combined swab), sputum, plasma, serum and urine were evaluated by rRT-PCR. RESULTS Demographic analysis showed males (86) twice more affected by COVID-19 than females (44) (p = 0.00001). Combined swabs showed a positivity rate of 100% followed by NPS (91.5%), OPS (72.3%), sputum (63%), while nCoV was found undetected in urine, plasma and serum specimens. The lowest cycle threshold (Ct) values of targeted genes E, ORF1b and RdRP are 10.56, 10.14 and 12.26 respectively and their lowest average Ct values were found in combined swab which indicates high viral load in combined swab among all other specimen types. Analysis of 665 follow-up multi-varied specimens also showed combined swab as the last specimen among all specimen types to become negative, after an average 6.6 (range 4-10) days post-treatment, having lowest (15.48) and average (29.96) Ct values of ORF1b respectively indicating posterior nasopharyngeal tract as primary nCoV afflicted site with high viral load. CONCLUSION The combined swab may be recommended as a more appropriate specimen for both diagnosis and monitoring of COVID-19 treatment by rRT-PCR for assessing virus clearance to help physicians in taking evidence-based decision before discharging patients. Implementing combined swabs globally will definitely help in management and control of the pandemic, as it is the need of the hour.
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Affiliation(s)
- Kuldeep Sharma
- Microbiology Department, AIIMS, Raipur, Chhattisgarh, India
| | | | - Deepa Gandhi
- Microbiology Department, AIIMS, Raipur, Chhattisgarh, India
| | | | - Priyanka Singh
- Microbiology Department, AIIMS, Raipur, Chhattisgarh, India
| | - Somya Sharma
- Microbiology Department, AIIMS, Raipur, Chhattisgarh, India
| | - Sanjay Singh Negi
- Microbiology Department, AIIMS, Raipur, Chhattisgarh, India
- * E-mail:
| | | | - Padma Das
- Microbiology Department, AIIMS, Raipur, Chhattisgarh, India
| | | | | | - Ajoy Behra
- Department of Pulmonary Medicine, AIIMS, Raipur, Chhattisgarh, India
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21
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Rao M, Rashid FA, Sabri FSAH, Jamil NN, Seradja V, Abdullah NA, Ahmad H, Aren SL, Ali SAS, Ghazali M, Manaf AA, Talib H, Hashim R, Zain R, Thayan R, Amran F, Aris T, Ahmad N. COVID-19 screening test by using random oropharyngeal saliva. J Med Virol 2021; 93:2461-2466. [PMID: 33393672 PMCID: PMC7986796 DOI: 10.1002/jmv.26773] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 12/20/2020] [Accepted: 12/30/2020] [Indexed: 12/13/2022]
Abstract
An optimal clinical specimen for accurate detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by minimizing the usage of consumables and reduce hazard exposure to healthcare workers is an urgent priority. The diagnostic performance of SARS-CoV-2 detection between healthcare worker-collected nasopharyngeal and oropharyngeal (NP + OP) swabs and patient performed self-collected random saliva was assessed. Paired NP + OP swabs and random saliva were collected and processed within 48 h of specimen collection from two cohort studies which recruited 562 asymptomatic adult candidates. Real-time reverse-transcription polymerase chain reaction targeting Open reading frame 1a (ORF1a) and nucleocapsid (N) genes was performed and the results were compared. Overall, 65 of 562 (28.1%) candidates tested positive for COVID-19 based on random saliva, NP + OP swabs, or both testing techniques. The detection rate of SARS-CoV-2 was higher in random saliva compared to NP + OP testing (92.3%; 60/65 vs. 73.8%; 48/65; p < .05). The estimated sensitivity and specificity of random saliva were higher than NP + OP swabs (95.0; 99.9 vs. 72.2; 99.4). The Ct values of ORF1a and N genes were significantly lower in random saliva compared to NP + OP swabs specimens. Our findings demonstrate that random saliva is an alternative diagnostic specimen for the detection of SARS-CoV-2. Self-collected random oropharyngeal saliva is a valuable specimen that provides accurate SARS-CoV-2 surveillance testing of a community.
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Affiliation(s)
- Mohan Rao
- Infectious Disease Research Centre, Institute for Medical ResearchMinistry of Health MalaysiaJalan PahangKuala LumpurMalaysia
| | - Fairuz A. Rashid
- Infectious Disease Research Centre, Institute for Medical ResearchMinistry of Health MalaysiaJalan PahangKuala LumpurMalaysia
| | - Fashihah S. A. H. Sabri
- Infectious Disease Research Centre, Institute for Medical ResearchMinistry of Health MalaysiaJalan PahangKuala LumpurMalaysia
| | - Nur Nadia Jamil
- Infectious Disease Research Centre, Institute for Medical ResearchMinistry of Health MalaysiaJalan PahangKuala LumpurMalaysia
| | - Valentinus Seradja
- Infectious Disease Research Centre, Institute for Medical ResearchMinistry of Health MalaysiaJalan PahangKuala LumpurMalaysia
| | | | | | - S. L. Aren
- Kota Setar District Health OfficeKedahMalaysia
| | | | - Mawaddah Ghazali
- Kuala Lumpur International Airport Health OfficeSelangorMalaysia
| | - Anizan A. Manaf
- Kuala Lumpur International Airport Health OfficeSelangorMalaysia
| | - Harishah Talib
- Kuala Lumpur International Airport Health OfficeSelangorMalaysia
| | - Rohaidah Hashim
- Infectious Disease Research Centre, Institute for Medical ResearchMinistry of Health MalaysiaJalan PahangKuala LumpurMalaysia
| | - Rozainanee Zain
- Infectious Disease Research Centre, Institute for Medical ResearchMinistry of Health MalaysiaJalan PahangKuala LumpurMalaysia
| | - Ravindran Thayan
- Infectious Disease Research Centre, Institute for Medical ResearchMinistry of Health MalaysiaJalan PahangKuala LumpurMalaysia
| | - Fairuz Amran
- Infectious Disease Research Centre, Institute for Medical ResearchMinistry of Health MalaysiaJalan PahangKuala LumpurMalaysia
| | - Tahir Aris
- Infectious Disease Research Centre, Institute for Medical ResearchMinistry of Health MalaysiaJalan PahangKuala LumpurMalaysia
| | - Norazah Ahmad
- Infectious Disease Research Centre, Institute for Medical ResearchMinistry of Health MalaysiaJalan PahangKuala LumpurMalaysia
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22
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Dias HG, Resck MEB, Caldas GC, Resck AF, da Silva NV, dos Santos AMV, Sousa TDC, Ogrzewalska MH, Siqueira MM, Pauvolid-Corrêa A, dos Santos FB. Neutralizing antibodies for SARS-CoV-2 in stray animals from Rio de Janeiro, Brazil. PLoS One 2021; 16:e0248578. [PMID: 33765012 PMCID: PMC7993851 DOI: 10.1371/journal.pone.0248578] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 03/02/2021] [Indexed: 02/07/2023] Open
Abstract
The epidemic of coronavirus disease 2019 (COVID-19), caused by a novel Betacoronavirus named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) became a public health emergency worldwide. Few reports indicate that owned pets from households with at least one human resident that was diagnosed with COVID-19 can be infected by SARS-CoV-2. However, the exposure to SARS-CoV-2 of pets from households with no COVID-19 cases or stray animals remains less assessed. Using real-time reverse transcriptase polymerase chain reaction (RT-PCR) and plaque reduction neutralization test (PRNT90), we investigated the infection and previous exposure of dogs and cats to SARS-CoV-2 during the ongoing COVID-19 epidemic in Rio de Janeiro, Brazil. From June to August 2020, 96 animals were sampled, including 49 cats (40 owned and 9 stray) and 47 dogs (42 owned and 5 stray). Regarding owned pets, 75.6% (62/82) belonged to households with no COVID-19 cases. Samples included serum, and rectal and oropharyngeal swabs. All swabs were negative for SARS-CoV-2 RNA, but serum samples of a stray cat and a stray dog presented neutralizing antibodies for SARS-CoV-2, with PRNT90 titer of 80 and 40, respectively. Serological data presented here suggest that not only owned pets from households with COVID19 cases, but also stray animals are being exposed to SARS-CoV-2 during the COVID-19 pandemic.
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Affiliation(s)
- Helver Gonçalves Dias
- Laboratório de Imunologia Viral, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brasil
| | - Maria Eduarda Barreto Resck
- Laboratório de Mosquitos Transmissores de Hematozoários, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brasil
| | - Gabriela Cardoso Caldas
- Laboratório de Morfologia e Morfogênese Viral, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brasil
| | | | - Natália Valente da Silva
- Laboratório de Vírus Respiratórios e Sarampo, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brasil
| | | | - Thiago das Chagas Sousa
- Laboratório de Vírus Respiratórios e Sarampo, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brasil
| | - Maria Halina Ogrzewalska
- Laboratório de Vírus Respiratórios e Sarampo, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brasil
| | - Marilda Mendonça Siqueira
- Laboratório de Vírus Respiratórios e Sarampo, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brasil
| | - Alex Pauvolid-Corrêa
- Laboratório de Vírus Respiratórios e Sarampo, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brasil
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas, United States of America
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Umair M, Ikram A, Salman M, Khurshid A, Alam M, Badar N, Suleman R, Tahir F, Sharif S, Montgomery J, Whitmer S, Klena J. Whole-genome sequencing of SARS-CoV-2 reveals the detection of G614 variant in Pakistan. PLoS One 2021; 16:e0248371. [PMID: 33755704 PMCID: PMC7987156 DOI: 10.1371/journal.pone.0248371] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 02/25/2021] [Indexed: 12/22/2022] Open
Abstract
Since its emergence in China, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread worldwide including Pakistan. During the pandemic, whole genome sequencing has played an important role in understanding the evolution and genomic diversity of SARS-CoV-2. Although an unprecedented number of SARS-CoV-2 full genomes have been submitted in GISAID and NCBI, data from Pakistan is scarce. We report the sequencing, genomic characterization, and phylogenetic analysis of five SARS-CoV-2 strains isolated from patients in Pakistan. The oropharyngeal swabs of patients that were confirmed positive for SARS-CoV-2 through real-time RT-PCR at National Institute of Health, Pakistan, were selected for whole-genome sequencing. Sequencing was performed using NEBNext Ultra II Directional RNA Library Prep kit for Illumina (NEW ENGLAND BioLabs Inc., MA, US) and Illumina iSeq 100 instrument (Illumina, San Diego, US). Based on whole-genome analysis, three Pakistani SARS-CoV-2 strains clustered into the 20A (GH) clade along with the strains from Oman, Slovakia, United States, and Pakistani strain EPI_ISL_513925. The two 19B (S)-clade strains were closely related to viruses from India and Oman. Overall, twenty-nine amino acid mutations were detected in the current study genome sequences, including fifteen missense and four novel mutations. Notably, we have found a D614G (aspartic acid to glycine) mutation in spike protein of the sequences from the GH clade. The G614 variant carrying the characteristic D614G mutation has been shown to be more infectious that lead to its rapid spread worldwide. This report highlights the detection of GH and S clade strains and G614 variant from Pakistan warranting large-scale whole-genome sequencing of strains prevalent in different regions to understand virus evolution and to explore their genetic diversity.
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Affiliation(s)
- Massab Umair
- National Institute of Health, Islamabad, Pakistan
- * E-mail:
| | - Aamer Ikram
- National Institute of Health, Islamabad, Pakistan
| | | | | | - Masroor Alam
- National Institute of Health, Islamabad, Pakistan
| | - Nazish Badar
- National Institute of Health, Islamabad, Pakistan
| | - Rana Suleman
- National Institute of Health, Islamabad, Pakistan
| | - Faheem Tahir
- National Institute of Health, Islamabad, Pakistan
| | | | - Joel Montgomery
- Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Shannon Whitmer
- Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - John Klena
- Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
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24
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Brogna B, Brogna C, Petrillo M, Conte AM, Benincasa G, Montano L, Piscopo M. SARS-CoV-2 Detection in Fecal Sample from a Patient with Typical Findings of COVID-19 Pneumonia on CT but Negative to Multiple SARS-CoV-2 RT-PCR Tests on Oropharyngeal and Nasopharyngeal Swab Samples. Medicina (Kaunas) 2021; 57:290. [PMID: 33804646 PMCID: PMC8003654 DOI: 10.3390/medicina57030290] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/15/2021] [Accepted: 03/17/2021] [Indexed: 02/07/2023]
Abstract
Reverse transcriptase polymerase chain reaction (RT-PCR) negative results in the upper respiratory tract represent a major concern for the clinical management of coronavirus disease 2019 (COVID-19) patients. Herein, we report the case of a 43-years-old man with a strong clinical suspicion of COVID-19, who resulted in being negative to multiple severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RT-PCR tests performed on different oropharyngeal and nasopharyngeal swabs, despite serology having confirmed the presence of SARS-CoV-2 IgM. The patient underwent a chest computed tomography (CT) that showed typical imaging findings of COVID-19 pneumonia. The presence of viral SARS-CoV-2 was confirmed only by performing a SARS-CoV-2 RT-PCR test on stool. Performing of SARS-CoV-2 RT-PCR test on fecal samples can be a rapid and useful approach to confirm COVID-19 diagnosis in cases where there is an apparent discrepancy between COVID-19 clinical symptoms coupled with chest CT and SARS-CoV-2 RT-PCR tests' results on samples from the upper respiratory tract.
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Affiliation(s)
- Barbara Brogna
- Department of Radiology, Moscati Hospital, Contrada Amoretta, 83100 Avellino, Italy
| | - Carlo Brogna
- Specialist-Craniomed Laboratory Group srl, Viale degli Astronauti, 45, 83038 Montemiletto, Italy;
| | - Mauro Petrillo
- European Commission, Joint Research Centre (JRC), Ispra, 21027 Via Enrico Fermi, Italy;
| | - Adriana Modestina Conte
- Chief U.O. Emergency Unit-OBI P.O., Pineta Grande Hospital, Via Domitiana 3000, 81030 Castel Volturno, Italy;
| | - Giulio Benincasa
- Chief Anatomy Pathology Department, Pineta Grande Hospital, Via Domitiana 3000, 81030 Castel Volturno, Italy;
| | - Luigi Montano
- Specialist Andrology Unit, Service of Lifestyle Medicine in Uro-Andrology, Local Health Authority (ASL), 84121 Salerno, Italy;
| | - Marina Piscopo
- Department of Biology, University of Naples Federico II, 80138 Naples, Italy;
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25
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Agarwal A, Fernando SM, Honarmand K, Bakaa L, Brar S, Granton D, Chaudhuri D, Chetan D, Hu M, Basmaji J, Muttalib F, Rochwerg B, Adhikari NKJ, Lamontagne F, Murthy S, Hui DS, Gomersall CD, Mubareka S, Diaz J, Burns KE, Couban R, Vandvik PO. Risk of dispersion or aerosol generation and infection transmission with nasopharyngeal and oropharyngeal swabs for detection of COVID-19: a systematic review. BMJ Open 2021; 11:e040616. [PMID: 33737418 PMCID: PMC7977073 DOI: 10.1136/bmjopen-2020-040616] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
OBJECTIVES SARS-CoV-2-related disease, referred to as COVID-19, has emerged as a global pandemic since December 2019. While there is growing recognition regarding possible airborne transmission, particularly in the setting of aerosol-generating procedures and treatments, whether nasopharyngeal and oropharyngeal swabs for SARS-CoV-2 generate aerosols remains unclear. DESIGN Systematic review. DATA SOURCES We searched Ovid MEDLINE and EMBASE up to 3 November 2020. We also searched the China National Knowledge Infrastructure, Chinese Medical Journal Network, medRxiv and ClinicalTrials.gov up to 29 March 2020. ELIGIBILITY CRITERIA All comparative and non-comparative studies that evaluated dispersion or aerosolisation of viable airborne organisms, or transmission of infection associated with nasopharyngeal or oropharyngeal swab testing. RESULTS Of 7702 citations, only one study was deemed eligible. Using a dedicated sampling room with negative pressure isolation room, personal protective equipment including N95 or higher masks, strict sterilisation protocols, structured training with standardised collection methods and a structured collection and delivery system, a tertiary care hospital proved a 0% healthcare worker infection rate among eight nurses conducting over 11 000 nasopharyngeal swabs. No studies examining transmissibility with other safety protocols, nor any studies quantifying the risk of aerosol generation with nasopharyngeal or oropharyngeal swabs for detection of SARS-CoV-2, were identified. CONCLUSIONS There is limited to no published data regarding aerosol generation and risk of transmission with nasopharyngeal and oropharyngeal swabs for the detection of SARS-CoV-2. Field experiments to quantify this risk are warranted. Vigilance in adhering to current standards for infection control is suggested.
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Affiliation(s)
- Arnav Agarwal
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
- Department of Health Research Methods, Evidence and Impact, McMaster University, Hamilton, Ontario, Canada
| | - Shannon M Fernando
- Division of Critical Care, Department of Medicine, University of Ottawa, Ottawa, Ontario, Canada
- Department of Emergency Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Kimia Honarmand
- Division of Critical Care, Department of Medicine, Western University, London, Ontario, Canada
| | - Layla Bakaa
- Faculty of Science, McMaster University, Hamilton, Ontario, Canada
| | - Sonia Brar
- School of Medicine and Biomedical Sciences, University of Buffalo, Buffalo, New York, USA
| | - David Granton
- Michael G. DeGroote School of Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Dipayan Chaudhuri
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Devin Chetan
- Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada
- Division of Cardiology, Labatt Family Heart Centre, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Malini Hu
- Michael G. DeGroote School of Medicine, McMaster University, Hamilton, Ontario, Canada
| | - John Basmaji
- Division of Critical Care, Department of Medicine, Western University, London, Ontario, Canada
| | - Fiona Muttalib
- Center for Global Child Health, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Bram Rochwerg
- Department of Health Research Methods, Evidence and Impact, McMaster University, Hamilton, Ontario, Canada
- Michael G. DeGroote School of Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Neill K J Adhikari
- Department of Critical Care Medicine, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
- Interdepartmental Division of Critical Care Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Francois Lamontagne
- Centre de recherche due CHU de Sherbrooke, Université de Sherbrooke, Sherbrooke, Quebec, Canada
- Département de Médecine, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Srinivas Murthy
- Faculty of Medicine, BC Children's Hospital, University of British Columbia, Vancouver, British Columbia, Canada
| | - David S Hui
- Department of Medicine and Therapeutics, Chinese University of Hong Kong, Shatin, Hong Kong
- Stanley Ho Center for Emerging Infectious Diseases, Chinese University of Hong Kong, Shatin, Hong Kong
| | - Charles D Gomersall
- Department of Anaesthesia and Intensive Care, Chinese University of Hong Kong, Shatin, Hong Kong
| | - Samira Mubareka
- Division of Infectious Diseases, University of Toronto, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Janet Diaz
- Pacific Medical Center, San Francisco, California, USA
- World Health Organization, Geneva, Switzerland
| | - Karen Ea Burns
- Interdepartmental Division of Critical Care Medicine, University of Toronto, Toronto, Ontario, Canada
- Division of Critical Care, Unity Health Toronto - St. Michael's Hospital, Toronto, Ontario, Canada
- Li Ka Shing Knowledge Institute, Unity Health Toronto - St. Michael's Hospital, Toronto, Ontario, Canada
| | - Rachel Couban
- Department of Health Research Methods, Evidence and Impact, McMaster University, Hamilton, Ontario, Canada
- Michael G. DeGroote Institute for Pain Research and Care, McMaster University, Hamilton, Ontario, Canada
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Sylverken AA, El-Duah P, Owusu M, Schneider J, Yeboah R, Ayisi-Boateng NK, Gorman R, Adu E, Kwarteng A, Frimpong M, Binger T, Aryeetey S, Asamoah JA, Amoako YA, Amuasi JH, Beheim-Schwarzbach J, Owusu-Dabo E, Adu-Sarkodie Y, Obiri-Danso K, Corman VM, Drosten C, Phillips R. Transmission of SARS-CoV-2 in northern Ghana: insights from whole-genome sequencing. Arch Virol 2021; 166:1385-1393. [PMID: 33723631 PMCID: PMC7959303 DOI: 10.1007/s00705-021-04986-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Accepted: 12/21/2020] [Indexed: 12/23/2022]
Abstract
Following the detection of the first imported case of COVID-19 in the northern sector of Ghana, we molecularly characterized and phylogenetically analysed sequences, including three complete genome sequences, of severe acute respiratory syndrome coronavirus 2 obtained from nine patients in Ghana. We performed high-throughput sequencing on nine samples that were found to have a high concentration of viral RNA. We also assessed the potential impact that long-distance transport of samples to testing centres may have on sequencing results. Here, two samples that were similar in terms of viral RNA concentration but were transported from sites that are over 400 km apart were analyzed. All sequences were compared to previous sequences from Ghana and representative sequences from regions where our patients had previously travelled. Three complete genome sequences and another nearly complete genome sequence with 95.6% coverage were obtained. Sequences with coverage in excess of 80% were found to belong to three lineages, namely A, B.1 and B.2. Our sequences clustered in two different clades, with the majority falling within a clade composed of sequences from sub-Saharan Africa. Less RNA fragmentation was seen in sample KATH23, which was collected 9 km from the testing site, than in sample TTH6, which was collected and transported over a distance of 400 km to the testing site. The clustering of several sequences from sub-Saharan Africa suggests regional circulation of the viruses in the subregion. Importantly, there may be a need to decentralize testing sites and build more capacity across Africa to boost the sequencing output of the subregion.
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Affiliation(s)
- Augustina Angelina Sylverken
- Kumasi Centre for Collaborative Research in Tropical Medicine, PMB, UPO, 00233 Kumasi, Ghana
- Department of Theoretical and Applied Biology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Philip El-Duah
- Kumasi Centre for Collaborative Research in Tropical Medicine, PMB, UPO, 00233 Kumasi, Ghana
- Institute of Virology, Charite, Universitätsmedizin Berlin, Berlin, Germany
| | - Michael Owusu
- Kumasi Centre for Collaborative Research in Tropical Medicine, PMB, UPO, 00233 Kumasi, Ghana
- Department of Medical Diagnostics, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Julia Schneider
- Institute of Virology, Charite, Universitätsmedizin Berlin, Berlin, Germany
| | - Richmond Yeboah
- Kumasi Centre for Collaborative Research in Tropical Medicine, PMB, UPO, 00233 Kumasi, Ghana
| | | | - Richmond Gorman
- Kumasi Centre for Collaborative Research in Tropical Medicine, PMB, UPO, 00233 Kumasi, Ghana
| | - Eric Adu
- Kumasi Centre for Collaborative Research in Tropical Medicine, PMB, UPO, 00233 Kumasi, Ghana
| | - Alexander Kwarteng
- Kumasi Centre for Collaborative Research in Tropical Medicine, PMB, UPO, 00233 Kumasi, Ghana
- Department of Biochemistry and Biotechnology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Michael Frimpong
- Kumasi Centre for Collaborative Research in Tropical Medicine, PMB, UPO, 00233 Kumasi, Ghana
- Department of Molecular Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Tabea Binger
- Kumasi Centre for Collaborative Research in Tropical Medicine, PMB, UPO, 00233 Kumasi, Ghana
| | - Sherihane Aryeetey
- Kumasi Centre for Collaborative Research in Tropical Medicine, PMB, UPO, 00233 Kumasi, Ghana
| | - Jesse Addo Asamoah
- Kumasi Centre for Collaborative Research in Tropical Medicine, PMB, UPO, 00233 Kumasi, Ghana
| | - Yaw Ampem Amoako
- Department of Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - John Humphrey Amuasi
- Kumasi Centre for Collaborative Research in Tropical Medicine, PMB, UPO, 00233 Kumasi, Ghana
- Department of Global and International Health, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | | | - Ellis Owusu-Dabo
- Department of Global and International Health, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Yaw Adu-Sarkodie
- Department of Clinical Microbiology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Kwasi Obiri-Danso
- Department of Theoretical and Applied Biology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Victor Max Corman
- Institute of Virology, Charite, Universitätsmedizin Berlin, Berlin, Germany
| | - Christian Drosten
- Institute of Virology, Charite, Universitätsmedizin Berlin, Berlin, Germany
| | - Richard Phillips
- Kumasi Centre for Collaborative Research in Tropical Medicine, PMB, UPO, 00233 Kumasi, Ghana
- Department of Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
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Di Carlo P, Falasca K, Ucciferri C, Sinjari B, Aruffo E, Antonucci I, Di Serafino A, Pompilio A, Damiani V, Mandatori D, De Fabritiis S, Dufrusine B, Capone E, Chiacchiaretta P, Brune WH, Di Bonaventura G, Vecchiet J. Normal breathing releases SARS-CoV-2 into the air. J Med Microbiol 2021; 70:001328. [PMID: 33629949 PMCID: PMC8346733 DOI: 10.1099/jmm.0.001328] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 01/29/2021] [Indexed: 01/22/2023] Open
Abstract
This study tests the release of SARS-CoV-2 RNA into the air during normal breathing, without any sign of possible risk of contagion such as coughing, sneezing or talking. Five patients underwent oropharyngeal, nasopharyngeal and salivary swabs for real-time reverse transcriptase PCR (RT-PCR) detection of SARS-CoV-2 RNA. Direct SARS-CoV-2 release during normal breathing was also investigated by RT-PCR in air samples collected using a microbiological sampler. Viral RNA was detected in air at 1 cm from the mouth of patients whose oropharyngeal, nasopharyngeal and salivary swabs tested positive for SARS-CoV-2 RNA. In contrast, the viral RNA was not identified in the exhaled air from patients with oropharyngeal, nasopharyngeal and salivary swabs that tested negative. Contagion of SARS-CoV-2 is possible by being very close to the mouth of someone who is infected, asymptomatic and simply breathing.
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Affiliation(s)
- Piero Di Carlo
- University "G. d'Annunzio" of Chieti-Pescara, Department of Advanced Technologies in Medicine & Dentistry, Chieti, Italy
- Center for Advanced Studies and Technology (CAST), University "G. d'Annunzio" of Chieti-Pescara, Chieti, Italy
| | - Katia Falasca
- University "G. d'Annunzio" of Chieti-Pescara, Department of Medicine and Aging Sciences, Chieti, Italy
- Clinic of Infectious Diseases, S.S. Annunziata Hospital, Chieti, Italy
| | - Claudio Ucciferri
- University "G. d'Annunzio" of Chieti-Pescara, Department of Medicine and Aging Sciences, Chieti, Italy
- Clinic of Infectious Diseases, S.S. Annunziata Hospital, Chieti, Italy
| | - Bruna Sinjari
- University "G. d'Annunzio" of Chieti-Pescara, Department of Advanced Technologies in Medicine & Dentistry, Chieti, Italy
| | - Eleonora Aruffo
- University "G. d'Annunzio" of Chieti-Pescara, Department of Advanced Technologies in Medicine & Dentistry, Chieti, Italy
- Center for Advanced Studies and Technology (CAST), University "G. d'Annunzio" of Chieti-Pescara, Chieti, Italy
| | - Ivana Antonucci
- Center for Advanced Studies and Technology (CAST), University "G. d'Annunzio" of Chieti-Pescara, Chieti, Italy
- Department of Psychological, Health and Territorial Sciences, University "G. d'Annunziio" of Chieti_Pescara, Chieti, Italy
| | - Alessandra Di Serafino
- Center for Advanced Studies and Technology (CAST), University "G. d'Annunzio" of Chieti-Pescara, Chieti, Italy
- Department of Psychological, Health and Territorial Sciences, University "G. d'Annunziio" of Chieti_Pescara, Chieti, Italy
| | - Arianna Pompilio
- Center for Advanced Studies and Technology (CAST), University "G. d'Annunzio" of Chieti-Pescara, Chieti, Italy
- University "G. d'Annunzio" of Chieti-Pescara, Department of Medical, Oral and Biotechnological Sciences, Chieti, Italy
| | - Verena Damiani
- Center for Advanced Studies and Technology (CAST), University "G. d'Annunzio" of Chieti-Pescara, Chieti, Italy
| | - Domitilla Mandatori
- Center for Advanced Studies and Technology (CAST), University "G. d'Annunzio" of Chieti-Pescara, Chieti, Italy
| | - Simone De Fabritiis
- Center for Advanced Studies and Technology (CAST), University "G. d'Annunzio" of Chieti-Pescara, Chieti, Italy
| | - Beatrice Dufrusine
- Center for Advanced Studies and Technology (CAST), University "G. d'Annunzio" of Chieti-Pescara, Chieti, Italy
| | - Emily Capone
- University "G. d'Annunzio" of Chieti-Pescara, Department of Neuroscience, Imaging and Clinical Sciences, Chieti, Italy
| | - Piero Chiacchiaretta
- University "G. d'Annunzio" of Chieti-Pescara, Department of Neuroscience, Imaging and Clinical Sciences, Chieti, Italy
| | - William H. Brune
- Pennsylvania State University, Department Meteorology and Atmospheric Science, University Park, PA, 16802, USA
| | - Giovanni Di Bonaventura
- Center for Advanced Studies and Technology (CAST), University "G. d'Annunzio" of Chieti-Pescara, Chieti, Italy
- University "G. d'Annunzio" of Chieti-Pescara, Department of Medical, Oral and Biotechnological Sciences, Chieti, Italy
| | - Jacopo Vecchiet
- University "G. d'Annunzio" of Chieti-Pescara, Department of Medicine and Aging Sciences, Chieti, Italy
- Clinic of Infectious Diseases, S.S. Annunziata Hospital, Chieti, Italy
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Dutescu RM, Banasik P, Schildgen O, Schrage N, Uthoff D. Detection of Coronavirus in Tear Samples of Hospitalized Patients With Confirmed SARS-CoV-2 From Oropharyngeal Swabs. Cornea 2021; 40:348-350. [PMID: 32897895 PMCID: PMC7526400 DOI: 10.1097/ico.0000000000002562] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 08/29/2020] [Indexed: 12/23/2022]
Abstract
PURPOSE This study was designed to detect CoV-RNA in the tears of polymerase chain reaction (PCR)-confirmed SARS-CoV-2 positive patients. METHODS We performed a prospective case series study of hospitalized patients who have been confirmed SARS-CoV-2 positive by oropharyngeal swab within the previous 5 days. Tear samples obtained with a laboratory capillary and oropharyngeal swabs were analyzed by real-time PCR using the Altona SARS-CoV-2 Assay or the Roche SARS-CoV-2 LightMix PCR, depending on the availability. Patient history was documented, and ophthalmoscopy was used to assess for ocular surface disease. RESULTS Of all 18 patients recruited in April 2020, 5 suffered from respiratory failure and were submitted to an intensive care unit. None of our patients had signs of viral conjunctivitis although all patients in intensive care showed chemosis and conjunctival hyperemia because of third-spacing or fluid overload. The presence of coronavirus RNA was confirmed by PCR in 5 of 18 patients (28%) in tears and 72% for oropharyngeal swabs. CONCLUSIONS Using a tear fluid sampling technique similar to oropharyngeal lavage presents a higher percentage of SARS-CoV-2 positive tears in contrast to earlier reports that used a conjunctival swab. This does not automatically indicate viral shedding in ocular tissue or contagiousness of tear fluid.
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Affiliation(s)
- R. Michael Dutescu
- Aachen Centre of Technology Transfer in Ophthalmology (ACTO e.V.), An-Institute, RWTH Aachen University, Aachen, Germany
| | - Peter Banasik
- GenExpress Gesellschaft für Proteindesign mbH, Berlin, Germany; and
| | - Oliver Schildgen
- Institut für Pathologie der Kliniken der Stadt Köln, Klinikum der Privaten Universität Witten/Herdecke, Witten, Germany
| | - Norbert Schrage
- Aachen Centre of Technology Transfer in Ophthalmology (ACTO e.V.), An-Institute, RWTH Aachen University, Aachen, Germany
| | - Daniel Uthoff
- Aachen Centre of Technology Transfer in Ophthalmology (ACTO e.V.), An-Institute, RWTH Aachen University, Aachen, Germany
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Laferl H, Kelani H, Seitz T, Holzer B, Zimpernik I, Steinrigl A, Schmoll F, Wenisch C, Allerberger F. An approach to lifting self-isolation for health care workers with prolonged shedding of SARS-CoV-2 RNA. Infection 2021; 49:95-101. [PMID: 33025521 PMCID: PMC7538033 DOI: 10.1007/s15010-020-01530-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Accepted: 09/16/2020] [Indexed: 12/23/2022]
Abstract
PURPOSE According to the European Public Health Authority guidance for ending isolation in the context of COVID-19, a convalescent healthcare worker (HCW) can end their isolation at home and resume work upon clinical improvement and two negative RT-PCR tests from respiratory specimens obtained at 24-h intervals at least 8 days after the onset of symptoms. However, convalescent HCWs may shed SARS-CoV-2 viral RNA for prolonged periods. METHODS 40 healthy HCWs off work because of ongoing positive RT-PCR results in combined nasopharyngeal (NP) and oropharyngeal (OP) swabs following SARS-CoV-2 infection were invited to participate in this study. These HCWs had been in self-isolation because of a PCR-confirmed SARS-CoV-2 infection. NP and OP swabs as well as a blood sample were collected from each participant. RT-PCR and virus isolation was performed with each swab sample and serum neutralization test as well as two different ELISA tests were performed on all serum samples. RESULTS No viable virions could be detected in any of 29 nasopharyngeal and 29 oropharyngeal swabs taken from 15 long-time carriers. We found SARSCoV- 2 RNA in 14/29 nasopharyngeal and 10/29 oropharyngeal swabs obtained from screening 15 HCWs with previous COVID-19 up to 55 days after symptom onset. Six (40%) of the 15 initially positive HCWs converted to negative and later reverted to positive again according to their medical records. All but one HCW, a healthy volunteer banned from work, showed the presence of neutralizing antibodies in concomitantly taken blood samples. Late threshold cycle (Ct) values in RT-PCR [mean 37.4; median 37.3; range 30.8-41.7] and the lack of virus growth in cell culture indicate that despite the positive PCR results no infectivity remained. CONCLUSION We recommend lifting isolation if the RT-PCR Ct-value of a naso- or oropharyngeal swab sample is over 30. Positive results obtained from genes targeted with Ct-values > 30 correspond to non-viable/noninfectious particles that are still detected by RT-PCR. In case of Ct-values lower than 30, a blood sample from the patient should be tested for the presence of neutralizing antibodies. If positive, non-infectiousness can also be assumed.
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Affiliation(s)
- H Laferl
- 4th Medical Department with Infectious Diseases and Tropical Medicine, Kaiser Franz Josef Hospital, 1100, Vienna, Austria.
| | - H Kelani
- 4th Medical Department with Infectious Diseases and Tropical Medicine, Kaiser Franz Josef Hospital, 1100, Vienna, Austria
| | - T Seitz
- 4th Medical Department with Infectious Diseases and Tropical Medicine, Kaiser Franz Josef Hospital, 1100, Vienna, Austria
| | - B Holzer
- Austrian Agency for Health and Food Safety (AGES), Institute for Veterinary Disease Control Mödling, 2340, Mödling, Austria
| | - I Zimpernik
- Austrian Agency for Health and Food Safety (AGES), Institute for Veterinary Disease Control Mödling, 2340, Mödling, Austria
| | - A Steinrigl
- Austrian Agency for Health and Food Safety (AGES), Institute for Veterinary Disease Control Mödling, 2340, Mödling, Austria
| | - F Schmoll
- Austrian Agency for Health and Food Safety (AGES), Institute for Veterinary Disease Control Mödling, 2340, Mödling, Austria
| | - C Wenisch
- 4th Medical Department with Infectious Diseases and Tropical Medicine, Kaiser Franz Josef Hospital, 1100, Vienna, Austria
| | - F Allerberger
- Austrian Agency for Health and Food Safety (AGES), Institute for Veterinary Disease Control Mödling, 2340, Mödling, Austria
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30
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Chan CPL, Chan JYK. Profiling severe acute respiratory syndrome coronavirus 2 and its relevance to otolaryngologic examinations during the coronavirus disease 2019 pandemic. Curr Opin Allergy Clin Immunol 2021; 21:38-45. [PMID: 33369568 DOI: 10.1097/aci.0000000000000709] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
PURPOSE OF REVIEW The WHO announced the coronavirus disease 2019 (COVID-19) outbreak as a pandemic in February 2020 with over 15 million confirmed cases of COVID-19 globally to date. Otolaryngologists are at a high risk of contracting COVID-19 during this pandemic if there is inadequate and improper personal protective equipment provision, as we are dealing with diseases of the upper-aerodigestive tract and routinely engaged in aerosol-generating procedures. RECENT FINDINGS This article discusses the background and transmission route for severe acute respiratory syndrome coronavirus 2, its viral load and temporal profile as well as precaution guidelines in outpatient and operative setting in otorhinolaryngology. SUMMARY As it is evident that COVID-19 can be transmitted at presymptomatic or asymptomatic period of infections, it is essential to practice ear, nose, and throat surgery with high vigilance in a safe and up-to-standard protection level during the pandemic. This article provides a summary for guidelines and recommendations in otorhinolaryngology.
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Affiliation(s)
- Catherine P L Chan
- Department of Otorhinolaryngology, Head and Neck Surgery, The Chinese University of Hong Kong, Hong Kong SAR, China
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31
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Wei J, Guo S, Long E, Zhang L, Shu B, Guo L. Why does the spread of COVID-19 vary greatly in different countries? Revealing the efficacy of face masks in epidemic prevention. Epidemiol Infect 2021; 149:e24. [PMID: 33441205 PMCID: PMC7844184 DOI: 10.1017/s0950268821000108] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 01/08/2021] [Accepted: 01/11/2021] [Indexed: 11/05/2022] Open
Abstract
The severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) is highly contagious, and the coronavirus disease 2019 (COVID-19) pandemic caused by it has forced many countries to adopt 'lockdown' measures to prevent the spread of the epidemic through social isolation of citizens. Some countries proposed universal mask wearing as a protection measure of public health to strengthen national prevention efforts and to limit the wider spread of the epidemic. In order to reveal the epidemic prevention efficacy of masks, this paper systematically evaluates the experimental studies of various masks and filter materials, summarises the general characteristics of the filtration efficiency of isolation masks with particle size, and reveals the actual efficacy of masks by combining the volume distribution characteristics of human exhaled droplets with different particle sizes and the SARS-CoV-2 virus load of nasopharynx and throat swabs from patients. The existing measured data show that the filtration efficiency of all kinds of masks for large particles and extra-large droplets is close to 100%. From the perspective of filtering the total number of pathogens discharged in the environment and protecting vulnerable individuals from breathing live viruses, the mask has a higher protective effect. If considering the weighted average filtration efficiency with different particle sizes, the filtration efficiencies of the N95 mask and the ordinary mask are 99.4% and 98.5%, respectively. The mask can avoid releasing active viruses to the environment from the source of infection, thus maximising the protection of vulnerable individuals by reducing the probability of inhaling a virus. Therefore, if the whole society strictly implements the policy of publicly wearing masks, the risk of large-scale spread of the epidemic can be greatly reduced. Compared with the overall cost of social isolation, limited personal freedoms and forced suspension of economic activities, the inconvenience for citizens caused by wearing masks is perfectly acceptable.
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Affiliation(s)
- Jincheng Wei
- MOE Key Laboratory of Deep Earth Science and Engineering, College of Architecture and Environment, Sichuan University, Chengdu, China
| | - Shurui Guo
- MOE Key Laboratory of Deep Earth Science and Engineering, College of Architecture and Environment, Sichuan University, Chengdu, China
| | - Enshen Long
- MOE Key Laboratory of Deep Earth Science and Engineering, College of Architecture and Environment, Sichuan University, Chengdu, China
| | - Li Zhang
- Department of Solid Waste Treatment Technology, Sichuan Environmental Protection Key Laboratory of Pollution Control for Heavy Metals, Sichuan Academy of Environmental Sciences, Chengdu, China
| | - Bizhen Shu
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, West China Second Hospital of Sichuan University, Chengdu, China
| | - Lei Guo
- MOE Key Laboratory of Deep Earth Science and Engineering, College of Architecture and Environment, Sichuan University, Chengdu, China
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Bhattacharya B, Kumar R, Meena VP, Soneja M, Singh A, Das R, Xess A, Arif N, Vig S, Rastogi V, Tiwari P, Bhatnagar S, Mohan A, Wig N, Dar L. SARS-CoV-2 RT-PCR profile in 298 Indian COVID-19 patients: a retrospective observational study. Pathog Dis 2021; 79:ftaa064. [PMID: 33053181 PMCID: PMC7665504 DOI: 10.1093/femspd/ftaa064] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 10/12/2020] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND despite being in the 5th month of pandemic, knowledge with respect to viral dynamics, infectivity and RT-PCR positivity continues to evolve. AIM to analyse the SARS CoV-2 nucleic acid RT-PCR profiles in COVID-19 patients. DESIGN it was a retrospective, observational study conducted at COVID facilities under AIIMS, New Delhi. METHODS patients admitted with laboratory confirmed COVID-19 were eligible for enrolment. Patients with incomplete details, or only single PCR tests were excluded. Data regarding demographic details, comorbidities, treatment received and results of SARS-CoV-2 RT-PCR performed on nasopharyngeal and oropharyngeal swabs, collected at different time points, was retrieved from the hospital records. RESULTS a total of 298 patients were included, majority were males (75·8%) with mean age of 39·07 years (0·6-88 years). The mean duration from symptom onset to first positive RT-PCR was 4·7 days (SD 3·67), while that of symptom onset to last positive test was 17·83 days (SD 6·22). Proportions of positive RT-PCR tests were 100%, 49%, 24%, 8·7% and 20·6% in the 1st, 2nd, 3rd, 4th and >4 weeks of illness. A total of 12 symptomatic patients had prolonged positive test results even after 3 weeks of symptom onset. Age > = 60 years was associated with prolonged RT-PCR positivity (statistically significant). CONCLUSION this study showed that the average period of PCR positivity is more than 2 weeks in COVID-19 patients; elderly patients have prolonged duration of RT-PCR positivity and requires further follow up.
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Affiliation(s)
- Bisakh Bhattacharya
- Department of Medicine, All India Institute of Medical Sciences, New Delhi (110029)
| | - Rohit Kumar
- Department of Medicine, All India Institute of Medical Sciences, New Delhi (110029)
| | - Ved Prakash Meena
- Department of Medicine, All India Institute of Medical Sciences, New Delhi (110029)
| | - Manish Soneja
- Department of Medicine, All India Institute of Medical Sciences, New Delhi (110029)
| | - Amit Singh
- Department of Mircobiology, All India Institute of Medical Sciences, New Delhi (110029)
| | - Rojaleen Das
- Department of Mircobiology, All India Institute of Medical Sciences, New Delhi (110029)
| | - Ashit Xess
- Department of Mircobiology, All India Institute of Medical Sciences, New Delhi (110029)
| | - Nazneen Arif
- Department of Mircobiology, All India Institute of Medical Sciences, New Delhi (110029)
| | - Saurabh Vig
- Department of Onco-anesthesia & Palliative Medicine, All India Institute of Medical Sciences, New Delhi (110029)
| | - Vandana Rastogi
- Department of Biostatistics, All India Institute of Medical Sciences, New Delhi (110029)
| | - Pavan Tiwari
- Department of Pulmonary Medicine & Sleep Disorders, All India Institute of Medical Sciences, New Delhi (110029)
| | - Sushma Bhatnagar
- Department of Onco-anesthesia & Palliative Medicine, All India Institute of Medical Sciences, New Delhi (110029)
| | - Anant Mohan
- Department of Pulmonary Medicine & Sleep Disorders, All India Institute of Medical Sciences, New Delhi (110029)
| | - Naveet Wig
- Department of Medicine, All India Institute of Medical Sciences, New Delhi (110029)
| | - Lalit Dar
- Department of Mircobiology, All India Institute of Medical Sciences, New Delhi (110029)
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Fabbris C, Cestaro W, Menegaldo A, Spinato G, Frezza D, Vijendren A, Borsetto D, Boscolo-Rizzo P. Is oro/nasopharyngeal swab for SARS-CoV-2 detection a safe procedure? Complications observed among a case series of 4876 consecutive swabs. Am J Otolaryngol 2021; 42:102758. [PMID: 33125901 PMCID: PMC7553130 DOI: 10.1016/j.amjoto.2020.102758] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 10/11/2020] [Indexed: 01/10/2023]
Affiliation(s)
- Cristoforo Fabbris
- Department of Neurosciences, Section of Otolaryngology, University of Padova, Treviso, Italy.
| | - Walter Cestaro
- Unit of Otorhinolaryngology, AULSS 2 - Marca Trevigiana, Montebelluna, Italy
| | - Anna Menegaldo
- Department of Neurosciences, Section of Otolaryngology, University of Padova, Treviso, Italy
| | - Giacomo Spinato
- Department of Neurosciences, Section of Otolaryngology, University of Padova, Treviso, Italy
| | - Daniele Frezza
- Department of Neurosciences, Section of Otolaryngology, University of Padova, Treviso, Italy
| | - Ananth Vijendren
- ENT Department, Lister Hospital, East and North Herts NHS Trust, Stevenage, UK
| | - Daniele Borsetto
- Department of Otolaryngology, Guy's and St. Thomas' Hospital NHS Foundation Trust, London, UK
| | - Paolo Boscolo-Rizzo
- Department of Neurosciences, Section of Otolaryngology, University of Padova, Treviso, Italy
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Abstract
Widespread testing is required to limit the current public health crisis caused by the COVID-19 pandemic. Multiple tests protocols have been authorized by the food and drugs administration (FDA) under an emergency use authorization (EUA). The majority of these protocols are based on the gold-standard RT-qPCR test pioneered by the U.S. Centers for Disease Control and Prevention (CDC). However, there is still a widespread lack of testing in the US and many of the clinical diagnostics protocols require extensive human labor and materials that could face supply shortages and present biosafety concerns. Given the need to develop alternative reagents and approaches to provide nucleic-acid testing in the face of heightened demand and potential shortages, we have developed a simplified SARS-CoV-2 testing protocol adapted for its use in research laboratories with minimal molecular biology equipment and expertise. The protocol utilizes TRIzol to purify the viral RNA from different types of clinical specimens, requires minimal BSL-1 precautions and, given its high sensitivity, can be easily adapted to pooling samples strategies.
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Affiliation(s)
- Sean Paz
- Charles E Schmidt College of Medicine, Florida Atlantic University, Boca Raton, Florida, United States of America
| | - Christopher Mauer
- Charles E Schmidt College of Medicine, Florida Atlantic University, Boca Raton, Florida, United States of America
| | - Anastasia Ritchie
- Charles E Schmidt College of Medicine, Florida Atlantic University, Boca Raton, Florida, United States of America
| | - Janet D. Robishaw
- Charles E Schmidt College of Medicine, Florida Atlantic University, Boca Raton, Florida, United States of America
| | - Massimo Caputi
- Charles E Schmidt College of Medicine, Florida Atlantic University, Boca Raton, Florida, United States of America
- * E-mail:
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Young S, Taylor SN, Cammarata CL, Varnado KG, Roger-Dalbert C, Montano A, Griego-Fullbright C, Burgard C, Fernandez C, Eckert K, Andrews JC, Ren H, Allen J, Ackerman R, Cooper CK. Clinical Evaluation of BD Veritor SARS-CoV-2 Point-of-Care Test Performance Compared to PCR-Based Testing and versus the Sofia 2 SARS Antigen Point-of-Care Test. J Clin Microbiol 2020; 59:e02338-20. [PMID: 33023911 PMCID: PMC7771450 DOI: 10.1128/jcm.02338-20] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 10/01/2020] [Indexed: 12/23/2022] Open
Abstract
The clinical performance of the BD Veritor System for Rapid Detection of SARS-CoV-2 nucleocapsid antigen (Veritor), a chromatographic immunoassay used for SARS-CoV-2 point-of-care testing, was evaluated using nasal specimens from individuals with COVID-19 symptoms. Two studies were completed to determine clinical performance. In the first study, nasal specimens and either nasopharyngeal or oropharyngeal specimens from 251 participants with COVID-19 symptoms (≤7 days from symptom onset [DSO], ≥18 years of age) were utilized to compare Veritor with the Lyra SARS-CoV-2 PCR assay (Lyra). In the second study, nasal specimens from 361 participants with COVID-19 symptoms (≤5 DSO, ≥18 years of age) were utilized to compare performance of Veritor to that of the Sofia 2 SARS Antigen FIA test (Sofia 2). The positive, negative, and overall percent agreement (PPA, NPA, and OPA, respectively) were the primary outcomes. In study 1, the PPA for Veritor, compared to Lyra, ranged from 81.8 to 87.5% across the 0 to 1 and 0 to 6 DSO ranges. In study 2, Veritor had PPA, NPA, and OPA values of 97.4, 98.1, and 98.1%, respectively, with Sofia 2. Discordant analysis showed one Lyra positive missed by Veritor and five Lyra positives missed by Sofia 2; one Veritor positive result was negative by Lyra. Veritor met FDA emergency use authorization (EUA) acceptance criteria for SARS-CoV-2 antigen testing for the 0 to 5 and 0 to 6 DSO ranges (PPA values of 83.9% and 82.4%, respectively). Veritor and Sofia 2 showed a high degree of agreement for SARS-CoV-2 detection. The Veritor test allows for more rapid COVID-19 testing utilizing easy-to-collect nasal swabs but demonstrated <100% PPA compared to PCR.
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Affiliation(s)
- Stephen Young
- Tricore Reference Laboratory, Albuquerque, New Mexico, USA
| | - Stephanie N Taylor
- Louisiana State University Health Sciences Center, New Orleans, Louisiana, USA
| | | | - Katey G Varnado
- Louisiana State University Health Sciences Center, New Orleans, Louisiana, USA
| | - Celine Roger-Dalbert
- Becton, Dickinson and Company, BD Life Sciences-Integrated Diagnostic Solutions, Sparks, Maryland, USA
| | - Amanda Montano
- Tricore Reference Laboratory, Albuquerque, New Mexico, USA
| | | | | | - Catherine Fernandez
- Becton, Dickinson and Company, BD Life Sciences-Integrated Diagnostic Solutions, San Diego, California, USA
| | - Karen Eckert
- Becton, Dickinson and Company, BD Life Sciences-Integrated Diagnostic Solutions, Sparks, Maryland, USA
| | - Jeffrey C Andrews
- Becton, Dickinson and Company, BD Life Sciences-Integrated Diagnostic Solutions, Sparks, Maryland, USA
| | - Huimiao Ren
- Becton, Dickinson and Company, BD Life Sciences-Integrated Diagnostic Solutions, San Diego, California, USA
| | | | - Ronald Ackerman
- Comprehensive Clinical Research, LLC, West Palm Beach, Florida, USA
| | - Charles K Cooper
- Becton, Dickinson and Company, BD Life Sciences-Integrated Diagnostic Solutions, Sparks, Maryland, USA
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36
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Paiva MHS, Guedes DRD, Docena C, Bezerra MF, Dezordi FZ, Machado LC, Krokovsky L, Helvecio E, da Silva AF, Vasconcelos LRS, Rezende AM, da Silva SJR, Sales KGDS, de Sá BSLF, da Cruz DL, Cavalcanti CE, Neto ADM, da Silva CTA, Mendes RPG, da Silva MAL, Gräf T, Resende PC, Bello G, Barros MDS, do Nascimento WRC, Arcoverde RML, Bezerra LCA, Brandão-Filho SP, Ayres CFJ, Wallau GL. Multiple Introductions Followed by Ongoing Community Spread of SARS-CoV-2 at One of the Largest Metropolitan Areas of Northeast Brazil. Viruses 2020; 12:v12121414. [PMID: 33316947 PMCID: PMC7763515 DOI: 10.3390/v12121414] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 11/16/2020] [Accepted: 11/22/2020] [Indexed: 01/08/2023] Open
Abstract
Multiple epicenters of the SARS-CoV-2 pandemic have emerged since the first pneumonia cases in Wuhan, China, such as Italy, USA, and Brazil. Brazil is the third-most affected country worldwide, but genomic sequences of SARS-CoV-2 strains are mostly restricted to states from the Southeast region. Pernambuco state, located in the Northeast region, is the sixth most affected Brazilian state, but very few genomic sequences from the strains circulating in this region are available. We sequenced 101 strains of SARS-CoV-2 from patients presenting Covid-19 symptoms that reside in Pernambuco. Phylogenetic reconstructions revealed that all genomes belong to the B lineage and most of the samples (88%) were classified as lineage B.1.1. We detected multiple viral introductions from abroad (likely from Europe) as well as six local B.1.1 clades composed by Pernambuco only strains. Local clades comprise sequences from the capital city (Recife) and other country-side cities, corroborating the community spread between different municipalities of the state. These findings demonstrate that different from Southeastern Brazilian states where the epidemics were majorly driven by one dominant lineage (B.1.1.28 or B.1.1.33), the early epidemic phase at the Pernambuco state was driven by multiple B.1.1 lineages seeded through both national and international traveling.
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Affiliation(s)
- Marcelo Henrique Santos Paiva
- Núcleo de Ciências da Vida, Universidade Federal de Pernambuco (UFPE), Centro Acadêmico do Agreste-Rodovia BR-104, km 59-Nova Caruaru, Caruaru 55002-970, Brazil;
- Departamento de Entomologia, Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife 50670-420, Brazil; (D.R.D.G.); (F.Z.D.); (L.C.M.); (L.K.); (E.H.); (A.F.d.S.); (D.L.d.C.); (C.F.J.A.)
| | - Duschinka Ribeiro Duarte Guedes
- Departamento de Entomologia, Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife 50670-420, Brazil; (D.R.D.G.); (F.Z.D.); (L.C.M.); (L.K.); (E.H.); (A.F.d.S.); (D.L.d.C.); (C.F.J.A.)
| | - Cássia Docena
- Núcleo de Plataformas Tecnológicas (NPT), Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife 50670-420, Brazil;
| | - Matheus Filgueira Bezerra
- Departamento de Microbiologia, Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife 50670-420, Brazil; (M.F.B.); (A.M.R.); (B.S.L.F.d.S.)
| | - Filipe Zimmer Dezordi
- Departamento de Entomologia, Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife 50670-420, Brazil; (D.R.D.G.); (F.Z.D.); (L.C.M.); (L.K.); (E.H.); (A.F.d.S.); (D.L.d.C.); (C.F.J.A.)
- Núcleo de Bioinformática (NBI), Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife 50670-420, Brazil
| | - Laís Ceschini Machado
- Departamento de Entomologia, Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife 50670-420, Brazil; (D.R.D.G.); (F.Z.D.); (L.C.M.); (L.K.); (E.H.); (A.F.d.S.); (D.L.d.C.); (C.F.J.A.)
| | - Larissa Krokovsky
- Departamento de Entomologia, Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife 50670-420, Brazil; (D.R.D.G.); (F.Z.D.); (L.C.M.); (L.K.); (E.H.); (A.F.d.S.); (D.L.d.C.); (C.F.J.A.)
| | - Elisama Helvecio
- Departamento de Entomologia, Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife 50670-420, Brazil; (D.R.D.G.); (F.Z.D.); (L.C.M.); (L.K.); (E.H.); (A.F.d.S.); (D.L.d.C.); (C.F.J.A.)
| | - Alexandre Freitas da Silva
- Departamento de Entomologia, Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife 50670-420, Brazil; (D.R.D.G.); (F.Z.D.); (L.C.M.); (L.K.); (E.H.); (A.F.d.S.); (D.L.d.C.); (C.F.J.A.)
- Núcleo de Bioinformática (NBI), Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife 50670-420, Brazil
| | - Luydson Richardson Silva Vasconcelos
- Departamento de Parasitologia, Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife 50670-420, Brazil; (L.R.S.V.); (A.d.M.N.); (C.T.A.d.S.); (R.P.G.M.); (M.A.L.d.S.); (W.R.C.d.N.); (R.M.L.A.); (S.P.B.-F.)
| | - Antonio Mauro Rezende
- Departamento de Microbiologia, Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife 50670-420, Brazil; (M.F.B.); (A.M.R.); (B.S.L.F.d.S.)
- Núcleo de Bioinformática (NBI), Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife 50670-420, Brazil
| | - Severino Jefferson Ribeiro da Silva
- Laboratório de Virologia e Terapia Experimental (LAVITE), Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife 50670-420, Brazil; (S.J.R.d.S.); (C.E.C.)
| | - Kamila Gaudêncio da Silva Sales
- Departamento de Imunologia, Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife 50670-420, Brazil; (K.G.d.S.S.); (M.d.S.B.)
| | - Bruna Santos Lima Figueiredo de Sá
- Departamento de Microbiologia, Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife 50670-420, Brazil; (M.F.B.); (A.M.R.); (B.S.L.F.d.S.)
| | - Derciliano Lopes da Cruz
- Departamento de Entomologia, Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife 50670-420, Brazil; (D.R.D.G.); (F.Z.D.); (L.C.M.); (L.K.); (E.H.); (A.F.d.S.); (D.L.d.C.); (C.F.J.A.)
| | - Claudio Eduardo Cavalcanti
- Laboratório de Virologia e Terapia Experimental (LAVITE), Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife 50670-420, Brazil; (S.J.R.d.S.); (C.E.C.)
| | - Armando de Menezes Neto
- Departamento de Parasitologia, Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife 50670-420, Brazil; (L.R.S.V.); (A.d.M.N.); (C.T.A.d.S.); (R.P.G.M.); (M.A.L.d.S.); (W.R.C.d.N.); (R.M.L.A.); (S.P.B.-F.)
| | - Caroline Targino Alves da Silva
- Departamento de Parasitologia, Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife 50670-420, Brazil; (L.R.S.V.); (A.d.M.N.); (C.T.A.d.S.); (R.P.G.M.); (M.A.L.d.S.); (W.R.C.d.N.); (R.M.L.A.); (S.P.B.-F.)
| | - Renata Pessôa Germano Mendes
- Departamento de Parasitologia, Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife 50670-420, Brazil; (L.R.S.V.); (A.d.M.N.); (C.T.A.d.S.); (R.P.G.M.); (M.A.L.d.S.); (W.R.C.d.N.); (R.M.L.A.); (S.P.B.-F.)
| | - Maria Almerice Lopes da Silva
- Departamento de Parasitologia, Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife 50670-420, Brazil; (L.R.S.V.); (A.d.M.N.); (C.T.A.d.S.); (R.P.G.M.); (M.A.L.d.S.); (W.R.C.d.N.); (R.M.L.A.); (S.P.B.-F.)
| | - Tiago Gräf
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador 40296-710, Brazil;
| | - Paola Cristina Resende
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro 21040-900, Brazil;
| | - Gonzalo Bello
- Laboratório de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro 21040-900, Brazil;
| | - Michelle da Silva Barros
- Departamento de Imunologia, Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife 50670-420, Brazil; (K.G.d.S.S.); (M.d.S.B.)
| | - Wheverton Ricardo Correia do Nascimento
- Departamento de Parasitologia, Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife 50670-420, Brazil; (L.R.S.V.); (A.d.M.N.); (C.T.A.d.S.); (R.P.G.M.); (M.A.L.d.S.); (W.R.C.d.N.); (R.M.L.A.); (S.P.B.-F.)
- Departamento de Medicina Tropical, Centro de Ciências Médicas, Universidade Federal de Pernambuco (UFPE), Recife 50670-901, Brazil
| | - Rodrigo Moraes Loyo Arcoverde
- Departamento de Parasitologia, Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife 50670-420, Brazil; (L.R.S.V.); (A.d.M.N.); (C.T.A.d.S.); (R.P.G.M.); (M.A.L.d.S.); (W.R.C.d.N.); (R.M.L.A.); (S.P.B.-F.)
| | | | - Sinval Pinto Brandão-Filho
- Departamento de Parasitologia, Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife 50670-420, Brazil; (L.R.S.V.); (A.d.M.N.); (C.T.A.d.S.); (R.P.G.M.); (M.A.L.d.S.); (W.R.C.d.N.); (R.M.L.A.); (S.P.B.-F.)
| | - Constância Flávia Junqueira Ayres
- Departamento de Entomologia, Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife 50670-420, Brazil; (D.R.D.G.); (F.Z.D.); (L.C.M.); (L.K.); (E.H.); (A.F.d.S.); (D.L.d.C.); (C.F.J.A.)
| | - Gabriel Luz Wallau
- Departamento de Entomologia, Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife 50670-420, Brazil; (D.R.D.G.); (F.Z.D.); (L.C.M.); (L.K.); (E.H.); (A.F.d.S.); (D.L.d.C.); (C.F.J.A.)
- Núcleo de Bioinformática (NBI), Instituto Aggeu Magalhães (IAM)-Fundação Oswaldo Cruz-FIOCRUZ, Recife 50670-420, Brazil
- Correspondence:
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37
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Amendola A, Bianchi S, Gori M, Colzani D, Canuti M, Borghi E, Raviglione MC, Zuccotti GV, Tanzi E. Evidence of SARS-CoV-2 RNA in an Oropharyngeal Swab Specimen, Milan, Italy, Early December 2019. Emerg Infect Dis 2020; 27:648-650. [PMID: 33292923 PMCID: PMC7853584 DOI: 10.3201/eid2702.204632] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
We identified severe acute respiratory syndrome coronavirus 2 RNA in an oropharyngeal swab specimen collected from a child with suspected measles in early December 2019, ≈3 months before the first identified coronavirus disease case in Italy. This finding expands our knowledge on timing and mapping of novel coronavirus transmission pathways.
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38
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Kemenesi G, Zeghbib S, Somogyi BA, Tóth GE, Bányai K, Solymosi N, Szabo PM, Szabó I, Bálint Á, Urbán P, Herczeg R, Gyenesei A, Nagy Á, Pereszlényi CI, Babinszky GC, Dudás G, Terhes G, Zöldi V, Lovas R, Tenczer S, Kornya L, Jakab F. Multiple SARS-CoV-2 Introductions Shaped the Early Outbreak in Central Eastern Europe: Comparing Hungarian Data to a Worldwide Sequence Data-Matrix. Viruses 2020; 12:v12121401. [PMID: 33291299 PMCID: PMC7762115 DOI: 10.3390/v12121401] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 12/02/2020] [Accepted: 12/04/2020] [Indexed: 11/16/2022] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 is the third highly pathogenic human coronavirus in history. Since the emergence in Hubei province, China, during late 2019, the situation evolved to pandemic level. Following China, Europe was the second epicenter of the pandemic. To better comprehend the detailed founder mechanisms of the epidemic evolution in Central-Eastern Europe, particularly in Hungary, we determined the full-length SARS-CoV-2 genomes from 32 clinical samples collected from laboratory confirmed COVID-19 patients over the first month of disease in Hungary. We applied a haplotype network analysis on all available complete genomic sequences of SARS-CoV-2 from GISAID database as of 21 April 2020. We performed additional phylogenetic and phylogeographic analyses to achieve the recognition of multiple and parallel introductory events into our region. Here, we present a publicly available network imaging of the worldwide haplotype relations of SARS-CoV-2 sequences and conclude the founder mechanisms of the outbreak in Central-Eastern Europe.
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Affiliation(s)
- Gábor Kemenesi
- National Laboratory of Virology, Szentágothai Research Centre, University of Pécs, 7624 Pécs, Hungary; (S.Z.); (B.A.S.); (G.E.T.)
- Institute of Biology, Faculty of Sciences, University of Pécs, 7624 Pécs, Hungary
- Correspondence: (G.K.); (F.J.)
| | - Safia Zeghbib
- National Laboratory of Virology, Szentágothai Research Centre, University of Pécs, 7624 Pécs, Hungary; (S.Z.); (B.A.S.); (G.E.T.)
- Institute of Biology, Faculty of Sciences, University of Pécs, 7624 Pécs, Hungary
| | - Balázs A Somogyi
- National Laboratory of Virology, Szentágothai Research Centre, University of Pécs, 7624 Pécs, Hungary; (S.Z.); (B.A.S.); (G.E.T.)
- Institute of Biology, Faculty of Sciences, University of Pécs, 7624 Pécs, Hungary
| | - Gábor Endre Tóth
- National Laboratory of Virology, Szentágothai Research Centre, University of Pécs, 7624 Pécs, Hungary; (S.Z.); (B.A.S.); (G.E.T.)
- Institute of Biology, Faculty of Sciences, University of Pécs, 7624 Pécs, Hungary
| | - Krisztián Bányai
- Institute for Veterinary Medical Research, Centre for Agricultural Research, 1093 Budapest, Hungary;
| | - Norbert Solymosi
- Centre for Bioinformatics, University of Veterinary Medicine Budapest, 1078 Budapest, Hungary;
| | - Peter M Szabo
- Translational Discovery, Stromal Biology, Bristol-Myers Squibb, Princeton, NJ 08648, USA;
| | - István Szabó
- Veterinary Diagnostic Directorate, National Food Safety Office, 1143 Budapest, Hungary; (I.S.); (Á.B.)
| | - Ádám Bálint
- Veterinary Diagnostic Directorate, National Food Safety Office, 1143 Budapest, Hungary; (I.S.); (Á.B.)
| | - Péter Urbán
- Bioinformatics Research Group, Genomics and Bioinformatics Core Facility, Szentágothai Research Centre, University of Pécs, 7624 Pécs, Hungary; (P.U.); (R.H.); (A.G.)
| | - Róbert Herczeg
- Bioinformatics Research Group, Genomics and Bioinformatics Core Facility, Szentágothai Research Centre, University of Pécs, 7624 Pécs, Hungary; (P.U.); (R.H.); (A.G.)
| | - Attila Gyenesei
- Bioinformatics Research Group, Genomics and Bioinformatics Core Facility, Szentágothai Research Centre, University of Pécs, 7624 Pécs, Hungary; (P.U.); (R.H.); (A.G.)
- Clinical Research Centre, Medical University of Bialystok, 15-089 Bialystok, Poland
| | - Ágnes Nagy
- Medical Centre, Hungarian Defense Forces, 1114 Budapest, Hungary; (Á.N.); (C.I.P.); (G.C.B.); (G.D.)
| | - Csaba István Pereszlényi
- Medical Centre, Hungarian Defense Forces, 1114 Budapest, Hungary; (Á.N.); (C.I.P.); (G.C.B.); (G.D.)
| | - Gergely Csaba Babinszky
- Medical Centre, Hungarian Defense Forces, 1114 Budapest, Hungary; (Á.N.); (C.I.P.); (G.C.B.); (G.D.)
| | - Gábor Dudás
- Medical Centre, Hungarian Defense Forces, 1114 Budapest, Hungary; (Á.N.); (C.I.P.); (G.C.B.); (G.D.)
| | - Gabriella Terhes
- Institute of Clinical Microbiology, Faculty of Medicine, University of Szeged, 6720 Szeged, Hungary;
| | | | - Róbert Lovas
- Institute for Computer Science and Control (SZTAKI), Eötvös Loránd Research Network, 1111 Budapest, Hungary; (R.L.); (S.T.)
| | - Szabolcs Tenczer
- Institute for Computer Science and Control (SZTAKI), Eötvös Loránd Research Network, 1111 Budapest, Hungary; (R.L.); (S.T.)
| | - László Kornya
- Central Hospital of Southern Pest—National Institute of Hematolgy and Infectious Diseases, 1476 Budapest, Hungary;
| | - Ferenc Jakab
- National Laboratory of Virology, Szentágothai Research Centre, University of Pécs, 7624 Pécs, Hungary; (S.Z.); (B.A.S.); (G.E.T.)
- Institute of Biology, Faculty of Sciences, University of Pécs, 7624 Pécs, Hungary
- Correspondence: (G.K.); (F.J.)
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Cardozo KHM, Lebkuchen A, Okai GG, Schuch RA, Viana LG, Olive AN, Lazari CDS, Fraga AM, Granato CFH, Pintão MCT, Carvalho VM. Establishing a mass spectrometry-based system for rapid detection of SARS-CoV-2 in large clinical sample cohorts. Nat Commun 2020; 11:6201. [PMID: 33273458 PMCID: PMC7713649 DOI: 10.1038/s41467-020-19925-0] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 11/05/2020] [Indexed: 12/13/2022] Open
Abstract
The outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is pressing public health systems around the world, and large population testing is a key step to control this pandemic disease. Here, we develop a high-throughput targeted proteomics assay to detect SARS-CoV-2 nucleoprotein peptides directly from nasopharyngeal and oropharyngeal swabs. A modified magnetic particle-based proteomics approach implemented on a robotic liquid handler enables fully automated preparation of 96 samples within 4 hours. A TFC-MS system allows multiplexed analysis of 4 samples within 10 min, enabling the processing of more than 500 samples per day. We validate this method qualitatively (Tier 3) and quantitatively (Tier 1) using 985 specimens previously analyzed by real-time RT-PCR, and detect up to 84% of the positive cases with up to 97% specificity. The presented strategy has high sample stability and should be considered as an option for SARS-CoV-2 testing in large populations.
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Affiliation(s)
| | - Adriana Lebkuchen
- Division of Research and Development, Fleury Group, 04344-070, São Paulo, SP, Brazil
| | | | | | - Luciana Godoy Viana
- Division of Research and Development, Fleury Group, 04344-070, São Paulo, SP, Brazil
| | - Aline Nogueira Olive
- Division of Research and Development, Fleury Group, 04344-070, São Paulo, SP, Brazil
| | | | - Ana Maria Fraga
- Division of Research and Development, Fleury Group, 04344-070, São Paulo, SP, Brazil
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Eckel F, Küsters F, Drossel B, Konert M, Mattes H, Schopf S. Variplex™ test system fails to reliably detect SARS-CoV-2 directly from respiratory samples without RNA extraction. Eur J Clin Microbiol Infect Dis 2020; 39:2373-2377. [PMID: 32681309 PMCID: PMC7367510 DOI: 10.1007/s10096-020-03983-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 07/03/2020] [Indexed: 12/22/2022]
Abstract
Diagnosis of COVID is performed by PCR methods, but their capacity is limited by the requirement of high-level facilities and instruments. The loop-mediated isothermal amplification (LAMP) method has been utilized for the detection of isolated virus-specific RNA. Preliminary data suggest the possibility of isothermal amplification directly from respiratory samples without RNA extraction. All patients admitted to our hospital were screened for SARS-CoV-2 by routine. Respiratory samples were tested by variplex system based on LAMP method directly without RNA extraction and by PCR. Primary endpoint was the false-negative rate of variplex test compared with PCR as gold standard. In 109 patients variplex test and PCR assay were performed simultaneously. Median age was 80 years and male/female ratio was 40/60%. The prevalence of PCR-confirmed COVID diagnosis was 43.1%. Variplex test was positive in 13.8%. False-negative rate of variplex test compared with PCR was 83.0%. The potential of LAMP technology using isolated RNA has been demonstrated impressively by others, and excellent sensitivity and specificity of detecting SARS-CoV-2 has been reported. However, without RNA extraction, the variplex test system failed to reliably detect SARS-CoV-2 directly in respiratory samples.
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Affiliation(s)
- Florian Eckel
- Internal Medicine II, Klinikum rechts der Isar, Technische Universität München, Munich, Germany.
- Medical Department, RoMed Klink Bad Aibling, Harthauser Str. 16, 83043, Bad Aibling, Germany.
| | - Franziska Küsters
- Medical Department, RoMed Klink Bad Aibling, Harthauser Str. 16, 83043, Bad Aibling, Germany
| | - Bernhard Drossel
- Hospital Laboratory, RoMed Klink Bad Aibling, Harthauser Str. 16, 83043, Bad Aibling, Germany
| | - Markus Konert
- Department of Anesthesia, RoMed Klink Bad Aibling, Harthauser Str. 16, 83043, Bad Aibling, Germany
| | - Hans Mattes
- Hospital Hygiene, RoMed Klinikum Rosenheim, Pettenkoferstr. 10, 83022, Rosenheim, Germany
| | - Stefan Schopf
- Surgical Department, RoMed Klink Bad Aibling, Harthauser Str. 16, 83043, Bad Aibling, Germany
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Abstract
BackgroundReverse-transcription PCR (RT-PCR) assays are used to test for infection with the SARS-CoV-2 virus. RT-PCR tests are highly specific and the probability of false positives is low, but false negatives are possible depending on swab type and time since symptom onset.AimTo determine how the probability of obtaining a false-negative test in infected patients is affected by time since symptom onset and swab type.MethodsWe used generalised additive mixed models to analyse publicly available data from patients who received multiple RT-PCR tests and were identified as SARS-CoV-2 positive at least once.ResultsThe probability of a positive test decreased with time since symptom onset, with oropharyngeal (OP) samples less likely to yield a positive result than nasopharyngeal (NP) samples. The probability of incorrectly identifying an uninfected individual due to a false-negative test was considerably reduced if negative tests were repeated 24 hours later. For a small false-positive test probability (<0.5%), the true number of infected individuals was larger than the number of positive tests. For a higher false-positive test probability, the true number of infected individuals was smaller than the number of positive tests.ConclusionNP samples are more sensitive than OP samples. The later an infected individual is tested after symptom onset, the less likely they are to test positive. This has implications for identifying infected patients, contact tracing and discharging convalescing patients who are potentially still infectious.
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Affiliation(s)
- Paul S Wikramaratna
- These authors contributed equally to this article and share first authorship
- Independent Researcher, London, United Kingdom (DPhil (Zoology) Oxon)
| | - Robert S Paton
- These authors contributed equally to this article and share first authorship
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Mahan Ghafari
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - José Lourenço
- Department of Zoology, University of Oxford, Oxford, United Kingdom
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Tirupathi R, Ramparas TR, Wadhwa G, Areti S, Kaur J, Salim S, Rabaan AA, Al-Tawfiq JA. Viral dynamics in the Upper Respiratory Tract (URT) of SARS-CoV-2. Infez Med 2020; 28:486-499. [PMID: 33257622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
To date, research on viral shedding (VS), live virus isolation and infection status remains ongoing as scientists and clinicians attempt to better understand the coronavirus disease of 2019 (COVID-19) pandemic. Viral RNA detection at different stages of the disease, quantitative changes and patterns of viral persistence and clearance all provide context for the pathogenesis and transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Given the highly infectious nature of SARS-CoV-2 and its impact on the global population and economy, clinicians continue to seek the best methods for controlling its spread, and data on public health preventative measures continue to emerge. In this paper we review the available evidence on the viral dynamics of SARS-CoV-2 in the URT to determine a timeline for infection based on molecular and viral culture findings and to assess the significance of persistently positive results. Keywords: viral shedding, viral load, viral culture, SARS-CoV-2, upper respiratory tract.
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Affiliation(s)
- Raghavendra Tirupathi
- Department of Medicine, Penn State University School of Medicine, Hershey, PA, USA; Keystone Infectious Diseases/HIV, Keystone Health, Chambersburg, PA, USA; Department of Medicine, Keystone Health, Chambersburg, PA, USA; Department of Medicine, Wellspan Chambersburg and Waynesboro (Pa.) Hospitals, Chambersburg, PA, USA
| | | | - Gautam Wadhwa
- Department of Medicine, Wellspan Chambersburg and Waynesboro (Pa.) Hospitals, Chambersburg, PA, USA
| | - Swetha Areti
- Department of Medicine, Wellspan Chambersburg and Waynesboro (Pa.) Hospitals, Chambersburg, PA, USA
| | - Jagdeep Kaur
- Department of Psychiatry, Keystone Health, Chambersburg, PA, USA
| | - Sohail Salim
- Department of Nephrology, University of Mississippi Medical Center, Jackson, MS, USA
| | - Ali A Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran, Saudi Arabia
| | - Jaffar A Al-Tawfiq
- Specialty Internal Medicine and Quality Department, Johns Hopkins Aramco Healthcare, Dhahran, Saudi Arabia; Indiana University School of Medicine, Indiana, USA; Infectious Disease Division, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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Abstract
BackgroundReverse-transcription PCR (RT-PCR) assays are used to test for infection with the SARS-CoV-2 virus. RT-PCR tests are highly specific and the probability of false positives is low, but false negatives are possible depending on swab type and time since symptom onset.AimTo determine how the probability of obtaining a false-negative test in infected patients is affected by time since symptom onset and swab type.MethodsWe used generalised additive mixed models to analyse publicly available data from patients who received multiple RT-PCR tests and were identified as SARS-CoV-2 positive at least once.ResultsThe probability of a positive test decreased with time since symptom onset, with oropharyngeal (OP) samples less likely to yield a positive result than nasopharyngeal (NP) samples. The probability of incorrectly identifying an uninfected individual due to a false-negative test was considerably reduced if negative tests were repeated 24 hours later. For a small false-positive test probability (<0.5%), the true number of infected individuals was larger than the number of positive tests. For a higher false-positive test probability, the true number of infected individuals was smaller than the number of positive tests.ConclusionNP samples are more sensitive than OP samples. The later an infected individual is tested after symptom onset, the less likely they are to test positive. This has implications for identifying infected patients, contact tracing and discharging convalescing patients who are potentially still infectious.
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Affiliation(s)
- Paul S Wikramaratna
- These authors contributed equally to this article and share first authorship
- Independent Researcher, London, United Kingdom (DPhil (Zoology) Oxon)
| | - Robert S Paton
- These authors contributed equally to this article and share first authorship
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Mahan Ghafari
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - José Lourenço
- Department of Zoology, University of Oxford, Oxford, United Kingdom
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Wikramaratna PS, Paton RS, Ghafari M, Lourenço J. Estimating the false-negative test probability of SARS-CoV-2 by RT-PCR. Euro Surveill 2020. [PMID: 33334398 DOI: 10.1101/2020.04.05.20053355v3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/18/2023] Open
Abstract
BackgroundReverse-transcription PCR (RT-PCR) assays are used to test for infection with the SARS-CoV-2 virus. RT-PCR tests are highly specific and the probability of false positives is low, but false negatives are possible depending on swab type and time since symptom onset.AimTo determine how the probability of obtaining a false-negative test in infected patients is affected by time since symptom onset and swab type.MethodsWe used generalised additive mixed models to analyse publicly available data from patients who received multiple RT-PCR tests and were identified as SARS-CoV-2 positive at least once.ResultsThe probability of a positive test decreased with time since symptom onset, with oropharyngeal (OP) samples less likely to yield a positive result than nasopharyngeal (NP) samples. The probability of incorrectly identifying an uninfected individual due to a false-negative test was considerably reduced if negative tests were repeated 24 hours later. For a small false-positive test probability (<0.5%), the true number of infected individuals was larger than the number of positive tests. For a higher false-positive test probability, the true number of infected individuals was smaller than the number of positive tests.ConclusionNP samples are more sensitive than OP samples. The later an infected individual is tested after symptom onset, the less likely they are to test positive. This has implications for identifying infected patients, contact tracing and discharging convalescing patients who are potentially still infectious.
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Affiliation(s)
- Paul S Wikramaratna
- These authors contributed equally to this article and share first authorship
- Independent Researcher, London, United Kingdom (DPhil (Zoology) Oxon)
| | - Robert S Paton
- These authors contributed equally to this article and share first authorship
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Mahan Ghafari
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - José Lourenço
- Department of Zoology, University of Oxford, Oxford, United Kingdom
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Chong YM, Sam IC, Chong J, Kahar Bador M, Ponnampalavanar S, Syed Omar SF, Kamarulzaman A, Munusamy V, Wong CK, Jamaluddin FH, Chan YF. SARS-CoV-2 lineage B.6 was the major contributor to early pandemic transmission in Malaysia. PLoS Negl Trop Dis 2020; 14:e0008744. [PMID: 33253226 PMCID: PMC7728384 DOI: 10.1371/journal.pntd.0008744] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 12/10/2020] [Accepted: 10/30/2020] [Indexed: 12/22/2022] Open
Abstract
Malaysia had 10,219 confirmed cases of COVID-19 as of September 20, 2020. About 33% were associated with a Tablighi Jamaat religious mass gathering held in Kuala Lumpur between February 27 and March 3, 2020, which drove community transmission during Malaysia’s second wave. We analysed genome sequences of SARS-CoV-2 from Malaysia to better understand the molecular epidemiology and spread. We obtained 58 SARS-CoV-2 whole genome sequences from patients in Kuala Lumpur and performed phylogenetic analyses on these and a further 57 Malaysian sequences available in the GISAID database. Nine different SARS-CoV-2 lineages (A, B, B.1, B.1.1, B.1.1.1, B.1.36, B.2, B.3 and B.6) were detected in Malaysia. The B.6 lineage was first reported a week after the Tablighi mass gathering and became predominant (65.2%) despite being relatively rare (1.4%) globally. Direct epidemiological links between lineage B.6 viruses and the mass gathering were identified. Increases in reported total cases, Tablighi-associated cases, and community-acquired B.6 lineage strains were temporally linked. Non-B.6 lineages were mainly travel-associated and showed limited onward transmission. There were also temporally correlated increases in B.6 sequences in other Southeast Asian countries, India and Australia, linked to participants returning from this event. Over 95% of global B.6 sequences originated from Asia Pacific. We also report a nsp3-C6310A substitution found in 47.3% of global B.6 sequences which was associated with reduced sensitivity using a commercial diagnostic real-time PCR assay. Lineage B.6 became the predominant cause of community transmission in Malaysia after likely introduction during a religious mass gathering. This event also contributed to spikes of lineage B.6 in other countries in the Asia-Pacific. Mass gatherings can be significant causes of local and global spread of COVID-19. Shared genomic surveillance can be used to identify SARS-CoV-2 transmission chains to aid prevention and control, and to monitor diagnostic molecular assays. Clinical Trial Registration: COVID-19 paper. The early COVID-19 pandemic in Malaysia was driven mainly by transmission following a religious mass gathering held in Kuala Lumpur at the end of February 2020. To study the genetic epidemiology of SARS-CoV-2 in Malaysia, we analysed 57 available and 58 newly generated Malaysian whole genome virus sequences. We found that lineage B.6, rare (1.4%) globally, first appeared after the mass gathering, was linked to attendees, and became predominant (65.2%) in Malaysia. Increases in COVID-19 cases and locally acquired B.6 strains were temporally linked. Non-B.6 viruses were mainly associated with travel and showed limited spread. Increases in B.6 viruses in Asia Pacific countries were temporally linked to participants returning from this mass gathering. Altogether, 95% of global B.6 sequences originated in Asia Pacific countries. We also report a mutation in the virus nsp3 gene found in 47.3% of global B.6 sequences and associated with reduced detection by a commercial diagnostic test. In conclusion, the religious mass gathering in Kuala Lumpur was associated with the second wave of COVID-19 cases of predominantly B.6 lineage in Malaysia, and subsequent spread of B.6 viruses regionally. Genome sequence data provides valuable insight into virus spread and is important for monitoring continued accuracy of diagnostic kits.
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Affiliation(s)
- Yoong Min Chong
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - I-Ching Sam
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
- Department of Medical Microbiology, University of Malaya Medical Centre, Kuala Lumpur, Malaysia
- * E-mail: (I-CS); (YFC)
| | - Jennifer Chong
- Department of Medical Microbiology, University of Malaya Medical Centre, Kuala Lumpur, Malaysia
| | - Maria Kahar Bador
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
- Department of Medical Microbiology, University of Malaya Medical Centre, Kuala Lumpur, Malaysia
| | | | | | - Adeeba Kamarulzaman
- Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Vijayan Munusamy
- Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Chee Kuan Wong
- Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Fadhil Hadi Jamaluddin
- Department of Anesthesiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Yoke Fun Chan
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
- * E-mail: (I-CS); (YFC)
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Alexandersen S, Chamings A, Bhatta TR. SARS-CoV-2 genomic and subgenomic RNAs in diagnostic samples are not an indicator of active replication. Nat Commun 2020; 11:6059. [PMID: 33247099 DOI: 10.1101/2020.06.01.20119750] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 11/03/2020] [Indexed: 05/23/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) was first detected in late December 2019 and has spread worldwide. Coronaviruses are enveloped, positive sense, single-stranded RNA viruses and employ a complicated pattern of virus genome length RNA replication as well as transcription of genome length and leader containing subgenomic RNAs. Although not fully understood, both replication and transcription are thought to take place in so-called double-membrane vesicles in the cytoplasm of infected cells. Here we show detection of SARS-CoV-2 subgenomic RNAs in diagnostic samples up to 17 days after initial detection of infection and provide evidence for their nuclease resistance and protection by cellular membranes suggesting that detection of subgenomic RNAs in such samples may not be a suitable indicator of active coronavirus replication/infection.
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Affiliation(s)
- Soren Alexandersen
- Geelong Centre for Emerging Infectious Diseases, Geelong, VIC, 3220, Australia.
- Deakin University, Geelong, VIC, 3220, Australia.
- Barwon Health, University Hospital Geelong, Geelong, VIC, 3220, Australia.
| | - Anthony Chamings
- Geelong Centre for Emerging Infectious Diseases, Geelong, VIC, 3220, Australia
- Deakin University, Geelong, VIC, 3220, Australia
| | - Tarka Raj Bhatta
- Geelong Centre for Emerging Infectious Diseases, Geelong, VIC, 3220, Australia
- Deakin University, Geelong, VIC, 3220, Australia
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47
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Alexandersen S, Chamings A, Bhatta TR. SARS-CoV-2 genomic and subgenomic RNAs in diagnostic samples are not an indicator of active replication. Nat Commun 2020; 11:6059. [PMID: 33247099 PMCID: PMC7695715 DOI: 10.1038/s41467-020-19883-7] [Citation(s) in RCA: 206] [Impact Index Per Article: 51.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 11/03/2020] [Indexed: 02/06/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) was first detected in late December 2019 and has spread worldwide. Coronaviruses are enveloped, positive sense, single-stranded RNA viruses and employ a complicated pattern of virus genome length RNA replication as well as transcription of genome length and leader containing subgenomic RNAs. Although not fully understood, both replication and transcription are thought to take place in so-called double-membrane vesicles in the cytoplasm of infected cells. Here we show detection of SARS-CoV-2 subgenomic RNAs in diagnostic samples up to 17 days after initial detection of infection and provide evidence for their nuclease resistance and protection by cellular membranes suggesting that detection of subgenomic RNAs in such samples may not be a suitable indicator of active coronavirus replication/infection.
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Affiliation(s)
- Soren Alexandersen
- Geelong Centre for Emerging Infectious Diseases, Geelong, VIC, 3220, Australia.
- Deakin University, Geelong, VIC, 3220, Australia.
- Barwon Health, University Hospital Geelong, Geelong, VIC, 3220, Australia.
| | - Anthony Chamings
- Geelong Centre for Emerging Infectious Diseases, Geelong, VIC, 3220, Australia
- Deakin University, Geelong, VIC, 3220, Australia
| | - Tarka Raj Bhatta
- Geelong Centre for Emerging Infectious Diseases, Geelong, VIC, 3220, Australia
- Deakin University, Geelong, VIC, 3220, Australia
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Hanege FM, Kocoglu E, Kalcioglu MT, Celik S, Cag Y, Esen F, Bayindir E, Pence S, Alp Mese E, Agalar C. SARS-CoV-2 Presence in the Saliva, Tears, and Cerumen of COVID-19 Patients. Laryngoscope 2020; 131:E1677-E1682. [PMID: 33094833 DOI: 10.1002/lary.29218] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 09/29/2020] [Accepted: 10/19/2020] [Indexed: 12/23/2022]
Abstract
OBJECTIVES/HYPOTHESIS The emergence of a new coronavirus strain (SARS-CoV-2) in December 2019 from China led to a global pandemic. The lack of herd immunity against this virus and the possibility of viral spread from asymptomatic individuals is still a major challenge for the prevention of viral transmission. The aim of this study was to evaluate the presence of the virus in different bodily secretions as a potential source of viral spread among patients infected with SARS-CoV-2. STUDY DESIGN Cross Sectional Study. METHODS The study included 38 COVID-19 patients with a positive real-time polymerase chain reaction (RT-PCR) test result for SARS-CoV-2, obtained from the combined nasopharyngeal-oropharyngeal swab samples. Saliva, tear, and cerumen samples were taken from the patients within 72 hours of the first RT-PCR test. SARS-CoV-2 N1 and N2 gene regions were studied with single-step RT-PCR in all samples. RESULTS Among the studied samples, the highest positivity rate was in saliva (76.3%) followed by tears (55.3%) and cerumen (39.5%). Viral load in saliva was also significantly higher compared to tears and cerumen (P < .001), while there was no significant difference between tears and cerumen. Higher viral load in combined nasopharyngeal-oropharyngeal swab samples was associated with higher viral load in tears, but not in saliva or cerumen. Half of the saliva, tear, and cerumen samples obtained from asymptomatic patients contained SARS-CoV-2 genome. CONCLUSIONS The virus was detected in the saliva, tears, and cerumen samples of both symptomatic and asymptomatic patients. The potential role of these bodily fluids on viral spread needs to be studied. LEVEL OF EVIDENCE 4 Laryngoscope, 131:E1677-E1682, 2021.
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Affiliation(s)
- Fatih M Hanege
- Department of Otorhinolaryngology and Head and Neck Surgery, Istanbul Medeniyet University Faculty of Medicine, Istanbul, Turkey
- Drhanege Clinic, Istanbul, Turkey
| | - Esra Kocoglu
- Department of Medical Microbiology, Istanbul Medeniyet University Faculty of Medicine, Istanbul, Turkey
| | - Mahmut T Kalcioglu
- Department of Otorhinolaryngology and Head and Neck Surgery, Istanbul Medeniyet University Faculty of Medicine, Istanbul, Turkey
| | - Serdal Celik
- Department of Otorhinolaryngology and Head and Neck Surgery, Istanbul Medeniyet University Faculty of Medicine, Istanbul, Turkey
| | - Yasemin Cag
- Department of Infectious Diseases and Clinical Microbiology, Istanbul Medeniyet University Faculty of Medicine, Istanbul, Turkey
| | - Fehim Esen
- Department of Ophthalmology, Istanbul Medeniyet University Faculty of Medicine, Istanbul, Turkey
| | - Eray Bayindir
- Department of Otorhinolaryngology and Head and Neck Surgery, Istanbul Medeniyet University Faculty of Medicine, Istanbul, Turkey
| | - Sadrettin Pence
- Department of Physiology, Istanbul Medeniyet University Faculty of Medicine, Istanbul, Turkey
| | - Emine Alp Mese
- Department of Infectious Diseases and Clinical Microbiology, Republic of Turkey Ministry of Health, Ankara, Turkey
| | - Canan Agalar
- Department of Infectious Diseases and Clinical Microbiology, Saglik Bilimleri University Fatih Sultan Mehmet Training and Research Hospital, Istanbul, Turkey
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Palop Larrea V, Hernández Rodríguez MÁ. [Use of oral antiseptics for SARS-CoV-2 infection]. Med Clin (Barc) 2020; 155:416-417. [PMID: 32778429 PMCID: PMC7383134 DOI: 10.1016/j.medcli.2020.07.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 07/06/2020] [Accepted: 07/09/2020] [Indexed: 11/30/2022]
Affiliation(s)
- Vicente Palop Larrea
- Medicina Familiar y Comunitaria, Grupo de Trabajo de Utilización de Fármacos de la Sociedad Española de Medicina Familiar y Comunitaria; Unidad de Aparato Locomotor, Consulta de Fibromialgia, Hospital de Dénia-Marina Salud, Asesor Médico de Ribera Salud, Dénia, Alicante, España
| | - Miguel Ángel Hernández Rodríguez
- Medicina Familiar y Comunitaria, Grupo de Trabajo de Utilización de Fármacos de la Sociedad Española de Medicina Familiar y Comunitaria; Servicio Canario de la Salud, Plan de Salud de Canarias, Santa Cruz de Tenerife, España.
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50
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Arnold MT, Temte JL, Barlow SK, Bell CJ, Goss MD, Temte EG, Checovich MM, Reisdorf E, Scott S, Guenther K, Wedig M, Shult P, Uzicanin A. Comparison of participant-collected nasal and staff-collected oropharyngeal specimens for human ribonuclease P detection with RT-PCR during a community-based study. PLoS One 2020; 15:e0239000. [PMID: 33027284 PMCID: PMC7540885 DOI: 10.1371/journal.pone.0239000] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 08/27/2020] [Indexed: 11/24/2022] Open
Abstract
We analyzed 4,352 participant- and staff-collected respiratory specimens from 2,796 subjects in the Oregon Child Absenteeism due to Respiratory Disease Study. Trained staff collected oropharyngeal specimens from school-aged children with acute respiratory illness while household participants of all ages collected their own midturbinate nasal specimens in year one and anterior nasal specimens in year two. Human ribonuclease P levels were measured using RT-PCR for all staff- and participant-collected specimens to determine adequacy, defined as Cycle threshold less than 38. Overall, staff- and participant-collected specimens were 99.9% and 96.4% adequate, respectively. Participant-collected midturbinate specimens were 95.2% adequate in year one, increasing to 97.2% in year two with anterior nasal collection. The mean human ribonuclease P Cycle threshold for participant-collected specimens was 31.18 in year one and 28.48 in year two. The results from this study suggest that community-based participant collection of respiratory specimens is comparable to staff-collected oropharyngeal specimens, is feasible, and may be optimal with anterior nasal collection.
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Affiliation(s)
- Mitchell T. Arnold
- Department of Family Medicine and Community Health, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI, United States of America
- * E-mail:
| | - Jonathan L. Temte
- Department of Family Medicine and Community Health, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI, United States of America
| | - Shari K. Barlow
- Department of Family Medicine and Community Health, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI, United States of America
| | - Cristalyne J. Bell
- Department of Family Medicine and Community Health, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI, United States of America
| | - Maureen D. Goss
- Department of Family Medicine and Community Health, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI, United States of America
| | - Emily G. Temte
- Department of Family Medicine and Community Health, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI, United States of America
| | - Mary M. Checovich
- Department of Family Medicine and Community Health, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI, United States of America
| | - Erik Reisdorf
- Wisconsin State Laboratory of Hygiene, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Samantha Scott
- Wisconsin State Laboratory of Hygiene, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Kyley Guenther
- Wisconsin State Laboratory of Hygiene, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Mary Wedig
- Wisconsin State Laboratory of Hygiene, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Peter Shult
- Wisconsin State Laboratory of Hygiene, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Amra Uzicanin
- US Centers for Disease Control and Prevention, Atlanta, GA, United States of America
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