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Mishra C, Meena S, Meena JK, Tiwari S, Mathur P. Detection of three pandemic causing coronaviruses from non-respiratory samples: systematic review and meta-analysis. Sci Rep 2021; 11:16131. [PMID: 34373501 PMCID: PMC8352881 DOI: 10.1038/s41598-021-95329-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 06/30/2021] [Indexed: 12/12/2022] Open
Abstract
SARS-CoV-2 has posed an unprecedented challenge to the world. Pandemics have been caused previously by viruses of this family like Middle East Respiratory Corona Virus (MERS CoV), Severe Acute Respiratory Syndrome Corona Virus (SARS CoV). Although these viruses are primarily respiratory viruses, but they have been isolated from non-respiratory samples as well. Presently, the detection rate of SARS-CoV-2 RNA from different clinical specimens using Real Time Reverse Transcriptase Polymerized Chain Reaction (qRT-PCR) after onset of symptoms is not yet well established. Therefore, the aim of this systematic review was to establish the profile of detecting SARS-CoV-2, MERS CoV, SARS CoV from different types of clinical specimens other than the respiratory using a standard diagnostic test (qRT-PCR). A total of 3429 non-respiratory specimens were recorded: SARS CoV (total sample-802), MERS CoV (total sample-155), SARS CoV-2 (total sample-2347). Out of all the samples studied high positive rate was seen for saliva with 96.7% (14/14; 95% CI 87.6-100.0%) for SARS CoV and 57.5% (58/250; 95% CI - 1.2 to 116.2%) for SARS CoV-2, while low detection rate in urine samples for SARS CoV-2 with 2.2% (8/318; 95% CI 0.6-3.7%) and 9.6% (12/61; 95% CI - 0.9 to 20.1%) for SARS CoV but there was relatively higher positivity in urine samples for MERS CoV with detection rate of 32.4% (2/38; 95% CI - 37.3 to 102.1%). In Stool sample positivity was 54.9% (396/779; 95% CI 41.0-68.8%), 45.2% (180/430; 95% CI 28.1-62.3%) and 34.7% (4/38; 95% CI - 29.5 to 98.9%) for SARS CoV-2, MERS CoV, and SARS CoV, respectively. In blood sample the positivity was 33.3% (7/21; 95% CI 13.2-53.5%), 23.7% (42/277; 95% CI 10.5-36.9%) and 2.5% (2/81; 95% CI 0.00-5.8%) for MERS CoV, SARS CoV-2 and SARS CoV respectively. SARS-CoV-2 along with previous two pandemic causing viruses from this family, were highly detected stool and saliva. A low positive rate was recorded in blood samples. Viruses were also detected in fluids along with unusual samples like semen and vaginal secretions thus highlighting unique pathogenic potential of SARS-CoV-2.
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Affiliation(s)
- Chandan Mishra
- Department of Laboratory Medicine, All India Institute of Medical Sciences, Delhi, India
| | - Suneeta Meena
- Department of Laboratory Medicine, All India Institute of Medical Sciences, Delhi, India.
| | - Jitendra Kumar Meena
- Preventive Oncology, NCI Jhajjar, All India Institute of Medical Sciences, Delhi, India
| | - Suman Tiwari
- Department of Anaesthesia and Intensive Care, VMMC and Safdarjung Hospital, Delhi, India
| | - Purva Mathur
- Department of Laboratory Medicine, JPNATC, All India Institute of Medical Sciences, Delhi, India
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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] [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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Banada P, Elson D, Daivaa N, Park C, Desind S, Montalvan I, Kwiatkowski R, Chakravorty S, Alland D, Xie YL. Evaluation of sample collection and transport strategies to enhance yield, accessibility, and biosafety of COVID-19 RT-PCR testing. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.03.03.21251172. [PMID: 33688680 PMCID: PMC7941657 DOI: 10.1101/2021.03.03.21251172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Sensitive, accessible, and biosafe sampling methods for COVID-19 reverse-transcriptase polymerase chain reaction (RT-PCR) assays are needed for frequent and widespread testing. We systematically evaluated diagnostic yield across different sample collection and transport workflows, including the incorporation of a viral inactivation buffer. We prospectively collected nasal swabs, oral swabs, and saliva, from 52 COVID-19 RT-PCR-confirmed patients, and nasopharyngeal (NP) swabs from 37 patients. Nasal and oral swabs were placed in both viral transport media (VTM) and eNAT™, a sterilizing transport buffer, prior to testing with the Xpert Xpress SARS-CoV-2 (Xpert) test. The sensitivity of each sampling strategy was compared using a composite positive standard. Overall, swab specimens collected in eNAT showed superior sensitivity compared to swabs in VTM (70% vs 57%, P=0.0022). Direct saliva 90.5%, (95% CI: 82%, 95%), followed by NP swabs in VTM and saliva in eNAT, was significantly more sensitive than nasal swabs in VTM (50%, P<0.001) or eNAT (67.8%, P=0.0012) and oral swabs in VTM (50%, P<0.0001) or eNAT (56%, P<0.0001). Saliva and use of eNAT buffer each increased detection of SARS-CoV-2 with the Xpert test; however, no single sample matrix identified all positive cases.
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Bognanni A, Schiaffino A, Pimpinelli F, Donzelli S, Celesti I, Strano S, Solari E, Schiaffino G, Solari G, Solari D, Delbue S, Rigoni M, Nollo G, Muti GE, Muti Schünemann GE, Schünemann HJ, Blandino G, Morrone A, Muti P. The Conundrum of Giglio Island: Unraveling the dynamics of an apparent resistance to COVID-19 - A descriptive study. Comput Struct Biotechnol J 2021; 19:1467-1471. [PMID: 33680349 PMCID: PMC7920805 DOI: 10.1016/j.csbj.2021.02.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 02/05/2021] [Accepted: 02/15/2021] [Indexed: 12/18/2022] Open
Abstract
OBJECTIVES Despite an extensive risk of exposure to COVID-19, the residents of Giglio Island, Italy, did not develop any symptom of SARS-CoV-2. The present study aims to characterize the nature of exposure and to describe the local population dynamics underlying its apparent resistance to COVID-19. METHODS Descriptive study of an islander partially-segregated population cohort based on a seroprevalence screening conducted from Aprile 29 to May 3, 2020 and including SARS-CoV-2 seroprevalence and viral prevalence in samples of saliva assessed through RT-qPCR. Serologic testing was performed using a COVID-19 IgG/IgM rapid test while molecular analyses were carried out by Allplex 2019-nCoV Assay (Seegene). RESULTS A total of 634 residents out of 748 (84.8%) present at the time, and 89 non-residents underwent serological testing. 364 males and 359 females with a median age of 58.5 years. The serological screening identified one positive, asymptomatic subject. The Nucleic Acid Amplification Tests (NAAT) did not yield any positive result. CONCLUSION Despite extensive exposure to SARS-CoV-2, possibly only one new asymptomatic infection occurred in this population, as documented by IgM positivity not confirmed by RT-qPCR. This may be due to unknown protective factors or chance. On the basis of this baseline study, using its population as a reference model, further investigations will be conducted to test the advanced hypotheses, focusing on the evaluation of a possible cross-reactivity to SARS-CoV-2 from exposure to endemic viruses.
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Affiliation(s)
- Antonio Bognanni
- Department of Health Research Methods, Evidence, and Impact, Faculty of Health Sciences, McMaster University, Hamilton, Ontario, Canada
- Department of Biomedical, Surgical and Dental Sciences, “Università degli Studi di Milano”, Milan, Italy
| | | | - Fulvia Pimpinelli
- Clinical Pathology and Microbiology, San Gallicano Dermatologic Institute IRCCS, Rome, Italy
| | - Sara Donzelli
- Oncogenomic and Epigenetic Unit, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Ilaria Celesti
- Clinical Pathology and Microbiology, San Gallicano Dermatologic Institute IRCCS, Rome, Italy
| | - Sabrina Strano
- Oncogenomic and Epigenetic Unit, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Elena Solari
- Università di Pisa, Nursing School, Department of Clinical Health and Experimental Medicine, Pisa, Italy
| | | | - Gabriele Solari
- Independent Health Professionist, Isola del Giglio, Grosseto, Italy
| | - Domenico Solari
- Tuscany Regional Health System – South Eastern Area (retired), Italy
| | - Serena Delbue
- Department of Biomedical, Surgical and Dental Sciences, “Università degli Studi di Milano”, Milan, Italy
| | - Marta Rigoni
- Department of Industrial Engineering, University of Trento, Trento, Italy
| | - Giandomenico Nollo
- Department of Industrial Engineering, University of Trento, Trento, Italy
| | - Greta E. Muti
- Università “Vita Salute” San Raffaele – International MD Program, Milan, Italy
| | - Giovanna E.U. Muti Schünemann
- Department of Health Research Methods, Evidence, and Impact, Faculty of Health Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Holger J Schünemann
- Department of Health Research Methods, Evidence, and Impact, Faculty of Health Sciences, McMaster University, Hamilton, Ontario, Canada
- Department of Medicine, McMaster University, Hamilton, Canada
| | - Giovanni Blandino
- Oncogenomic and Epigenetic Unit, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Aldo Morrone
- Scientific Direction, San Gallicano Dermatological Institute IRCCS, Rome, Italy
| | - Paola Muti
- Department of Health Research Methods, Evidence, and Impact, Faculty of Health Sciences, McMaster University, Hamilton, Ontario, Canada
- Department of Biomedical, Surgical and Dental Sciences, “Università degli Studi di Milano”, Milan, Italy
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Swarnakar R, Gupta NM, Halder I, Khilnani GC. Guidance for nebulization during the COVID-19 pandemic. Lung India 2021; 38:S86-S91. [PMID: 33686989 PMCID: PMC8104341 DOI: 10.4103/lungindia.lungindia_681_20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Affiliation(s)
- Rajesh Swarnakar
- Department of Pulmonology, Getwell Hospital and Research Institute, Nagpur, Maharashtra, India
| | - Neeraj M Gupta
- Department of Respiratory Medicine, JLN Medical College, Ajmer, Rajasthan, India,, India
| | - Indranil Halder
- Department of Pulmonary Medicine, College of Medicine and JNM Hospital, Kolkata, West Bengal, India
| | - Gopi C Khilnani
- PSRI Institute of Pulmonary, Critical Care and Sleep Medicine, PSRI Hospital, New Delhi, India
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Ana Laura GO, Abraham Josué NR, Briceida LM, Israel PO, Tania AF, Nancy MR, Lourdes JB, Daniela DLRZ, Fernando OR, Carlos Mauricio JE, Sergio René BP, Irineo RT, Horacio MG, Oscar MC, Héctor Q. Sensitivity of the Molecular Test in Saliva for Detection of COVID-19 in Pediatric Patients With Concurrent Conditions. Front Pediatr 2021; 9:642781. [PMID: 33912522 PMCID: PMC8071854 DOI: 10.3389/fped.2021.642781] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 03/17/2021] [Indexed: 01/27/2023] Open
Abstract
Background: The reference standard for the molecular diagnostic testing for COVID-19 is the use of nasopharyngeal or combined nasopharyngeal and oropharyngeal (NP/OP) swabs. Saliva has been proposed as a minimally invasive specimen whose collection reduces the risks for health care personnel. Objective: To assess the suitability of saliva for COVID-19 diagnosis as a replacement of the reference standard NP/OP swab in the setting of a tertiary care pediatric unit. Study design: A paired study based in the prospective cohort design in patients suspected of having COVID-19. Methods: RT-PCR was used to detect SARS-CoV-2 in paired samples of saliva and NP/OP swab collected from May through August 2020 from 156 pediatric participants, of whom 128 has at least one comorbidity and 91 showed clinical symptoms related to SARS-CoV-2 infection. Additionally, we studied a group of 326 members of the hospital staff, of whom 271 had symptoms related to SARS-CoV-2 infection. Results: In the group of pediatric participants the sensitivity of the diagnostic test in saliva was 82.3% (95% CI 56.6-96.2) and the specificity 95.6% (95% CI 90.8-98.4). The prevalence of COVID-19 was 10.9% (17/156). In 6 of the 23 participants who tested positive for SARS-CoV-2 in at least one specimen type, the virus was detected in saliva but not in NP/OP swab, while in 3 participants the NP/OP swab was positive and saliva negative. In the group of adults, the sensitivity of the test in saliva was 77.8% (95% CI 67.2-86.3) and prevalence 24.8% (81/326). Discordant results between the two types of specimens showed a significant association with low viral load in the pharynx of adults but not of pediatric participants. Interpretation: In the context of a pediatric tertiary care hospital, the sensibility of the test in saliva is not high enough to replace the use of NP/OP swab for COVID-19 diagnosis. Neither NP/OP swab nor saliva could detect all the participants infected with SARS-CoV-2.
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Affiliation(s)
- Guzmán-Ortiz Ana Laura
- Laboratorio de Investigación en Inmunología y Proteómica, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Nevárez-Ramírez Abraham Josué
- Laboratorio de Investigación en Inmunología y Proteómica, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | | | - Parra-Ortega Israel
- Laboratorio Clínico, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | | | - Martínez-Rodríguez Nancy
- Unidad de Investigación Epidemiológica en Endocrinología y Nutrición, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | | | - De la Rosa-Zamboni Daniela
- Departamento de Epidemiología Hospitalaria, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | | | | | | | - Reyna-Trinidad Irineo
- Departamento de Enfermería, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Márquez-González Horacio
- Departamento de Investigación Clínica, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Medina-Contreras Oscar
- Unidad de Investigación Epidemiológica en Endocrinología y Nutrición, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Quezada Héctor
- Laboratorio de Investigación en Inmunología y Proteómica, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
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Torrente-Rodríguez RM, Lukas H, Tu J, Min J, Yang Y, Xu C, Rossiter HB, Gao W. SARS-CoV-2 RapidPlex: A Graphene-Based Multiplexed Telemedicine Platform for Rapid and Low-Cost COVID-19 Diagnosis and Monitoring. MATTER 2020; 3:1981-1998. [PMID: 33043291 PMCID: PMC7535803 DOI: 10.1016/j.matt.2020.09.027] [Citation(s) in RCA: 269] [Impact Index Per Article: 67.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 09/20/2020] [Accepted: 09/29/2020] [Indexed: 05/15/2023]
Abstract
The COVID-19 pandemic is an ongoing global challenge for public health systems. Ultrasensitive and early identification of infection is critical in preventing widespread COVID-19 infection by presymptomatic and asymptomatic individuals, especially in the community and in-home settings. We demonstrate a multiplexed, portable, wireless electrochemical platform for ultra-rapid detection of COVID-19: the SARS-CoV-2 RapidPlex. It detects viral antigen nucleocapsid protein, IgM and IgG antibodies, as well as the inflammatory biomarker C-reactive protein, based on our mass-producible laser-engraved graphene electrodes. We demonstrate ultrasensitive, highly selective, and rapid electrochemical detection in the physiologically relevant ranges. We successfully evaluated the applicability of our SARS-CoV-2 RapidPlex platform with COVID-19-positive and COVID-19-negative blood and saliva samples. Based on this pilot study, our multiplexed immunosensor platform may allow for high-frequency at-home testing for COVID-19 telemedicine diagnosis and monitoring.
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Affiliation(s)
- Rebeca M Torrente-Rodríguez
- Andrew and Peggy Cherng Department of Medical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Heather Lukas
- Andrew and Peggy Cherng Department of Medical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Jiaobing Tu
- Andrew and Peggy Cherng Department of Medical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Jihong Min
- Andrew and Peggy Cherng Department of Medical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Yiran Yang
- Andrew and Peggy Cherng Department of Medical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Changhao Xu
- Andrew and Peggy Cherng Department of Medical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Harry B Rossiter
- Rehabilitation Clinical Trials Center, Division of Respiratory and Critical Care Physiology and Medicine, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Wei Gao
- Andrew and Peggy Cherng Department of Medical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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