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Howard LM, Grijalva CG. Impact of respiratory viral infections on nasopharyngeal pneumococcal colonization dynamics in children. Curr Opin Infect Dis 2024; 37:170-175. [PMID: 38437245 DOI: 10.1097/qco.0000000000001008] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2024]
Abstract
PURPOSE OF REVIEW Prevention of acute respiratory illnesses (ARI) in children is a global health priority, as these remain a leading cause of pediatric morbidity and mortality throughout the world. As new products and strategies to prevent respiratory infections caused by important pathogens such as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), influenza, respiratory syncytial virus and pneumococcus are advancing, increasing evidence suggests that these and other respiratory viruses and pneumococci may exhibit interactions that are associated with altered colonization and disease dynamics. We aim to review recent data evaluating interactions between respiratory viruses and pneumococci in the upper respiratory tract and their potential impact on pneumococcal colonization patterns and disease outcomes. RECENT FINDINGS While interactions between influenza infection and subsequent increased susceptibility and transmissibility of colonizing pneumococci have been widely reported in the literature, emerging evidence suggests that human rhinovirus, SARS-CoV-2, and other viruses may also exhibit interactions with pneumococci and alter pneumococcal colonization patterns. Additionally, colonizing pneumococci may play a role in modifying outcomes associated with respiratory viral infections. Recent evidence suggests that vaccination with pneumococcal conjugate vaccines, and prevention of colonization with pneumococcal serotypes included in these vaccines, may be associated with reducing the risk of subsequent viral infection and the severity of the associated illnesses. SUMMARY Understanding the direction and dynamics of viral-pneumococcal interactions may elucidate the potential effects of existing and emerging viral and bacterial vaccines and other preventive strategies on the health impact of these important respiratory pathogens.
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Affiliation(s)
- Leigh M Howard
- Department of Pediatrics, Division of Infectious Diseases
| | - Carlos G Grijalva
- Departments of Health Policy and Biomedical Informatics, Division of Pharmacoepidemiology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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2
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Saeed U, Uppal R, Khan AA, Uppal MR, Piracha ZZ, Uppal SR. Analytical assessment of clinical sensitivity and specificities of pharmaceutical rapid SARS-CoV-2 detection nasopharyngeal swab testing kits in Pakistan. BRAZ J BIOL 2024; 84:e265550. [PMID: 38451627 DOI: 10.1590/1519-6984.265550] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 10/28/2022] [Indexed: 03/08/2024] Open
Abstract
Despite of the global unity against COVID-19 pandemic, the threat of SARS-CoV-2 variants on the lives of human being is still not over. SARS-CoV-2 pandemic has urged the need of rapid viral detection at earliest. To cope with gradually expanding scenario of SARS-CoV-2, accurate diagnosis is extremely crucial factor which should be noticed by international health organizations. Limited research followed by sporadic marketing of SARS-CoV-2 rapid pharmaceutical detection kits raises critical questions against quality assurance and quality control measures. Herein we aimed to interrogate effectivity and specificity analysis of SARS-CoV-2 pharmaceutical rapid detection kits (nasopharyngeal swab based) using conventional gold standard triple target real-time polymerase chain reaction (USFDA approved). A cross-sectional study was conducted over 1500 suspected SARS-CoV-2 patients. 100 real time-PCR confirmed patients were evaluated for pharmaceutical RDT kits based upon nasopharyngeal swab based kits. The SARS-CoV-2 nasopharyngeal swab based rapid diagnostic kit (NSP RDTs) analysis showed 78% reactivity. Among real time PCR confirmed negative subjects, 49.3% represented false positivity. The positive predictive analysis revealed 67.82%, while negative predictive values were 64.40%. The NSP RDTs showed limited sensitivities and specificities as compared to gold standard real time PCR. Valid and authentic detection of SARS-CoV-2 is deemed necessary for accurate COVID-19 surveillance across the globe. Current study highlights the potential consequences of inadequate detection of SARS-CoV-2 and emerging novel mutants, compromising vaccine preventable diseases. Current study emphasizes need to wake higher authorities including strategic organizations for designing adequate measures to prevent future SARS-CoV-2 epidemics.
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Affiliation(s)
- U Saeed
- Islamabad Diagnostic Center - IDC, Department of Research and Development, Islamabad, Pakistan
- Foundation University Islamabad Pakistan, Foundation University School of Health Sciences, Clinical and Biomedical Research Center, Islamabad, Pakistan
| | - R Uppal
- Islamabad Diagnostic Center - IDC, Department of Research and Development, Islamabad, Pakistan
| | - A A Khan
- Islamabad Diagnostic Center - IDC, Department of Research and Development, Islamabad, Pakistan
| | - M R Uppal
- Islamabad Diagnostic Center - IDC, Department of Research and Development, Islamabad, Pakistan
| | - Z Z Piracha
- International Center of Medical Sciences Research - ICMSR, Islamabad, Pakistan
- International Center of Medical Sciences Research - ICMSR, Austin, TX, United States of America
- International Center of Medical Sciences Research - ICMSR, Chadwell Health, United Kingdom
| | - S R Uppal
- Islamabad Diagnostic Center - IDC, Department of Research and Development, Islamabad, Pakistan
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3
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Jalving HT, Heimdal I, Valand J, Risnes K, Krokstad S, Nordbø SA, Døllner H, Christensen A. The Burden of Human Bocavirus 1 in Hospitalized Children With Respiratory Tract Infections. J Pediatric Infect Dis Soc 2023; 12:282-289. [PMID: 37099765 PMCID: PMC10231390 DOI: 10.1093/jpids/piad027] [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] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 04/27/2023] [Indexed: 04/28/2023]
Abstract
BACKGROUND Human bocavirus 1 (HBoV1) is frequently codetected with other viruses, and detected in asymptomatic children. Thus, the burden of HBoV1 respiratory tract infections (RTI) has been unknown. Using HBoV1-mRNA to indicate true HBoV1 RTI, we assessed the burden of HBoV1 in hospitalized children and the impact of viral codetections, compared with respiratory syncytial virus (RSV). METHODS Over 11 years, we enrolled 4879 children <16 years old admitted with RTI. Nasopharyngeal aspirates were analyzed with polymerase chain reaction for HBoV1-DNA, HBoV1-mRNA, and 19 other pathogens. RESULTS HBoV1-mRNA was detected in 2.7% (130/4850) samples, modestly peaking in autumn and winter. Forty-three percent with HBoV1 mRNA were 12-17 months old, and only 5% were <6 months old. A total of 73.8% had viral codetections. It was more likely to detect HBoV1-mRNA if HBoV1-DNA was detected alone (odds ratio [OR]: 3.9, 95% confidence interval [CI]: 1.7-8.9) or with 1 viral codetection (OR: 1.9, 95% CI: 1.1-3.3), compared to ≥2 codetections. Codetection of severe viruses like RSV had lower odds for HBoV1-mRNA (OR: 0.34, 95% CI: 0.19-0.61). The yearly lower RTI hospitalization rate per 1000 children <5 years was 0.7 for HBoV1-mRNA and 8.7 for RSV. CONCLUSIONS True HBoV1 RTI is most likely when HBoV1-DNA is detected alone, or with 1 codetected virus. Hospitalization due to HBoV1 LRTI is 10-12 times less common than RSV.
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Affiliation(s)
- Hedda Trømborg Jalving
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Inger Heimdal
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Jonas Valand
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Kari Risnes
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Children’s Department, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Sidsel Krokstad
- Department of Medical Microbiology, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Svein Arne Nordbø
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Department of Medical Microbiology, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Henrik Døllner
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Children’s Department, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Andreas Christensen
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Department of Medical Microbiology, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
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4
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Waggoner JJ, Tyburski EA, Lam WA. SARS-CoV-2 Results in Self-collected Nasal Swabs vs Swabs Collected by Health Care Workers in Children and Adolescents-Reply. JAMA 2023; 329:425-426. [PMID: 36749337 DOI: 10.1001/jama.2022.21599] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
| | | | - Wilbur A Lam
- Emory University School of Medicine, Children's Healthcare of Atlanta, Atlanta, Georgia
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Hong KH, Sung H. SARS-CoV-2 Results in Self-collected Nasal Swabs vs Swabs Collected by Health Care Workers in Children and Adolescents. JAMA 2023; 329:424-425. [PMID: 36749340 DOI: 10.1001/jama.2022.21596] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Ki Ho Hong
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, South Korea
| | - Heungsup Sung
- Department of Laboratory Medicine, University of Ulsan College of Medicine, Seoul, South Korea
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Andrés C, Piñana M, Borràs-Bermejo B, González-Sánchez A, García-Cehic D, Esperalba J, Rando A, Zules-Oña RG, Campos C, Codina MG, Blanco-Grau A, Colomer-Castell S, Martín MC, Castillo C, García-Comuñas K, Vásquez-Mercado R, Martins-Martins R, Saubi N, Campins-Martí M, Pumarola T, Quer J, Antón A. A year living with SARS-CoV-2: an epidemiological overview of viral lineage circulation by whole-genome sequencing in Barcelona city (Catalonia, Spain). Emerg Microbes Infect 2022; 11:172-181. [PMID: 34842496 PMCID: PMC8741249 DOI: 10.1080/22221751.2021.2011617] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [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: 08/09/2021] [Accepted: 11/23/2021] [Indexed: 12/24/2022]
Abstract
Herein, we describe the genetic diversity of circulating SARS-CoV-2 viruses by whole-genome sequencing (WGS) in Barcelona city (Catalonia, Spain) throughout the first four pandemic waves. From weeks 11/2020-24/2021, SARS-CoV-2-positive respiratory samples were randomly selected per clinical setting (80% from primary care or 20% from the hospital), age group, and week. WGS was performed following the ARTICv3 protocol on MiSeq or NextSeq2000 Illumina platforms. Nearly complete consensus sequences were used for genetic characterization based on GISAID and PANGOLIN nomenclatures. From 2475 samples, 2166 (87%) were fully sequenced (78% from primary care and 22% from hospital settings). Multiple genetic lineages were co-circulating, but four were predominant at different periods. While B.1.5 (50.68%) and B.1.1 (32.88%) were the major lineages during the first pandemic wave, B.1.177 (66.85%) and B.1.1.7 (83.80%) were predominant during the second, third, and fourth waves, respectively. Almost all (96.4%) were carrying D614G mutation in the S protein, with additional mutations that define lineages or variants. But some mutations of concern, such as E484K from B.1.351 and P.1 lineages are currently under monitoring, together with those observed in the receptor-binding domain or N-terminal domain, such as L452R and T478K from B.1.617.2 lineage. The fact that a predominant lineage was observed in each pandemic wave suggests advantageous properties over other contemporary co-circulating variants. This genetic variability should be monitored, especially when a massive vaccination campaign is ongoing because the potential selection and emergence of novel antigenic SARS-CoV-2 strains related to immunological escapement events.
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Affiliation(s)
- Cristina Andrés
- Respiratory Viruses Unit, Microbiology Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital CampusBarcelona, Spain
| | - Maria Piñana
- Respiratory Viruses Unit, Microbiology Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital CampusBarcelona, Spain
| | - Blanca Borràs-Bermejo
- Preventive Medicine and Epidemiology Department, Vall d´Hebron Research Institute (VHIR), Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Alejandra González-Sánchez
- Respiratory Viruses Unit, Microbiology Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital CampusBarcelona, Spain
| | - Damir García-Cehic
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Juliana Esperalba
- Respiratory Viruses Unit, Microbiology Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital CampusBarcelona, Spain
| | - Ariadna Rando
- Respiratory Viruses Unit, Microbiology Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital CampusBarcelona, Spain
| | - Ricardo-Gabriel Zules-Oña
- Preventive Medicine and Epidemiology Department, Vall d´Hebron Research Institute (VHIR), Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Carolina Campos
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Maria Gema Codina
- Respiratory Viruses Unit, Microbiology Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital CampusBarcelona, Spain
| | - Albert Blanco-Grau
- Clinical Biochemistry (Clinical Laboratories), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Sergi Colomer-Castell
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Maria Carmen Martín
- Respiratory Viruses Unit, Microbiology Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital CampusBarcelona, Spain
| | - Carla Castillo
- Respiratory Viruses Unit, Microbiology Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital CampusBarcelona, Spain
| | - Karen García-Comuñas
- Respiratory Viruses Unit, Microbiology Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital CampusBarcelona, Spain
| | - Rodrigo Vásquez-Mercado
- Respiratory Viruses Unit, Microbiology Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital CampusBarcelona, Spain
| | - Reginaldo Martins-Martins
- Respiratory Viruses Unit, Microbiology Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital CampusBarcelona, Spain
| | - Narcís Saubi
- Respiratory Viruses Unit, Microbiology Department, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron, Barcelona, Spain
| | - Magda Campins-Martí
- Preventive Medicine and Epidemiology Department, Vall d´Hebron Research Institute (VHIR), Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Tomàs Pumarola
- Respiratory Viruses Unit, Microbiology Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital CampusBarcelona, Spain
| | - Josep Quer
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Andrés Antón
- Respiratory Viruses Unit, Microbiology Department, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital CampusBarcelona, Spain
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Lai MY, Bukhari FDM, Zulkefli NZ, Ismail I, Mustapa NI, Soh TST, Hassan AH, Peariasamy KM, Lee YL, Suppiah J, Thayan R, Isa MKM, Wahid NZA, Lau YL. Clinical testing on SARS-CoV-2 swab samples using reverse-transcription loop-mediated isothermal amplification (RT-LAMP). BMC Infect Dis 2022; 22:697. [PMID: 35982419 PMCID: PMC9387413 DOI: 10.1186/s12879-022-07684-w] [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: 03/25/2022] [Accepted: 07/28/2022] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND High cost of commercial RNA extraction kits limits the testing efficiency of SARS-CoV-2. Here, we developed a simple nucleic acid extraction method for the detection of SARS-CoV-2 directly from nasopharyngeal swab samples. METHODS A pH sensitive dye was used as the end point detection method. The obvious colour changes between positive and negative reactions eliminates the need of other equipment. RESULTS Clinical testing using 260 samples showed 92.7% sensitivity (95% CI 87.3-96.3%) and 93.6% specificity (95% CI 87.3-97.4%) of RT-LAMP. CONCLUSIONS The simple RNA extraction method minimizes the need for any extensive laboratory set-up. We suggest combining this simple nucleic acid extraction method and RT-LAMP technology as the point-of care diagnostic tool.
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Affiliation(s)
- Meng Yee Lai
- Department of Parasitology, Faculty of Medicine, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | | | - Nur Zulaikha Zulkefli
- Department of Parasitology, Faculty of Medicine, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | - Ilyiana Ismail
- Department of Pathology, Hospital Sungai Buloh, Ministry of Health, Kuala Lumpur, Malaysia
| | - Nur Izati Mustapa
- Department of Pathology, Hospital Sungai Buloh, Ministry of Health, Kuala Lumpur, Malaysia
| | - Tuan Suhaila Tuan Soh
- Department of Pathology, Hospital Sungai Buloh, Ministry of Health, Kuala Lumpur, Malaysia
| | - Afifah Haji Hassan
- Department of Pathology, Hospital Sungai Buloh, Ministry of Health, Kuala Lumpur, Malaysia
| | - Kalaiarasu M Peariasamy
- Institute for Clinical Research, National Institutes of Health, Ministry of Health, Kuala Lumpur, Malaysia
| | - Yee Leng Lee
- Clinical Research Centre, Hospital Sungai Buloh, Ministry of Health, Kuala Lumpur, Malaysia
| | - Jeyanthi Suppiah
- Virology Unit, Infectious Disease Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health, Kuala Lumpur, Malaysia
| | - Ravindran Thayan
- Virology Unit, Infectious Disease Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health, Kuala Lumpur, Malaysia
| | - Mohd Khairi Mat Isa
- Selia-Tek Holdings Sdn Bhd, Lot 18, Jalan Teknologi 3/5, Taman Sains Selangor, 47810, Kota Damansara, Selangor, Malaysia
| | - Nur Zafirah Abdul Wahid
- Selia-Tek Holdings Sdn Bhd, Lot 18, Jalan Teknologi 3/5, Taman Sains Selangor, 47810, Kota Damansara, Selangor, Malaysia
| | - Yee Ling Lau
- Department of Parasitology, Faculty of Medicine, Universiti Malaya, 50603, Kuala Lumpur, Malaysia.
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8
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Kim DH, Kim D, Moon JW, Chae SW, Rhyu IJ. Complications of Nasopharyngeal Swabs and Safe Procedures for COVID-19 Testing Based on Anatomical Knowledge. J Korean Med Sci 2022; 37:e88. [PMID: 35315599 PMCID: PMC8938608 DOI: 10.3346/jkms.2022.37.e88] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 02/25/2022] [Indexed: 11/23/2022] Open
Abstract
Nasopharyngeal swabs have been widely to prevent the spread of coronavirus disease 2019 (COVID-19). Nasopharyngeal COVID-19 testing is a generally safe and well-tolerated procedure, but numerous complications have been reported in the media. Therefore, the present study aimed to review and document adverse events and suggest procedural references to minimize preventable but often underestimated risks. A total of 27 articles were selected for the review of 842 related documents in PubMed, Embase, and KoreaMed. The complications related to nasopharyngeal COVID-19 testing were reported to be rarely happened, ranging from 0.0012 to 0.026%. Frequently documented adverse events were retained swabs, epistaxis, and cerebrospinal fluid leakage, often associated with high-risk factors, including severe septal deviations, pre-existing skull base defects, and previous sinus or transsphenoidal pituitary surgery. Appropriate techniques based on sufficient anatomical knowledge are mandatory for clinicians to perform nasopharyngeal COVID-19 testing. The nasal floor can be predicted by the line between the nostril and external ear canal. For safe testing, the angle of swab insertion in the nasal passage should remain within 30° of the nasal floor. The swab was gently inserted along the nasal septum just above the nasal floor to the nasopharynx and remained on the nasopharynx for several seconds before removal. Forceful insertion should be attempted, and alternative examinations should be considered, especially in vulnerable patients. In conclusion, patients and clinicians should be aware of rare but possible complications and associated high-risk factors. The suggested procedural pearls enable more comfortable and safe nasopharyngeal COVID-19 testing for both clinicians and patients.
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Affiliation(s)
- Dai Hyun Kim
- Department of Dermatology, Korea University College of Medicine, Seoul, Korea
- Department of Anatomy, Korea University College of Medicine, Seoul, Korea
| | - Dasom Kim
- Department of Anatomy, Korea University College of Medicine, Seoul, Korea
| | - Jee Won Moon
- Department of Otorhinolaryngology-Head and Neck Surgery, Korea University Guro Hospital, Korea University Medicine, Seoul, Korea
| | - Sung-Won Chae
- Department of Otorhinolaryngology-Head and Neck Surgery, Korea University Guro Hospital, Korea University Medicine, Seoul, Korea.
| | - Im Joo Rhyu
- Department of Anatomy, Korea University College of Medicine, Seoul, Korea
- Division of Brain Korea 21 Plus Program for Biomedical Science, Korea University College of Medicine, Seoul, Korea.
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9
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O’Laughlin K, Espinosa CC, Smith-Jeffcoat SE, Koh M, Khalil GM, Hoffman A, Rebolledo PA, Schechter MC, Stewart RJ, da Silva J, Biedron C, Bankamp B, Folster J, Gargis AS, Bowen MD, Paulick A, Wang YF, Tate JE, Kirking HL. Specimen self-collection for SARS-CoV-2 testing: Patient performance and preferences—Atlanta, Georgia, August-October 2020. PLoS One 2022; 17:e0264085. [PMID: 35263342 PMCID: PMC8906601 DOI: 10.1371/journal.pone.0264085] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 08/26/2021] [Accepted: 02/02/2022] [Indexed: 11/19/2022] Open
Abstract
Self-collected specimens can expand access to SARS-CoV-2 testing. At a large inner-city hospital 1,082 participants self-collected saliva and anterior nasal swab (ANS) samples before healthcare workers collected nasopharyngeal swab (NPS) samples on the same day. To characterize patient preferences for self-collection, this investigation explored ability, comfort, and ease of ANS and saliva self-collection for SARS-CoV-2 testing along with associated patient characteristics, including medical history and symptoms of COVID-19. With nearly all participants successfully submitting a specimen, favorable ratings from most participants (at least >79% in ease and comfort), and equivocal preference between saliva and ANS, self-collection is a viable SARS-CoV-2 testing option.
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Affiliation(s)
- Kevin O’Laughlin
- COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
- Epidemic Intelligence Service, CDC, Atlanta, GA, United States of America
- * E-mail:
| | - Catherine C. Espinosa
- COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Sarah E. Smith-Jeffcoat
- COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Mitsuki Koh
- COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - George M. Khalil
- COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Adam Hoffman
- Grady Memorial Hospital, Atlanta, GA, United States of America
- Emory University Atlanta, Atlanta, GA, United States of America
| | | | - Marcos C. Schechter
- Grady Memorial Hospital, Atlanta, GA, United States of America
- Emory University Atlanta, Atlanta, GA, United States of America
| | - Rebekah J. Stewart
- COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Juliana da Silva
- COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Caitlin Biedron
- COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Bettina Bankamp
- COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Jennifer Folster
- COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Amy S. Gargis
- COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Michael D. Bowen
- COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Ashley Paulick
- COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Yun F. Wang
- Grady Memorial Hospital, Atlanta, GA, United States of America
- Emory University Atlanta, Atlanta, GA, United States of America
| | - Jacqueline E. Tate
- COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Hannah L. Kirking
- COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
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Kotwa JD, Jamal AJ, Mbareche H, Yip L, Aftanas P, Barati S, Bell NG, Bryce E, Coomes E, Crowl G, Duchaine C, Faheem A, Farooqi L, Hiebert R, Katz K, Khan S, Kozak R, Li AX, Mistry HP, Mozafarihashjin M, Nasir JA, Nirmalarajah K, Panousis EM, Paterson A, Plenderleith S, Powis J, Prost K, Schryer R, Taylor M, Veillette M, Wong T, Zoe Zhong X, McArthur AG, McGeer AJ, Mubareka S. Surface and Air Contamination With Severe Acute Respiratory Syndrome Coronavirus 2 From Hospitalized Coronavirus Disease 2019 Patients in Toronto, Canada, March-May 2020. J Infect Dis 2022; 225:768-776. [PMID: 34850051 DOI: 10.1101/2021.05.17.21257122] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 11/24/2021] [Indexed: 05/19/2023] Open
Abstract
BACKGROUND We determined the burden of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in air and on surfaces in rooms of patients hospitalized with coronavirus disease 2019 (COVID-19) and investigated patient characteristics associated with SARS-CoV-2 environmental contamination. METHODS Nasopharyngeal swabs, surface, and air samples were collected from the rooms of 78 inpatients with COVID-19 at 6 acute care hospitals in Toronto from March to May 2020. Samples were tested for SARS-CoV-2 ribonucleic acid (RNA), cultured to determine potential infectivity, and whole viral genomes were sequenced. Association between patient factors and detection of SARS-CoV-2 RNA in surface samples were investigated. RESULTS Severe acute respiratory syndrome coronavirus 2 RNA was detected from surfaces (125 of 474 samples; 42 of 78 patients) and air (3 of 146 samples; 3 of 45 patients); 17% (6 of 36) of surface samples from 3 patients yielded viable virus. Viral sequences from nasopharyngeal and surface samples clustered by patient. Multivariable analysis indicated hypoxia at admission, polymerase chain reaction-positive nasopharyngeal swab (cycle threshold of ≤30) on or after surface sampling date, higher Charlson comorbidity score, and shorter time from onset of illness to sampling date were significantly associated with detection of SARS-CoV-2 RNA in surface samples. CONCLUSIONS The infrequent recovery of infectious SARS-CoV-2 virus from the environment suggests that the risk to healthcare workers from air and near-patient surfaces in acute care hospital wards is likely limited.
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Affiliation(s)
| | | | | | - Lily Yip
- Sunnybrook Research Institute, Toronto, Ontario, Canada
| | | | | | | | - Elizabeth Bryce
- Division of Medical Microbiology and Infection Prevention, Vancouver Coastal Health, Vancouver, British Colombia, Canada
- Department of Pathology and Laboratory Medicine, Vancouver General Hospital, Vancouver, British Colombia, Canada
| | - Eric Coomes
- Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | | | - Caroline Duchaine
- Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec - Université de Laval, Québec City, Québec, Canada
- Départment de Biochimie, de Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université de Laval, Québec City, Québec, Canada
| | - Amna Faheem
- Sinai Health System, Toronto, Ontario, Canada
| | | | - Ryan Hiebert
- Sunnybrook Research Institute, Toronto, Ontario, Canada
| | - Kevin Katz
- North York General Hospital, Toronto, Ontario, Canada
| | - Saman Khan
- Sinai Health System, Toronto, Ontario, Canada
| | - Robert Kozak
- Sunnybrook Research Institute, Toronto, Ontario, Canada
| | - Angel X Li
- Sinai Health System, Toronto, Ontario, Canada
| | | | | | - Jalees A Nasir
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
- Department of Biochemistry and Biomedical Science, McMaster University, Hamilton, Ontario, Canada
| | | | - Emily M Panousis
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
- Department of Biochemistry and Biomedical Science, McMaster University, Hamilton, Ontario, Canada
| | | | | | - Jeff Powis
- Michael Garron Hospital, Toronto, Ontario, Canada
| | - Karren Prost
- Sunnybrook Research Institute, Toronto, Ontario, Canada
| | - Renée Schryer
- Sunnybrook Research Institute, Toronto, Ontario, Canada
| | | | - Marc Veillette
- Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec - Université de Laval, Québec City, Québec, Canada
| | - Titus Wong
- Division of Medical Microbiology and Infection Prevention, Vancouver Coastal Health, Vancouver, British Colombia, Canada
- Department of Pathology and Laboratory Medicine, Vancouver General Hospital, Vancouver, British Colombia, Canada
| | | | - Andrew G McArthur
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
- Department of Biochemistry and Biomedical Science, McMaster University, Hamilton, Ontario, Canada
| | - Allison J McGeer
- Sinai Health System, Toronto, Ontario, Canada
- Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Samira Mubareka
- Sunnybrook Research Institute, Toronto, Ontario, Canada
- Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
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11
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Sarchet JJ, Pollreisz JP, Bechtol DT, Blanding MR, Saltman RL, Taube PC. Limitations of bacterial culture, viral PCR, and tulathromycin susceptibility from upper respiratory tract samples in predicting clinical outcome of tulathromycin control or treatment of bovine respiratory disease in high-risk feeder heifers. PLoS One 2022; 17:e0247213. [PMID: 35143504 PMCID: PMC8830659 DOI: 10.1371/journal.pone.0247213] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 02/02/2021] [Accepted: 01/09/2022] [Indexed: 01/08/2023] Open
Abstract
A cross-sectional prospective cohort study including 1026 heifers administered tulathromycin due to high risk of clinical signs of bovine respiratory disease (BRD), measured poor association between BRD clinical outcomes and results of bacterial culture and tulathromycin susceptibility from BRD isolates of deep nasopharyngeal swabs (DNS) and adequate association with viral polymerase chain reaction (PCR) results from nasal swabs. Isolation rates from DNS collected on day-0 and at 1st BRD-treatment respectively were: Mannheimia haemolytica (10.9% & 34.1%); Pasteurella multocida (10.4% & 7.4%); Mycoplasma bovis (1.0% & 36.6%); and Histophilus somni (0.7% & 6.3%). Prevalence of BRD viral nucleic acid on nasal swabs collected exclusively at 1st BRD-treatment were: bovine parainfluenza virus type-3 (bPIV-3) 34.1%; bovine viral diarrhea virus (BVDV) 26.3%; bovine herpes virus type-1 (BHV-1) 10.8%; and bovine respiratory syncytial virus (BRSV) 54.1%. Increased relative risk, at 95% confidence intervals, of 1st BRD-treatment failure was associated with positive viral PCR results: BVDV 1.39 (1.17-1.66), bPIV-3 1.26 (1.06-1.51), BHV-1 1.52 (1.25-1.83), and BRSV 1.35 (1.11-1.63) from nasal swabs collected at 1st BRD-treatment and culture of M. haemolytica 1.23 (1.00-1.51) from DNS collected at day-0. However, in this population of high-risk feeder heifers, the predictive values of susceptible and resistant isolates had inadequate association with BRD clinical outcome. These results indicate, that using tulathromycin susceptibility testing of isolates of M. haemolytica or P. multocida from DNS collected on arrival or at 1st BRD-treatment to evaluate tulathromycin clinical efficacy, is unreliable.
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MESH Headings
- Animals
- Anti-Bacterial Agents/pharmacology
- Anti-Bacterial Agents/therapeutic use
- Bovine Respiratory Disease Complex/drug therapy
- Bovine Respiratory Disease Complex/microbiology
- Bovine Respiratory Disease Complex/pathology
- Cattle
- Cattle Diseases/drug therapy
- Cattle Diseases/microbiology
- Cattle Diseases/pathology
- Cross-Sectional Studies
- DNA, Viral/genetics
- DNA, Viral/metabolism
- Diarrhea Viruses, Bovine Viral/drug effects
- Diarrhea Viruses, Bovine Viral/genetics
- Diarrhea Viruses, Bovine Viral/isolation & purification
- Disaccharides/pharmacology
- Disaccharides/therapeutic use
- Herpesvirus 1, Bovine/drug effects
- Herpesvirus 1, Bovine/genetics
- Herpesvirus 1, Bovine/isolation & purification
- Heterocyclic Compounds/pharmacology
- Heterocyclic Compounds/therapeutic use
- Mannheimia haemolytica/drug effects
- Mannheimia haemolytica/isolation & purification
- Microbial Sensitivity Tests
- Nasopharynx/microbiology
- Nasopharynx/virology
- Pasteurella multocida/drug effects
- Pasteurella multocida/isolation & purification
- Polymerase Chain Reaction
- Prospective Studies
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Respiratory Syncytial Virus, Bovine/drug effects
- Respiratory Syncytial Virus, Bovine/genetics
- Respiratory Syncytial Virus, Bovine/isolation & purification
- Risk Factors
- Treatment Failure
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Affiliation(s)
- Jeffrey J. Sarchet
- Zoetis, Parsippany-Troy Hills, New Jersey, United States of America
- * E-mail:
| | | | | | | | - Roger L. Saltman
- Zoetis, Parsippany-Troy Hills, New Jersey, United States of America
| | - Patrick C. Taube
- Zoetis, Parsippany-Troy Hills, New Jersey, United States of America
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12
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Zainulabid UA, Mat Yassim AS, Hussain M, Aslam A, Soffian SN, Mohd Ibrahim MS, Kamarudin N, Kamarulzaman MN, Hin HS, Ahmad HF. Whole genome sequence analysis showing unique SARS-CoV-2 lineages of B.1.524 and AU.2 in Malaysia. PLoS One 2022; 17:e0263678. [PMID: 35213571 PMCID: PMC8880882 DOI: 10.1371/journal.pone.0263678] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 08/10/2021] [Accepted: 01/25/2022] [Indexed: 12/23/2022] Open
Abstract
SARS-CoV-2 has spread throughout the world since its discovery in China, and Malaysia is no exception. WGS has been a crucial approach in studying the evolution and genetic diversity of SARS-CoV-2 in the ongoing pandemic. Despite considerable number of SARS-CoV-2 genome sequences have been submitted to GISAID and NCBI databases, there is still scarcity of data from Malaysia. This study aims to report new Malaysian lineages of the virus, responsible for the sustained spikes in COVID-19 cases during the third wave of the pandemic. Patients with nasopharyngeal and/or oropharyngeal swabs confirmed COVID-19 positive by real-time RT-PCR with CT value < 25 were chosen for WGS. The selected SARS-CoV-2 isolates were then sequenced, characterized and analyzed along with 986 sequences of the dominant lineages of D614G variants currently circulating throughout Malaysia. The prevalence of clade GH and G formed strong ground for the presence of two Malaysian lineages of AU.2 and B.1.524 that has caused sustained spikes of cases in the country. Statistical analysis on the association of gender and age group with Malaysian lineages revealed a significant association (p <0.05). Phylogenetic analysis revealed dispersion of 41 lineages, of these, 22 lineages are still active. Mutational analysis showed presence of unique G1223C missense mutation in transmembrane domain of the spike protein. For better understanding of the SARS-CoV-2 evolution in Malaysia especially with reference to the reported lineages, large scale studies based on WGS are warranted.
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Affiliation(s)
- Ummu Afeera Zainulabid
- Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang, Gambang, Pahang, Malaysia
- Department of Internal Medicine, Kulliyyah of Medicine, International Islamic University of Malaysia, Kuantan, Pahang, Malaysia
| | | | - Mushtaq Hussain
- Bioinformatics and Molecular Medicine Research Group, Dow Research Institute of Biotechnology and Biomedical Sciences, Dow College of Biotechnology, Dow University of Health Sciences, Karachi, Pakistan
| | - Ayesha Aslam
- Bioinformatics and Molecular Medicine Research Group, Dow Research Institute of Biotechnology and Biomedical Sciences, Dow College of Biotechnology, Dow University of Health Sciences, Karachi, Pakistan
| | - Sharmeen Nellisa Soffian
- Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang, Gambang, Pahang, Malaysia
| | - Mohamad Shafiq Mohd Ibrahim
- Department of Paediatric and Dental Public Health, Kulliyyah of Dentistry, International Islamic University Malaysia, Kuantan, Pahang, Malaysia
| | - Norhidayah Kamarudin
- Department of Pathology and Laboratory Medicine, Kulliyyah of Medicine, International Islamic University of Malaysia, Kuantan, Pahang, Malaysia
| | - Mohd Nazli Kamarulzaman
- Department of Surgery, Kulliyyah of Medicine, International Islamic University of Malaysia, Kuantan, Pahang, Malaysia
| | - How Soon Hin
- Department of Internal Medicine, Kulliyyah of Medicine, International Islamic University of Malaysia, Kuantan, Pahang, Malaysia
| | - Hajar Fauzan Ahmad
- Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang, Gambang, Pahang, Malaysia
- Centre for Research in Advanced Tropical Bioscience (Biotropic Centre), Universiti Malaysia Pahang, Gambang, Pahang, Malaysia
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13
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Kundrod KA, Natoli ME, Chang MM, Smith CA, Paul S, Ogoe D, Goh C, Santhanaraj A, Price A, Eldin KW, Patel KP, Baker E, Schmeler KM, Richards-Kortum R. Sample-to-answer, extraction-free, real-time RT-LAMP test for SARS-CoV-2 in nasopharyngeal, nasal, and saliva samples: Implications and use for surveillance testing. PLoS One 2022; 17:e0264130. [PMID: 35213596 PMCID: PMC8880874 DOI: 10.1371/journal.pone.0264130] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [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: 08/06/2021] [Accepted: 02/03/2022] [Indexed: 12/19/2022] Open
Abstract
The global COVID-19 pandemic has highlighted the need for rapid, accurate and accessible nucleic acid tests to enable timely identification of infected individuals. We optimized a sample-to-answer nucleic acid test for SARS-CoV-2 that provides results in <1 hour using inexpensive and readily available reagents. The test workflow includes a simple lysis and viral inactivation protocol followed by direct isothermal amplification of viral RNA using RT-LAMP. The assay was validated using two different instruments, a portable isothermal fluorimeter and a standard thermocycler. Results of the RT-LAMP assay were compared to traditional RT-qPCR for nasopharyngeal swabs, nasal swabs, and saliva collected from a cohort of patients hospitalized due to COVID-19. For all three sample types, positive agreement with RT-LAMP performed using the isothermal fluorimeter was 100% for samples with Ct <30 and 69-91% for samples with Ct <40. Following validation, the test was successfully scaled to test the saliva of up to 400 asymptomatic individuals per day as part of the campus surveillance program at Rice University. Successful development, validation, and scaling of this sample-to-answer, extraction-free real-time RT-LAMP test for SARS-CoV-2 adds a highly adaptable tool to efforts to control the COVID-19 pandemic, and can inform test development strategies for future infectious disease threats.
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Affiliation(s)
- Kathryn A. Kundrod
- Department of Bioengineering, Rice University, Houston, Texas, United States of America
| | - Mary E. Natoli
- Department of Bioengineering, Rice University, Houston, Texas, United States of America
| | - Megan M. Chang
- Department of Bioengineering, Rice University, Houston, Texas, United States of America
| | - Chelsey A. Smith
- Department of Bioengineering, Rice University, Houston, Texas, United States of America
| | - Sai Paul
- Department of Bioengineering, Rice University, Houston, Texas, United States of America
| | - Dereq Ogoe
- Rice 360° Institute of Global Health, Rice University, Houston, Texas, United States of America
| | - Christopher Goh
- Rice 360° Institute of Global Health, Rice University, Houston, Texas, United States of America
| | - Akshaya Santhanaraj
- Rice 360° Institute of Global Health, Rice University, Houston, Texas, United States of America
| | - Anthony Price
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Karen W. Eldin
- McGovern Medical School, The University of Texas Health Science Center, Houston, Texas, United States of America
| | - Keyur P. Patel
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Ellen Baker
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Kathleen M. Schmeler
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
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14
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Wölfl-Duchek M, Bergmann F, Jorda A, Weber M, Müller M, Seitz T, Zoufaly A, Strassl R, Zeitlinger M, Herkner H, Schnidar H, Anderle K, Derhaschnig U. Sensitivity and Specificity of SARS-CoV-2 Rapid Antigen Detection Tests Using Oral, Anterior Nasal, and Nasopharyngeal Swabs: a Diagnostic Accuracy Study. Microbiol Spectr 2022; 10:e0202921. [PMID: 35107327 PMCID: PMC8809344 DOI: 10.1128/spectrum.02029-21] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [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: 11/02/2021] [Accepted: 01/06/2022] [Indexed: 12/23/2022] Open
Abstract
The objective of our study was to evaluate the sensitivity and specificity of rapid antigen detection tests versus those of reverse transcriptase PCR (RT-PCR) using oral, anterior nasal, and nasopharyngeal swabs. The underlying prospective, diagnostic case-control-type accuracy study included 87 hospitalized and nonhospitalized participants in a positive and a negative sample cohort between 16 March and 14 May 2021 in two hospitals in Vienna. SARS-CoV-2 infection status was confirmed by RT-PCR. Participants self-performed one oral and one anterior nasal swab for the rapid antigen test, immediately followed by two nasopharyngeal swabs for the rapid antigen test and RT-PCR by the investigator. Test results were read after 15 min, and participants completed a questionnaire in the meantime. Test parameters were calculated based on the evaluation of 87 participants. The overall sensitivity of rapid antigen detection tests versus that of RT-PCR with oral, anterior nasal, and nasopharyngeal samples was 18.18% (95% confidence interval [CI] 8.19% to 32.71%), 63.04% (95% CI 47.55% to 76.79%), and 73.33% (95% CI 58.06% to 85.4%), respectively. All sampling methods had a test specificity of 100% regardless of the cycle threshold (CT) value. Rapid antigen detection tests using self-collected anterior nasal swabs proved to be as sensitive as and more tolerable than professionally collected nasopharyngeal swabs for CT values up to 30 determined by RT-PCR. This finding illustrates the reliability of tests obtained by adequate self-collected anterior nasal specimen. Sensitivity was dependent upon the CT value for each sampling method. While the main advantage of rapid antigen detection tests is the immediate availability of results, PCR should be preferred in crucial settings wherever possible. IMPORTANCE Rapid antigen detection devices for SARS-CoV-2 represent a valuable tool for monitoring the spread of infection. However, the reliability of the tests depends largely on the test performance and the respective sampling method. Nasopharyngeal swabs mark the gold standard for sample collection in suspected respiratory tract infections but are unsuitable for widespread application, as they must be performed by medically trained personnel. With the underlying study, the head-to-head test performance and the usability of self-collected samples for SARS-CoV-2 detection using rapid antigen detection devices were evaluated. The results confirm similar sensitivity of self-collected anterior nasal swabs to that of professionally collected nasopharyngeal swabs for patients with a CT of < 30 determined by RT-PCR.
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Affiliation(s)
- Michael Wölfl-Duchek
- Department of Clinical Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Felix Bergmann
- Department of Clinical Pharmacology, Medical University of Vienna, Vienna, Austria
- Department of Plastic, Reconstructive and Aesthetic Surgery, Medical University of Vienna, Vienna, Austria
| | - Anselm Jorda
- Department of Clinical Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Maria Weber
- Department of Clinical Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Matthias Müller
- Department of Clinical Pharmacology, Medical University of Vienna, Vienna, Austria
- Department of Emergency Medicine, Medical University of Vienna, Vienna, Austria
| | - Tamara Seitz
- Fourth Medical Department for Infectious Diseases and Tropical Medicine, Clinic Favoriten, Vienna, Austria
| | - Alexander Zoufaly
- Fourth Medical Department for Infectious Diseases and Tropical Medicine, Clinic Favoriten, Vienna, Austria
- Faculty of Medicine, Sigmund Freud University, Vienna, Austria
| | - Robert Strassl
- Department of Laboratory Medicine, Division of Clinical Virology, Medical University of Vienna, Vienna, Austria
| | - Markus Zeitlinger
- Department of Clinical Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Harald Herkner
- Department of Emergency Medicine, Medical University of Vienna, Vienna, Austria
| | | | - Karolina Anderle
- Department of Clinical Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Ulla Derhaschnig
- Department of Clinical Pharmacology, Medical University of Vienna, Vienna, Austria
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15
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Manna S, McAuley J, Jacobson J, Nguyen CD, Ullah MA, Sebina I, Williamson V, Mulholland EK, Wijburg O, Phipps S, Satzke C. Synergism and Antagonism of Bacterial-Viral Coinfection in the Upper Respiratory Tract. mSphere 2022; 7:e0098421. [PMID: 35044807 PMCID: PMC8769199 DOI: 10.1128/msphere.00984-21] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [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: 12/17/2021] [Accepted: 12/28/2021] [Indexed: 01/03/2023] Open
Abstract
Streptococcus pneumoniae (the pneumococcus) is a leading cause of pneumonia in children under 5 years of age. Coinfection by pneumococci and respiratory viruses enhances disease severity. Little is known about pneumococcal coinfections with respiratory syncytial virus (RSV). Here, we developed a novel infant mouse model of coinfection using pneumonia virus of mice (PVM), a murine analogue of RSV, to examine the dynamics of coinfection in the upper respiratory tract, an anatomical niche that is essential for host-to-host transmission and progression to disease. Coinfection increased damage to the nasal tissue and increased production of the chemokine CCL3. Nasopharyngeal pneumococcal density and shedding in nasal secretions were increased by coinfection. In contrast, coinfection reduced PVM loads in the nasopharynx, an effect that was independent of pneumococcal strain and the order of infection. We showed that this "antagonistic" effect was absent using either ethanol-killed pneumococci or a pneumococcal mutant deficient in capsule production and incapable of nasopharyngeal carriage. Colonization with a pneumococcal strain naturally unable to produce capsule also reduced viral loads. The pneumococcus-mediated reduction in PVM loads was caused by accelerated viral clearance from the nasopharynx. Although these synergistic and antagonistic effects occurred with both wild-type pneumococcal strains used in this study, the magnitude of the effects was strain dependent. Lastly, we showed that pneumococci can also antagonize influenza virus. Taken together, our study has uncovered multiple novel facets of bacterial-viral coinfection. Our findings have important public health implications, including for bacterial and viral vaccination strategies in young children. IMPORTANCE Respiratory bacterial-viral coinfections (such as pneumococci and influenza virus) are often synergistic, resulting in enhanced disease severity. Although colonization of the nasopharynx is the precursor to disease and transmission, little is known about bacterial-viral interactions that occur within this niche. In this study, we developed a novel mouse model to examine pneumococcal-viral interactions in the nasopharynx with pneumonia virus of mice (PVM) and influenza. We found that PVM infection benefits pneumococci by increasing their numbers in the nasopharynx and shedding of these bacteria in respiratory secretions. In contrast, we discovered that pneumococci decrease PVM numbers by accelerating viral clearance. We also report a similar effect of pneumococci on influenza. By showing that coinfections lead to both synergistic and antagonistic outcomes, our findings challenge the existing dogma in the field. Our work has important applications and implications for bacterial and viral vaccines that target these microbes.
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Affiliation(s)
- Sam Manna
- Infection and Immunity, Murdoch Children’s Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, Victoria, Australia
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Julie McAuley
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Jonathan Jacobson
- Infection and Immunity, Murdoch Children’s Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Cattram D. Nguyen
- Infection and Immunity, Murdoch Children’s Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, Victoria, Australia
| | - Md. Ashik Ullah
- Respiratory Immunology Laboratory, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Ismail Sebina
- Respiratory Immunology Laboratory, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Victoria Williamson
- Infection and Immunity, Murdoch Children’s Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
| | - E. Kim Mulholland
- Infection and Immunity, Murdoch Children’s Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, Victoria, Australia
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Odilia Wijburg
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Simon Phipps
- Respiratory Immunology Laboratory, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Catherine Satzke
- Infection and Immunity, Murdoch Children’s Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Parkville, Victoria, Australia
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
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16
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Nóra M, Déri D, Veres DS, Kis Z, Barcsay E, Pályi B. Evaluating the field performance of multiple SARS-Cov-2 antigen rapid tests using nasopharyngeal swab samples. PLoS One 2022; 17:e0262399. [PMID: 35157700 PMCID: PMC8843216 DOI: 10.1371/journal.pone.0262399] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [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: 08/19/2021] [Accepted: 12/23/2021] [Indexed: 12/16/2022] Open
Abstract
The SARS-CoV-2 pandemic, which started in December 2019, has been posing significant challenges to the health care system worldwide. As the pandemic spreads with rapidly increasing number of positive cases, early diagnosis of infected patients is crucial to successfully limit the spread of the virus. Although the real-time reverse-transcription polymerase chain reaction (RT-qPCR) is the recommended laboratory method to diagnose COVID-19 infection, many factors such as availability of laboratory equipment, reagents and trained personnel affect the use of time-consuming molecular techniques. To facilitate on-the-spot diagnosis of COVID-19, SARS-CoV-2 rapid antigen tests were developed by several different manufacturers. The evaluation of such rapid tests is particularly important due to the recent unanimous agreement by the European Commission Member States on a recommendation setting out a framework for the use of antigen rapid tests that contains a list of the mutually recognized assays and the basis of independent validation protocols. To evaluate the on-field performance of ten commercially available SARS-CoV-2 antigen rapid tests (CLINITEST Rapid COVID-19 Antigen Test, GenBody COVID-19 Antigen Test, GENEDIA W COVID-19 Ag Test, Healgen Coronavirus Antigen Rapid Test, Humasis COVID-19 Ag Test, VivaDiag SARS-CoV-2 Ag Rapid Test, Helix i-SARS-CoV-2 Ag Rapid Test, Roche SARS-CoV-2 Rapid Antigen Test, Abbot COVID-19 Ag Rapid Test and Vazyme SARS-CoV-2 Antigen Detection Kit) and compare with RT-qPCR as a reference method, the Hungarian National Public Health Center provided 1,597 antigen rapid tests to the National Ambulance Service, COVID-testing trucks and two hospitals treating COVID-19 patients. Sensitivity, specificity and accuracy were determined by performing the rapid test directly from nasopharyngeal swab samples of symptomatic individuals. For strongly positive samples (Ct < 25) sensitivities ranged between 66.7% and 100%, while for positive samples (Ct < 30) they gave a maximum sensitivity of 87.5%. The specificity of the tests was ranging between 79% to 100%. The results presented here are of high importance to the European Commission and also help governmental decision-making regarding the application of the proper rapid tests for screening different at-risk populations. Nonetheless, SARS-Cov-2 rapid tests play an important role in early and on-the-spot diagnosis of potentially infected individuals.
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Affiliation(s)
- Magyar Nóra
- National Biosafety Laboratory, National Public Health Center, Budapest, Hungary
- Schools of Doctoral Studies, Semmelweis University, Budapest, Hungary
- Department of Virology, National Public Health Center, Budapest, Hungary
| | - Dániel Déri
- National Biosafety Laboratory, National Public Health Center, Budapest, Hungary
- Department of Virology, National Public Health Center, Budapest, Hungary
- Doctoral School of Biology, Institute of Biology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Dániel Sándor Veres
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - Zoltán Kis
- National Biosafety Laboratory, National Public Health Center, Budapest, Hungary
- Department of Virology, National Public Health Center, Budapest, Hungary
- Department of Microbiology, Semmelweis University, Budapest, Hungary
| | - Erzsébet Barcsay
- Department of Virology, National Public Health Center, Budapest, Hungary
| | - Bernadett Pályi
- National Biosafety Laboratory, National Public Health Center, Budapest, Hungary
- Department of Virology, National Public Health Center, Budapest, Hungary
- * E-mail:
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17
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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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18
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Shetty SA, van Beek J, Bijvank E, Groot J, Kuiling S, Bosch T, van Baarle D, Fuentes S. Associations and recovery dynamics of the nasopharyngeal microbiota during influenza-like illness in the aging population. Sci Rep 2022; 12:1915. [PMID: 35115596 PMCID: PMC8813934 DOI: 10.1038/s41598-022-05618-9] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 01/12/2022] [Indexed: 11/09/2022] Open
Abstract
Influenza-like illness (ILI), a disease caused by respiratory pathogens including influenza virus, is a major health concern in older adults. There is little information on changes and recovery dynamics of the nasopharyngeal (NP) microbiota of older adults associated with an ILI. Here, we compared the NP microbiota in older adults reporting (n = 240) or not (n = 157) ILI during the 2014-2015 influenza season at different times of the ILI event. A small but significant effect of the ILI was observed on the microbiota community composition and structure when compared to controls and samples collected at recovery. Corynebacterium was negatively associated with ILI and its abundance increased after recovery. Potential pathobionts such as Haemophilus, Porphyromonas and Gemella had higher abundances during acute-ILI. Stability and changes in the NP microbial community showed individual dynamics. Key core genera, Corynebacterium, Moraxella and Dolosigranulum exhibited higher inter-individual variability in acute-ILI, but showed comparable variability to controls after recovery. Participants in the ILI group with higher core microbiota abundances at the acute phase showed higher microbiota stability after recovery. Our findings demonstrate that acute-ILI is associated with alterations in the phylogenetic structure of the NP microbiota in older adults. The variation in the core microbiota suggests imbalances in the ecosystem, which could potentially play a role in the susceptibility and recovery of the NP microbiota after an ILI event.
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Affiliation(s)
- Sudarshan A Shetty
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Department of Medical Microbiology and Infection Prevention, Virology and Immunology Research Group, University Medical Center Groningen, Groningen, The Netherlands
| | - Josine van Beek
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Elske Bijvank
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - James Groot
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Sjoerd Kuiling
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Thijs Bosch
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Debbie van Baarle
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Department of Medical Microbiology and Infection Prevention, Virology and Immunology Research Group, University Medical Center Groningen, Groningen, The Netherlands
| | - Susana Fuentes
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands.
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19
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Fronza F, Groff N, Martinelli A, Passerini BZ, Rensi N, Cortelletti I, Vivori N, Adami V, Helander A, Bridi S, Pancher M, Greco V, Garritano SI, Piffer E, Stefani L, De Sanctis V, Bertorelli R, Pancheri S, Collini L, Dassi E, Quattrone A, Capobianchi MR, Icardi G, Poli G, Caciagli P, Ferro A, Pizzato M. A Community Study of SARS-CoV-2 Detection by RT-PCR in Saliva: A Reliable and Effective Method. Viruses 2022; 14:313. [PMID: 35215902 PMCID: PMC8878650 DOI: 10.3390/v14020313] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [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: 01/05/2022] [Revised: 01/24/2022] [Accepted: 01/31/2022] [Indexed: 01/27/2023] Open
Abstract
Efficient, wide-scale testing for SARS-CoV-2 is crucial for monitoring the incidence of the infection in the community. The gold standard for COVID-19 diagnosis is the molecular analysis of epithelial secretions from the upper respiratory system captured by nasopharyngeal (NP) or oropharyngeal swabs. Given the ease of collection, saliva has been proposed as a possible substitute to support testing at the population level. Here, we used a novel saliva collection device designed to favour the safe and correct acquisition of the sample, as well as the processivity of the downstream molecular analysis. We tested 1003 nasopharyngeal swabs and paired saliva samples self-collected by individuals recruited at a public drive-through testing facility. An overall moderate concordance (68%) between the two tests was found, with evidence that neither system can diagnose the infection in 100% of the cases. While the two methods performed equally well in symptomatic individuals, their discordance was mainly restricted to samples from convalescent subjects. The saliva test was at least as effective as NP swabs in asymptomatic individuals recruited for contact tracing. Our study describes a testing strategy of self-collected saliva samples, which is reliable for wide-scale COVID-19 screening in the community and is particularly effective for contact tracing.
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Affiliation(s)
- Filippo Fronza
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123 Trento, Italy; (F.F.); (N.G.); (A.M.); (B.Z.P.); (N.R.); (I.C.); (N.V.); (V.A.); (A.H.); (S.B.); (M.P.); (V.G.); (S.I.G.); (E.P.); (L.S.); (V.D.S.); (R.B.); (E.D.); (A.Q.); (P.C.)
| | - Nelli Groff
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123 Trento, Italy; (F.F.); (N.G.); (A.M.); (B.Z.P.); (N.R.); (I.C.); (N.V.); (V.A.); (A.H.); (S.B.); (M.P.); (V.G.); (S.I.G.); (E.P.); (L.S.); (V.D.S.); (R.B.); (E.D.); (A.Q.); (P.C.)
| | - Angela Martinelli
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123 Trento, Italy; (F.F.); (N.G.); (A.M.); (B.Z.P.); (N.R.); (I.C.); (N.V.); (V.A.); (A.H.); (S.B.); (M.P.); (V.G.); (S.I.G.); (E.P.); (L.S.); (V.D.S.); (R.B.); (E.D.); (A.Q.); (P.C.)
| | - Beatrice Zita Passerini
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123 Trento, Italy; (F.F.); (N.G.); (A.M.); (B.Z.P.); (N.R.); (I.C.); (N.V.); (V.A.); (A.H.); (S.B.); (M.P.); (V.G.); (S.I.G.); (E.P.); (L.S.); (V.D.S.); (R.B.); (E.D.); (A.Q.); (P.C.)
| | - Nicolò Rensi
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123 Trento, Italy; (F.F.); (N.G.); (A.M.); (B.Z.P.); (N.R.); (I.C.); (N.V.); (V.A.); (A.H.); (S.B.); (M.P.); (V.G.); (S.I.G.); (E.P.); (L.S.); (V.D.S.); (R.B.); (E.D.); (A.Q.); (P.C.)
| | - Irene Cortelletti
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123 Trento, Italy; (F.F.); (N.G.); (A.M.); (B.Z.P.); (N.R.); (I.C.); (N.V.); (V.A.); (A.H.); (S.B.); (M.P.); (V.G.); (S.I.G.); (E.P.); (L.S.); (V.D.S.); (R.B.); (E.D.); (A.Q.); (P.C.)
| | - Nicolò Vivori
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123 Trento, Italy; (F.F.); (N.G.); (A.M.); (B.Z.P.); (N.R.); (I.C.); (N.V.); (V.A.); (A.H.); (S.B.); (M.P.); (V.G.); (S.I.G.); (E.P.); (L.S.); (V.D.S.); (R.B.); (E.D.); (A.Q.); (P.C.)
| | - Valentina Adami
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123 Trento, Italy; (F.F.); (N.G.); (A.M.); (B.Z.P.); (N.R.); (I.C.); (N.V.); (V.A.); (A.H.); (S.B.); (M.P.); (V.G.); (S.I.G.); (E.P.); (L.S.); (V.D.S.); (R.B.); (E.D.); (A.Q.); (P.C.)
| | - Anna Helander
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123 Trento, Italy; (F.F.); (N.G.); (A.M.); (B.Z.P.); (N.R.); (I.C.); (N.V.); (V.A.); (A.H.); (S.B.); (M.P.); (V.G.); (S.I.G.); (E.P.); (L.S.); (V.D.S.); (R.B.); (E.D.); (A.Q.); (P.C.)
| | - Simone Bridi
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123 Trento, Italy; (F.F.); (N.G.); (A.M.); (B.Z.P.); (N.R.); (I.C.); (N.V.); (V.A.); (A.H.); (S.B.); (M.P.); (V.G.); (S.I.G.); (E.P.); (L.S.); (V.D.S.); (R.B.); (E.D.); (A.Q.); (P.C.)
| | - Michael Pancher
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123 Trento, Italy; (F.F.); (N.G.); (A.M.); (B.Z.P.); (N.R.); (I.C.); (N.V.); (V.A.); (A.H.); (S.B.); (M.P.); (V.G.); (S.I.G.); (E.P.); (L.S.); (V.D.S.); (R.B.); (E.D.); (A.Q.); (P.C.)
| | - Valentina Greco
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123 Trento, Italy; (F.F.); (N.G.); (A.M.); (B.Z.P.); (N.R.); (I.C.); (N.V.); (V.A.); (A.H.); (S.B.); (M.P.); (V.G.); (S.I.G.); (E.P.); (L.S.); (V.D.S.); (R.B.); (E.D.); (A.Q.); (P.C.)
| | - Sonia Iolanda Garritano
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123 Trento, Italy; (F.F.); (N.G.); (A.M.); (B.Z.P.); (N.R.); (I.C.); (N.V.); (V.A.); (A.H.); (S.B.); (M.P.); (V.G.); (S.I.G.); (E.P.); (L.S.); (V.D.S.); (R.B.); (E.D.); (A.Q.); (P.C.)
| | - Elena Piffer
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123 Trento, Italy; (F.F.); (N.G.); (A.M.); (B.Z.P.); (N.R.); (I.C.); (N.V.); (V.A.); (A.H.); (S.B.); (M.P.); (V.G.); (S.I.G.); (E.P.); (L.S.); (V.D.S.); (R.B.); (E.D.); (A.Q.); (P.C.)
| | - Lara Stefani
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123 Trento, Italy; (F.F.); (N.G.); (A.M.); (B.Z.P.); (N.R.); (I.C.); (N.V.); (V.A.); (A.H.); (S.B.); (M.P.); (V.G.); (S.I.G.); (E.P.); (L.S.); (V.D.S.); (R.B.); (E.D.); (A.Q.); (P.C.)
| | - Veronica De Sanctis
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123 Trento, Italy; (F.F.); (N.G.); (A.M.); (B.Z.P.); (N.R.); (I.C.); (N.V.); (V.A.); (A.H.); (S.B.); (M.P.); (V.G.); (S.I.G.); (E.P.); (L.S.); (V.D.S.); (R.B.); (E.D.); (A.Q.); (P.C.)
| | - Roberto Bertorelli
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123 Trento, Italy; (F.F.); (N.G.); (A.M.); (B.Z.P.); (N.R.); (I.C.); (N.V.); (V.A.); (A.H.); (S.B.); (M.P.); (V.G.); (S.I.G.); (E.P.); (L.S.); (V.D.S.); (R.B.); (E.D.); (A.Q.); (P.C.)
| | - Serena Pancheri
- Azienda Provinciale per i Servizi Sanitari, 38123 Trento, Italy; (S.P.); (L.C.); (A.F.)
| | - Lucia Collini
- Azienda Provinciale per i Servizi Sanitari, 38123 Trento, Italy; (S.P.); (L.C.); (A.F.)
| | - Erik Dassi
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123 Trento, Italy; (F.F.); (N.G.); (A.M.); (B.Z.P.); (N.R.); (I.C.); (N.V.); (V.A.); (A.H.); (S.B.); (M.P.); (V.G.); (S.I.G.); (E.P.); (L.S.); (V.D.S.); (R.B.); (E.D.); (A.Q.); (P.C.)
| | - Alessandro Quattrone
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123 Trento, Italy; (F.F.); (N.G.); (A.M.); (B.Z.P.); (N.R.); (I.C.); (N.V.); (V.A.); (A.H.); (S.B.); (M.P.); (V.G.); (S.I.G.); (E.P.); (L.S.); (V.D.S.); (R.B.); (E.D.); (A.Q.); (P.C.)
| | | | - Giancarlo Icardi
- Department of Health Sciences, University of Genova, 16132 Genova, Italy;
| | - Guido Poli
- Vita-Salute San Raffaele University, 20132 Milano, Italy;
| | - Patrizio Caciagli
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123 Trento, Italy; (F.F.); (N.G.); (A.M.); (B.Z.P.); (N.R.); (I.C.); (N.V.); (V.A.); (A.H.); (S.B.); (M.P.); (V.G.); (S.I.G.); (E.P.); (L.S.); (V.D.S.); (R.B.); (E.D.); (A.Q.); (P.C.)
- Azienda Provinciale per i Servizi Sanitari, 38123 Trento, Italy; (S.P.); (L.C.); (A.F.)
| | - Antonio Ferro
- Azienda Provinciale per i Servizi Sanitari, 38123 Trento, Italy; (S.P.); (L.C.); (A.F.)
| | - Massimo Pizzato
- Department of Cellular, Computational and Integrative Biology, University of Trento, 38123 Trento, Italy; (F.F.); (N.G.); (A.M.); (B.Z.P.); (N.R.); (I.C.); (N.V.); (V.A.); (A.H.); (S.B.); (M.P.); (V.G.); (S.I.G.); (E.P.); (L.S.); (V.D.S.); (R.B.); (E.D.); (A.Q.); (P.C.)
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20
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Nagakubo Y, Hirotsu Y, Maejima M, Shibusawa M, Hosaka K, Amemiya K, Sueki H, Hayakawa M, Mochizuki H, Tsutsui T, Kakizaki Y, Miyashita Y, Omata M. Non-pharmaceutical interventions during the COVID-19 epidemic changed detection rates of other circulating respiratory pathogens in Japan. PLoS One 2022; 17:e0262874. [PMID: 35061862 PMCID: PMC8782330 DOI: 10.1371/journal.pone.0262874] [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: 07/04/2021] [Accepted: 01/06/2022] [Indexed: 12/21/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has circulated worldwide and causes coronavirus disease 2019 (COVID-19). At the onset of the COVID-19 pandemic, infection control measures were taken, such as hand washing, mask wearing, and behavioral restrictions. However, it is not fully clear how the effects of these non-pharmaceutical interventions changed the prevalence of other pathogens associated with respiratory infections. In this study, we collected 3,508 nasopharyngeal swab samples from 3,249 patients who visited the Yamanashi Central Hospital in Japan from March 1, 2020 to February 28, 2021. We performed multiplex polymerase chain reaction (PCR) using the FilmArray Respiratory Panel and singleplex quantitative reverse transcription PCR targeting SARS-CoV-2 to detect respiratory disease-associated pathogens. At least one pathogen was detected in 246 (7.0%) of the 3,508 samples. Eleven types of pathogens were detected in the samples collected from March-May 2020, during which non-pharmaceutical interventions were not well implemented. In contrast, after non-pharmaceutical interventions were thoroughly implemented, only five types of pathogens were detected, and the majority were SARS-CoV-2, adenoviruses, or human rhinoviruses / enteroviruses. The 0-9 year age group had a higher prevalence of infection with adenoviruses and human rhinoviruses / enteroviruses compared with those 10 years and older, while those 10 years and older had a higher prevalence of infection with SARS-CoV-2 and other pathogens. These results indicated that non-pharmaceutical interventions likely reduced the diversity of circulating pathogens. Moreover, differences in the prevalence of pathogens were observed among the different age groups.
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Affiliation(s)
- Yuki Nagakubo
- Genome Analysis Center, Yamanashi Central Hospital, Kofu, Yamanashi, Japan
- Division of Microbiology in Clinical Laboratory, Yamanashi Central Hospital, Kofu, Yamanashi, Japan
- Division of Genetics and Clinical Laboratory, Yamanashi Central Hospital, Kofu, Yamanashi, Japan
| | - Yosuke Hirotsu
- Genome Analysis Center, Yamanashi Central Hospital, Kofu, Yamanashi, Japan
- * E-mail:
| | - Makoto Maejima
- Division of Microbiology in Clinical Laboratory, Yamanashi Central Hospital, Kofu, Yamanashi, Japan
| | - Masahiro Shibusawa
- Division of Microbiology in Clinical Laboratory, Yamanashi Central Hospital, Kofu, Yamanashi, Japan
| | - Kazuhiro Hosaka
- Division of Microbiology in Clinical Laboratory, Yamanashi Central Hospital, Kofu, Yamanashi, Japan
| | - Kenji Amemiya
- Division of Genetics and Clinical Laboratory, Yamanashi Central Hospital, Kofu, Yamanashi, Japan
| | - Hitomi Sueki
- Division of Microbiology in Clinical Laboratory, Yamanashi Central Hospital, Kofu, Yamanashi, Japan
| | - Miyoko Hayakawa
- Central Clinical Laboratory, Yamanashi Central Hospital, Kofu, Yamanashi, Japan
| | - Hitoshi Mochizuki
- Genome Analysis Center, Yamanashi Central Hospital, Kofu, Yamanashi, Japan
- Central Clinical Laboratory, Yamanashi Central Hospital, Kofu, Yamanashi, Japan
- Department of Gastroenterology, Yamanashi Central Hospital, Kofu, Yamanashi, Japan
| | - Toshiharu Tsutsui
- Lung Cancer and Respiratory Disease Center, Yamanashi Central Hospital, Kofu, Yamanashi, Japan
| | - Yumiko Kakizaki
- Lung Cancer and Respiratory Disease Center, Yamanashi Central Hospital, Kofu, Yamanashi, Japan
| | - Yoshihiro Miyashita
- Lung Cancer and Respiratory Disease Center, Yamanashi Central Hospital, Kofu, Yamanashi, Japan
| | - Masao Omata
- Department of Gastroenterology, Yamanashi Central Hospital, Kofu, Yamanashi, Japan
- The University of Tokyo, Bunkyo-ku, Tokyo, Japan
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21
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Candoni A, Petruzzellis G, Sperotto A, Andreotti V, Giavarra M, Corvaja C, Minisini A, Comuzzi C, Tascini C, Fanin R, Fasola G. Detection of SARS-CoV-2 infection prevalence in 860 cancer patients with a combined screening procedure including triage, molecular nasopharyngeal swabs and rapid serological test. A report from the first epidemic wave. PLoS One 2022; 17:e0262784. [PMID: 35108300 PMCID: PMC8809545 DOI: 10.1371/journal.pone.0262784] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 05/27/2021] [Accepted: 01/04/2022] [Indexed: 01/09/2023] Open
Abstract
INTRODUCTION Even if now we have available the weapon of vaccination against SARS-CoV-2, the patients with cancer remains a very frail population in which frequently the immunologic response to vaccination may be impaired. In this setting, the SARS-CoV-2 infection screening retains a great value. However, there are still limited data on the feasibility and efficacy of combined screening procedures to assess the prevalence of SARS-CoV-2 infection (including asymptomatic cases) in cancer outpatients undergoing antineoplastic therapy. PATIENTS AND RESULTS From May 1, 2020, to June 15, 2020, during the first wave of SARS-CoV-2 pandemic, 860 consecutive patients, undergoing active anticancer therapy, were evaluated and tested for SARS-CoV-2 with a combined screening procedure, including a self-report questionnaire, a molecular nasopharyngeal swab (NPS) and a rapid serological immunoassay (for anti-SARS-CoV-2 IgG/IgM antibodies). The primary endpoint of the study was to estimate the prevalence of SARS-CoV-2 infection (including asymptomatic cases) in consecutive and unselected cancer outpatients by a combined screening modality. A total of 2955 SARS-CoV-2 NPS and 860 serological tests, in 475 patients with hematologic cancers and in 386 with solid tumors, were performed. A total of 112 (13%) patients self-reported symptoms potentially COVID-19 related. In 1/860 cases (< 1%) SARS-CoV-2 NPS was positive and in 14 cases (1.62%) the specific serological test was positive (overall prevalence of SARS-CoV-2 infection 1.62%). Of the 112 cases who declared symptoms potentially COVID-19-related, only 2.7% (3/112) were found SARS-CoV-2 positive. CONCLUSIONS This is the largest study reporting the feasibility of a combined screening procedure (including triage, NPS and serologic test) to evaluate the prevalence of SARS-CoV-2 infection in cancer patients receiving active therapy, during the first epidemic wave and under the restrictive lockdown measures, in one of the active areas of the SARS-CoV-2 circulation. Lacking specific recommendations for the detection of asymptomatic SARS-CoV-2 cases, a combined diagnostic screening might be more effective to detect the exact prevalence of SARS-CoV-2 in neoplastic patient population. The prevalence can obviously change according to the territorial context, the entity of the restrictive measures adopted and the phase of the epidemic curve. However, its exact and real-time knowledge could be important to balance risks/benefits of oncologic treatments, avoiding (if the prevalence is low) the reduction of dose intensity or the selection of less intensive (but also less effective) anti-cancer therapies.
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Affiliation(s)
- Anna Candoni
- Department of Hematology and SCT, Santa Maria della Misericordia Hospital, ASUFC, Udine, Italy
- * E-mail:
| | - Giuseppe Petruzzellis
- Department of Hematology and SCT, Santa Maria della Misericordia Hospital, ASUFC, Udine, Italy
| | - Alessandra Sperotto
- Department of Hematology and SCT, Santa Maria della Misericordia Hospital, ASUFC, Udine, Italy
| | - Victoria Andreotti
- Department of Oncology, Santa Maria della Misericordia Hospital, ASUFC, Udine, Italy
| | - Marco Giavarra
- Department of Oncology, Santa Maria della Misericordia Hospital, ASUFC, Udine, Italy
| | - Carla Corvaja
- Department of Oncology, Santa Maria della Misericordia Hospital, ASUFC, Udine, Italy
| | - Alessandro Minisini
- Department of Oncology, Santa Maria della Misericordia Hospital, ASUFC, Udine, Italy
| | - Chiara Comuzzi
- Department of Hematology and SCT, Santa Maria della Misericordia Hospital, ASUFC, Udine, Italy
| | - Carlo Tascini
- Department of Infectious Diseases, Santa Maria della Misericordia Hospital, ASUFC, Udine, Italy
- DAME, University of Udine, Udine, Italy
| | - Renato Fanin
- Department of Hematology and SCT, Santa Maria della Misericordia Hospital, ASUFC, Udine, Italy
- DAME, University of Udine, Udine, Italy
| | - Gianpiero Fasola
- Department of Oncology, Santa Maria della Misericordia Hospital, ASUFC, Udine, Italy
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22
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Pierri B, Mancusi A, Proroga YTR, Capuano F, Cerino P, Girardi S, Vassallo L, Lo Conte G, Tafuro M, Cuomo MC, Di Concilio D, Vicenza T, Cozzi L, Di Pasquale S, La Rosa G, Beikpour F, Suffredini E. SARS-CoV-2 detection in nasopharyngeal swabs: Performance characteristics of a real-time RT-qPCR and a droplet digital RT-PCR assay based on the exonuclease region (ORF1b, nsp 14). J Virol Methods 2022; 300:114420. [PMID: 34902456 PMCID: PMC8660663 DOI: 10.1016/j.jviromet.2021.114420] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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: 06/27/2021] [Revised: 11/07/2021] [Accepted: 12/08/2021] [Indexed: 12/12/2022]
Abstract
The emergence and spread of SARS-CoV-2 has led to a compelling request for accurate diagnostic tests. The aim of this study was assessing the performance of a real-time RT-qPCR (rt RT-qPCR) assay and of a droplet digital RT-PCR (dd RT-PCR) targeting the nsp14 genome region for the detection of SARS-CoV-2 in nasopharyngeal swabs. A total of 258 nasopharyngeal swabs were analyzed with the nsp14 assays and, for comparison, with a reference assay targeting the RdRp and E genes. Conflicting results were further investigated by two additional protocols, the Centers for Disease Control and Prevention (CDC) real-time targeting N1/N2, and a nested RT-PCR for the spike region. Agreement of results was achieved on 226 samples (156 positive and 70 negative), 8 samples were positive in the reference assay and in the nsp14 rt RT-qPCR but negative with the dd RT-PCR, and 24 samples provided different combinations of results with the three assays. Sensitivity, specificity and accuracy (95 %C.I.) of the nsp14 assays were: 100.0 % (97.4-100.0), 98.7 % (92.1-100.0), and 99.6 % (97.5-100.0) for the rt RT-qPCR; 92.4 % (87.4-95.6), 100.0 % (94.2-100.0), and 94.7 % (91.1-97.0) for the dd RT-PCR. The results of the study support the use of the nsp14 real-time RT-qPCR and ddPCR for the detection of SARS-CoV-2 in nasopharyngeal swabs.
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Affiliation(s)
- Biancamaria Pierri
- Centro di Referenza Nazionale per l'analisi e studio di correlazione tra ambiente, animale e uomo, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, NA, Italy; Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi, SA, Italy
| | - Andrea Mancusi
- Department of Food Microbiology, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, NA, Italy
| | - Yolande T R Proroga
- Department of Food Microbiology, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, NA, Italy
| | - Federico Capuano
- Department of Food Microbiology, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, NA, Italy
| | - Pellegrino Cerino
- Centro di Referenza Nazionale per l'analisi e studio di correlazione tra ambiente, animale e uomo, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, NA, Italy
| | - Santa Girardi
- Department of Food Microbiology, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, NA, Italy
| | - Lucia Vassallo
- Centro di Referenza Nazionale per l'analisi e studio di correlazione tra ambiente, animale e uomo, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, NA, Italy
| | - Gabriella Lo Conte
- Centro di Referenza Nazionale per l'analisi e studio di correlazione tra ambiente, animale e uomo, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, NA, Italy
| | - Maria Tafuro
- Centro di Referenza Nazionale per l'analisi e studio di correlazione tra ambiente, animale e uomo, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, NA, Italy
| | - Maria Concetta Cuomo
- Centro di Referenza Nazionale per l'analisi e studio di correlazione tra ambiente, animale e uomo, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, NA, Italy
| | - Denise Di Concilio
- Centro di Referenza Nazionale per l'analisi e studio di correlazione tra ambiente, animale e uomo, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, NA, Italy
| | - Teresa Vicenza
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | - Loredana Cozzi
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | - Simona Di Pasquale
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | - Giuseppina La Rosa
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
| | - Farzad Beikpour
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy; Department of Veterinary Medicine, University of Bari 'Aldo Moro', Bari, Italy
| | - Elisabetta Suffredini
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy.
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23
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de Steenhuijsen Piters WAA, Watson RL, de Koff EM, Hasrat R, Arp K, Chu MLJN, de Groot PCM, van Houten MA, Sanders EAM, Bogaert D. Early-life viral infections are associated with disadvantageous immune and microbiota profiles and recurrent respiratory infections. Nat Microbiol 2022; 7:224-237. [PMID: 35058634 DOI: 10.1038/s41564-021-01043-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 12/06/2021] [Indexed: 12/17/2022]
Abstract
The respiratory tract is populated by a specialized microbial ecosystem, which is seeded during and directly following birth. Perturbed development of the respiratory microbial community in early-life has been associated with higher susceptibility to respiratory tract infections (RTIs). Given a consistent gap in time between first signs of aberrant microbial maturation and the observation of the first RTIs, we hypothesized that early-life host-microbe cross-talk plays a role in this process. We therefore investigated viral presence, gene expression profiles and nasopharyngeal microbiota from birth until 12 months of age in 114 healthy infants. We show that the strongest dynamics in gene expression profiles occurred within the first days of life, mostly involving Toll-like receptor (TLR) and inflammasome signalling. These gene expression dynamics coincided with rapid microbial niche differentiation. Early asymptomatic viral infection co-occurred with stronger interferon activity, which was related to specific microbiota dynamics following, including early enrichment of Moraxella and Haemophilus spp. These microbial trajectories were in turn related to a higher number of subsequent (viral) RTIs over the first year of life. Using a multi-omic approach, we found evidence for species-specific host-microbe interactions related to consecutive susceptibility to RTIs. Although further work will be needed to confirm causality of our findings, together these data indicate that early-life viral encounters could impact subsequent host-microbe cross-talk, which is linked to later-life infections.
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Affiliation(s)
- Wouter A A de Steenhuijsen Piters
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Utrecht, the Netherlands
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Rebecca L Watson
- Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Emma M de Koff
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Utrecht, the Netherlands
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
- Spaarne Gasthuis Academy, Hoofddorp and Haarlem, the Netherlands
| | - Raiza Hasrat
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Utrecht, the Netherlands
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Kayleigh Arp
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Utrecht, the Netherlands
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Mei Ling J N Chu
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Utrecht, the Netherlands
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Pieter C M de Groot
- Department of Obstetrics and Gynaecology, Spaarne Gasthuis, Hoofddorp and Haarlem, the Netherlands
| | - Marlies A van Houten
- Spaarne Gasthuis Academy, Hoofddorp and Haarlem, the Netherlands
- Department of Paediatrics, Spaarne Gasthuis, Hoofddorp and Haarlem, the Netherlands
| | - Elisabeth A M Sanders
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Utrecht, the Netherlands
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Debby Bogaert
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Utrecht, the Netherlands.
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands.
- Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK.
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24
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Pérez-Abeledo M, Ramos B, Candel FJ, Sanz JC. Performance of the Procleix SARS-CoV-2 transcriptase-mediated amplification (TMA) assay for the diagnosis of COVID-19 in nasopharyngeal sample pools. Small pilot study. Rev Esp Quimioter 2022; 35:103-104. [PMID: 34953472 PMCID: PMC8790640 DOI: 10.37201/req/101.2021] [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] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
| | | | | | - J C Sanz
- Juan Carlos Sanz Moreno, Unidad de Microbiología Clínica. Laboratorio Regional de Salud Pública de la Comunidad de Madrid. Dirección General de Salud Pública de la Comunidad de Madrid. Edificio Usos Múltiples Hospital Enfermera Isabel Zendal, Planta 1ª. Avenida de Manuel Fraga Iribarne 2, Madrid 28055. Spain.
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25
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Saad Menezes MC, Santinelli Pestana DV, Ferreira JC, Ribeiro de Carvalho CR, Felix MC, Marcilio IO, da Silva KR, Junior VC, Marchini JF, Alencar JC, Gomez LMG, Mauá DD, Souza HP. Distinct Outcomes in COVID-19 Patients with Positive or Negative RT-PCR Test. Viruses 2022; 14:v14020175. [PMID: 35215772 PMCID: PMC8874612 DOI: 10.3390/v14020175] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 01/08/2022] [Accepted: 01/15/2022] [Indexed: 02/01/2023] Open
Abstract
Identification of the SARS-CoV-2 virus by RT-PCR from a nasopharyngeal swab sample is a common test for diagnosing COVID-19. However, some patients present clinical, laboratorial, and radiological evidence of COVID-19 infection with negative RT-PCR result(s). Thus, we assessed whether positive results were associated with intubation and mortality. This study was conducted in a Brazilian tertiary hospital from March to August of 2020. All patients had clinical, laboratory, and radiological diagnosis of COVID-19. They were divided into two groups: positive (+) RT-PCR group, with 2292 participants, and negative (−) RT-PCR group, with 706 participants. Patients with negative RT-PCR testing and an alternative most probable diagnosis were excluded from the study. The RT-PCR(+) group presented increased risk of intensive care unit (ICU) admission, mechanical ventilation, length of hospital stay, and 28-day mortality, when compared to the RT-PCR(−) group. A positive SARS-CoV-2 RT-PCR result was independently associated with intubation and 28 day in-hospital mortality. Accordingly, we concluded that patients with a COVID-19 diagnosis based on clinical data, despite a negative RT-PCR test from nasopharyngeal samples, presented more favorable outcomes than patients with positive RT-PCR test(s).
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Affiliation(s)
- Maria Clara Saad Menezes
- Emergency Medicine Department, Faculdade de Medicina da Universidade de São Paulo, São Paulo 01246-903, Brazil; (D.V.S.P.); (L.M.G.G.); (H.P.S.)
- Correspondence:
| | - Diego Vinicius Santinelli Pestana
- Emergency Medicine Department, Faculdade de Medicina da Universidade de São Paulo, São Paulo 01246-903, Brazil; (D.V.S.P.); (L.M.G.G.); (H.P.S.)
| | - Juliana Carvalho Ferreira
- Hospital das Clínicas, Faculdade de Medicina da Universidade de São Paulo, São Paulo 01246-903l, Brazil; (J.C.F.); (C.R.R.d.C.); (M.C.F.); (I.O.M.); (K.R.d.S.); (V.C.J.); (J.F.M.); (J.C.A.)
| | - Carlos Roberto Ribeiro de Carvalho
- Hospital das Clínicas, Faculdade de Medicina da Universidade de São Paulo, São Paulo 01246-903l, Brazil; (J.C.F.); (C.R.R.d.C.); (M.C.F.); (I.O.M.); (K.R.d.S.); (V.C.J.); (J.F.M.); (J.C.A.)
| | - Marcelo Consorti Felix
- Hospital das Clínicas, Faculdade de Medicina da Universidade de São Paulo, São Paulo 01246-903l, Brazil; (J.C.F.); (C.R.R.d.C.); (M.C.F.); (I.O.M.); (K.R.d.S.); (V.C.J.); (J.F.M.); (J.C.A.)
| | - Izabel Oliva Marcilio
- Hospital das Clínicas, Faculdade de Medicina da Universidade de São Paulo, São Paulo 01246-903l, Brazil; (J.C.F.); (C.R.R.d.C.); (M.C.F.); (I.O.M.); (K.R.d.S.); (V.C.J.); (J.F.M.); (J.C.A.)
| | - Katia Regina da Silva
- Hospital das Clínicas, Faculdade de Medicina da Universidade de São Paulo, São Paulo 01246-903l, Brazil; (J.C.F.); (C.R.R.d.C.); (M.C.F.); (I.O.M.); (K.R.d.S.); (V.C.J.); (J.F.M.); (J.C.A.)
| | - Vilson Cobello Junior
- Hospital das Clínicas, Faculdade de Medicina da Universidade de São Paulo, São Paulo 01246-903l, Brazil; (J.C.F.); (C.R.R.d.C.); (M.C.F.); (I.O.M.); (K.R.d.S.); (V.C.J.); (J.F.M.); (J.C.A.)
| | - Julio Flavio Marchini
- Hospital das Clínicas, Faculdade de Medicina da Universidade de São Paulo, São Paulo 01246-903l, Brazil; (J.C.F.); (C.R.R.d.C.); (M.C.F.); (I.O.M.); (K.R.d.S.); (V.C.J.); (J.F.M.); (J.C.A.)
| | - Julio Cesar Alencar
- Hospital das Clínicas, Faculdade de Medicina da Universidade de São Paulo, São Paulo 01246-903l, Brazil; (J.C.F.); (C.R.R.d.C.); (M.C.F.); (I.O.M.); (K.R.d.S.); (V.C.J.); (J.F.M.); (J.C.A.)
| | - Luz Marina Gomez Gomez
- Emergency Medicine Department, Faculdade de Medicina da Universidade de São Paulo, São Paulo 01246-903, Brazil; (D.V.S.P.); (L.M.G.G.); (H.P.S.)
| | - Denis Deratani Mauá
- Institute of Mathematics and Statistics, Universidade de São Paulo, São Paulo 05508-090, Brazil;
| | - Heraldo Possolo Souza
- Emergency Medicine Department, Faculdade de Medicina da Universidade de São Paulo, São Paulo 01246-903, Brazil; (D.V.S.P.); (L.M.G.G.); (H.P.S.)
| | - Emergency USP COVID-19 Group
- Emergency Medicine Department, Faculdade de Medicina da Universidade de São Paulo, São Paulo 01246-903, Brazil; (D.V.S.P.); (L.M.G.G.); (H.P.S.)
| | - HCFMUSP COVID-19 Study Group
- Hospital das Clínicas, Faculdade de Medicina da Universidade de São Paulo, São Paulo 01246-903l, Brazil; (J.C.F.); (C.R.R.d.C.); (M.C.F.); (I.O.M.); (K.R.d.S.); (V.C.J.); (J.F.M.); (J.C.A.)
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Barbagallo D, Palermo CI, Barbagallo C, Battaglia R, Caponnetto A, Spina V, Ragusa M, Di Pietro C, Scalia G, Purrello M. Competing endogenous RNA network mediated by circ_3205 in SARS-CoV-2 infected cells. Cell Mol Life Sci 2022; 79:75. [PMID: 35039944 PMCID: PMC8763136 DOI: 10.1007/s00018-021-04119-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [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: 10/21/2021] [Revised: 12/24/2021] [Accepted: 12/27/2021] [Indexed: 12/19/2022]
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a new member of the Betacoronaviridae family, responsible for the recent pandemic outbreak of COVID-19. To start exploring the molecular events that follow host cell infection, we queried VirusCircBase and identified a circular RNA (circRNA) predicted to be synthesized by SARS-CoV-2, circ_3205, which we used to probe: (i) a training cohort comprised of two pools of cells from three nasopharyngeal swabs of SARS-CoV-2 infected (positive) or uninfected (negative, UCs) individuals; (ii) a validation cohort made up of 12 positive and 3 negative samples. The expression of circRNAs, miRNAs and miRNA targets was assayed through real-time PCR. CircRNA-miRNA interactions were predicted by TarpMiR, Analysis of Common Targets for circular RNAs (ACT), and STarMir tools. Enrichment of the biological processes and the list of predicted miRNA targets were retrieved from DIANA miRPath v3.0. Our results showed that the predicted SARS-CoV-2 circ_3205 was expressed only in positive samples and its amount positively correlated with that of SARS-CoV-2 Spike (S) mRNA and the viral load (r values = 0.80952 and 0.84867, Spearman's correlation test, respectively). Human (hsa) miR-298 was predicted to interact with circ_3205 by all three predictive tools. KCNMB4 and PRKCE were predicted as hsa-miR-298 targets. Interestingly, the function of both is correlated with blood coagulation and immune response. KCNMB4 and PRKCE mRNAs were upregulated in positive samples as compared to UCs (6 and 8.1-fold, p values = 0.049 and 0.02, Student's t test, respectively) and their expression positively correlated with that of circ_3205 (r values = 0.6 and 0.25, Spearman's correlation test, respectively). We propose that our results convincingly suggest that circ_3205 is a circRNA synthesized by SARS-CoV-2 upon host cell infection and that it may behave as a competitive endogenous RNA (ceRNA), sponging hsa-miR-298 and contributing to the upregulation of KCNMB4 and PRKCE mRNAs.
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Affiliation(s)
- Davide Barbagallo
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics Giovanni Sichel, University of Catania, 95123, Catania, Italy.
| | - Concetta Ilenia Palermo
- U.O.C. Laboratory Analysis Unit, A.O.U. Policlinico‑Vittorio Emanuele, 95123, Catania, Italy
| | - Cristina Barbagallo
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics Giovanni Sichel, University of Catania, 95123, Catania, Italy
| | - Rosalia Battaglia
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics Giovanni Sichel, University of Catania, 95123, Catania, Italy
| | - Angela Caponnetto
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics Giovanni Sichel, University of Catania, 95123, Catania, Italy
| | - Vittoria Spina
- Department of Biomedical and Biotechnological Sciences, Section of Medical Biochemistry, University of Catania, 95123, Catania, Italy
| | - Marco Ragusa
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics Giovanni Sichel, University of Catania, 95123, Catania, Italy
| | - Cinzia Di Pietro
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics Giovanni Sichel, University of Catania, 95123, Catania, Italy
| | - Guido Scalia
- Department of Biomedical and Biotechnological Sciences, Section of Microbiology, University of Catania, 95123, Catania, Italy
| | - Michele Purrello
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics Giovanni Sichel, University of Catania, 95123, Catania, Italy
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27
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Tonelotto V, Davini A, Cardarelli L, Calderone M, Marin P. Efficacy of Fluorecare SARS-CoV-2 Spike Protein Test Kit for SARS-CoV-2 detection in nasopharyngeal samples of 121 individuals working in a manufacturing company. PLoS One 2022; 17:e0262174. [PMID: 35025944 PMCID: PMC8757945 DOI: 10.1371/journal.pone.0262174] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 12/17/2021] [Indexed: 11/23/2022] Open
Abstract
OBJECTIVES The aim of this study was to evaluate the clinical performance of the Fluorecare SARS-CoV-2 Spike Protein Test Kit, a rapid immunochromatographic assay for SARS-CoV-2 detection. Moreover, we sought to point out the strategy adopted by a local company to lift the lockdown without leading to an increase in the number of COVID-19 cases, by performing a precise and timely health surveillance. METHODS The rapid Fluorecare SARS-CoV-2 Spike Protein Test was performed immediately after sampling following the manufacturer's instructions. RT-PCRs were performed within 24 hours of specimen collection. A total amount of 253 nasopharyngeal samples from 121 individuals were collected between March 16 and April 2, 2021 and tested. RESULTS Of 253 nasopharyngeal samples, 11 (9.1%) were positive and 242 (90.9%) were negative for SARS-CoV-2 RNA by RT-PCR assays. The rapid SARS-CoV-2 antigen detection test's mean sensitivity and specificity were 84,6% (95% CI, 54.6-98.1%) and 100% (95% CI, 98.6-100%), respectively. Two false negative test results were obtained from samples with high RT-PCR cycle threshold (Ct). CONCLUSION Our study suggested that Fluorecare SARS-CoV-2 Spike Protein Test can be introduced into daily diagnostic practice, as its mean sensitivity and specificity follow the standards recommended by WHO and IFCC Task Force. In addition, we underlined how the strategy adopted by a local company to risk assessment and health surveillance was appropriate for infection containment. This real-life scenario gave us the possibility to experience potential approaches aimed to preserve public health and work activities.
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Affiliation(s)
| | - Annamaria Davini
- C.M.S.R. Veneto Medica S.r.l., Altavilla Vicentina, Vicenza, Italy
| | - Laura Cardarelli
- Lifebrain S.r.l–Gruppo Cerba HealthCare c/o RDI—Rete Diagnostica Italiana S.r.l, Limena, Padova, Italy
| | - Milena Calderone
- C.M.S.R. Veneto Medica S.r.l., Altavilla Vicentina, Vicenza, Italy
| | - Paola Marin
- C.M.S.R. Veneto Medica S.r.l., Altavilla Vicentina, Vicenza, Italy
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Mills MG, Bruce E, Huang ML, Crothers JW, Hyrien O, Oura CAL, Blake L, Brown Jordan A, Hester S, Wehmas L, Mari B, Barby P, Lacoux C, Fassy J, Vial P, Vial C, Martinez JRW, Oladipo OO, Inuwa B, Shittu I, Meseko CA, Chammas R, Santos CF, Dionísio TJ, Garbieri TF, Parisi VA, Mendes-Correa MC, de Paula AV, Romano CM, Góes LGB, Minoprio P, Campos AC, Cunha MP, Vilela APP, Nyirenda T, Mkakosya RS, Muula AS, Dumm RE, Harris RM, Mitchell CA, Pettit S, Botten J, Jerome KR. An international, interlaboratory ring trial confirms the feasibility of an extraction-less "direct" RT-qPCR method for reliable detection of SARS-CoV-2 RNA in clinical samples. PLoS One 2022; 17:e0261853. [PMID: 35025926 PMCID: PMC8758094 DOI: 10.1371/journal.pone.0261853] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 12/11/2021] [Indexed: 11/29/2022] Open
Abstract
Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) is used worldwide to test and trace the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). "Extraction-less" or "direct" real time-reverse transcription polymerase chain reaction (RT-PCR) is a transparent and accessible qualitative method for SARS-CoV-2 detection from nasopharyngeal or oral pharyngeal samples with the potential to generate actionable data more quickly, at a lower cost, and with fewer experimental resources than full RT-qPCR. This study engaged 10 global testing sites, including laboratories currently experiencing testing limitations due to reagent or equipment shortages, in an international interlaboratory ring trial. Participating laboratories were provided a common protocol, common reagents, aliquots of identical pooled clinical samples, and purified nucleic acids and used their existing in-house equipment. We observed 100% concordance across laboratories in the correct identification of all positive and negative samples, with highly similar cycle threshold values. The test also performed well when applied to locally collected patient nasopharyngeal samples, provided the viral transport media did not contain charcoal or guanidine, both of which appeared to potently inhibit the RT-PCR reaction. Our results suggest that direct RT-PCR assay methods can be clearly translated across sites utilizing readily available equipment and expertise and are thus a feasible option for more efficient COVID-19 coronavirus disease testing as demanded by the continuing pandemic.
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Affiliation(s)
- Margaret G. Mills
- Virology Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Emily Bruce
- Division of Immunobiology, Department of Medicine, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, Vermont, United States of America
| | - Meei-Li Huang
- Virology Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Jessica W. Crothers
- Division of Immunobiology, Department of Medicine, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, Vermont, United States of America
| | - Ollivier Hyrien
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Christopher A. L. Oura
- School of Veterinary Medicine, University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Lemar Blake
- School of Veterinary Medicine, University of the West Indies, St. Augustine, Trinidad and Tobago
| | | | - Susan Hester
- Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina, United States of America
| | - Leah Wehmas
- Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina, United States of America
| | - Bernard Mari
- Université Côte d’Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, FHU-OncoAge, Valbonne, France
| | - Pascal Barby
- Université Côte d’Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, FHU-OncoAge, Valbonne, France
| | - Caroline Lacoux
- Université Côte d’Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, FHU-OncoAge, Valbonne, France
| | - Julien Fassy
- Université Côte d’Azur, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, FHU-OncoAge, Valbonne, France
| | - Pablo Vial
- Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Programa Hantavirus, Instituto de Ciencias e Innovación en Medicina, Santiago, Chile
| | - Cecilia Vial
- Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Programa Hantavirus, Instituto de Ciencias e Innovación en Medicina, Santiago, Chile
| | - Jose R. W. Martinez
- Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Programa Hantavirus, Instituto de Ciencias e Innovación en Medicina, Santiago, Chile
| | | | - Bitrus Inuwa
- Infectious and Transboundary Animal Diseases, National Veterinary Research Institute, Vom, Nigeria
| | - Ismaila Shittu
- Infectious and Transboundary Animal Diseases, National Veterinary Research Institute, Vom, Nigeria
| | - Clement A. Meseko
- Infectious and Transboundary Animal Diseases, National Veterinary Research Institute, Vom, Nigeria
| | - Roger Chammas
- Faculdade de Medicina da Universidade de São Paulo, Departamento de Radiologia e Oncologia, Centro de Investigação Translacional em Oncologia, Instituto do Cancer do Estado de São Paulo, São Paulo, Brazil
| | - Carlos Ferreira Santos
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Bauru, São Paulo, Brazil
| | - Thiago José Dionísio
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Bauru, São Paulo, Brazil
| | - Thais Francini Garbieri
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Bauru, São Paulo, Brazil
| | - Viviane Aparecida Parisi
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Bauru, São Paulo, Brazil
| | | | - Anderson V. de Paula
- Department of Infectious Diseases, Institute of Tropical Medicine of São Paulo, São Paulo, Brazil
| | - Camila M. Romano
- Department of Infectious Diseases, Institute of Tropical Medicine of São Paulo, São Paulo, Brazil
| | - Luiz Gustavo Bentim Góes
- Scientific Platform Pasteur-USP, Universidade de São Paulo, São Paulo, Brazil
- Department of Microbiology, Biomedical Sciences Institute, University of São Paulo, São Paulo, Brazil
| | - Paola Minoprio
- Scientific Platform Pasteur-USP, Universidade de São Paulo, São Paulo, Brazil
| | - Angelica C. Campos
- Scientific Platform Pasteur-USP, Universidade de São Paulo, São Paulo, Brazil
| | - Marielton P. Cunha
- Scientific Platform Pasteur-USP, Universidade de São Paulo, São Paulo, Brazil
| | - Ana Paula P. Vilela
- Scientific Platform Pasteur-USP, Universidade de São Paulo, São Paulo, Brazil
| | - Tonney Nyirenda
- Department of Pathology, College of Medicine, University of Malawi, Blantyre, Malawi
| | | | - Adamson S. Muula
- Department of Public Health, College of Medicine, University of Malawi, Blantyre, Malawi
| | - Rebekah E. Dumm
- Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Rebecca M. Harris
- Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Constance A. Mitchell
- Health and Environmental Sciences Institute, Washington, DC, United States of America
| | - Syril Pettit
- Health and Environmental Sciences Institute, Washington, DC, United States of America
| | - Jason Botten
- Division of Immunobiology, Department of Medicine, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, Vermont, United States of America
- Department of Microbiology and Molecular Genetics, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, Vermont, United States of America
| | - Keith R. Jerome
- Virology Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
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Bulfoni M, Sozio E, Marcon B, De Martino M, Cesselli D, De Carlo C, Martinella R, Migotti A, Vania E, Zanus-Fortes A, De Piero J, Nencioni E, Tascini C, Isola M, Curcio F. Validation of a Saliva-Based Test for the Molecular Diagnosis of SARS-CoV-2 Infection. Dis Markers 2022; 2022:6478434. [PMID: 35035611 PMCID: PMC8759915 DOI: 10.1155/2022/6478434] [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] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 11/22/2021] [Accepted: 12/13/2021] [Indexed: 12/15/2022]
Abstract
BACKGROUND Since the beginning of the pandemic, clinicians and researchers have been searching for alternative tests to improve the screening and diagnosis of the SARS-CoV-2 infection. Currently, the gold standard for virus identification is the nasopharyngeal (NP) swab. Saliva samples, however, offer clear, practical, and logistical advantages but due to a lack of collection, transport, and storage solutions, high-throughput saliva-based laboratory tests are difficult to scale up as a screening or diagnostic tool. With this study, we aimed to validate an intralaboratory molecular detection method for SARS-CoV-2 on saliva samples collected in a new storage saline solution, comparing the results to NP swabs to determine the difference in sensitivity between the two tests. METHODS In this study, 156 patients (cases) and 1005 asymptomatic subjects (controls) were enrolled and tested simultaneously for the detection of the SARS-CoV-2 viral genome by RT-PCR on both NP swab and saliva samples. Saliva samples were collected in a preservative and inhibiting saline solution (Biofarma Srl). Internal method validation was performed to standardize the entire workflow for saliva samples. RESULTS The identification of SARS-CoV-2 conducted on saliva samples showed a clinical sensitivity of 95.1% and specificity of 97.8% compared to NP swabs. The positive predictive value (PPV) was 81% while the negative predictive value (NPV) was 99.5%. Test concordance was 97.6% (Cohen's Kappa = 0.86; 95% CI 0.81-0.91). The LoD of the test was 5 viral copies for both samples. CONCLUSIONS RT-PCR assays conducted on a stored saliva sample achieved similar performance to those on NP swabs, and this may provide a very effective tool for population screening and diagnosis. Collection of saliva in a stabilizing solution makes the test more convenient and widely available; furthermore, the denaturing properties of the solution reduce the infective risks belonging to sample manipulation.
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Affiliation(s)
- Michela Bulfoni
- Department of Medicine, University of Udine, Udine, Italy
- Institute of Pathology, ASU FC, Udine, Italy
| | - Emanuela Sozio
- Infectious Disease Unit, Department of Medicine, ASU FC, Udine, Italy
| | | | | | - Daniela Cesselli
- Department of Medicine, University of Udine, Udine, Italy
- Institute of Pathology, ASU FC, Udine, Italy
| | - Chiara De Carlo
- Infectious Disease Unit, Department of Medicine, ASU FC, Udine, Italy
| | | | | | - Eleonora Vania
- Infectious Disease Unit, Department of Medicine, ASU FC, Udine, Italy
| | | | - Jessica De Piero
- Infectious Disease Unit, Department of Medicine, ASU FC, Udine, Italy
| | | | - Carlo Tascini
- Department of Medicine, University of Udine, Udine, Italy
- Infectious Disease Unit, Department of Medicine, ASU FC, Udine, Italy
| | - Miriam Isola
- Department of Medicine, University of Udine, Udine, Italy
| | - Francesco Curcio
- Department of Medicine, University of Udine, Udine, Italy
- Department of Laboratory Medicine, ASU FC, Udine, Italy
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Mboumba Bouassa RS, Tonen-Wolyec S, Veyer D, Péré H, Bélec L. Analytical performances of the AMPLIQUICK® Respiratory Triplex assay for simultaneous detection and differentiation of SARS-CoV-2, influenza A/B and respiratory syncytial viruses in respiratory specimens. PLoS One 2022; 17:e0262258. [PMID: 34986156 PMCID: PMC8730414 DOI: 10.1371/journal.pone.0262258] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 02/23/2021] [Accepted: 12/21/2021] [Indexed: 12/28/2022] Open
Abstract
Although patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), influenza A, influenza B and respiratory syncytial virus (RSV) show comparable or very similar manifestations, the therapeutic approaches of these respiratory viral infections are different, which requires an accurate diagnosis. Recently, the novel multiplex real-time reverse transcription-polymerase chain reaction assay AMPLIQUICK® Respiratory Triplex (BioSynex SA, Illkirch-Graffenstaden, France) allows simultaneous detection and differentiation of SARS-CoV-2, influenza A, influenza B, and RSV in respiratory tract samples. We herein evaluated the performance of the AMPLIQUICK® Respiratory Triplex for the detection of the four viruses in respiratory specimens, using Allplex™ Respiratory Panel 1 and 2019-nCoV assays (Seegene, Seoul, Korea) as reference comparator assays. A total of 359 archived predetermined respiratory samples, including 83, 145, 19 and 95 positive specimens for SARS-CoV-2, influenza A, influenza B and RSV respectively, were included. The AMPLIQUICK® Respiratory Triplex showed high concordance with the reference assays, with an overall agreement for SARS-CoV-2, influenza A, influenza B, and RSV at 97.6%, 98.8%, 98.3% and 100.0%, respectively, and high κ values ranging from 0.93 to 1.00, indicating an almost perfect agreement between assays. Furthermore, high correlations of cycle threshold (Ct) values were observed for positive samples of the four viruses between the AMPLIQUICK® Respiratory Triplex and comparator assays, with an overall high agreement between Ct values assessed by Bland-Altman analyses. In conclusion, these observations demonstrate that the multiplex AMPLIQUICK® Respiratory Triplex is a reliable assay for the qualitative detection and differentiation of SARS-CoV-2, influenza A, influenza B, and RSV in respiratory specimens, which may prove useful for streamlining diagnostics during the winter influenza-seasons.
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Affiliation(s)
- Ralph-Sydney Mboumba Bouassa
- Ecole Doctorale d’Infectiologie Tropicale, Franceville, Gabon
- Laboratoire de Virologie, Hôpital Européen Georges Pompidou, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Serge Tonen-Wolyec
- Ecole Doctorale d’Infectiologie Tropicale, Franceville, Gabon
- Faculty of Medicine and Pharmacy, University of Kisangani, Kisangani, The Democratic Republic of the Congo
| | - David Veyer
- Laboratoire de Virologie, Hôpital Européen Georges Pompidou, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Hélène Péré
- Laboratoire de Virologie, Hôpital Européen Georges Pompidou, Assistance Publique-Hôpitaux de Paris, Paris, France
- Université de Paris, Sorbonne Paris Cité, Paris, France
| | - Laurent Bélec
- Laboratoire de Virologie, Hôpital Européen Georges Pompidou, Assistance Publique-Hôpitaux de Paris, Paris, France
- Université de Paris, Sorbonne Paris Cité, Paris, France
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31
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Huang F, Song K, Jiang Y, Hirose K, Umezu S. 3D-printed swab with cover for precision diagnosis. J Mater Sci Mater Med 2022; 33:8. [PMID: 34982267 PMCID: PMC8724228 DOI: 10.1007/s10856-021-06635-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Accepted: 12/13/2021] [Indexed: 06/14/2023]
Abstract
The collection capacity of common nasopharyngeal swabs and irregularities of medical personnel limit the accuracy of PCR testing. This study describes a newly designed 3D-printed swab that is combined with a 3D-printed cover to prevent the extraction of undesired nasal secretions. This swab improved the accuracy of PCR test results. The results of a series of experiments showed that, because of the mucus extraction effect, 3D-printed swabs can replace ordinary cotton swabs. The crisis of the worldwide medical supply shortage can be ameliorated to a certain extent by applying 3D printing technology.
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Affiliation(s)
- Fan Huang
- Department of Modern Mechanical Engineering, Waseda University, Tokyo, Japan
| | - Kewei Song
- Department of Modern Mechanical Engineering, Waseda University, Tokyo, Japan
| | - Yue Jiang
- Department of Modern Mechanical Engineering, Waseda University, Tokyo, Japan
| | - Kayo Hirose
- Department of Anesthesiology and Pain Relief Center, The University of Tokyo Hospital, Tokyo, Japan
| | - Shinjiro Umezu
- Department of Modern Mechanical Engineering, Waseda University, Tokyo, Japan.
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32
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Bräunlich J, Hoheisel R, Dinse-Lambracht A. Comparison of SARS-CoV-2 antigen testing to RT-PCR in a real-world setting-an observational cohort study. Diagn Microbiol Infect Dis 2022; 102:115531. [PMID: 34656818 PMCID: PMC8457903 DOI: 10.1016/j.diagmicrobio.2021.115531] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 06/14/2021] [Revised: 08/19/2021] [Accepted: 08/22/2021] [Indexed: 11/17/2022]
Abstract
A total of 2978 patients with validated paired results (SARS-CoV2-antigen and PCR) were identified. Our results show that only 45 antigen tests from 90 patients with positive validated PCR were correctly identified by antigen testing (sensitivity 50%). Roughly 50% of these patients had ongoing respiratory symptoms.
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33
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Chen Y, Huang S, Zhou L, Wang X, Yang H, Li W. Coronavirus Disease 2019 (COVID-19): Emerging detection technologies and auxiliary analysis. J Clin Lab Anal 2022; 36:e24152. [PMID: 34894011 PMCID: PMC8761422 DOI: 10.1002/jcla.24152] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [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: 09/04/2021] [Revised: 11/09/2021] [Accepted: 11/18/2021] [Indexed: 12/11/2022] Open
Abstract
The ongoing COVID-19 pandemic constitutes a new challenge for public health. Prevention and control of infection have become urgent and serious issues. To meet the clinical demand for higher accuracy of COVID-19 detection, the development of fast and efficient methods represents an important step. The most common methods of COVID-19 diagnosis, relying on real-time fluorescent quantitative PCR(RT-qPCR), computed tomography, and new-generation sequencing technologies, have a series of advantages, especially for early diagnosis and screening. In addition, joint efforts of researchers all over the world have led to the development of other rapid detection methods with high sensitivity, ease of use, cost-effectiveness, or allowing multiplex analysis based on technologies such as dPCR, ELISA, fluorescence immunochromatography assay, and the microfluidic detection chip method. The main goal of this review was to provide a critical discussion on the development and application of these different analytical methods, which based on etiology, serology, and molecular biology, as well as to compare their respective advantages and disadvantages. In addition to these methods, hematology and biochemistry, as well as auxiliary analysis based on pathological anatomy, ultrasonography, and cytokine detection, will help understand COVID-19 pathogenesis. Together, these technologies may promote and open new windows to unravel issues surrounding symptomatic and asymptomatic COVID-19 infections and improve clinical strategies toward reducing mortality.
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Affiliation(s)
- Ying Chen
- School of Medical Technology, Xuzhou Medical University, Xuzhou, China
| | - Shengxiong Huang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, China
| | - Liuyan Zhou
- School of Anesthesiology, Xuzhou Medical University, Xuzhou, China
| | - Xin Wang
- Centralized and Point of Care Solutions & Molecular Diagnostics, Roche Diagnostics (Shanghai) Limited, Shanghai, China
| | - Huan Yang
- School of Medical Technology, Xuzhou Medical University, Xuzhou, China
| | - Wenqing Li
- School of Medical Technology, Xuzhou Medical University, Xuzhou, China
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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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Golbets E, Kaplan A, Shafat T, Yagel Y, Jotkowitz A, Awesat J, Barski L. Secondary organizing pneumonia after recovery of mild COVID-19 infection. J Med Virol 2022; 94:417-423. [PMID: 34581458 PMCID: PMC8661567 DOI: 10.1002/jmv.27360] [Citation(s) in RCA: 4] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 04/16/2021] [Accepted: 09/23/2021] [Indexed: 11/12/2022]
Abstract
A 36-year-old male with diffuse large B-cell lymphoma on maintenance rituximab therapy presented to the emergency department with high fever and fatigue. A chest X-ray showed a lobar infiltrate, 40 days before admission the patient suffered from a mild coronavirus disease 2019 (COVID-19) infection and fully recovered. PCR nasopharyngeal swab was negative for COVID-19. Comprehensive biochemical, radiological, and pathological evaluation including 18-fluorodeoxyglucose positron emission tomography with computed tomography and transbronchial lung biopsy found no pathogen or lymphoma recurrence. Treatment for pneumonia with antibiotic and antifungal agents was nonbeneficial. A diagnosis of secondary organizing pneumonia (OP) was made after pneumonia migration and a rapid response to corticosteroids. OP secondary to a viral respiratory infection has been well described. Raising awareness for post-COVID-19 OP has therapeutic and prognostic importance because those patients benefit from steroid therapy. We believe the condition described here is underdiagnosed and undertreated by doctors worldwide. Because of the ongoing global pandemic we are now encountering a new kind of patient, patients that have recovered from COVID-19. We hope that this case may contribute to gaining more knowledge about this growing patient population.
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Affiliation(s)
- Evgeny Golbets
- Department of Internal Medicine F, Soroka Medical Center, Beersheba, Israel
| | - Alon Kaplan
- Department of Internal Medicine F, Soroka Medical Center, Beersheba, Israel
| | - Tali Shafat
- Division of Internal Medicine, Infectious Disease Institute, Soroka Medical Center, Beersheba, Israel
| | - Yael Yagel
- Division of Internal Medicine, Infectious Disease Institute, Soroka Medical Center, Beersheba, Israel
| | - Alan Jotkowitz
- Faculty of Health Sciences, Ben-Gurion University of the Negev, Beersheba, Israel
| | - Jenan Awesat
- Department of Internal Medicine F, Soroka Medical Center, Beersheba, Israel
| | - Leonid Barski
- Department of Internal Medicine F, Soroka Medical Center, Beersheba, Israel
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36
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Naito A, Kiyasu Y, Akashi Y, Sugiyama A, Michibuchi M, Takeuchi Y, Notake S, Nakamura K, Ishikawa H, Suzuki H. The evaluation of the utility of the GENECUBE HQ SARS-CoV-2 for anterior nasal samples and saliva samples with a new rapid examination protocol. PLoS One 2021; 16:e0262159. [PMID: 34972195 PMCID: PMC8719657 DOI: 10.1371/journal.pone.0262159] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 12/16/2021] [Indexed: 11/19/2022] Open
Abstract
INTRODUCTION GENECUBE® is a rapid molecular identification system, and previous studies demonstrated that GENECUBE® HQ SARS-CoV-2 showed excellent analytical performance for the detection of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) with nasopharyngeal samples. However, other respiratory samples have not been evaluated. METHODS This prospective comparison between GENECUBE® HQ SARS-CoV-2 and reference real-time reverse transcriptase polymerase chain reaction (RT-PCR) was performed for the detection of SARS-CoV-2 using anterior nasal samples and saliva samples. Additionally, we evaluated a new rapid examination protocol using GENECUBE® HQ SARS-CoV-2 for the detection of SARS-CoV-2 with saliva samples. For the rapid protocol, in the preparation of saliva samples, purification and extraction processes were adjusted, and the total process time was shortened to approximately 35 minutes. RESULTS For 359 anterior nasal samples, the total-, positive-, and negative concordance of the two assays was 99.7% (358/359), 98.1% (51/52), and 100% (307/307), respectively. For saliva samples, the total-, positive-, and negative concordance of the two assays was 99.6% (239/240), 100% (56/56), and 99.5% (183/184), respectively. With the new protocol, total-, positive-, and negative concordance of the two assays was 98.8% (237/240), 100% (56/56), and 98.4% (181/184), respectively. In all discordance cases, SARS-CoV-2 was detected by additional molecular examinations. CONCLUSION GENECUBE® HQ SARS-CoV-2 provided high analytical performance for the detection of SARS-CoV-2 in anterior nasal samples and saliva samples.
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Affiliation(s)
- Asami Naito
- Tsukuba i-Laboratory LLP, Tsukuba, Ibaraki, Japan
| | - Yoshihiko Kiyasu
- Division of Infectious Diseases, Department of Medicine, Tsukuba Medical Center Hospital, Tsukuba, Ibaraki, Japan
- Department of Infectious Diseases, University of Tsukuba Hospital, Tsukuba, Ibaraki, Japan
| | - Yusaku Akashi
- Division of Infectious Diseases, Department of Medicine, Tsukuba Medical Center Hospital, Tsukuba, Ibaraki, Japan
- Akashi Internal Medicine Clinic, Kashiwara, Osaka, Japan
| | - Akio Sugiyama
- Diagnostic System Department, TOYOBO Co., Ltd., Kita-ku, Osaka, Japan
| | | | - Yuto Takeuchi
- Division of Infectious Diseases, Department of Medicine, Tsukuba Medical Center Hospital, Tsukuba, Ibaraki, Japan
- Department of Infectious Diseases, University of Tsukuba Hospital, Tsukuba, Ibaraki, Japan
| | - Shigeyuki Notake
- Department of Clinical Laboratory, Tsukuba Medical Center Hospital, Tsukuba, Ibaraki, Japan
| | - Koji Nakamura
- Department of Clinical Laboratory, Tsukuba Medical Center Hospital, Tsukuba, Ibaraki, Japan
| | - Hiroichi Ishikawa
- Department of Respiratory Medicine, Tsukuba Medical Center Hospital, Tsukuba, Ibaraki, Japan
| | - Hiromichi Suzuki
- Division of Infectious Diseases, Department of Medicine, Tsukuba Medical Center Hospital, Tsukuba, Ibaraki, Japan
- Department of Infectious Diseases, University of Tsukuba Hospital, Tsukuba, Ibaraki, Japan
- Department of Infectious Diseases, Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan
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Igloi Z, Velzing J, Huisman R, Geurtsvankessel C, Comvalius A, IJpelaar J, van Beek J, Ensing R, Boelsums T, Koopmans M, Molenkamp R. Clinical evaluation of the SD Biosensor SARS-CoV-2 saliva antigen rapid test with symptomatic and asymptomatic, non-hospitalized patients. PLoS One 2021; 16:e0260894. [PMID: 34936659 PMCID: PMC8694432 DOI: 10.1371/journal.pone.0260894] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [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: 07/08/2021] [Accepted: 11/18/2021] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Performance of the SD Biosensor saliva antigen rapid test was evaluated at a large designated testing site in non-hospitalized patients, with or without symptoms. METHOD All eligible people over 18 years of age presenting for a booked appointment at the designated SARS-CoV-2 testing site were approached for inclusion and enrolled following verbal informed consent. One nasopharyngeal swab was taken to carry out the default antigen rapid test from which the results were reported back to the patient and one saliva sample was self-taken according to verbal instruction on site. This was used for the saliva antigen rapid test, the RT-PCR and for virus culture. Sensitivity of the saliva antigen rapid test was analyzed in two ways: i, compared to saliva RT-PCR; and ii, compared to virus culture of the saliva samples. Study participants were also asked to fill in a short questionnaire stating age, sex, date of symptom onset. Recommended time of ≥30mins since last meal, drink or cigarette if applicable was also recorded. The study was carried out in February-March 2021 for 4 weeks. RESULTS We could include 789 people with complete records and results. Compared to saliva RT-PCR, overall sensitivity and specificity of the saliva antigen rapid test was 66.1% and 99.6% which increased to 88.6% with Ct ≤30 cutoff. Analysis by days post onset did not result in higher sensitivities because the large majority of people were in the very early phase of disease ie <3 days post onset. When breaking down the data for symptomatic and asymptomatic individuals, sensitivity ranged from 69.2% to 50% respectively, however the total number of RT-PCR positive asymptomatic participants was very low (n = 5). Importantly, almost all culture positive samples were detected by the rapid test. CONCLUSION Overall, the potential benefits of saliva antigen rapid test, could outweigh the lower sensitivity compared to nasopharyngeal antigen rapid test in a comprehensive testing strategy, especially for home/self-testing and in vulnerable populations like elderly, disabled or children where in intrusive testing is either not possible or causes unnecessary stress.
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Affiliation(s)
- Zsofia Igloi
- Department of Viroscience, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Jans Velzing
- Department of Viroscience, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Robin Huisman
- Department of Viroscience, Erasmus Medical Centre, Rotterdam, The Netherlands
| | | | - Anoushka Comvalius
- Department of Viroscience, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Jeroen IJpelaar
- Department of Viroscience, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Janko van Beek
- Department of Viroscience, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Roel Ensing
- Public Health Service Rotterdam-Rijnmond, Rotterdam, The Netherlands
| | - Timo Boelsums
- Public Health Service Rotterdam-Rijnmond, Rotterdam, The Netherlands
| | - Marion Koopmans
- Department of Viroscience, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Richard Molenkamp
- Department of Viroscience, Erasmus Medical Centre, Rotterdam, The Netherlands
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Forinová M, Pilipenco A, Víšová I, Lynn NS, Dostálek J, Mašková H, Hönig V, Palus M, Selinger M, Kočová P, Dyčka F, Štěrba J, Houska M, Vrabcová M, Horák P, Anthi J, Tung CP, Yu CM, Chen CY, Huang YC, Tsai PH, Lin SY, Hsu HJ, Yang AS, Dejneka A, Vaisocherová-Lísalová H. Functionalized Terpolymer-Brush-Based Biointerface with Improved Antifouling Properties for Ultra-Sensitive Direct Detection of Virus in Crude Clinical Samples. ACS Appl Mater Interfaces 2021; 13:60612-60624. [PMID: 34902239 DOI: 10.1021/acsami.1c16930] [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] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
New analytical techniques that overcome major drawbacks of current routinely used viral infection diagnosis methods, i.e., the long analysis time and laboriousness of real-time reverse-transcription polymerase chain reaction (qRT-PCR) and the insufficient sensitivity of "antigen tests", are urgently needed in the context of SARS-CoV-2 and other highly contagious viruses. Here, we report on an antifouling terpolymer-brush biointerface that enables the rapid and sensitive detection of SARS-CoV-2 in untreated clinical samples. The developed biointerface carries a tailored composition of zwitterionic and non-ionic moieties and allows for the significant improvement of antifouling capabilities when postmodified with biorecognition elements and exposed to complex media. When deployed on a surface of piezoelectric sensor and postmodified with human-cell-expressed antibodies specific to the nucleocapsid (N) protein of SARS-CoV-2, it made possible the quantitative analysis of untreated samples by a direct detection assay format without the need of additional amplification steps. Natively occurring N-protein-vRNA complexes, usually disrupted during the sample pre-treatment steps, were detected in the untreated clinical samples. This biosensor design improved the bioassay sensitivity to a clinically relevant limit of detection of 1.3 × 104 PFU/mL within a detection time of only 20 min. The high specificity toward N-protein-vRNA complexes was validated both by mass spectrometry and qRT-PCR. The performance characteristics were confirmed by qRT-PCR through a comparative study using a set of clinical nasopharyngeal swab samples. We further demonstrate the extraordinary fouling resistance of this biointerface through exposure to other commonly used crude biological samples (including blood plasma, oropharyngeal, stool, and nasopharyngeal swabs), measured via both the surface plasmon resonance and piezoelectric measurements, which highlights the potential to serve as a generic platform for a wide range of biosensing applications.
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Affiliation(s)
- Michala Forinová
- Institute of Physics of the Czech Academy of Sciences, Na Slovance 2, 182 21 Prague, Czech Republic
| | - Alina Pilipenco
- Institute of Physics of the Czech Academy of Sciences, Na Slovance 2, 182 21 Prague, Czech Republic
| | - Ivana Víšová
- Institute of Physics of the Czech Academy of Sciences, Na Slovance 2, 182 21 Prague, Czech Republic
| | - N Scott Lynn
- Institute of Physics of the Czech Academy of Sciences, Na Slovance 2, 182 21 Prague, Czech Republic
| | - Jakub Dostálek
- Institute of Physics of the Czech Academy of Sciences, Na Slovance 2, 182 21 Prague, Czech Republic
- Austrian Institute of Technology GmbH, Konrad-Lorenz-Strasse 24, 3430 Tulln, Austria
| | - Hana Mašková
- Faculty of Science, University of South Bohemia, Branišovská 31a, 370 05 České Budějovice, Czech Republic
| | - Václav Hönig
- Institute of Parasitology, Biology Centre CAS, Branišovská 31, 370 05 České Budějovice, Czech Republic
- Veterinary Research Institute, Hudcova 70, 621 00 Brno, Czech Republic
| | - Martin Palus
- Institute of Parasitology, Biology Centre CAS, Branišovská 31, 370 05 České Budějovice, Czech Republic
- Veterinary Research Institute, Hudcova 70, 621 00 Brno, Czech Republic
| | - Martin Selinger
- Faculty of Science, University of South Bohemia, Branišovská 31a, 370 05 České Budějovice, Czech Republic
- Institute of Parasitology, Biology Centre CAS, Branišovská 31, 370 05 České Budějovice, Czech Republic
| | - Pavlína Kočová
- Faculty of Science, University of South Bohemia, Branišovská 31a, 370 05 České Budějovice, Czech Republic
| | - Filip Dyčka
- Faculty of Science, University of South Bohemia, Branišovská 31a, 370 05 České Budějovice, Czech Republic
| | - Jan Štěrba
- Faculty of Science, University of South Bohemia, Branišovská 31a, 370 05 České Budějovice, Czech Republic
| | - Milan Houska
- Institute of Physics of the Czech Academy of Sciences, Na Slovance 2, 182 21 Prague, Czech Republic
| | - Markéta Vrabcová
- Institute of Physics of the Czech Academy of Sciences, Na Slovance 2, 182 21 Prague, Czech Republic
| | - Petr Horák
- Institute of Physics of the Czech Academy of Sciences, Na Slovance 2, 182 21 Prague, Czech Republic
| | - Judita Anthi
- Institute of Physics of the Czech Academy of Sciences, Na Slovance 2, 182 21 Prague, Czech Republic
| | - Chao-Ping Tung
- Genomics Research Center, Academia Sinica, 128 Academia Rd., Sec.2, Nankang Dist., Taipei 115, Taiwan
| | - Chung-Ming Yu
- Genomics Research Center, Academia Sinica, 128 Academia Rd., Sec.2, Nankang Dist., Taipei 115, Taiwan
| | - Chi-Yung Chen
- Genomics Research Center, Academia Sinica, 128 Academia Rd., Sec.2, Nankang Dist., Taipei 115, Taiwan
| | - Yu-Chuan Huang
- Genomics Research Center, Academia Sinica, 128 Academia Rd., Sec.2, Nankang Dist., Taipei 115, Taiwan
| | - Pei-Hsun Tsai
- Genomics Research Center, Academia Sinica, 128 Academia Rd., Sec.2, Nankang Dist., Taipei 115, Taiwan
| | - Szu-Yu Lin
- Genomics Research Center, Academia Sinica, 128 Academia Rd., Sec.2, Nankang Dist., Taipei 115, Taiwan
| | - Hung-Ju Hsu
- Genomics Research Center, Academia Sinica, 128 Academia Rd., Sec.2, Nankang Dist., Taipei 115, Taiwan
| | - An-Suei Yang
- Genomics Research Center, Academia Sinica, 128 Academia Rd., Sec.2, Nankang Dist., Taipei 115, Taiwan
| | - Alexandr Dejneka
- Institute of Physics of the Czech Academy of Sciences, Na Slovance 2, 182 21 Prague, Czech Republic
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Leitão IDC, Calil PT, Galliez RM, Moreira FRR, Mariani D, Castiñeiras ACP, da Silva GPD, Maia RA, Corrêa IA, Monteiro FLL, de Souza MRM, Gonçalves CCA, Higa LM, de Jesus Ribeiro L, Fonseca VWP, Bastos VC, Voloch CM, Faffe DS, da Costa Ferreira O, Tanuri A, Castiñeiras TMPP, da Costa LJ. Prolonged SARS-CoV-2 Positivity in Immunocompetent Patients: Virus Isolation, Genomic Integrity, and Transmission Risk. Microbiol Spectr 2021; 9:e0085521. [PMID: 34787498 PMCID: PMC8597635 DOI: 10.1128/spectrum.00855-21] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 10/21/2021] [Indexed: 12/23/2022] Open
Abstract
Current guidelines for patient isolation in COVID-19 cases recommend a symptom-based approach, averting the use of control real-time reverse transcription PCR (rRT-PCR) testing. However, we hypothesized that patients with persistently positive results by RT-PCR for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) could be potentially infectious for a prolonged time, even if immunocompetent and asymptomatic, which would demand a longer social isolation period than presently recommended. To test this hypothesis, 72 samples from 51 mildly symptomatic immunocompetent patients with long-lasting positive rRT-PCR results for SARS-CoV-2 were tested for their infectiousness in cell culture. The serological response of samples from those patients and virus genomic integrity were also analyzed. Infectious viruses were successfully isolated from 34.38% (22/64) of nasopharynx samples obtained 14 days or longer after symptom onset. Indeed, we observed successful virus isolation up to 128 days. Complete SARS-COV-2 genome integrity was demonstrated, suggesting the presence of replication-competent viruses. No correlation was found between the isolation of infectious viruses and rRT-PCR cycle threshold values or the humoral immune response. These findings call attention to the need to review current isolation guidelines, particularly in scenarios involving high-risk individuals. IMPORTANCE In this study, we evaluated mildly symptomatic immunocompetent patients with long-lasting positive rRT-PCR results for SARS-CoV-2. Infectious viruses were successfully isolated in cell cultures from nasopharynx samples obtained 14 days or longer after symptom onset. Indeed, we observed successful virus isolation for up to 128 days. Moreover, SARS-CoV-2 genome integrity was demonstrated by sequencing, suggesting the presence of replication-competent viruses. These data point out the risk of continuous SARS-CoV-2 transmission from patients with prolonged detection of SARS-CoV-2 in the upper respiratory tract, which has important implications for current precaution guidelines, particularly in settings where vulnerable individuals may be exposed (e.g., nursing homes and hospitals).
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Affiliation(s)
- Isabela de Carvalho Leitão
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
| | - Pedro Telles Calil
- Laboratório de Genética e Imunologia das Infecções Virais, Departamento de Virologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
| | - Rafael Mello Galliez
- Departamento de Doenças Infecciosas e Parasitárias, Faculdade de Medicina, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
| | - Filipe Romero Rebello Moreira
- Laboratório de Virologia Molecular, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
| | - Diana Mariani
- Laboratório de Virologia Molecular, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
| | | | - Gustavo Peixoto Duarte da Silva
- Laboratório de Genética e Imunologia das Infecções Virais, Departamento de Virologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
| | - Richard Araújo Maia
- Laboratório de Virologia Molecular, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
| | - Isadora Alonso Corrêa
- Laboratório de Genética e Imunologia das Infecções Virais, Departamento de Virologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
| | - Fábio Luís Lima Monteiro
- Laboratório de Genética e Imunologia das Infecções Virais, Departamento de Virologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
| | - Marcos Romário Matos de Souza
- Laboratório de Genética e Imunologia das Infecções Virais, Departamento de Virologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
| | | | - Luiza Mendonça Higa
- Laboratório de Virologia Molecular, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
| | - Liane de Jesus Ribeiro
- Laboratório de Virologia Molecular, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
| | | | - Victoria Cortes Bastos
- Departamento de Doenças Infecciosas e Parasitárias, Faculdade de Medicina, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
| | - Carolina Moreira Voloch
- Laboratório de Virologia Molecular, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
| | - Débora Souza Faffe
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
| | - Orlando da Costa Ferreira
- Laboratório de Virologia Molecular, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
| | - Amilcar Tanuri
- Laboratório de Virologia Molecular, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
| | | | - Luciana Jesus da Costa
- Laboratório de Genética e Imunologia das Infecções Virais, Departamento de Virologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
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Torretta S, Pignataro L, Marchisio P, Capaccio P. SARS-CoV-2 tropism across the upper aerodigestive tract. Int J Immunopathol Pharmacol 2021; 35:20587384211056840. [PMID: 34928176 PMCID: PMC8724987 DOI: 10.1177/20587384211056840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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] [Indexed: 11/29/2022] Open
Affiliation(s)
- Sara Torretta
- Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
- Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Milan, Italy
- Sara Torretta, Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Via F. Sforza 35, Milano 20122, Italy.
| | - Lorenzo Pignataro
- Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
- Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Milan, Italy
| | - Paola Marchisio
- Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
| | - Pasquale Capaccio
- Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
- Department of Department of Biomedical Surgical Dental Science, Università degli Studi di Milano, Milan, Italy
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Costa-Martins AG, Mane K, Lindsey BB, Ogava RL, Castro Í, Jagne YJ, Sallah HJ, Armitage EP, Jarju S, Ahadzie B, Ellis-Watson R, Tregoning JS, Bingle CD, Bogaert D, Clarke E, Ordovas-Montanes J, Jeffries D, Kampmann B, Nakaya HI, de Silva TI. Prior upregulation of interferon pathways in the nasopharynx impacts viral shedding following live attenuated influenza vaccine challenge in children. Cell Rep Med 2021; 2:100465. [PMID: 35028607 PMCID: PMC8714852 DOI: 10.1016/j.xcrm.2021.100465] [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] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 09/28/2021] [Accepted: 11/12/2021] [Indexed: 02/06/2023]
Abstract
In children lacking influenza-specific adaptive immunity, upper respiratory tract innate immune responses may influence viral replication and disease outcome. We use trivalent live attenuated influenza vaccine (LAIV) as a surrogate challenge model in children aged 24-59 months to identify pre-infection mucosal transcriptomic signatures associated with subsequent viral shedding. Upregulation of interferon signaling pathways prior to LAIV is significantly associated with lower strain-specific viral loads (VLs) at days 2 and 7. Several interferon-stimulated genes are differentially expressed in children with pre-LAIV asymptomatic respiratory viral infections and negatively correlated with LAIV VLs. Upregulation of genes enriched in macrophages, neutrophils, and eosinophils is associated with lower VLs and found more commonly in children with asymptomatic viral infections. Variability in pre-infection mucosal interferon gene expression in children may impact the course of subsequent influenza infections. This variability may be due to frequent respiratory viral infections, demonstrating the potential importance of mucosal virus-virus interactions in children.
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Affiliation(s)
- André G. Costa-Martins
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
- Scientific Platform Pasteur, University of São Paulo, São Paulo, Brazil
| | - Karim Mane
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, P.O. Box 273, Fajara, The Gambia
| | - Benjamin B. Lindsey
- The Florey Institute for Host-Pathogen Interactions and Department of Infection, Immunity and Cardiovascular Disease, The University of Sheffield, Sheffield S10 2RX, UK
| | - Rodrigo L.T. Ogava
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Ícaro Castro
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Ya Jankey Jagne
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, P.O. Box 273, Fajara, The Gambia
| | - Hadijatou J. Sallah
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, P.O. Box 273, Fajara, The Gambia
| | - Edwin P. Armitage
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, P.O. Box 273, Fajara, The Gambia
| | - Sheikh Jarju
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, P.O. Box 273, Fajara, The Gambia
| | - Bankole Ahadzie
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, P.O. Box 273, Fajara, The Gambia
| | - Rebecca Ellis-Watson
- The University of Edinburgh/MRC Centre for Inflammation Research, The Queen’s Medical Research Institute, Edinburgh EH16 4TJ, UK
| | - John S. Tregoning
- Department of Infectious Disease, Imperial College London, London W2 1NY, UK
| | - Colin D. Bingle
- The Florey Institute for Host-Pathogen Interactions and Department of Infection, Immunity and Cardiovascular Disease, The University of Sheffield, Sheffield S10 2RX, UK
| | - Debby Bogaert
- The University of Edinburgh/MRC Centre for Inflammation Research, The Queen’s Medical Research Institute, Edinburgh EH16 4TJ, UK
| | - Ed Clarke
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, P.O. Box 273, Fajara, The Gambia
| | - Jose Ordovas-Montanes
- Division of Gastroenterology, Hepatology, and Nutrition, Boston Children’s Hospital, Boston, MA 02115, USA
- Program in Immunology, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - David Jeffries
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, P.O. Box 273, Fajara, The Gambia
| | - Beate Kampmann
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, P.O. Box 273, Fajara, The Gambia
- The Vaccine Centre, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - Helder I. Nakaya
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
- Scientific Platform Pasteur, University of São Paulo, São Paulo, Brazil
- Corresponding author
| | - Thushan I. de Silva
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, P.O. Box 273, Fajara, The Gambia
- The Florey Institute for Host-Pathogen Interactions and Department of Infection, Immunity and Cardiovascular Disease, The University of Sheffield, Sheffield S10 2RX, UK
- Corresponding author
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Delaroche L, Bertine M, Oger P, Descamps D, Damond F, Genauzeau E, Meicler P, Le Hingrat Q, Lamazou F, Gschwind R, Ruppé E, Visseaux B. Evaluation of SARS-CoV-2 in semen, seminal plasma, and spermatozoa pellet of COVID-19 patients in the acute stage of infection. PLoS One 2021; 16:e0260187. [PMID: 34905541 PMCID: PMC8670700 DOI: 10.1371/journal.pone.0260187] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 08/14/2021] [Accepted: 11/03/2021] [Indexed: 02/06/2023] Open
Abstract
To date, there is limited information about the presence of SARS-CoV-2 in semen especially in the acute phase of the infection. While available data from cohort studies including a total of 342 patients in the acute or recovery phase of the infection are reassuring, one study mentioned detecting virus in the semen of 6/38 COVID-19 patients. Here we assessed SARS-CoV-2 presence in the semen of COVID-19 positive patients in the acute stage of infection, within 24 hours of the positive nasopharyngeal swabs. Semen, seminal plasma and spermatozoa pellet were screened for SARS-CoV-2 and manual or airborne contamination during semen sampling. Among the 32 COVID-19 volunteers, the median interval from the onset of symptoms to semen collection was 4 days [IQR: 0-8]. Only one presented positive SARS-CoV-2 PCR in semen and seminal plasma fractions, although the spermatozoa pellet was negative. Viral cultures were all negative. We observed slightly higher concentrations of bacterial DNA in the SARS-CoV-2 positive specimen than in all negative samples. The bacteria identified neither confirm nor rule out contamination by oropharyngeal secretions during collection. SARS-CoV-2 was rarely present in semen during the acute phase of the disease. This very rare situation could be connected to oral or manual contamination during semen collection. The possible presence of SARS-CoV-2 in semen calls for nasopharyngeal viral testing and strict hygiene protocols during semen collection before assisted reproductive attempts.
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Affiliation(s)
- Lucie Delaroche
- Ramsay Santé, Hôpital Privé de Parly 2, Institut Fertilité Maternité Parly 2, Le Chesnay, France
- Centre de Biologie Médicale, Hôpital Privé de Parly 2, Le Chesnay, France
- * E-mail:
| | - Mélanie Bertine
- Université de Paris, INSERM, IAME, Paris, France
- AP-HP, Hôpital Bichat, Laboratoire de Virologie, Paris, France
| | - Pierre Oger
- Ramsay Santé, Hôpital Privé de Parly 2, Institut Fertilité Maternité Parly 2, Le Chesnay, France
| | - Diane Descamps
- Université de Paris, INSERM, IAME, Paris, France
- AP-HP, Hôpital Bichat, Laboratoire de Virologie, Paris, France
| | - Florence Damond
- Université de Paris, INSERM, IAME, Paris, France
- AP-HP, Hôpital Bichat, Laboratoire de Virologie, Paris, France
| | - Emmanuel Genauzeau
- Ramsay Santé, Hôpital Privé de Parly 2, Institut Fertilité Maternité Parly 2, Le Chesnay, France
- Centre de Biologie Médicale, Hôpital Privé de Parly 2, Le Chesnay, France
| | - Philippe Meicler
- Ramsay Santé, Hôpital Privé de Parly 2, Institut Fertilité Maternité Parly 2, Le Chesnay, France
| | - Quentin Le Hingrat
- Université de Paris, INSERM, IAME, Paris, France
- AP-HP, Hôpital Bichat, Laboratoire de Virologie, Paris, France
| | - Frédéric Lamazou
- Ramsay Santé, Hôpital Privé de Parly 2, Institut Fertilité Maternité Parly 2, Le Chesnay, France
| | | | - Etienne Ruppé
- Université de Paris, INSERM, IAME, Paris, France
- AP-HP, Hôpital Bichat, Laboratoire de Bactériologie, Paris, France
| | - Benoit Visseaux
- Université de Paris, INSERM, IAME, Paris, France
- AP-HP, Hôpital Bichat, Laboratoire de Virologie, Paris, France
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Mio C, Dal Secco C, Marzinotto S, Bruno C, Pimpo S, Betto E, Bertoni M, Pipan C, Sozio E, Tascini C, Damante G, Curcio F. Local occurrence and fast spread of B.1.1.7 lineage: A glimpse into Friuli Venezia Giulia. PLoS One 2021; 16:e0261229. [PMID: 34905574 PMCID: PMC8670677 DOI: 10.1371/journal.pone.0261229] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 11/24/2021] [Indexed: 11/27/2022] Open
Abstract
In-depth study of the entire SARS-CoV-2 genome has uncovered many mutations, which have replaced the lineage that characterized the first wave of infections all around the world. In December 2020, the outbreak of variant of concern (VOC) 202012/01 (lineage B.1.1.7) in the United Kingdom defined a turning point during the pandemic, immediately posing a worldwide threat on the Covid-19 vaccination campaign. Here, we reported the evolution of B.1.1.7 lineage-related infections, analyzing samples collected from January 1st 2021, until April 15th 2021, in Friuli Venezia Giulia, a northeastern region of Italy. A cohort of 1508 nasopharyngeal swabs was analyzed by High Resolution Melting (HRM) and 479 randomly selected samples underwent Next Generation Sequencing analysis (NGS), uncovering a steady and continuous accumulation of B.1.1.7 lineage-related specimens, joined by sporadic cases of other known lineages (i.e. harboring the Spike glycoprotein p.E484K mutation). All the SARS-CoV-2 genome has been analyzed in order to highlight all the rare mutations that may eventually result in a new variant of interest. This work suggests that a thorough monitoring of the SARS-CoV-2 genome by NGS is essential to contain any new variant that could jeopardize all the efforts that have been made so far to resolve the emergence of the pandemic.
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Affiliation(s)
- Catia Mio
- Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Chiara Dal Secco
- Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Stefania Marzinotto
- Department of Laboratory Medicine, University Hospital of Udine, Udine, Italy
| | - Claudio Bruno
- Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Santa Pimpo
- Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Elena Betto
- Department of Laboratory Medicine, University Hospital of Udine, Udine, Italy
| | - Martina Bertoni
- Department of Laboratory Medicine, University Hospital of Udine, Udine, Italy
| | - Corrado Pipan
- Department of Medicine (DAME), University of Udine, Udine, Italy
- Department of Laboratory Medicine, University Hospital of Udine, Udine, Italy
| | - Emanuela Sozio
- Infectious Diseases Clinic, University Hospital of Udine, Udine, Italy
| | - Carlo Tascini
- Department of Medicine (DAME), University of Udine, Udine, Italy
- Infectious Diseases Clinic, University Hospital of Udine, Udine, Italy
| | - Giuseppe Damante
- Department of Medicine (DAME), University of Udine, Udine, Italy
- Department of Laboratory Medicine, University Hospital of Udine, Udine, Italy
| | - Francesco Curcio
- Department of Medicine (DAME), University of Udine, Udine, Italy
- Department of Laboratory Medicine, University Hospital of Udine, Udine, Italy
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Yun J, Park JH, Kim N, Roh EY, Shin S, Yoon JH, Kim TS, Park H. Evaluation of Three Multiplex Real-time Reverse Transcription PCR Assays for Simultaneous Detection of SARS-CoV-2, Influenza A/B, and Respiratory Syncytial Virus in Nasopharyngeal Swabs. J Korean Med Sci 2021; 36:e328. [PMID: 34904407 PMCID: PMC8668494 DOI: 10.3346/jkms.2021.36.e328] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 11/10/2021] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND In the coronavirus disease 2019 (COVID-19) pandemic era, the simultaneous detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), influenza virus (Flu), and respiratory syncytial virus (RSV) is important in the rapid differential diagnosis in patients with respiratory symptoms. Three multiplex real-time reverse transcription polymerase chain reaction (rRT-PCR) assays have been recently developed commercially in Korea: PowerChek™ SARS-CoV-2, Influenza A&B Multiplex Real-time PCR Kit (PowerChek; KogeneBiotech); STANDARD™ M Flu/SARS-CoV-2 Real-time Detection Kit (STANDARD M; SD BioSensor); and Allplex™ SARS-CoV-2/FluA/FluB/RSV Assay (Allplex; Seegene). We evaluated the analytical and clinical performances of these kits. METHODS A limit of detection tests were performed and cross-reactivity analysis was executed using clinical respiratory samples. Ninety-seven SARS-CoV-2-positive, 201 SARS-CoV-2-negative, 71 influenza A-positive, 50 influenza B-positive, 78 RSV-positive, and 207 other respiratory virus-positive nasopharyngeal swabs were tested using the three assays. The AdvanSure™ respiratory viruses rRT-PCR assay (AdvanSure; LG Life Sciences) was used as a comparator assay for RSV. RESULTS Except in influenza B, in SARS-CoV-2 and influenza A, there were no significant differences in detecting specific genes of the viruses among the three assays. All three kits did not cross-react with common respiratory viruses. All three kits had greater than 92% positive percent agreement and negative percent agreement and ≥ 0.95 kappa value in the detection of SARS-CoV-2 and flu A/B. Allplex detected RSV more sensitively than AdvanSure. CONCLUSION The overall performance of three multiplex rRT-PCR assays for the concurrent detection of SARS-CoV-2, influenza A/B, and RSV was comparable. These kits will promote prompt differential diagnosis of COVID-19, influenza, and RSV infection in the COVID-19 pandemic era.
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Affiliation(s)
- Jiwon Yun
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Korea
| | - Jae Hyeon Park
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Korea
| | - Namhee Kim
- Department of Laboratory Medicine, Seoul National University Boramae Medical Center, Seoul, Korea
| | - Eun Youn Roh
- Department of Laboratory Medicine, Seoul National University Boramae Medical Center, Seoul, Korea
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Sue Shin
- Department of Laboratory Medicine, Seoul National University Boramae Medical Center, Seoul, Korea
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Jong Hyun Yoon
- Department of Laboratory Medicine, Seoul National University Boramae Medical Center, Seoul, Korea
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Taek Soo Kim
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Korea
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Hyunwoong Park
- Department of Laboratory Medicine, Seoul National University Boramae Medical Center, Seoul, Korea
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Korea.
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Goubet AG, Dubuisson A, Geraud A, Danlos FX, Terrisse S, Silva CAC, Drubay D, Touri L, Picard M, Mazzenga M, Silvin A, Dunsmore G, Haddad Y, Pizzato E, Ly P, Flament C, Melenotte C, Solary E, Fontenay M, Garcia G, Balleyguier C, Lassau N, Maeurer M, Grajeda-Iglesias C, Nirmalathasan N, Aprahamian F, Durand S, Kepp O, Ferrere G, Thelemaque C, Lahmar I, Fahrner JE, Meziani L, Ahmed-Belkacem A, Saïdani N, La Scola B, Raoult D, Gentile S, Cortaredona S, Ippolito G, Lelouvier B, Roulet A, Andre F, Barlesi F, Soria JC, Pradon C, Gallois E, Pommeret F, Colomba E, Ginhoux F, Kazandjian S, Elkrief A, Routy B, Miyara M, Gorochov G, Deutsch E, Albiges L, Stoclin A, Gachot B, Florin A, Merad M, Scotte F, Assaad S, Kroemer G, Blay JY, Marabelle A, Griscelli F, Zitvogel L, Derosa L. Prolonged SARS-CoV-2 RNA virus shedding and lymphopenia are hallmarks of COVID-19 in cancer patients with poor prognosis. Cell Death Differ 2021; 28:3297-3315. [PMID: 34230615 PMCID: PMC8259103 DOI: 10.1038/s41418-021-00817-9] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 05/26/2021] [Accepted: 05/28/2021] [Indexed: 12/13/2022] Open
Abstract
Patients with cancer are at higher risk of severe coronavirus infectious disease 2019 (COVID-19), but the mechanisms underlying virus-host interactions during cancer therapies remain elusive. When comparing nasopharyngeal swabs from cancer and noncancer patients for RT-qPCR cycle thresholds measuring acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in 1063 patients (58% with cancer), we found that malignant disease favors the magnitude and duration of viral RNA shedding concomitant with prolonged serum elevations of type 1 IFN that anticorrelated with anti-RBD IgG antibodies. Cancer patients with a prolonged SARS-CoV-2 RNA detection exhibited the typical immunopathology of severe COVID-19 at the early phase of infection including circulation of immature neutrophils, depletion of nonconventional monocytes, and a general lymphopenia that, however, was accompanied by a rise in plasmablasts, activated follicular T-helper cells, and non-naive Granzyme B+FasL+, EomeshighTCF-1high, PD-1+CD8+ Tc1 cells. Virus-induced lymphopenia worsened cancer-associated lymphocyte loss, and low lymphocyte counts correlated with chronic SARS-CoV-2 RNA shedding, COVID-19 severity, and a higher risk of cancer-related death in the first and second surge of the pandemic. Lymphocyte loss correlated with significant changes in metabolites from the polyamine and biliary salt pathways as well as increased blood DNA from Enterobacteriaceae and Micrococcaceae gut family members in long-term viral carriers. We surmise that cancer therapies may exacerbate the paradoxical association between lymphopenia and COVID-19-related immunopathology, and that the prevention of COVID-19-induced lymphocyte loss may reduce cancer-associated death.
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Affiliation(s)
- Anne-Gaëlle Goubet
- Université Paris-Saclay, Faculté de Médecine, Le Kremlin-Bicêtre, France
- Gustave Roussy Cancer Campus, Villejuif, France
- Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France
| | - Agathe Dubuisson
- Gustave Roussy Cancer Campus, Villejuif, France
- Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France
| | - Arthur Geraud
- Gustave Roussy Cancer Campus, Villejuif, France
- Département d'Oncologie Médicale, Gustave Roussy, Villejuif, France
- Département d'Innovation Thérapeutique et d'Essais Précoces, Gustave Roussy, Villejuif, France
| | - François-Xavier Danlos
- Gustave Roussy Cancer Campus, Villejuif, France
- Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France
| | - Safae Terrisse
- Gustave Roussy Cancer Campus, Villejuif, France
- Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France
| | - Carolina Alves Costa Silva
- Gustave Roussy Cancer Campus, Villejuif, France
- Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France
| | - Damien Drubay
- Gustave Roussy Cancer Campus, Villejuif, France
- Département de Biostatistique et d'Epidémiologie, Gustave Roussy, Université Paris-Saclay, Villejuif, France
- Institut National de la Santé et de la Recherche Médicale Oncostat, U1018, Equipe labellisée par la Ligue Contre le Cancer, Gustave Roussy, Villejuif, France
| | - Lea Touri
- Gustave Roussy Cancer Campus, Villejuif, France
- Médecine du travail, Gustave Roussy, Villejuif, France
| | - Marion Picard
- Gustave Roussy Cancer Campus, Villejuif, France
- Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France
- Institut Pasteur, Unit Biology and Genetics of the Bacterial Cell Wall, Paris, France
- CNRS UMR2001, Paris, France
- INSERM, Equipe Avenir, Paris, France
| | - Marine Mazzenga
- Gustave Roussy Cancer Campus, Villejuif, France
- Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France
| | - Aymeric Silvin
- Gustave Roussy Cancer Campus, Villejuif, France
- Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France
| | - Garett Dunsmore
- Gustave Roussy Cancer Campus, Villejuif, France
- Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France
| | - Yacine Haddad
- Gustave Roussy Cancer Campus, Villejuif, France
- Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France
| | - Eugenie Pizzato
- Gustave Roussy Cancer Campus, Villejuif, France
- Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France
| | - Pierre Ly
- Gustave Roussy Cancer Campus, Villejuif, France
- Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France
| | - Caroline Flament
- Gustave Roussy Cancer Campus, Villejuif, France
- Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France
| | - Cléa Melenotte
- Gustave Roussy Cancer Campus, Villejuif, France
- Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France
| | - Eric Solary
- Université Paris-Saclay, Faculté de Médecine, Le Kremlin-Bicêtre, France
- Gustave Roussy Cancer Campus, Villejuif, France
- Institut National de la Santé et de la Recherche Médicale, U1287, Gustave Roussy, Villejuif, France
- Département d'Hématologie, Gustave Roussy, Villejuif, France
| | - Michaela Fontenay
- Université de Paris, Institut Cochin, Centre National de la Recherche Scientifique UMR8104, Institut National de la Santé et de la Recherche Médicale, Paris, France
- Service d'hématologie biologique, Hôpital Cochin, Assistance Publique-Hôpitaux de Paris.Centre-Université de Paris, Paris, France
| | - Gabriel Garcia
- Gustave Roussy Cancer Campus, Villejuif, France
- Département d'Imagerie Médicale, Gustave Roussy, Villejuif, France
| | - Corinne Balleyguier
- Gustave Roussy Cancer Campus, Villejuif, France
- Département d'Imagerie Médicale, Gustave Roussy, Villejuif, France
| | - Nathalie Lassau
- Université Paris-Saclay, Faculté de Médecine, Le Kremlin-Bicêtre, France
- Gustave Roussy Cancer Campus, Villejuif, France
- Département d'Imagerie Médicale, Gustave Roussy, Villejuif, France
- Biomaps, UMR1281, INSERM, CNRS, CEA, Université Paris Saclay, Paris, France
| | - Markus Maeurer
- Immunotherapy/Immunosurgery, Champalimaud foundation, Lisboa, Portugal
| | - Claudia Grajeda-Iglesias
- Gustave Roussy Cancer Campus, Villejuif, France
- Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France
- Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue contre le cancer, Université de Paris, Sorbonne Université, Inserm U1138, Institut Universitaire de France, Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Center, Université Paris Saclay, Villejuif, France
| | - Nitharsshini Nirmalathasan
- Gustave Roussy Cancer Campus, Villejuif, France
- Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue contre le cancer, Université de Paris, Sorbonne Université, Inserm U1138, Institut Universitaire de France, Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Center, Université Paris Saclay, Villejuif, France
| | - Fanny Aprahamian
- Gustave Roussy Cancer Campus, Villejuif, France
- Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue contre le cancer, Université de Paris, Sorbonne Université, Inserm U1138, Institut Universitaire de France, Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Center, Université Paris Saclay, Villejuif, France
| | - Sylvère Durand
- Gustave Roussy Cancer Campus, Villejuif, France
- Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue contre le cancer, Université de Paris, Sorbonne Université, Inserm U1138, Institut Universitaire de France, Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Center, Université Paris Saclay, Villejuif, France
| | - Oliver Kepp
- Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue contre le cancer, Université de Paris, Sorbonne Université, Inserm U1138, Institut Universitaire de France, Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Center, Université Paris Saclay, Villejuif, France
| | - Gladys Ferrere
- Gustave Roussy Cancer Campus, Villejuif, France
- Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France
| | - Cassandra Thelemaque
- Gustave Roussy Cancer Campus, Villejuif, France
- Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France
| | - Imran Lahmar
- Gustave Roussy Cancer Campus, Villejuif, France
- Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France
| | - Jean-Eudes Fahrner
- Gustave Roussy Cancer Campus, Villejuif, France
- Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France
| | - Lydia Meziani
- Gustave Roussy Cancer Campus, Villejuif, France
- Institut National de la Santé et de la Recherche Médicale, U1030, Gustave Roussy, Villejuif, France
| | | | - Nadia Saïdani
- Service de maladies infectieuses, Centre Hospitalier de Cornouaille, Quimper, France
| | - Bernard La Scola
- Aix-Marseille Université, Institut de Recherche pour le Développement, Assistance Publique - Hôpitaux de Marseille, Microbes Evolution Phylogeny and Infections, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Didier Raoult
- Aix-Marseille Université, Institut de Recherche pour le Développement, Assistance Publique - Hôpitaux de Marseille, Microbes Evolution Phylogeny and Infections, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Stéphanie Gentile
- Aix Marseille Univ, School of medicine-La Timone Medical Campus, EA 3279: CEReSS-Health Service Research and Quality of life Center, Marseille, France
| | - Sébastien Cortaredona
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - Giuseppe Ippolito
- Scientific Direction, National Institute for Infectious Diseases Lazzaro Spallanzani, Rome, Italy
| | | | | | - Fabrice Andre
- Université Paris-Saclay, Faculté de Médecine, Le Kremlin-Bicêtre, France
- Gustave Roussy Cancer Campus, Villejuif, France
- Département d'Oncologie Médicale, Gustave Roussy, Villejuif, France
- Institut National de la Santé et de la Recherche Médicale, U981, Gustave Roussy, Villejuif, France
| | - Fabrice Barlesi
- Gustave Roussy Cancer Campus, Villejuif, France
- Département d'Oncologie Médicale, Gustave Roussy, Villejuif, France
- Aix Marseille University, CNRS, INSERM, CRCM, Marseille, France
| | - Jean-Charles Soria
- Université Paris-Saclay, Faculté de Médecine, Le Kremlin-Bicêtre, France
- Gustave Roussy Cancer Campus, Villejuif, France
| | - Caroline Pradon
- Gustave Roussy Cancer Campus, Villejuif, France
- Centre de ressources biologiques, ET-EXTRA, Gustave Roussy, Villejuif, France
- Département de Biologie Médicale et Pathologie Médicales, service de biochimie, Gustave Roussy, Villejuif, France
| | - Emmanuelle Gallois
- Gustave Roussy Cancer Campus, Villejuif, France
- Département de Biologie Médicale et Pathologie Médicales, service de microbiologie, Gustave Roussy, Villejuif, France
| | - Fanny Pommeret
- Gustave Roussy Cancer Campus, Villejuif, France
- Département d'Oncologie Médicale, Gustave Roussy, Villejuif, France
| | - Emeline Colomba
- Gustave Roussy Cancer Campus, Villejuif, France
- Département d'Oncologie Médicale, Gustave Roussy, Villejuif, France
| | - Florent Ginhoux
- Singapore Immunology Network, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Shanghai Institute of Immunology, Shangai, China
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Center, Singapore, Singapore
| | - Suzanne Kazandjian
- Cedar's Cancer Center, McGill University Healthcare Centre, Montreal, QC, Canada
| | - Arielle Elkrief
- Cedar's Cancer Center, McGill University Healthcare Centre, Montreal, QC, Canada
- Centre de recherche du Centre hospitalier de l'Université de Montréal (CRCHUM), Montreal, QC, Canada
| | - Bertrand Routy
- Centre de recherche du Centre hospitalier de l'Université de Montréal (CRCHUM), Montreal, QC, Canada
- Department of Hematology-Oncology, Centre hospitalier de l'Université de Montréal, Montreal, QC, Canada
| | - Makoto Miyara
- Institut National de la Santé et de la Recherche Médicale, U1135, Centre d'Immunologie et des Maladies Infectieuses, Hôpital Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Guy Gorochov
- Institut National de la Santé et de la Recherche Médicale, U1135, Centre d'Immunologie et des Maladies Infectieuses, Hôpital Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Eric Deutsch
- Université Paris-Saclay, Faculté de Médecine, Le Kremlin-Bicêtre, France
- Gustave Roussy Cancer Campus, Villejuif, France
- Institut National de la Santé et de la Recherche Médicale, U1030, Gustave Roussy, Villejuif, France
- Département de Radiothérapie, Gustave Roussy, Villejuif, France
| | - Laurence Albiges
- Université Paris-Saclay, Faculté de Médecine, Le Kremlin-Bicêtre, France
- Gustave Roussy Cancer Campus, Villejuif, France
- Département d'Oncologie Médicale, Gustave Roussy, Villejuif, France
| | - Annabelle Stoclin
- Gustave Roussy Cancer Campus, Villejuif, France
- Service de Réanimation Médicale, Gustave Roussy, Villejuif, France
| | - Bertrand Gachot
- Gustave Roussy Cancer Campus, Villejuif, France
- Service de Pathologie Infectieuse, Gustave Roussy, Villejuif, France
| | - Anne Florin
- Gustave Roussy Cancer Campus, Villejuif, France
- Médecine du travail, Gustave Roussy, Villejuif, France
| | - Mansouria Merad
- Gustave Roussy Cancer Campus, Villejuif, France
- Service de médecine aigue d'urgence en cancérologie, Gustave Roussy, Villejuif, France
| | - Florian Scotte
- Gustave Roussy Cancer Campus, Villejuif, France
- Département Interdisciplinaire d'Organisation des Parcours Patients, Gustave Roussy, Villejuif, France
| | - Souad Assaad
- Centre Léon Bérard, Lyon, France
- Université Claude Bernard, Lyon, France
- Unicancer, Paris, France
| | - Guido Kroemer
- Gustave Roussy Cancer Campus, Villejuif, France
- Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue contre le cancer, Université de Paris, Sorbonne Université, Inserm U1138, Institut Universitaire de France, Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Center, Université Paris Saclay, Villejuif, France
- Université de Paris, Paris, France
- Department of Women's and Children's Health, Karolinska Institute, Karolinska University Hospital, Stockholm, Sweden
- Pôle de Biologie, Hôpital Européen George Pompidou, Assistance Publique-Hôpitaux de Paris, Paris, France
- Suzhou Institute for Systems Biology, Chinese Academy of Medical Sciences, Suzhou, China
| | - Jean-Yves Blay
- Centre Léon Bérard, Lyon, France
- Université Claude Bernard, Lyon, France
- Unicancer, Paris, France
| | - Aurélien Marabelle
- Gustave Roussy Cancer Campus, Villejuif, France
- Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France
- Département d'Oncologie Médicale, Gustave Roussy, Villejuif, France
- Département d'Innovation Thérapeutique et d'Essais Précoces, Gustave Roussy, Villejuif, France
- Center of Clinical Investigations BIOTHERIS, Gustave Roussy, Villejuif, France
| | - Frank Griscelli
- Gustave Roussy Cancer Campus, Villejuif, France
- Département de Biologie Médicale et Pathologie Médicales, service de microbiologie, Gustave Roussy, Villejuif, France
- Institut National de la Santé et de la Recherche Médicale-UMR935/UA9, Université Paris-Saclay, Villejuif, France
- INGESTEM National IPSC Infrastructure, Université de Paris-Saclay, Villejuif, France
- Université de Paris, Faculté des Sciences Pharmaceutiques et Biologiques, Paris, France
| | - Laurence Zitvogel
- Université Paris-Saclay, Faculté de Médecine, Le Kremlin-Bicêtre, France.
- Gustave Roussy Cancer Campus, Villejuif, France.
- Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France.
- Center of Clinical Investigations BIOTHERIS, Gustave Roussy, Villejuif, France.
| | - Lisa Derosa
- Université Paris-Saclay, Faculté de Médecine, Le Kremlin-Bicêtre, France.
- Gustave Roussy Cancer Campus, Villejuif, France.
- Institut National de la Santé et de la Recherche Médicale, UMR1015, Gustave Roussy, Villejuif, France.
- Département d'Oncologie Médicale, Gustave Roussy, Villejuif, France.
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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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Zhao Y, Lee A, Composto K, Cunningham MH, Mediavilla JR, Fennessey S, Corvelo A, Chow KF, Zody M, Chen L, Kreiswirth BN, Perlin DS. A novel diagnostic test to screen SARS-CoV-2 variants containing E484K and N501Y mutations. Emerg Microbes Infect 2021; 10:994-997. [PMID: 33977858 PMCID: PMC8168736 DOI: 10.1080/22221751.2021.1929504] [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: 03/26/2021] [Revised: 04/27/2021] [Accepted: 05/09/2021] [Indexed: 12/12/2022]
Abstract
Spike protein mutations E484K and N501Y carried by SARS-CoV-2 variants have been associated with concerning changes of the virus, including resistance to neutralizing antibodies and increased transmissibility. While the concerning variants are fast spreading in various geographical areas, identification and monitoring of these variants are lagging far behind, due in large part to the slow speed and insufficient capacity of viral sequencing. In response to the unmet need for a fast and efficient screening tool, we developed a single-tube duplex molecular assay for rapid and simultaneous identification of E484K and N501Y mutations from nasopharyngeal swab (NS) samples within 2.5 h from sample preparation to report. Using this tool, we screened a total of 1135 clinical NS samples collected from COVID patients at 8 hospitals within the Hackensack Meridian Health network in New Jersey between late December 2020 and March 2021. Our data revealed dramatic increases in the frequencies of both E484K and N501Y over time, underscoring the need for continuous epidemiological monitoring.
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Affiliation(s)
- Yanan Zhao
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA
- Hackensack Meridian School of Medicine, Nutley, NJ, USA
| | - Annie Lee
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA
| | - Kaelea Composto
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA
| | - Marcus H. Cunningham
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA
| | - Jose R. Mediavilla
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA
| | | | | | - Kar Fai Chow
- Core Laboratory, Department of Pathology, Hackensack University Medical Center, Hackensack, NJ, USA
| | | | - Liang Chen
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA
- Hackensack Meridian School of Medicine, Nutley, NJ, USA
| | - Barry N. Kreiswirth
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA
- Hackensack Meridian School of Medicine, Nutley, NJ, USA
- Georgetown University Lombardi Comprehensive Cancer Center, Washington, DC, USA
| | - David S. Perlin
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA
- Hackensack Meridian School of Medicine, Nutley, NJ, USA
- Georgetown University Lombardi Comprehensive Cancer Center, Washington, DC, USA
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Boschi C, Aherfi S, Houhamdi L, Colson P, Raoult D, Scola BL. Isolation of 4000 SARS-CoV-2 shows that contagiousness is associated with viral load, not vaccine or symptomatic status. Emerg Microbes Infect 2021; 10:2276-2278. [PMID: 34792434 PMCID: PMC8648030 DOI: 10.1080/22221751.2021.2008776] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/15/2021] [Accepted: 11/16/2021] [Indexed: 12/23/2022]
Abstract
Culture inoculation of 6722 nasopharyngeal samples since February 2020 allowed isolation of 3637 SARS-CoV-2 and confirmed that isolation rate is correlated to viral load, regardless symptomatology or vaccination status. Moreover, the delta variant is associated with higher viral loads and therefore higher rates of viral isolation, explaining its greater contagiousness.
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Affiliation(s)
- Celine Boschi
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Aix-Marseille University, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Sarah Aherfi
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Aix-Marseille University, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | | | - Philippe Colson
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Aix-Marseille University, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Didier Raoult
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Aix-Marseille University, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Bernard La Scola
- Microbes, Evolution, Phylogeny and Infection (MEPHI), UM63, Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Aix-Marseille University, Marseille, France
- IHU Méditerranée Infection, Marseille, France
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Rodriguez-Paredes MB, Vallejo-Janeta PA, Morales-Jadan D, Freire-Paspuel B, Ortiz-Prado E, Henriquez-Trujillo AR, Rivera-Olivero IA, Jaramillo T, Lozada T, Garcia-Bereguiain MA. COVID-19 Community Transmission and Super Spreaders in Rural Villages from Manabi Province in the Coastal Region of Ecuador Assessed by Massive Testing of Community-Dwelling Population. Am J Trop Med Hyg 2021; 106:121-126. [PMID: 34788738 PMCID: PMC8733526 DOI: 10.4269/ajtmh.21-0582] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 05/24/2021] [Accepted: 10/05/2021] [Indexed: 11/17/2022] Open
Abstract
Neglected rural communities in Latin America are highly vulnerable to COVID-19 due to a poor health infrastructure and limited access to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) diagnosis. Manabí is a province of the Coastal Region of Ecuador characterized by a high prevalence of rural population living under poverty conditions. In the current study, we present the retrospective analysis of the results of a massive SARS-CoV-2 testing operation in nonhospitalized populations from Manabí carried out from August to September 2020. A total of 4,003 people from 15 cantons were tested for SARS-CoV-2 by reverse-transcriptase quantitative polymerase chain reaction, resulting in an overall infection rate of 16.13% for SARS-CoV-2, with several communities > 30%. Moreover, 29 SARS-CoV-2 super-spreader community-dwelling individuals with viral loads above 108 copies/mL were found. These results support that uncontrolled COVID-19 community transmission was happening in Manabí during the first semester of COVID-19 pandemic. This report endorses the utility of massive SARS-CoV-2 testing among asymptomatic population for control and surveillance of COVID-19.
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Affiliation(s)
- Maria Belén Rodriguez-Paredes
- One Health Research Group, Universidad de Las Américas, Quito, Ecuador
- “UDLA-COVID-19 Team,” Universidad de Las Américas, Quito, Ecuador
| | - Paolo Alexander Vallejo-Janeta
- One Health Research Group, Universidad de Las Américas, Quito, Ecuador
- “UDLA-COVID-19 Team,” Universidad de Las Américas, Quito, Ecuador
| | | | | | | | | | | | | | - Tannya Lozada
- Dirección General de Investigación, Universidad de Las Américas, Quito, Ecuador
| | - Miguel Angel Garcia-Bereguiain
- One Health Research Group, Universidad de Las Américas, Quito, Ecuador
- Address correspondence to Miguel Angel Garcia-Bereguiain, One Health Research Group, Universidad de Las Américas, Quito, Ecuador. E-mail:
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Abstract
We used serial rectal swabs to investigate the amount and duration of virus secretion through the gastrointestinal tract and assessed the association between fecal shedding and gastrointestinal symptoms and to clarify the clinical usefulness testing rectal swabs. We enrolled ten adult patients hospitalized with symptomatic coronavirus disease 2019 (COVID-19). Respiratory and stool specimens were collected by physicians. The presence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was confirmed using real-time reverse-transcription polymerase chain reaction. All ten patients had respiratory symptoms, six had diarrhea, and seven were positive for SARS-CoV-2 on rectal swabs. The viral loads in the respiratory specimens was higher than those in the rectal specimens, and no rectal specimens were positive after the respiratory specimens became negative. There was no association between gastrointestinal symptoms, pneumonia, severity, and rectal viral load. Rectal swabs may play a role in detecting SARS-CoV-2 in individuals with suspected COVID-19, regardless of gastrointestinal symptoms.
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Affiliation(s)
- Sung Hoon Jung
- Division of Gastroenterology, Department of Internal Medicine, Eunpyeong St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Sei Won Kim
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, Eunpyeong St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Heayon Lee
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, Eunpyeong St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Jung Hwan Oh
- Division of Gastroenterology, Department of Internal Medicine, Eunpyeong St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea.
| | - Jihyang Lim
- Department of Laboratory Medicine, Eunpyeong St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea.
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