1
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Patiño LH, Guerra S, Muñoz M, Luna N, Farrugia K, van de Guchte A, Khalil Z, Gonzalez-Reiche AS, Hernandez MM, Banu R, Shrestha P, Liggayu B, Firpo Betancourt A, Reich D, Cordon-Cardo C, Albrecht R, Pearl R, Simon V, Rooker A, Sordillo EM, van Bakel H, García-Sastre A, Bogunovic D, Palacios G, Paniz Mondolfi A, Ramírez JD. Phylogenetic landscape of Monkeypox Virus (MPV) during the early outbreak in New York City, 2022. Emerg Microbes Infect 2023; 12:e2192830. [PMID: 36927408 PMCID: PMC10114986 DOI: 10.1080/22221751.2023.2192830] [Citation(s) in RCA: 3] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 03/14/2023] [Indexed: 03/18/2023]
Abstract
Monkeypox (MPOX) is a zoonotic disease endemic to regions of Central/Western Africa. The geographic endemicity of MPV has expanded, broadening the human-monkeypox virus interface and its potential for spillover. Since May 2022, a large multi-country MPV outbreak with no proven links to endemic countries has originated in Europe and has rapidly expanded around the globe, setting off genomic surveillance efforts. Here, we conducted a genomic analysis of 23 MPV-infected patients from New York City during the early outbreak, assessing the phylogenetic relationship of these strains against publicly available MPV genomes. Additionally, we compared the genomic sequences of clinical isolates versus culture-passaged samples from a subset of samples. Phylogenetic analysis revealed that MPV genomes included in this study cluster within the B.1 lineage (Clade IIb), with some of the samples displaying further differentiation into five different sub-lineages of B.1. Mutational analysis revealed 55 non-synonymous polymorphisms throughout the genome, with some of these mutations located in critical regions required for viral multiplication, structural and assembly functions, as well as the target region for antiviral treatment. In addition, we identified a large majority of polymorphisms associated with GA > AA and TC > TT nucleotide replacements, suggesting the action of human APOBEC3 enzyme. A comparison between clinical isolates and cell culture-passaged samples failed to reveal any difference. Our results provide a first glance at the mutational landscape of early MPV-2022 (B.1) circulating strains in NYC.
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Affiliation(s)
- Luz H. Patiño
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Susana Guerra
- Department of Preventive Medicine, Public Health and Microbiology, Universidad Autónoma de Madrid, Madrid, Spain
| | - Marina Muñoz
- Facultad de Ciencias Naturales, Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Universidad del Rosario, Bogotá, Colombia
| | - Nicolas Luna
- Facultad de Ciencias Naturales, Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Universidad del Rosario, Bogotá, Colombia
| | - Keith Farrugia
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Adriana van de Guchte
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Zain Khalil
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Matthew M. Hernandez
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Radhika Banu
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Paras Shrestha
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Bernadette Liggayu
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Adolfo Firpo Betancourt
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - David Reich
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Carlos Cordon-Cardo
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Randy Albrecht
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Rebecca Pearl
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Viviana Simon
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VARPP), Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Aria Rooker
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VARPP), Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Emilia Mia Sordillo
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Harm van Bakel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Adolfo García-Sastre
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VARPP), Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Dusan Bogunovic
- Department of Microbiology, Centre for Inborn Errors of Immunity, Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gustavo Palacios
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VARPP), Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alberto Paniz Mondolfi
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Juan David Ramírez
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Facultad de Ciencias Naturales, Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Universidad del Rosario, Bogotá, Colombia
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2
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Gonzalez-Reiche AS, Alshammary H, Schaefer S, Patel G, Polanco J, Carreño JM, Amoako AA, Rooker A, Cognigni C, Floda D, van de Guchte A, Khalil Z, Farrugia K, Assad N, Zhang J, Alburquerque B, Sominsky LA, Gleason C, Srivastava K, Sebra R, Ramirez JD, Banu R, Shrestha P, Krammer F, Paniz-Mondolfi A, Sordillo EM, Simon V, van Bakel H. Sequential intrahost evolution and onward transmission of SARS-CoV-2 variants. Nat Commun 2023; 14:3235. [PMID: 37270625 PMCID: PMC10239218 DOI: 10.1038/s41467-023-38867-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [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: 10/07/2022] [Accepted: 05/16/2023] [Indexed: 06/05/2023] Open
Abstract
Persistent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections have been reported in immune-compromised individuals and people undergoing immune-modulatory treatments. Although intrahost evolution has been documented, direct evidence of subsequent transmission and continued stepwise adaptation is lacking. Here we describe sequential persistent SARS-CoV-2 infections in three individuals that led to the emergence, forward transmission, and continued evolution of a new Omicron sublineage, BA.1.23, over an eight-month period. The initially transmitted BA.1.23 variant encoded seven additional amino acid substitutions within the spike protein (E96D, R346T, L455W, K458M, A484V, H681R, A688V), and displayed substantial resistance to neutralization by sera from boosted and/or Omicron BA.1-infected study participants. Subsequent continued BA.1.23 replication resulted in additional substitutions in the spike protein (S254F, N448S, F456L, M458K, F981L, S982L) as well as in five other virus proteins. Our findings demonstrate not only that the Omicron BA.1 lineage can diverge further from its already exceptionally mutated genome but also that patients with persistent infections can transmit these viral variants. Thus, there is, an urgent need to implement strategies to prevent prolonged SARS-CoV-2 replication and to limit the spread of newly emerging, neutralization-resistant variants in vulnerable patients.
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Affiliation(s)
- Ana S Gonzalez-Reiche
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Hala Alshammary
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Sarah Schaefer
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Gopi Patel
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Jose Polanco
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Juan Manuel Carreño
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Angela A Amoako
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Aria Rooker
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Christian Cognigni
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Daniel Floda
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Adriana van de Guchte
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Zain Khalil
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Keith Farrugia
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Nima Assad
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Jian Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Bremy Alburquerque
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Levy A Sominsky
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Charles Gleason
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Komal Srivastava
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- The Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Juan David Ramirez
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Radhika Banu
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Paras Shrestha
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Alberto Paniz-Mondolfi
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Emilia Mia Sordillo
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Viviana Simon
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- The Global Health Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Harm van Bakel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
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3
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Paniz-Mondolfi A, Guerra S, Muñoz M, Luna N, Hernandez MM, Patino LH, Reidy J, Banu R, Shrestha P, Liggayu B, Umeaku A, Chen F, Cao L, Patel A, Hanna A, Li S, Look A, Pagani N, Albrecht R, Pearl R, Garcia-Sastre A, Bogunovic D, Palacios G, Bonnier L, Cera F, Lopez H, Calderon Y, Eiting E, Mullen K, Shin SJ, Lugo LA, Urbina AE, Starks C, Koo T, Uychiat P, Look A, van Bakel H, Gonzalez-Reiche A, Betancourt AF, Reich D, Cordon-Cardo C, Simon V, Sordillo EM, Ramírez JD. Evaluation and validation of an RT-PCR assay for specific detection of monkeypox virus (MPXV). J Med Virol 2023; 95:e28247. [PMID: 36271493 DOI: 10.1002/jmv.28247] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 10/11/2022] [Accepted: 10/19/2022] [Indexed: 01/11/2023]
Abstract
Monkeypox virus (MPXV) is a zoonotic orthopoxvirus within the Poxviridae family. MPXV is endemic to Central and West Africa. However, the world is currently witnessing an international outbreak with no clear epidemiological links to travel or animal exposure and with ever-increasing numbers of reported cases worldwide. Here, we evaluated and validated a new, sensitive, and specific real-time PCR-assay for MPXV diagnosis in humans and compare the performance of this novel assay against a Food & Drug Administration-cleared pan-Orthopox RT-PCR assay. We determined specificity, sensitivity, and analytic performance of the PKamp™ Monkeypox Virus RT-PCR assay targeting the viral F3L-gene. In addition, we further evaluated MPXV-PCR-positive specimens by viral culture, electron microscopy, and viral inactivation assays. The limit of detection was established at 7.2 genome copies/reaction, and MPXV was successfully identified in 20 clinical specimens with 100% correlation against the reference method with 100% sensitivity and specificity. Our results demonstrated the validity of this rapid, robust, and reliable RT-PCR assay for specific and accurate diagnosis of MPXV infection in human specimens collected both as dry swabs and in viral transport media. This assay has been approved by NYS Department of Health for clinical use.
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Affiliation(s)
- Alberto Paniz-Mondolfi
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Susana Guerra
- Department of Preventive Medicine, Public Health and Microbiology, Universidad Autónoma de Madrid, Madrid, Spain
| | - Marina Muñoz
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Nicolas Luna
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Matthew M Hernandez
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Luz H Patino
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Jason Reidy
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Radhika Banu
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Paras Shrestha
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Bernadette Liggayu
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Audrey Umeaku
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Feng Chen
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Liyong Cao
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Armi Patel
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ayman Hanna
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Sunny Li
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Andy Look
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Nina Pagani
- Department of Biotechnology Laboratory Sciences, Valencia College, Orlando, Florida, USA.,Infectious Diseases Research Branch, Venezuelan Science Incubator and The Zoonosis and Emerging Pathogens Regional Collaborative Network, Cabudare, Lara, Venezuela
| | - Randy Albrecht
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Rebecca Pearl
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Adolfo Garcia-Sastre
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Dusan Bogunovic
- Department of Microbiology, Center for Inborn Errors of Immunity, Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Gustavo Palacios
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Lucia Bonnier
- Department of Pathology and Laboratory Medicine, Mount Sinai Beth Israel, New York, New York, USA
| | - Freddy Cera
- Department of Pathology and Laboratory Medicine, Mount Sinai Beth Israel, New York, New York, USA
| | - Heidi Lopez
- Department of Pathology and Laboratory Medicine, Mount Sinai Beth Israel, New York, New York, USA
| | - Yvette Calderon
- Department of Emergency Medicine, Mount Sinai Beth Israel, New York, New York, USA
| | - Erick Eiting
- Department of Emergency Medicine, Mount Sinai Beth Israel, New York, New York, USA
| | - Karr Mullen
- Department of Emergency Medicine, Mount Sinai Beth Israel, New York, New York, USA
| | - Sangyoon Jason Shin
- Department of Medicine, Ambulatory Care, The Center for Transgender Medicine and Surgery (CTMS) of Mount Sinai, Mount Sinai Beth Israel, New York, New York, USA
| | - Luz Amarilis Lugo
- Division of Infectious Diseases, Institute for Advanced Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Antonio E Urbina
- Division of Infectious Diseases, Institute for Advanced Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Carlotta Starks
- Mount Sinai Institute for Advanced Medicine, Jack Martin Fund Clinic and Comprehensive Health Clinic, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Tonny Koo
- Laboratory of Medical Microbiology, Mount Sinai Hospital, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Patricia Uychiat
- Department of Pathology and Laboratory Medicine, Mount Sinai West, New York, New York, USA
| | - Avery Look
- Cornell University College of Agriculture and Life Sciences, Ithaca, New York, USA
| | - Harm van Bakel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ana Gonzalez-Reiche
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Adolfo Firpo Betancourt
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - David Reich
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Carlos Cordon-Cardo
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Viviana Simon
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Center for Vaccine Research and Pandemic Preparedness (C-VARPP), Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Emilia M Sordillo
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Juan David Ramírez
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
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4
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Hernandez MM, Banu R, Shrestha P, Gonzalez-Reiche AS, van de Guchte A, Farrugia K, Sebra R, Gitman MR, Nowak MD, Cordon-Cardo C, Simon V, van Bakel H, Sordillo EM, Luna N, Ramirez A, Castañeda SA, Patiño LH, Ballesteros N, Muñoz M, Ramírez JD, Paniz-Mondolfi AE. A Robust, Highly Multiplexed Mass Spectrometry Assay to Identify SARS-CoV-2 Variants. Microbiol Spectr 2022; 10:e0173622. [PMID: 36069609 PMCID: PMC9604185 DOI: 10.1128/spectrum.01736-22] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 08/12/2022] [Indexed: 12/31/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants are characterized by differences in transmissibility and response to therapeutics. Therefore, discriminating among them is vital for surveillance, infection prevention, and patient care. While whole-genome sequencing (WGS) is the "gold standard" for variant identification, molecular variant panels have become increasingly available. Most, however, are based on limited targets and have not undergone comprehensive evaluation. We assessed the diagnostic performance of the highly multiplexed Agena MassARRAY SARS-CoV-2 Variant Panel v3 to identify variants in a diverse set of 391 SARS-CoV-2 clinical RNA specimens collected across our health systems in New York City, USA and Bogotá, Colombia (September 2, 2020 to March 2, 2022). We demonstrated almost perfect levels of interrater agreement between this assay and WGS for 9 of 11 variant calls (κ ≥ 0.856) and 25 of 30 targets (κ ≥ 0.820) tested on the panel. The assay had a high diagnostic sensitivity (≥93.67%) for contemporary variants (e.g., Iota, Alpha, Delta, and Omicron [BA.1 sublineage]) and a high diagnostic specificity for all 11 variants (≥96.15%) and all 30 targets (≥94.34%) tested. Moreover, we highlighted distinct target patterns that could be utilized to identify variants not yet defined on the panel, including the Omicron BA.2 and other sublineages. These findings exemplified the power of highly multiplexed diagnostic panels to accurately call variants and the potential for target result signatures to elucidate new ones. IMPORTANCE The continued circulation of SARS-CoV-2 amid limited surveillance efforts and inconsistent vaccination of populations has resulted in the emergence of variants that uniquely impact public health systems. Thus, in conjunction with functional and clinical studies, continuous detection and identification are quintessential to informing diagnostic and public health measures. Furthermore, until WGS becomes more accessible in the clinical microbiology laboratory, the ideal assay for identifying variants must be robust, provide high resolution, and be adaptable to the evolving nature of viruses like SARS-CoV-2. Here, we highlighted the diagnostic capabilities of a highly multiplexed commercial assay to identify diverse SARS-CoV-2 lineages that circulated from September 2, 2020 to March 2, 2022 among patients seeking care in our health systems. This assay demonstrated variant-specific signatures of nucleotide/amino acid polymorphisms and underscored its utility for the detection of contemporary and emerging SARS-CoV-2 variants of concern.
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Affiliation(s)
- Matthew M. Hernandez
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Radhika Banu
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Paras Shrestha
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ana S. Gonzalez-Reiche
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Adriana van de Guchte
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Keith Farrugia
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Sema4, a Mount Sinai venture, Stamford, Connecticut, USA
| | - Mount Sinai PSP Study Group
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VARPP), Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Melissa R. Gitman
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Michael D. Nowak
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Carlos Cordon-Cardo
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Viviana Simon
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VARPP), Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- The Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Harm van Bakel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Emilia Mia Sordillo
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Nicolas Luna
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Angie Ramirez
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Sergio Andres Castañeda
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Luz Helena Patiño
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Nathalia Ballesteros
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Marina Muñoz
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Juan David Ramírez
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Alberto E. Paniz-Mondolfi
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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5
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Ramírez JD, Cao L, Cruz-Saavedra L, Hernandez C, Castañeda S, Muñoz M, Ballesteros N, Banu R, Shrestha P, Cordon-Cardo C, Sordillo EM, Paniz-Mondolfi A. Pan-stage real-time PCR for quantitation of Trypanosoma cruzi parasitic loads in blood samples. Int J Infect Dis 2022; 122:310-312. [PMID: 35690365 DOI: 10.1016/j.ijid.2022.06.006] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/19/2022] [Accepted: 06/04/2022] [Indexed: 11/24/2022] Open
Abstract
Chagas disease is a complex zoonosis caused by Trypanosoma cruzi. The diagnosis of this infection is complex and molecular tools are suggested to detect the parasite in blood samples. A long-standing question arises in Chagas disease molecular diagnostics and is related to the feasibility of using epimastigotes in standard curves to quantify parasitic loads. Herein, we conducted experiments running standard curves with all the known life stages of T. cruzi. Our results indicate that regardless of the life stage employed, there are no statistically significant differences when calculating parasitic loads in blood samples. Our results have practical implications from a laboratory perspective in terms of the usability of epimastigotes to build standard curves for T. cruzi pan-stage assessment. Future studies are needed to further improve T. cruzi molecular diagnostic methods and enhance their impact in clinical practice.
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Affiliation(s)
- Juan David Ramírez
- Molecular Microbiology Laboratory, Department of Pathology, Molecular and Cell-based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.; Centro de Investigaciones en Microbiología y Biotecnología-UR (CIM BIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia..
| | - Liyong Cao
- Molecular Microbiology Laboratory, Department of Pathology, Molecular and Cell-based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lissa Cruz-Saavedra
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIM BIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Carolina Hernandez
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIM BIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia.; Centro de Tecnología en Salud (CETESA), Innovaseq SAS, Bogotá, Colombia
| | - Sergio Castañeda
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIM BIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Marina Muñoz
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIM BIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Nathalia Ballesteros
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIM BIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Radhika Banu
- Molecular Microbiology Laboratory, Department of Pathology, Molecular and Cell-based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Paras Shrestha
- Molecular Microbiology Laboratory, Department of Pathology, Molecular and Cell-based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Carlos Cordon-Cardo
- Molecular Microbiology Laboratory, Department of Pathology, Molecular and Cell-based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Emilia Mia Sordillo
- Molecular Microbiology Laboratory, Department of Pathology, Molecular and Cell-based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alberto Paniz-Mondolfi
- Molecular Microbiology Laboratory, Department of Pathology, Molecular and Cell-based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.; Instituto de Investigaciones Biomédicas IDB/Incubadora Venezolana de la Ciencia, Barquisimeto, Venezuela
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6
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Hernandez MM, Banu R, Shrestha P, Gonzalez-Reiche AS, van de Guchte A, Farrugia K, Sebra R, Gitman MR, Nowak MD, Cordon-Cardo C, Simon V, van Bakel H, Sordillo EM, Luna N, Ramirez A, Castañeda SA, Patiño LH, Ballesteros N, Muñoz M, Ramírez JD, Paniz-Mondolfi AE. A robust, highly multiplexed mass spectrometry assay to identify SARS-CoV-2 variants. medRxiv 2022:2022.05.28.22275691. [PMID: 35665019 PMCID: PMC9164449 DOI: 10.1101/2022.05.28.22275691] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants are characterized by differences in transmissibility and response to therapeutics. Therefore, discriminating among them is vital for surveillance, infection prevention, and patient care. While whole viral genome sequencing (WGS) is the "gold standard" for variant identification, molecular variant panels have become increasingly available. Most, however, are based on limited targets and have not undergone comprehensive evaluation. We assessed the diagnostic performance of the highly multiplexed Agena MassARRAY ® SARS-CoV-2 Variant Panel v3 to identify variants in a diverse set of 391 SARS-CoV-2 clinical RNA specimens collected across our health systems in New York City, USA as well as in Bogotá, Colombia (September 2, 2020 - March 2, 2022). We demonstrate almost perfect levels of interrater agreement between this assay and WGS for 9 of 11 variant calls (κ ≥ 0.856) and 25 of 30 targets (κ ≥ 0.820) tested on the panel. The assay had a high diagnostic sensitivity (≥93.67%) for contemporary variants (e.g., Iota, Alpha, Delta, Omicron [BA.1 sublineage]) and a high diagnostic specificity for all 11 variants (≥96.15%) and all 30 targets (≥94.34%) tested. Moreover, we highlight distinct target patterns that can be utilized to identify variants not yet defined on the panel including the Omicron BA.2 and other sublineages. These findings exemplify the power of highly multiplexed diagnostic panels to accurately call variants and the potential for target result signatures to elucidate new ones. Importance The continued circulation of SARS-CoV-2 amidst limited surveillance efforts and inconsistent vaccination of populations has resulted in emergence of variants that uniquely impact public health systems. Thus, in conjunction with functional and clinical studies, continuous detection and identification are quintessential to inform diagnostic and public health measures. Furthermore, until WGS becomes more accessible in the clinical microbiology laboratory, the ideal assay for identifying variants must be robust, provide high resolution, and be adaptable to the evolving nature of viruses like SARS-CoV-2. Here, we highlight the diagnostic capabilities of a highly multiplexed commercial assay to identify diverse SARS-CoV-2 lineages that circulated at over September 2, 2020 - March 2, 2022 among patients seeking care at our health systems. This assay demonstrates variant-specific signatures of nucleotide/amino acid polymorphisms and underscores its utility for detection of contemporary and emerging SARS-CoV-2 variants of concern.
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Affiliation(s)
- Matthew M. Hernandez
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Radhika Banu
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Paras Shrestha
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ana S. Gonzalez-Reiche
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Adriana van de Guchte
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Keith Farrugia
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Sema4, a Mount Sinai venture, Stamford, CT 06902, USA
| | - Mount Sinai PSP Study Group
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VARPP), Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Melissa R. Gitman
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Michael D. Nowak
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Carlos Cordon-Cardo
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Viviana Simon
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VARPP), Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- The Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Harm van Bakel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Emilia Mia Sordillo
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Nicolas Luna
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Angie Ramirez
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Sergio Andres Castañeda
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Luz Helena Patiño
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Nathalia Ballesteros
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Marina Muñoz
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Juan David Ramírez
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Alberto E. Paniz-Mondolfi
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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7
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Hernandez MM, Banu R, Gonzalez-Reiche AS, Gray B, Shrestha P, Cao L, Chen F, Shi H, Hanna A, Ramírez JD, van de Guchte A, Sebra R, Gitman MR, Nowak MD, Cordon-Cardo C, Schutzbank TE, Simon V, van Bakel H, Sordillo EM, Paniz-Mondolfi AE. RT-PCR and Matrix-Assisted Laser Desorption-Ionization Time-of-Flight Mass Spectrometry Diagnostic Target Performance Reflects Circulating Severe Acute Respiratory Syndrome Coronavirus 2 Variant Diversity in New York City. J Mol Diagn 2022; 24:738-749. [PMID: 35525388 PMCID: PMC9067105 DOI: 10.1016/j.jmoldx.2022.04.003] [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: 12/03/2021] [Revised: 03/07/2022] [Accepted: 04/06/2022] [Indexed: 12/20/2022] Open
Abstract
As severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to circulate, multiple variants of concern have emerged. New variants pose challenges for diagnostic platforms because sequence diversity can alter primer/probe-binding sites (PBSs), causing false-negative results. The Agena MassARRAY SARS-CoV-2 Panel (Agena Bioscience) uses RT-PCR and mass spectrometry to detect five multiplex targets across N and ORF1ab genes. Herein, we use a data set of 256 SARS-CoV-2-positive specimens collected between April 11, 2021, and August 28, 2021, to evaluate target performance with paired sequencing data. During this time frame, two targets in the N gene (N2 and N3) were subject to the greatest sequence diversity. In specimens with N3 dropout, 69% harbored the Alpha-specific A28095U polymorphism that introduces a 3'-mismatch to the N3 forward PBS and increases risk of target dropout relative to specimens with 28095A (relative risk, 20.02; 95% CI, 11.36 to 35.72; P < 0.0001). Furthermore, among specimens with N2 dropout, 90% harbored the Delta-specific G28916U polymorphism that creates a 3'-mismatch to the N2 probe PBS and increases target dropout risk (relative risk, 11.92; 95% CI, 8.17 to 14.06; P < 0.0001). These findings highlight the robust capability of Agena MassARRAY SARS-CoV-2 Panel target results to reveal circulating virus diversity, and they underscore the power of multitarget design to capture variants of concern.
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Affiliation(s)
- Matthew M Hernandez
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York.
| | - Radhika Banu
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Ana S Gonzalez-Reiche
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Brandon Gray
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Paras Shrestha
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Liyong Cao
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Feng Chen
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Huanzhi Shi
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Ayman Hanna
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Juan David Ramírez
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York; Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Adriana van de Guchte
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York; Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Sema4, a Mount Sinai venture, Stamford, Connecticut
| | - Melissa R Gitman
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Michael D Nowak
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Carlos Cordon-Cardo
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | | | - Viviana Simon
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York; Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York; The Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Harm van Bakel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Emilia Mia Sordillo
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Alberto E Paniz-Mondolfi
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York.
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8
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Hernandez MM, Riollano‐Cruz M, Boyle MC, Banu R, Shrestha P, Gray B, Cao L, Chen F, Shi H, Paniz‐Perez DE, Paniz‐Perez PA, Rishi AL, Dubinsky J, Dubinsky D, Dubinsky O, Baine S, Baine L, Arinsburg S, Baine I, Ramirez JD, Cordon‐Cardo C, Sordillo EM, Paniz‐Mondolfi AE. Back Cover Image, Volume 94, Number 6, June 2022. J Med Virol 2022. [DOI: 10.1002/jmv.27787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Matthew M. Hernandez
- Department of Pathology, Molecular, and Cell‐Based Medicine Icahn School of Medicine at Mount Sinai New York New York USA
| | - Mariawy Riollano‐Cruz
- Department of Medicine, Division of Infectious Diseases Icahn School of Medicine at Mount Sinai New York New York USA
| | - Mary C. Boyle
- Department of Medicine, Division of Infectious Diseases Icahn School of Medicine at Mount Sinai New York New York USA
| | - Radhika Banu
- Department of Pathology, Molecular, and Cell‐Based Medicine Icahn School of Medicine at Mount Sinai New York New York USA
| | - Paras Shrestha
- Department of Pathology, Molecular, and Cell‐Based Medicine Icahn School of Medicine at Mount Sinai New York New York USA
| | - Brandon Gray
- Department of Pathology, Molecular, and Cell‐Based Medicine Icahn School of Medicine at Mount Sinai New York New York USA
| | - Liyong Cao
- Department of Pathology, Molecular, and Cell‐Based Medicine Icahn School of Medicine at Mount Sinai New York New York USA
| | - Feng Chen
- Department of Pathology, Molecular, and Cell‐Based Medicine Icahn School of Medicine at Mount Sinai New York New York USA
| | - Huanzhi Shi
- Department of Pathology, Molecular, and Cell‐Based Medicine Icahn School of Medicine at Mount Sinai New York New York USA
| | - Daniel E. Paniz‐Perez
- Department of Pathology, Molecular and Cell‐Based Medicine Kids Laboratory and Science Hub, Icahn School of Medicine at Mount Sinai New York New York USA
| | - Paul A. Paniz‐Perez
- Department of Pathology, Molecular and Cell‐Based Medicine Kids Laboratory and Science Hub, Icahn School of Medicine at Mount Sinai New York New York USA
| | - Aryan L. Rishi
- Department of Pathology, Molecular and Cell‐Based Medicine Kids Laboratory and Science Hub, Icahn School of Medicine at Mount Sinai New York New York USA
| | - Jacob Dubinsky
- Department of Pathology, Molecular and Cell‐Based Medicine Kids Laboratory and Science Hub, Icahn School of Medicine at Mount Sinai New York New York USA
| | - Dylan Dubinsky
- Department of Pathology, Molecular and Cell‐Based Medicine Kids Laboratory and Science Hub, Icahn School of Medicine at Mount Sinai New York New York USA
| | - Owen Dubinsky
- Department of Pathology, Molecular and Cell‐Based Medicine Kids Laboratory and Science Hub, Icahn School of Medicine at Mount Sinai New York New York USA
| | - Sophie Baine
- Department of Pathology, Molecular and Cell‐Based Medicine Kids Laboratory and Science Hub, Icahn School of Medicine at Mount Sinai New York New York USA
| | - Lily Baine
- Department of Pathology, Molecular and Cell‐Based Medicine Kids Laboratory and Science Hub, Icahn School of Medicine at Mount Sinai New York New York USA
| | - Suzanne Arinsburg
- Department of Pathology, Molecular, and Cell‐Based Medicine Icahn School of Medicine at Mount Sinai New York New York USA
| | - Ian Baine
- Department of Pathology, Molecular, and Cell‐Based Medicine Icahn School of Medicine at Mount Sinai New York New York USA
| | - Juan David Ramirez
- Department of Pathology, Molecular, and Cell‐Based Medicine Icahn School of Medicine at Mount Sinai New York New York USA
| | - Carlos Cordon‐Cardo
- Department of Pathology, Molecular, and Cell‐Based Medicine Icahn School of Medicine at Mount Sinai New York New York USA
| | - Emilia Mia Sordillo
- Department of Pathology, Molecular, and Cell‐Based Medicine Icahn School of Medicine at Mount Sinai New York New York USA
| | - Alberto E. Paniz‐Mondolfi
- Department of Pathology, Molecular, and Cell‐Based Medicine Icahn School of Medicine at Mount Sinai New York New York USA
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9
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Ramírez JD, Castañeda S, Ballesteros N, Muñoz M, Hernández M, Banu R, Shrestha P, Chen F, Shi H, van Bakel H, Simon V, Cordon-Cardo C, Sordillo EM, Paniz-Mondolfi AE. Hotspots for SARS-CoV-2 Omicron Variant Spread: Lessons from New York City. J Med Virol 2022; 94:2911-2914. [PMID: 35243662 PMCID: PMC9088473 DOI: 10.1002/jmv.27691] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 02/24/2022] [Accepted: 03/02/2022] [Indexed: 11/10/2022]
Abstract
The coronavirus disease‐2019 (COVID‐19) pandemic is still challenging public health systems worldwide, particularly with the emergence of novel SARS‐CoV‐2 variants with mutations that increase their transmissibility and immune escape. This is the case of the variant of concern Omicron that rapidly spread globally. Here, using epidemiological and genomic data we compared the situations in South Africa as the epicenter of emergence, United Kingdom, and with particular interest New York City. This rapid global dispersal from the place of first report reemphasizes the high transmissibility of Omicron, which needed only two weeks to become dominant in the United Kingdom and New York City. Our analyses suggest that as SARS‐CoV‐2 continues to evolve, global authorities must prioritize equity in vaccine access and continued genomic surveillance. Future studies are still needed to fully unveil the biological properties of Omicron, but what is certain is that vaccination, large‐scale testing, and infection prevention efforts are the greatest arsenal against the COVID‐19 pandemic.
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Affiliation(s)
- Juan David Ramírez
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Sergio Castañeda
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del, Rosario, Bogotá, Colombia
| | - Nathalia Ballesteros
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del, Rosario, Bogotá, Colombia
| | - Marina Muñoz
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del, Rosario, Bogotá, Colombia
| | - Matthew Hernández
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Radhika Banu
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Paras Shrestha
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Feng Chen
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
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- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Harm van Bakel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Viviana Simon
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Carlos Cordon-Cardo
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Emilia Mia Sordillo
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Alberto E Paniz-Mondolfi
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
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10
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Hernandez MM, Riollano-Cruz M, Boyle MC, Banu R, Shrestha P, Gray B, Cao L, Chen F, Shi H, Paniz-Perez DE, Paniz-Perez PA, Rishi AL, Dubinsky J, Dubinsky D, Dubinsky O, Baine S, Baine L, Arinsburg S, Baine I, Ramirez JD, Cordon-Cardo C, Sordillo EM, Paniz-Mondolfi AE. Food for thought: Eating before saliva collection and interference with SARS-CoV-2 detection. J Med Virol 2022; 94:2471-2478. [PMID: 35171508 PMCID: PMC9088375 DOI: 10.1002/jmv.27660] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 02/08/2022] [Accepted: 02/09/2022] [Indexed: 11/20/2022]
Abstract
Saliva is a promising specimen for the detection of viruses that cause upper respiratory infections including severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) due to its cost‐effectiveness and noninvasive collection. However, together with intrinsic enzymes and oral microbiota, children's unique dietary habits may introduce substances that interfere with diagnostic testing. To determine whether children's dietary choices impact SARS‐CoV‐2 molecular detection in saliva, we performed a diagnostic study that simulates testing of real‐life specimens provided from healthy children (n = 5) who self‐collected saliva at home before and at 0, 20, and 60 min after eating 20 foods they selected. Each of 72 specimens was split into two volumes and spiked with SARS‐CoV‐2‐negative or SARS‐CoV‐2‐positive clinical standards before side‐by‐side testing by reverse‐transcription polymerase chain reaction matrix‐assisted laser desorption ionization time‐of‐flight (RT‐PCR/MALDI‐TOF) assay. Detection of internal extraction control and SARS‐CoV‐2 nucleic acids was reduced in replicates of saliva collected at 0 min after eating 11 of 20 foods. Interference resolved at 20 and 60 min after eating all foods except hot dogs in one participant. This represented a significant improvement in the detection of nucleic acids compared to saliva collected at 0 min after eating (p = 0.0005). We demonstrate successful detection of viral nucleic acids in saliva self‐collected by children before and after eating a variety of foods. Fasting is not required before saliva collection for SARS‐CoV‐2 testing by RT‐PCR/MALDI‐TOF, but waiting for 20 min after eating is sufficient for accurate testing. These findings should be considered for SARS‐CoV‐2 testing and broader viral diagnostics in saliva specimens. Inconsistent collection and dietary habits impact viral nucleic acid detection in saliva. Various foods interfere with severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) detection in saliva self‐collected by children. Waiting 20 min after eating is sufficient for accurate SARS‐CoV‐2 testing in saliva.
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Affiliation(s)
- Matthew M Hernandez
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Mariawy Riollano-Cruz
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Mary C Boyle
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Radhika Banu
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Paras Shrestha
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Brandon Gray
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Liyong Cao
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Feng Chen
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Huanzhi Shi
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Daniel E Paniz-Perez
- Department of Pathology, Molecular and Cell-Based Medicine, Kids Laboratory and Science Hub, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Paul A Paniz-Perez
- Department of Pathology, Molecular and Cell-Based Medicine, Kids Laboratory and Science Hub, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Aryan L Rishi
- Department of Pathology, Molecular and Cell-Based Medicine, Kids Laboratory and Science Hub, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Jacob Dubinsky
- Department of Pathology, Molecular and Cell-Based Medicine, Kids Laboratory and Science Hub, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Dylan Dubinsky
- Department of Pathology, Molecular and Cell-Based Medicine, Kids Laboratory and Science Hub, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Owen Dubinsky
- Department of Pathology, Molecular and Cell-Based Medicine, Kids Laboratory and Science Hub, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Sophie Baine
- Department of Pathology, Molecular and Cell-Based Medicine, Kids Laboratory and Science Hub, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Lily Baine
- Department of Pathology, Molecular and Cell-Based Medicine, Kids Laboratory and Science Hub, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Suzanne Arinsburg
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Ian Baine
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Juan David Ramirez
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Carlos Cordon-Cardo
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Emilia Mia Sordillo
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Alberto E Paniz-Mondolfi
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
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11
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Hernandez MM, Banu R, Gonzalez-Reiche AS, van de Guchte A, Khan Z, Shrestha P, Cao L, Chen F, Shi H, Hanna A, Alshammary H, Fabre S, Amoako A, Obla A, Alburquerque B, Patiño LH, Ramírez JD, Sebra R, Gitman MR, Nowak MD, Cordon-Cardo C, Schutzbank TE, Simon V, van Bakel H, Sordillo EM, Paniz-Mondolfi AE. Robust clinical detection of SARS-CoV-2 variants by RT-PCR/MALDI-TOF multitarget approach. J Med Virol 2021; 94:1606-1616. [PMID: 34877674 DOI: 10.1002/jmv.27510] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 11/30/2021] [Accepted: 12/03/2021] [Indexed: 12/24/2022]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has sparked the rapid development of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) diagnostics. However, emerging variants pose the risk for target dropout and false-negative results secondary to primer/probe binding site (PBS) mismatches. The Agena MassARRAY® SARS-CoV-2 Panel combines reverse-transcription polymerase chain reaction and matrix-assisted laser desorption/ionization time-of-flight mass-spectrometry to probe for five targets across N and ORF1ab genes, which provides a robust platform to accommodate PBS mismatches in divergent viruses. Herein, we utilize a deidentified data set of 1262 SARS-CoV-2-positive specimens from Mount Sinai Health System (New York City) from December 2020 to April 2021 to evaluate target results and corresponding sequencing data. Overall, the level of PBS mismatches was greater in specimens with target dropout. Of specimens with N3 target dropout, 57% harbored an A28095T substitution that is highly specific for the Alpha (B.1.1.7) variant of concern. These data highlight the benefit of redundancy in target design and the potential for target performance to illuminate the dynamics of circulating SARS-CoV-2 variants.
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Affiliation(s)
- Matthew M Hernandez
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Radhika Banu
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ana S Gonzalez-Reiche
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Adriana van de Guchte
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Zenab Khan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Paras Shrestha
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Liyong Cao
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Feng Chen
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Huanzhi Shi
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ayman Hanna
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Hala Alshammary
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Shelcie Fabre
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Angela Amoako
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ajay Obla
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Bremy Alburquerque
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Luz Helena Patiño
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Juan David Ramírez
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Sema4, a Mount Sinai Venture, Stamford, Connecticut, USA
| | - Melissa R Gitman
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Michael D Nowak
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Carlos Cordon-Cardo
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ted E Schutzbank
- Senior Scientific Affairs Manager, Infectious Diseases, Agena Bioscience, San Diego, California, USA
| | - Viviana Simon
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,The Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Harm van Bakel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Emilia Mia Sordillo
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Alberto E Paniz-Mondolfi
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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12
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Hernandez MM, Banu R, Shrestha P, Patel A, Chen F, Cao L, Fabre S, Tan J, Lopez H, Chiu N. Comparison of real-time RT-PCR and RT-PCR/MALDI-TOF methods for SARS-CoV-2 detection in saliva. Am J Clin Pathol 2021. [DOI: 10.1093/ajcp/aqab189.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Background
The coronavirus disease 2019 pandemic has accelerated the need for rapid validation and implementation of assays for detection of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in diagnostic specimens. Multiple molecular methods have received emergency use authorization by the U.S. Food and Drug Administration for detection of SARS-CoV-2 in upper respiratory specimens, with testing of nasopharyngeal (NP) specimens serving as the foundation for these assays. However, supply chain constraints and the need for improved ease and safety of collection have prompted consideration of other specimen types as alternatives to NP specimens for detection of SARS-CoV-2. Here, we compared two methods for SARS-CoV-2 detection in saliva: the Roche cobas® 6800 SARS-CoV-2 real-time RT-PCR Test (“Roche”), which tests for viral ORF1ab (target 1, T1) and envelope E genes (target 2, T2); and the Agena Biosciences MassARRAY® SARS-CoV-2 Panel/MassARRAY® System (“Agena”), which tests for targets in the ORF1ab gene (ORF1, Orf1ab) and nucleocapsid N gene (N1, N2, N3).
Methods
Sixty saliva specimens collected within 48 hours of SARS-CoV-2 detection in an upper respiratory (anterior nares or NP) specimen from the same individual were tested in both the Roche and Agena platforms. Each system was evaluated for overall detection results and agreement with results of matched upper respiratory specimens. In addition, we determined the limit of detection (LoD) for each system and its component targets using an in-house SARS-CoV-2 standard generated from pooled positive saliva specimens quantitated against a commercially available standard (ZeptoMetrix NATSARS(COV2)-ERC).
Results
Both platforms demonstrated a similarly high sensitivity (97%) and specificity (100%) when compared to matched patient upper respiratory specimens and had high agreement with one another (Cohen’s κ = 0.9321, p = 2.6x10-13). Overall, the LoD (copies/mL) for the Roche assay was four times lower than that of Agena for saliva specimens (390.6 v. 1562.5). Furthermore, we determined that the LoD differed among the target components of each assay. The experimental LoD was comparable across Roche targets, but probit analyses indicate T2 has greater sensitivity (LoD: 228.6), Of the five Agena targets, the N2 target had the lowest LoD (1562.5).
Conclusions
In sum, we demonstrate that saliva is an acceptable specimen for testing in both the Roche cobas® 6800 SARS-CoV-2 real-time RT-PCR Test and the Agena Biosciences MassARRAY® SARS-CoV-2 Panel/MassARRAY® System, and both provide sensitive and specific detection of SARS-CoV-2 in saliva specimens. Although there was a high level of agreement between platforms, the LoD was lower for the Roche compared to the Agena assay with T2 and N2 being the most sensitive targets on each platform, respectively. The addition of saliva as an acceptable specimen and understanding the sensitivity for testing on these platforms can further inform public health measures for screening and detection to combat the pandemic.
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13
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Hernandez MM, Banu R, Shrestha P, Patel A, Chen F, Cao L, Fabre S, Tan J, Lopez H, Chiu N, Shifrin B, Zapolskaya I, Flores V, Lee PY, Castañeda S, Ramírez JD, Jhang J, Osorio G, Gitman MR, Nowak MD, Reich DL, Cordon-Cardo C, Sordillo EM, Paniz-Mondolfi AE. RT-PCR/MALDI-TOF mass spectrometry-based detection of SARS-CoV-2 in saliva specimens. J Med Virol 2021; 93:5481-5486. [PMID: 33963565 PMCID: PMC8242556 DOI: 10.1002/jmv.27069] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/06/2021] [Accepted: 05/07/2021] [Indexed: 12/24/2022]
Abstract
As severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infections continue, there is a substantial need for cost-effective and large-scale testing that utilizes specimens that can be readily collected from both symptomatic and asymptomatic individuals in various community settings. Although multiple diagnostic methods utilize nasopharyngeal specimens, saliva specimens represent an attractive alternative as they can rapidly and safely be collected from different populations. While saliva has been described as an acceptable clinical matrix for the detection of SARS-CoV-2, evaluations of analytic performance across platforms for this specimen type are limited. Here, we used a novel sensitive RT-PCR/MALDI-TOF mass spectrometry-based assay (Agena MassARRAY®) to detect SARS-CoV-2 in saliva specimens. The platform demonstrated high diagnostic sensitivity and specificity when compared to matched patient upper respiratory specimens. We also evaluated the analytical sensitivity of the platform and determined the limit of detection of the assay to be 1562.5 copies/ml. Furthermore, across the five individual target components of this assay, there was a range in analytic sensitivities for each target with the N2 target being the most sensitive. Overall, this system also demonstrated comparable performance when compared to the detection of SARS-CoV-2 RNA in saliva by the cobas® 6800/8800 SARS-CoV-2 real-time RT-PCR Test (Roche). Together, we demonstrate that saliva represents an appropriate matrix for SARS-CoV-2 detection on the novel Agena system as well as on a conventional real-time RT-PCR assay. We conclude that the MassARRAY® system is a sensitive and reliable platform for SARS-CoV-2 detection in saliva, offering scalable throughput in a large variety of clinical laboratory settings.
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Affiliation(s)
- Matthew M Hernandez
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Radhika Banu
- Clinical Microbiology Laboratory, Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Paras Shrestha
- Clinical Microbiology Laboratory, Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Armi Patel
- Clinical Microbiology Laboratory, Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Feng Chen
- Clinical Microbiology Laboratory, Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Liyong Cao
- Clinical Microbiology Laboratory, Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Shelcie Fabre
- Clinical Microbiology Laboratory, Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Jessica Tan
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Heidi Lopez
- Clinical Microbiology Laboratory, Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Numthip Chiu
- Clinical Microbiology Laboratory, Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Biana Shifrin
- Clinical Microbiology Laboratory, Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Inessa Zapolskaya
- Clinical Microbiology Laboratory, Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Vanessa Flores
- Clinical Microbiology Laboratory, Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Pui Yiu Lee
- Clinical Microbiology Laboratory, Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Sergio Castañeda
- Departamento de Biología, Facultad de Ciencias Naturales, Grupo de Investigaciones Microbiológicas-UR (GIMUR), Universidad del Rosario, Bogotá, Colombia
| | - Juan David Ramírez
- Departamento de Biología, Facultad de Ciencias Naturales, Grupo de Investigaciones Microbiológicas-UR (GIMUR), Universidad del Rosario, Bogotá, Colombia
| | - Jeffrey Jhang
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Giuliana Osorio
- Clinical Microbiology Laboratory, Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Melissa R Gitman
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Clinical Microbiology Laboratory, Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Michael D Nowak
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Clinical Microbiology Laboratory, Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - David L Reich
- Department of Anesthesiology, Perioperative and Pain Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Carlos Cordon-Cardo
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Emilia Mia Sordillo
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Clinical Microbiology Laboratory, Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Alberto E Paniz-Mondolfi
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Clinical Microbiology Laboratory, Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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Das A, Dutta S, Chattopadhyay S, Chhaule S, Mitra T, Banu R, Mandal P, Chandra M. Pain relief after ambulatory hand surgery: A comparison between dexmedetomidine and clonidine as adjuvant in axillary brachial plexus block: A prospective, double-blinded, randomized controlled study. Saudi J Anaesth 2016; 10:6-12. [PMID: 26955303 PMCID: PMC4760045 DOI: 10.4103/1658-354x.169443] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
BACKGROUND For ages various adjuvants have been tried to prolong axillary brachial plexus block. We compared the effect of adding dexmedetomidine versus clonidine to ropivacaine for axillary brachial plexus blockade. The primary endpoints were the onset and duration of sensory and motor block and duration of analgesia. MATERIALS AND METHODS A total of 90 patients (20-40 years) posted for ambulatory elective hand surgery under axillary brachial plexus block were divided into two equal groups (groups ropivacaine dexmedetomidine [RD] and ropivacaine clonidine [RC]) in a randomized, double-blind fashion. In group RD (n = 45) 30 ml 0.5% ropivacaine + 100 μg of dexmedetomidine and group RC (n = 45) 30 ml 0.5% ropivacaine + 75 μg clonidine were administered in axillary plexus block. Sensory and motor block onset times and block durations, time to first analgesic use, total analgesic need, postoperative visual analog scale (VAS), hemodynamics and side-effects were recorded for each patient. RESULTS Though with similar demographic profile in both groups, sensory and motor block in group RD (P < 0.05) was earlier than group RC. Sensory and motor block duration and time to first analgesic use were significantly longer and the total need for rescue analgesics was lower in group RD (P < 0.05) than group RC. Postoperative VAS value at 18 h were significantly lower in group RD (P < 0.05). Intraoperative hemodynamics were insignificantly lower in group RD (P < 0.05) without any appreciable side-effects. CONCLUSION It can be concluded that adding dexmedetomidine to axillary plexus block increases the sensory and motor block duration and time to first analgesic use, and decreases total analgesic use with no side-effects.
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Affiliation(s)
- A Das
- Department of Anaesthesiology, College of Medicine and Sagore Dutta Hospital, Kolkata, West Bengal, India
| | - S Dutta
- Department of Orthopedics, R. G. Kar Medical College, Kolkata, West Bengal, India
| | - S Chattopadhyay
- Department of Anaesthesiology, College of Medicine and Sagore Dutta Hospital, Kolkata, West Bengal, India
| | - S Chhaule
- Department of Anaesthesiology, College of Medicine and Sagore Dutta Hospital, Kolkata, West Bengal, India
| | - T Mitra
- Department of Anaesthesiology, Murshidabad Medical College, Berhampore, West Bengal, India
| | - R Banu
- Department of G and O, Berhampore, West Bengal, India
| | - P Mandal
- Department of G and O, College of Medicine and Sagore Dutta Hospital, Kolkata, West Bengal, India
| | - M Chandra
- Department of Orthopedics, R. G. Kar Medical College, Kolkata, West Bengal, India
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15
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Ansa ED, Awuah E, Andoh A, Banu R, Dorgbetor WH, Lubberding HJ, Gijzen HJ. A Review of the Mechanisms of Faecal Coliform Removal from Algal and Duckweed Waste Stabilization Pond Systems. ACTA ACUST UNITED AC 2015. [DOI: 10.3844/ajessp.2015.28.34] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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