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Mancon A, Raccagni AR, Gagliardi G, Moschese D, Rizzo A, Giacomelli A, Cutrera M, Salari F, Bracchitta F, Antinori S, Gori A, Rizzardini G, Castagna A, Gismondo MR, Nozza S, Mileto D. Evaluation of analytical performance of the STANDARD TM M10 MPX/OPX assay for the simultaneous DNA detection and clade attribution of Monkeypox virus. Emerg Microbes Infect 2024; 13:2337666. [PMID: 38572513 PMCID: PMC11018020 DOI: 10.1080/22221751.2024.2337666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Accepted: 03/27/2024] [Indexed: 04/05/2024]
Abstract
Monkeypox virus (MPXV) infection confirmation needs reliable polymerase chain reaction (PCR) assays; in addition, viral clade attribution is a key factor in containment measures, considering a more severe syndrome in clade I and the possibility of simultaneous circulation. This study evaluates the performance of all-in-one STANDARD M10 MPX/OPX (SD BIOSENSOR, South Korea - M10). Frozen samples from 205 subjects were selected and stratified according to routine test results (RealStar® Orthopoxvirus PCR Kit 1.0, Altona DIAGNOTICS, Germany - RS; RS-1): in detail, 100 negative skin lesions (SL) and 200 positive samples at the variable stage of infection were analysed. Positive samples were retested with RS (RS-2). Positive and Negative Percent Agreements (PPA, NPA) were calculated. The median (IQR) Ct values of RS and M10 (OPXV target) assays were highly similar. The PPA of M10 compared to RS-1 was 89.5% considering system interpretation, and 96.0% when the operator classified results as positive if any target was detected; NPA was 100%. Comparing the RS-2 run and M10, an overall concordance of 95.3% between assays was found; however, considering operator interpretation, M10 returned more positive results than RS-2. The occurrence of False-Negative results was likely associated with the influence of thawing on low viral concentration; no False-Positive tests were observed. All samples collected at the time of Mpox diagnosis were positive and M10 correctly attributed the clade (West-Africa/II). The M10 MPX/OPX assay demonstrated high reliability in confirming MPXV infection and clade attribution.
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Affiliation(s)
- Alessandro Mancon
- Laboratory of Clincal Microbiology, Virology and Bioemergencies, ASST Fatebenefratelli Sacco, Milan, Italy
| | | | | | - Davide Moschese
- Department of Infectious Diseases, ASST Fatebenefratelli Sacco, Milan, Italy
| | - Alberto Rizzo
- Laboratory of Clincal Microbiology, Virology and Bioemergencies, ASST Fatebenefratelli Sacco, Milan, Italy
| | - Andrea Giacomelli
- Department of Infectious Diseases, ASST Fatebenefratelli Sacco, Milan, Italy
| | | | | | | | - Spinello Antinori
- University of Milan, Milan, Italy
- Department of Infectious Diseases, ASST Fatebenefratelli Sacco, Milan, Italy
| | - Andrea Gori
- University of Milan, Milan, Italy
- Department of Infectious Diseases, ASST Fatebenefratelli Sacco, Milan, Italy
| | - Giuliano Rizzardini
- Department of Infectious Diseases, ASST Fatebenefratelli Sacco, Milan, Italy
| | - Antonella Castagna
- Vita-Salute San Raffaele University, Milan, Italy
- Department of Infectious Diseases, San Raffaele Hospital, Milan, Italy
| | - Maria Rita Gismondo
- Laboratory of Clincal Microbiology, Virology and Bioemergencies, ASST Fatebenefratelli Sacco, Milan, Italy
- University of Milan, Milan, Italy
| | - Silvia Nozza
- Vita-Salute San Raffaele University, Milan, Italy
| | - Davide Mileto
- Laboratory of Clincal Microbiology, Virology and Bioemergencies, ASST Fatebenefratelli Sacco, Milan, Italy
- CNR-SCITEC, Istituto di Scienze e Tecnologie Chimiche “Giulio Natta”, via C. Golgi 19, 20133Milan, Italy
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Patiño LH, Castañeda S, Camargo M, Cao LY, Liggayu B, Paniz-Mondolfi A, Ramírez JD. Validation of real-time PCR assays for detecting Plasmodium and Babesia DNA species in blood samples. Acta Trop 2024; 258:107350. [PMID: 39134111 DOI: 10.1016/j.actatropica.2024.107350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Revised: 07/11/2024] [Accepted: 08/02/2024] [Indexed: 08/17/2024]
Abstract
Malaria and babesiosis are global health threats affecting humans, wildlife, and domestic animals, particularly in Africa, the Americas, and Europe. Malaria can lead to severe outcomes, while babesiosis usually resembles a mild illness but can be severe and fatal in individuals with weakened immune systems. Swift, accurate detection of these parasites is crucial for treatment and control. We evaluated a real-time PCR assay for diagnosing five Plasmodium and three Babesia species from blood samples, assessing its sensitivity, specificity, and analytical performance by analyzing 46 malaria-positive and 32 Babesia spp-positive samples diagnosed through microscopy. The limit of detection for Plasmodium species ranged from 30 to 0.0003 copies/µL. For mixed infections, it was 0.3 copies/µL for P. falciparum/P. vivax and 3 copies/µL for P. malariae/P. knowlesi. Babesia species had a detection limit of 0.2 copies/µL. No cross-reactivity was observed among 64 DNA samples from various microorganisms. The assay showed good sensitivity, detecting Plasmodium and Babesia species with 100 % accuracy overall, except for P. falciparum (97.7 %) and B. microti (12.5 %). The low sensitivity of detecting B. microti was attributed to limitations in microscopy for species identification. This technique heavily relies on the proficiency of the examiner, as species within the genus cannot be distinguished under a microscope. Additionally, Babesia can be confused with the early trophozoite stage (ring forms) of Plasmodium parasites. The findings support multiplex qPCR's diagnostic superiority over the gold standard, despite higher costs. It offers enhanced sensitivity, specificity, and detects mixed infections, crucial for effective monitoring and diagnosis of malaria and babesiosis in endemic regions with significant public health challenges.
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Affiliation(s)
- Luz Helena Patiño
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia; Molecular Microbiology Laboratory, 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
| | - Milena Camargo
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Li Yong Cao
- Molecular Microbiology Laboratory, Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Bernadette Liggayu
- Molecular Microbiology Laboratory, Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, 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 10029, USA
| | - Juan David Ramírez
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia; Molecular Microbiology Laboratory, Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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3
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Peng Y, Hu R, Xue S, He Y, Tian L, Pang Z, He Y, Dong Y, Shi Y, Wang S, Hong B, Liu K, Wang R, Song L, Fan H, Li M, Tong Y. Rapid and highly sensitive colorimetric LAMP assay and integrated device for visual detection of monkeypox virus. Anal Chim Acta 2024; 1311:342720. [PMID: 38816155 DOI: 10.1016/j.aca.2024.342720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 04/30/2024] [Accepted: 05/12/2024] [Indexed: 06/01/2024]
Abstract
BACKGROUND The monkeypox virus (MPXV) is a linear double-stranded DNA virus with a large genome that causes tens of thousands of infections and hundreds of deaths in at least 40 countries and regions worldwide. Therefore, timely and accurate diagnostic testing could be an important measure to prevent the ongoing spread of MPXV and widespread epidemics. RESULTS Here, we designed multiple sets of primers for the target region of MPXV for loop-mediated isothermal amplification (LAMP) detection and identified the optimal primer set. Then, the specificity in fluorescent LAMP detection was verified using the plasmids containing the target gene, pseudovirus and other DNA/RNA viruses. We also evaluated the sensitivity of the colorimetric LAMP detection system using the plasmid and pseudovirus samples, respectively. Besides, we used monkeypox pseudovirus to simulate real samples for detection. Subsequent to the establishment and introduction of a magnetic beads (MBs)-based nucleic acid extraction technique, an integrated device was developed, characterized by rapidity, high sensitivity, and remarkable specificity. This portable system demonstrated a visual detection limit of 137 copies/mL, achieving sample-to-answer detection within 1 h. SIGNIFICANCE The device has the advantages of integration, simplicity, miniaturization, and visualization, which help promote the realization of accurate, rapid, portable, and low-cost testing. Meanwhile, this platform could facilitate efficient, cost-effective and easy-operable point-of-care testing (POCT) in diverse resource-limited settings in addition to the laboratory.
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Affiliation(s)
- Yadan Peng
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Ruolan Hu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Shuang Xue
- College of Mechanical and Electrical Engineering, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Yugan He
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Lili Tian
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Zehan Pang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Yile He
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Yuqi Dong
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Yinghan Shi
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Shuqi Wang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Bixia Hong
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Ke Liu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Ruixue Wang
- College of Mechanical and Electrical Engineering, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Lihua Song
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Huahao Fan
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China; School of Life Sciences, Tianjin University, Tianjin, 300072, China.
| | - Mengzhe Li
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China.
| | - Yigang Tong
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China; Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, China.
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Lee JC, Ryu SM, Lee Y, Jang H, Song J, Kang T, Lee KH, Park S. CRISPR/Cas12a antifouling nanocomposite electrochemical biosensors enable amplification-free detection of Monkeypox virus in complex biological fluids. NANOSCALE 2024; 16:11318-11326. [PMID: 38804270 DOI: 10.1039/d4nr01618a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
The escalating global threat of infectious diseases, including monkeypox virus (MPXV), necessitates advancements in point-of-care diagnostics, moving beyond the constraints of conventional methods tethered to centralized laboratories. Here, we introduce multiple CRISPR RNA (crRNA)-based biosensors that can directly detect MPXV within 35 minutes without pre-amplification, leveraging the enhanced sensitivity and antifouling attributes of the BSA-based nanocomposite. Multiple crRNAs, strategically targeting diverse regions of the F3L gene of MPXV, are designed and combined to amplify Cas12a activation and its collateral cleavage of reporter probes. Notably, our electrochemical sensors exhibit the detection limit of 669 fM F3L gene without amplification, which is approximately a 15-fold improvement compared to fluorescence detection. This sensor also shows negligible changes in peak current after exposure to complex biological fluids, such as whole blood and serum, maintaining its sensitivity at 682 fM. This sensitivity is nearly identical to the conditions when only the F3L gene was present in PBS. In summary, our CRISPR-based electrochemical biosensors can be utilized as a high-performance diagnostic tool in resource-limited settings, representing a transformative leap forward in point-of-care testing. Beyond infectious diseases, the implications of this technology extend to various molecular diagnostics, establishing itself as a rapid, accurate, and versatile platform for detection of target analytes.
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Affiliation(s)
- Jeong-Chan Lee
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Seuk-Min Ryu
- Center for Advanced Biomolecular Recognition, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - YongJin Lee
- KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul 02841, Republic of Korea
| | - Hyowon Jang
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Jayeon Song
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
- Department of Forensic Sciences, Sungkyunkwan University (SKKU), Suwon-si, Gyeongi-do 16419, Republic of Korea
- School of Pharmacy, Sungkyunkwan University (SKKU), Suwon-si, Gyeongi-do 16419, Republic of Korea
| | - Taejoon Kang
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
- School of Pharmacy, Sungkyunkwan University (SKKU), Suwon-si, Gyeongi-do 16419, Republic of Korea
| | - Kwan Hyi Lee
- Center for Advanced Biomolecular Recognition, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
- KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul 02841, Republic of Korea
| | - Steve Park
- Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
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Paniz-Mondolfi AE, Ramírez JD. FDA's proposed rule and its regulatory impact on emerging and reemerging neglected tropical diseases in the United States. PLoS Negl Trop Dis 2024; 18:e0012116. [PMID: 38722919 PMCID: PMC11081280 DOI: 10.1371/journal.pntd.0012116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2024] Open
Abstract
Diagnosing infectious diseases significantly influences patient care, aiding in outbreak identification, response, and public health monitoring. However, the range of FDA-approved molecular tests remains notably limited, especially concerning neglected tropical diseases (NTDs). Drawing upon our experience as one of the largest healthcare networks in the greater New York metropolitan area, this viewpoint manuscript aims to spotlight the existing diagnostic landscape and unmet clinical needs for 4 emerging NTDs increasingly prevalent in the United States, additionally, it delves into the possible adverse effects of the FDA's Proposed Rule on Laboratory-Developed Tests for these clinical conditions and the broader spectrum of NTDs.
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Affiliation(s)
- Alberto E. Paniz-Mondolfi
- Molecular Microbiology Laboratory, Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Juan David Ramírez
- Molecular Microbiology Laboratory, Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
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De Pace V, Bruzzone B, Ricucci V, Domnich A, Guarona G, Garzillo G, Qosja R, Ciccarese G, Di Biagio A, Orsi A, Icardi G. Molecular Diagnosis of Human Monkeypox Virus during 2022-23 Outbreak: Preliminary Evaluation of Novel Real-Time Qualitative PCR Assays. Microorganisms 2024; 12:664. [PMID: 38674608 PMCID: PMC11052509 DOI: 10.3390/microorganisms12040664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 03/11/2024] [Accepted: 03/18/2024] [Indexed: 04/28/2024] Open
Abstract
In 2022-23, the human monkeypox virus (MPXV) caused a global outbreak in several non-endemic countries. Here, we evaluated the diagnostic performance of four real-time qualitative PCR assays for the laboratory diagnosis of mpox (monkeypox) monkeypox disease. From July to August 2022, 27 positive and 10 negative specimens (lesion, crust and exudate swabs) were tested in the laboratory of the Hygiene Unit of the San Martino Hospital (Genoa, Italy) by using home-made real-time PCR to detect MPXV generic G2R_G DNA. According to the manufacturer's instructions, we also retrospectively analyzed these specimens using RealCycler MONK-UX/-GX (Progenie Molecular), STANDARD M10 MPX/OPX (SD Biosensor), Novaplex MPXV (Seegene Inc.) and RealStar Orthopoxvirus PCR Kit 1.0 (Altona Diagnostics) assays, recognized as research-use-only tests. The diagnostic accuracy and sensitivity of these assays ranged from 97.3% (95% CI: 86.2-99.5%) to 100% (95% CI: 90.6-100%) and 96.3% (95% CI: 81.72-99.34%) to 100% (95% CI: 72.2-100%), respectively. The RealCycler MONK-UX and STANDARD M10 MPX/OPX did not detect one positive sample with a cycle threshold of 36. The overall specificity was 100% (95% CI: 72.2-100%), and Cohen's Kappa values ranged from 1 (95% CI: 0.67-1) to 0.93 (95% CI: 0.61-1). As they are highly accurate, reliable and user-friendly, these tests should be recommended for the routine or rapid laboratory discrimination of mpox from other rash illnesses.
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Affiliation(s)
- Vanessa De Pace
- Hygiene Unit, San Martino Policlinico Hospital-IRCCS for Oncology and Neurosciences, 16132 Genoa, Italy; (B.B.); (V.R.); (A.D.); (R.Q.); (A.O.); (G.I.)
- Laboratorio di Riferimento Regionale per le Emergenze di Sanità Pubblica (LaRESP), 16132 Genoa, Italy; (G.G.); (G.G.)
| | - Bianca Bruzzone
- Hygiene Unit, San Martino Policlinico Hospital-IRCCS for Oncology and Neurosciences, 16132 Genoa, Italy; (B.B.); (V.R.); (A.D.); (R.Q.); (A.O.); (G.I.)
- Laboratorio di Riferimento Regionale per le Emergenze di Sanità Pubblica (LaRESP), 16132 Genoa, Italy; (G.G.); (G.G.)
| | - Valentina Ricucci
- Hygiene Unit, San Martino Policlinico Hospital-IRCCS for Oncology and Neurosciences, 16132 Genoa, Italy; (B.B.); (V.R.); (A.D.); (R.Q.); (A.O.); (G.I.)
- Laboratorio di Riferimento Regionale per le Emergenze di Sanità Pubblica (LaRESP), 16132 Genoa, Italy; (G.G.); (G.G.)
| | - Alexander Domnich
- Hygiene Unit, San Martino Policlinico Hospital-IRCCS for Oncology and Neurosciences, 16132 Genoa, Italy; (B.B.); (V.R.); (A.D.); (R.Q.); (A.O.); (G.I.)
- Laboratorio di Riferimento Regionale per le Emergenze di Sanità Pubblica (LaRESP), 16132 Genoa, Italy; (G.G.); (G.G.)
| | - Giulia Guarona
- Laboratorio di Riferimento Regionale per le Emergenze di Sanità Pubblica (LaRESP), 16132 Genoa, Italy; (G.G.); (G.G.)
- Department of Health Sciences, University of Genoa, 16132 Genoa, Italy
| | - Giada Garzillo
- Laboratorio di Riferimento Regionale per le Emergenze di Sanità Pubblica (LaRESP), 16132 Genoa, Italy; (G.G.); (G.G.)
- Department of Health Sciences, University of Genoa, 16132 Genoa, Italy
| | - Rexhina Qosja
- Hygiene Unit, San Martino Policlinico Hospital-IRCCS for Oncology and Neurosciences, 16132 Genoa, Italy; (B.B.); (V.R.); (A.D.); (R.Q.); (A.O.); (G.I.)
- Laboratorio di Riferimento Regionale per le Emergenze di Sanità Pubblica (LaRESP), 16132 Genoa, Italy; (G.G.); (G.G.)
| | - Giulia Ciccarese
- Dermatology Unit, San Martino Policlinico Hospital-IRCCS for Oncology and Neurosciences, 16132 Genoa, Italy;
| | - Antonio Di Biagio
- Infectious Disease Unit, San Martino Policlinico Hospital-IRCCS for Oncology and Neurosciences, 16132 Genoa, Italy;
| | - Andrea Orsi
- Hygiene Unit, San Martino Policlinico Hospital-IRCCS for Oncology and Neurosciences, 16132 Genoa, Italy; (B.B.); (V.R.); (A.D.); (R.Q.); (A.O.); (G.I.)
- Laboratorio di Riferimento Regionale per le Emergenze di Sanità Pubblica (LaRESP), 16132 Genoa, Italy; (G.G.); (G.G.)
- Department of Health Sciences, University of Genoa, 16132 Genoa, Italy
| | - Giancarlo Icardi
- Hygiene Unit, San Martino Policlinico Hospital-IRCCS for Oncology and Neurosciences, 16132 Genoa, Italy; (B.B.); (V.R.); (A.D.); (R.Q.); (A.O.); (G.I.)
- Laboratorio di Riferimento Regionale per le Emergenze di Sanità Pubblica (LaRESP), 16132 Genoa, Italy; (G.G.); (G.G.)
- Department of Health Sciences, University of Genoa, 16132 Genoa, Italy
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7
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Fattouh R, Boissinot K, Jeong E, Mendlowitz AB, Sjaarda CP, Wong H, Kozak R, Sheth PM, Matukas LM. Evaluation of 5 Polymerase Chain Reaction Assays for the Detection of Mpox Virus. J Infect Dis 2024; 229:S156-S162. [PMID: 38531075 DOI: 10.1093/infdis/jiad464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2024] Open
Abstract
BACKGROUND In 2022, the global dissemination of mpox virus (MPXV) outside endemic regions prompted the expansion of diagnostic testing worldwide. This study assesses the performance characteristics of 5 real-time polymerase chain reaction (PCR) assays in detecting MPXV during the 2022 outbreak. METHODS Clinical specimens collected from patients across Ontario, Canada, were tested on the following assays: RealStar Orthopoxyvirus PCR and FlexStar Monkeypox virus PCR (Altona Diagnostics), Novaplex MPXV (Seegene), VIASURE Monkeypox virus Real Time PCR Reagents (CerTest Biotec), and a laboratory-developed test. Positive percent agreement (PPA), negative percent agreement (NPA), relative limit of detection (LOD), and precision were evaluated and MPXV lineages were determined using an amplicon-based whole-genome sequencing (WGS) assay. RESULTS Swabs were collected from various anatomic sites (65 positive and 30 negative). All assays demonstrated 100% NPA (95% confidence interval, 88.4%/88.1%-100.0%), with PPA ranging from 92.2% (82.7%-97.4%) to 96.9% (89.3%-99.6%). LOD and precision were comparable across assays, with coefficient of variations <3%. WGS analysis identified 6 lineages, all belonging to subclade IIb. CONCLUSIONS The assays exhibited excellent PPA, NPA, LOD, and precision. Ongoing performance monitoring is essential to detect assay escape mutants and ensure universal detection of evolving MPXV strains.
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Affiliation(s)
- Ramzi Fattouh
- Department of Laboratory Medicine, St Michael's Hospital, Unity Health Toronto, Toronto, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
- Li Ka Shing Knowledge Institute, Unity Health Toronto, Toronto, Canada
| | - Karel Boissinot
- Department of Laboratory Medicine, St Michael's Hospital, Unity Health Toronto, Toronto, Canada
| | - Esther Jeong
- Department of Laboratory Medicine, St Michael's Hospital, Unity Health Toronto, Toronto, Canada
| | - Andrew B Mendlowitz
- Toronto Centre for Liver Disease/Viral Hepatitis Care Network (VIRCAN), University Health Network, Toronto, Canada
| | - Calvin P Sjaarda
- Division of Microbiology, Kingston Health Sciences Centre, Kingston, Canada
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, Canada
| | - Henry Wong
- Division of Microbiology, Kingston Health Sciences Centre, Kingston, Canada
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, Canada
| | - Robert Kozak
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
- Sunnybrook Health Sciences Centre, Toronto, Canada
| | - Prameet M Sheth
- Division of Microbiology, Kingston Health Sciences Centre, Kingston, Canada
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, Canada
| | - Larissa M Matukas
- Department of Laboratory Medicine, St Michael's Hospital, Unity Health Toronto, Toronto, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
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8
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Park SY, Trinh KTL, Song YJ, Lee NY. Pipette-free field-deployable molecular diagnostic kit for bimodal visual detection of infectious RNA viruses. Biotechnol J 2024; 19:e2300521. [PMID: 38403439 DOI: 10.1002/biot.202300521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 12/22/2023] [Accepted: 01/08/2024] [Indexed: 02/27/2024]
Abstract
Here, we developed a field-deployable molecular diagnostic kit for the detection of RNA viruses that operates in a pipette-free manner. The kit is composed of acrylic sticks, PCR tubes, and palm-sized three-dimensional(3D)-printed heaters operated by batteries. The kit performs RNA extraction, reverse transcriptase loop-mediated isothermal amplification (RT-LAMP), and visual detection in one kit. An acrylic stick was engraved with one shallow and one deep cylindrical chamber at each end for the insertion of an FTA card and ethidium homodimer-1 (EthD-1), respectively, to perform RNA extraction/purification and bimodal visual detection of the target amplicons. First, an intercalation of EthD-1 into the target DNA initially produces fluorescence upon UV illumination. Next, the addition of a strong oxidant, in this case sodium (meta) periodate (NaIO4 ), produces intense aggregates in the presence of EthD-1-intercalated DNA, realized by electrostatic interaction. In the absence of the target amplicon, no fluorescence or aggregates are observed. Using this kit, two major infectious viruses-severe fever with thrombocytopenia syndrome virus (SFTSV) and severe acute respiratory syndrome coronavirus (SARS-CoV-2)-were successfully detected in 1 h, and the limits of detection (LOD) were approximately 1 virus μL-1 for SFTSV and 103 copies μL-1 for SARS-CoV-2 RNA. The introduced kit is portable, end-user-friendly, and can be operated in a pipette-free manner, paving the way for simple and convenient virus detection in resource-limited settings.
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Affiliation(s)
- So Yeon Park
- Department of BioNano Technology, Gachon University, Seongnam-si, Gyeonggi-do, Republic of Korea
| | - Kieu The Loan Trinh
- BioNano Applications Research Center, Gachon University, Seongnam-si, Gyeonggi-do, Republic of Korea
| | - Yoon-Jae Song
- Department of Life Science, Gachon University, Seongnam-si, Gyeonggi-do, Republic of Korea
| | - Nae Yoon Lee
- Department of BioNano Technology, Gachon University, Seongnam-si, Gyeonggi-do, Republic of Korea
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Kasuki L, Lamback E, Antunes X, Gadelha MR. Biomarkers of response to treatment in acromegaly. Expert Rev Endocrinol Metab 2024; 19:71-80. [PMID: 38078447 DOI: 10.1080/17446651.2023.2293107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 12/06/2023] [Indexed: 01/03/2024]
Abstract
INTRODUCTION Medical treatment of acromegaly is based in a `trial and error` approach. First-generation somatostatin receptor ligands (fg-SRL) are prescribed as first-line medical therapy to the vast majority of patients, despite lack of disease control in approximately 60% of patients. However, other drugs used in acromegaly treatment are available (cabergoline, pasireotide and pegvisomant). AREAS COVERED In this article, we review and discuss the biomarkers of response to medical treatment in acromegaly. EXPERT OPINION Biomarkers for fg-SRL that can already be applied in clinical practice are: gender, age, pretreatment GH and IGF-I levels, cytokeratin granulation pattern, and the expression of somatostatin receptor type 2. Using biomarkers of response could guide treatment towards precision medicine with greater efficacy and lower costs.
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Affiliation(s)
- Leandro Kasuki
- Neuroendocrinology Research Center/Endocrinology Division, Medical School and Hospital Universitário Clementino Fraga Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Neuroendocrinology Division, Instituto Estadual do Cérebro Paulo Niemeyer, Secretaria Estadual de Saúde, Rio de Janeiro, Brazil
- Endocrinology Division, Hospital Federal de Bonsucesso, Rio de Janeiro, Brazil
| | - Elisa Lamback
- Neuroendocrinology Research Center/Endocrinology Division, Medical School and Hospital Universitário Clementino Fraga Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Neuroendocrinology Division, Instituto Estadual do Cérebro Paulo Niemeyer, Secretaria Estadual de Saúde, Rio de Janeiro, Brazil
- Neuropathology and Molecular Genetics Laboratory, Instituto Estadual do Cérebro Paulo Niemeyer, Secretaria Estadual de Saúde, Rio de Janeiro, Brazil
| | - Ximene Antunes
- Neuroendocrinology Research Center/Endocrinology Division, Medical School and Hospital Universitário Clementino Fraga Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Mônica R Gadelha
- Neuroendocrinology Research Center/Endocrinology Division, Medical School and Hospital Universitário Clementino Fraga Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Neuroendocrinology Division, Instituto Estadual do Cérebro Paulo Niemeyer, Secretaria Estadual de Saúde, Rio de Janeiro, Brazil
- Neuropathology and Molecular Genetics Laboratory, Instituto Estadual do Cérebro Paulo Niemeyer, Secretaria Estadual de Saúde, Rio de Janeiro, Brazil
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10
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Jain N, Umar TP, Sayad R, Mokresh ME, Tandarto K, Siburian R, Liana P, Laivacuma S, Reinis A. Monkeypox Diagnosis in Clinical Settings: A Comprehensive Review of Best Laboratory Practices. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1451:253-271. [PMID: 38801583 DOI: 10.1007/978-3-031-57165-7_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
An outbreak of monkeypox (Mpox) was reported in more than 40 countries in early 2022. Accurate diagnosis of Mpox can be challenging, but history, clinical findings, and laboratory diagnosis can establish the diagnosis. The pre-analytic phase of testing includes collecting, storing, and transporting specimens. It is advised to swab the lesion site with virus transport medium (VTM) containing Dacron or polyester flock swabs from two different sites. Blood, urine, and semen samples may also be used. Timely sampling is necessary to obtain a sufficient amount of virus or antibodies. The analytical phase of infectious disease control involves diagnostic tools to determine the presence of the virus. While polymerase chain reaction (PCR) is the gold standard for detecting Mpox, genome sequencing is for identifying new or modified viruses. As a complement to these methods, isothermal amplification methods have been designed. ELISA assays are also available for the determination of antibodies. Electron microscopy is another effective diagnostic method for tissue identification of the virus. Wastewater fingerprinting provides some of the most effective diagnostic methods for virus identification at the community level. The advantages and disadvantages of these methods are further discussed. Post-analytic phase requires proper interpretation of test results and the preparation of accurate patient reports that include relevant medical history, clinical guidelines, and recommendations for follow-up testing or treatment.
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Affiliation(s)
- Nityanand Jain
- Faculty of Medicine, Riga Stradiņš University, Dzirciema Street 16, Riga, 1007, Latvia.
- Joint Microbiology Laboratory, Pauls Stradins Clinical University Hospital, Pilsonu Street 13, Riga, 1002, Latvia.
| | - Tungki Pratama Umar
- Faculty of Medicine, Sriwijaya University, Dr. Mohammad Ali Street-RSMH Complex, Palembang, 30126, Indonesia.
| | - Reem Sayad
- Faculty of Medicine, Assiut University, Saad Zaghloul, Assiut, 71515, Egypt
| | - Muhammed Edib Mokresh
- Faculty of International Medicine, University of Health Sciences, Tibbiye, Istanbul, 34668, Turkey
| | - Kevin Tandarto
- Faculty of Medicine and Health Sciences, Atma Jaya Catholic University of Indonesia, Pluit Raya Street No. 2, North Jakarta, Special Capital Region of Jakarta, 14440, Indonesia
| | - Reynold Siburian
- Faculty of Medicine, Sriwijaya University, Dr. Mohammad Ali Street-RSMH Complex, Palembang, 30126, Indonesia
| | - Phey Liana
- Department of Clinical Pathology, Faculty of Medicine, Sriwijaya University-Mohammad Hoesin General Hospital, Palembang, 30126, Indonesia
| | - Sniedze Laivacuma
- Faculty of Medicine, Riga Stradiņš University, Dzirciema Street 16, Riga, 1007, Latvia
- Department of Infectious Diseases, Riga East Clinical University Hospital, Hipokrata Street 2, Riga, 1038, Latvia
| | - Aigars Reinis
- Faculty of Medicine, Riga Stradiņš University, Dzirciema Street 16, Riga, 1007, Latvia
- Joint Microbiology Laboratory, Pauls Stradins Clinical University Hospital, Pilsonu Street 13, Riga, 1002, Latvia
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11
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Brusati A, Agostinetto G, Bruno A, Casiraghi M, Pescini D, Sandionigi A, Balech B. Exploration and Retrieval of Virus-Related Molecular Data Using ExTaxsI: The Monkeypox Use Case. Methods Mol Biol 2024; 2732:145-154. [PMID: 38060123 DOI: 10.1007/978-1-0716-3515-5_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
Abstract
Retrieval and visualization of biological data are essential for understanding complex systems. With the increasing volume of data generated from high-throughput sequencing technologies, effective and optimized data visualization tools have become indispensable. This is particularly relevant in the COVID-19 postpandemic period, where understanding the diversity and interactions of microbial communities (i.e., viral and bacterial) constitutes an important asset to develop and plan suitable interventions.In this chapter, we show the usage and the potentials of ExTaxsI (Exploring Taxonomy Information) tool to retrieve viral biodiversity data stored in National Center for Biotechnology Information (NCBI) databases and create the related visualization. In addition, by integrating different functions and modules, the tool generates relevant types of visualization plots to facilitate the exploration of microbial biodiversity communities useful to deep dive into ecological and taxonomic relationships among different species and identify potential significant targets.Using the Monkeypox virus as a case study, this work points out significant perspectives on biological data visualization, which can be used to gain insights into the ecology, evolution, and pathogenesis of viruses. Accordingly, we show the potentiality of ExTaxsI to organize and describe the available/downloaded data in an easy, simple, and interpretable way allowing the user to interact dynamically with the visualization plots through specific filters, zoom, and explore functions.
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Affiliation(s)
- Alberto Brusati
- University of Pavia, Department of Brain and Behavioral Sciences, Pavia, Italy
| | - Giulia Agostinetto
- University of Milano-Bicocca, Department of Biotechnology and Biosciences, Milan, Italy.
| | - Antonia Bruno
- University of Milano-Bicocca, Department of Biotechnology and Biosciences, Milan, Italy
| | - Maurizio Casiraghi
- University of Milano-Bicocca, Department of Biotechnology and Biosciences, Milan, Italy
| | - Dario Pescini
- University of Milano-Bicocca, Department of Statistics and Quantitative Methods, Milan, Italy
| | - Anna Sandionigi
- University of Milano-Bicocca, Department of Biotechnology and Biosciences, Milan, Italy
- Quantia Consulting srl, Department of Data Science and Education, Remote Company, Milan, Italy
| | - Bachir Balech
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (CNR), Bari, Italy
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12
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Patiño LH, Ballesteros N, Muñoz M, Jaimes J, Castillo-Castañeda AC, Madigan R, Paniz-Mondolfi A, Ramírez JD. Validation of Oxford nanopore sequencing for improved New World Leishmania species identification via analysis of 70-kDA heat shock protein. Parasit Vectors 2023; 16:458. [PMID: 38111024 PMCID: PMC10726620 DOI: 10.1186/s13071-023-06073-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 11/29/2023] [Indexed: 12/20/2023] Open
Abstract
BACKGROUND Leishmaniasis is a parasitic disease caused by obligate intracellular protozoa of the genus Leishmania. This infection is characterized by a wide range of clinical manifestations, with symptoms greatly dependent on the causal parasitic species. Here we present the design and application of a new 70-kDa heat shock protein gene (hsp70)-based marker of 771 bp (HSP70-Long). We evaluated its sensitivity, specificity and diagnostic performance employing an amplicon-based MinION™ DNA sequencing assay to identify different Leishmania species in clinical samples from humans and reservoirs with cutaneous leishmaniasis (CL) and visceral leishmaniasis (VL). We also conducted a comparative analysis between our novel marker and a previously published HSP70 marker known as HSP70-Short, which spans 330 bp. METHODS A dataset of 27 samples from Colombia, Venezuela and the USA was assembled, of which 26 samples were collected from humans, dogs and cats affected by CL and one sample was collected from a dog with VL in the USA (but originally from Greece). DNA was extracted from each sample and underwent conventional PCR amplification utilizing two distinct HSP70 markers: HSP70-Short and HSP70-Long. The subsequent products were then sequenced using the MinION™ sequencing platform. RESULTS The results highlight the distinct characteristics of the newly devised HSP70-Long primer, showcasing the notable specificity of this primer, although its sensitivity is lower than that of the HSP70-Short marker. Notably, both markers demonstrated strong discriminatory capabilities, not only in distinguishing between different species within the Leishmania genus but also in identifying instances of coinfection. CONCLUSIONS This study underscores the outstanding specificity and effectiveness of HSP70-based MinION™ sequencing, in successfully discriminating between diverse Leishmania species and identifying coinfection events within samples sourced from leishmaniasis cases.
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Affiliation(s)
- 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
| | - Jesús Jaimes
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Adriana C Castillo-Castañeda
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Roy Madigan
- Animal Hospital of Smithson Valley, 286 Singing Oaks, Ste 113, Spring Branch, TX, 78070, 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, 10029, USA
| | - Juan David Ramírez
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia.
- Molecular Microbiology Laboratory, Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
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13
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Yang X, Cheng X, Wei H, Tu Z, Rong Z, Wang C, Wang S. Fluorescence-enhanced dual signal lateral flow immunoassay for flexible and ultrasensitive detection of monkeypox virus. J Nanobiotechnology 2023; 21:450. [PMID: 38001482 PMCID: PMC10675944 DOI: 10.1186/s12951-023-02215-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 11/14/2023] [Indexed: 11/26/2023] Open
Abstract
The outbreak of the monkeypox virus (MPXV) worldwide in 2022 highlights the need for a rapid and low-cost MPXV detection tool for effectively monitoring and controlling monkeypox disease. In this study, we developed a flexible lateral flow immunoassay (LFIA) with strong colorimetric and enhanced fluorescence dual-signal output for the rapid, on-site, and highly sensitive detection of the MPXV antigen in different scenarios. A multilayered SiO2-Au core dual-quantum dot (QD) shell nanocomposite (named SiO2-Au/DQD), which consists of a large SiO2 core (~ 200 nm), one layer of density-controlled gold nanoparticles (AuNPs, 20 nm), and thousands of small QDs, was fabricated instead of a traditional colorimetric nanotag (i.e., AuNPs) and a fluorescent nanotag (QD nanobead) to simultaneously provide good stability, strong colorimetric ability and superior fluorescence intensity. With the dual-signal output LFIA, we achieved the specific screening of the MPXV antigen (A29L) in 15 min, with detection limits of 0.5 and 0.0021 ng/mL for the colorimetric and fluorometric modes, respectively. Moreover, the colorimetric mode of SiO2-Au/DQD-LFIA exhibits the same sensitivity as the traditional AuNP- LFIA, whereas the overall sensitivity of this method on the basis of the fluorescent signal can achieve 238- and 3.3-fold improvements in sensitivity for MPXV compared with the AuNP-based LFIA and ELISA methods, respectively, indicating the powerful performance and good versatility of the dual-signal method in the point-of-care testing of the MPXV.
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Affiliation(s)
- Xingsheng Yang
- Bioinformatics Center of AMMS, Beijing, 100850, P. R. China
- Beijing Key Laboratory of New Molecular Diagnosis Technologies for Infectious Diseases, Beijing, 100850, P. R. China
| | - Xiaodan Cheng
- Bioinformatics Center of AMMS, Beijing, 100850, P. R. China
- Beijing Key Laboratory of New Molecular Diagnosis Technologies for Infectious Diseases, Beijing, 100850, P. R. China
| | - Hongjuan Wei
- Bioinformatics Center of AMMS, Beijing, 100850, P. R. China
- Beijing Key Laboratory of New Molecular Diagnosis Technologies for Infectious Diseases, Beijing, 100850, P. R. China
| | - Zhijie Tu
- Bioinformatics Center of AMMS, Beijing, 100850, P. R. China
- Beijing Key Laboratory of New Molecular Diagnosis Technologies for Infectious Diseases, Beijing, 100850, P. R. China
| | - Zhen Rong
- Bioinformatics Center of AMMS, Beijing, 100850, P. R. China.
- Beijing Key Laboratory of New Molecular Diagnosis Technologies for Infectious Diseases, Beijing, 100850, P. R. China.
| | - Chongwen Wang
- Bioinformatics Center of AMMS, Beijing, 100850, P. R. China.
- Laboratory Medicine, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510000, PR China.
| | - Shengqi Wang
- Bioinformatics Center of AMMS, Beijing, 100850, P. R. China.
- Beijing Key Laboratory of New Molecular Diagnosis Technologies for Infectious Diseases, Beijing, 100850, P. R. China.
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14
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Paniz-Mondolfi A, Reidy J, Pagani N, Lednicky JA, McGrail JP, Kasminskaya Y, Patino LH, Garcia-Sastre A, Palacios G, Gonzalez-Reiche AS, van Bakel H, Firpo Betancourt A, Hernandez MM, Cordon-Cardo C, Simon V, Sordillo EM, Ramírez JD, Guerra S. Genomic and ultrastructural analysis of monkeypox virus in skin lesions and in human/animal infected cells reveals further morphofunctional insights into viral pathogenicity. J Med Virol 2023; 95:e28878. [PMID: 37322614 DOI: 10.1002/jmv.28878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/23/2023] [Accepted: 05/25/2023] [Indexed: 06/17/2023]
Abstract
Monkeypox (MPOX) is a zoonotic disease that affects humans and other primates, resulting in a smallpox-like illness. It is caused by monkeypox virus (MPXV), which belongs to the Poxviridae family. Clinically manifested by a range of cutaneous and systemic findings, as well as variable disease severity phenotypes based on the genetic makeup of the virus, the cutaneous niche and respiratory mucosa are the epicenters of MPXV pathogenicity. Herein, we describe the ultrastructural features of MPXV infection in both human cultured cells and cutaneous clinical specimens collected during the 2022-2023 MPOX outbreak in New York City that were revealed through electron microscopy. We observed typical enveloped virions with brick-shaped morphologies that contained surface protrusions, consistent with the classic ultrastructural features of MPXV. In addition, we describe morpho-functional evidence that point to roles of distinct cellular organelles in viral assembly during clinical MPXV infection. Interestingly, in skin lesions, we found abundant melanosomes near viral assembly sites, particularly in the vicinity of mature virions, which provides further insight into virus-host interactions at the subcellular level that contribute to MPXV pathogenesis. These findings not only highlight the importance of electron microscopic studies for further investigation of this emerging pathogen but also in characterizing MPXV pathogenesis during human infection.
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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, USA
| | - Jason Reidy
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Nina Pagani
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, USA
- Department of Biotechnology Laboratory Sciences, Valencia College, Orlando, Florida, USA
- Infectious Diseases Research Department, Division of Virology, Venezuelan Science Incubator and The Zoonosis and Emerging Pathogens Regional Collaborative Network, Cabudare, Lara, Venezuela
| | - John A Lednicky
- Department of Environmental and Global Health, College of Public Health and Health Professions, Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
| | - Joseph Patrick McGrail
- Department of Preventive Medicine, Public Health and Microbiology, Universidad Autónoma de Madrid, Madrid, Spain
| | - Yana Kasminskaya
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Luz H Patino
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Adolfo Garcia-Sastre
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, USA
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Gustavo Palacios
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, USA
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, USA
| | | | - Harm van Bakel
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Adolfo Firpo Betancourt
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Matthew M Hernandez
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Carlos Cordon-Cardo
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Viviana Simon
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, USA
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VARPP), Icahn School of Medicine at Mount Sinai, New York, USA
| | - Emilia M Sordillo
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Juan David Ramírez
- Department of Pathology, Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, USA
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Susana Guerra
- Department of Preventive Medicine, Public Health and Microbiology, Universidad Autónoma de Madrid, Madrid, Spain
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15
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Nayak T, Chadaga K, Sampathila N, Mayrose H, Gokulkrishnan N, Bairy G M, Prabhu S, S SK, Umakanth S. Deep learning based detection of monkeypox virus using skin lesion images. MEDICINE IN NOVEL TECHNOLOGY AND DEVICES 2023; 18:100243. [PMID: 37293134 PMCID: PMC10236906 DOI: 10.1016/j.medntd.2023.100243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 05/25/2023] [Accepted: 05/26/2023] [Indexed: 06/10/2023] Open
Abstract
As we set into the second half of 2022, the world is still recovering from the two-year COVID-19 pandemic. However, over the past three months, the outbreak of the Monkeypox Virus (MPV) has led to fifty-two thousand confirmed cases and over one hundred deaths. This caused the World Health Organisation to declare the outbreak a Public Health Emergency of International Concern (PHEIC). If this outbreak worsens, we could be looking at the Monkeypox virus causing the next global pandemic. As Monkeypox affects the human skin, the symptoms can be captured with regular imaging. Large samples of these images can be used as a training dataset for machine learning-based detection tools. Using a regular camera to capture the skin image of the infected person and running it against computer vision models is beneficial. In this research, we use deep learning to diagnose monkeypox from skin lesion images. Using a publicly available dataset, we tested the dataset on five pre-trained deep neural networks: GoogLeNet, Places365-GoogLeNet, SqueezeNet, AlexNet and ResNet-18. Hyperparameter was done to choose the best parameters. Performance metrics such as accuracy, precision, recall, f1-score and AUC were considered. Among the above models, ResNet18 was able to obtain the highest accuracy of 99.49%. The modified models obtained validation accuracies above 95%. The results prove that deep learning models such as the proposed model based on ResNet-18 can be deployed and can be crucial in battling the monkeypox virus. Since the used networks are optimized for efficiency, they can be used on performance limited devices such as smartphones with cameras. The addition of explainable artificial intelligence techniques LIME and GradCAM enables visual interpretation of the prediction made, helping health professionals using the model.
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Affiliation(s)
- Tushar Nayak
- Department of Biomedical Engineering, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Krishnaraj Chadaga
- Department of Computer Science and Engineering, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Niranjana Sampathila
- Department of Biomedical Engineering, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Hilda Mayrose
- Department of Biomedical Engineering, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Nitila Gokulkrishnan
- Department of Biomedical Engineering, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Muralidhar Bairy G
- Department of Biomedical Engineering, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Srikanth Prabhu
- Department of Computer Science and Engineering, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Swathi K S
- Prasanna School of Public Health, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Shashikiran Umakanth
- Department of Medicine, Dr. T.M.A. Pai Hospital, Manipal Academy of Higher Education, Udupi, Karnataka, 576101, India
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16
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Zhao F, Wang P, Wang H, Liu S, Sohail M, Zhang X, Li B, Huang H. CRISPR/Cas12a-mediated ultrasensitive and on-site monkeypox viral testing. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2023; 15:2105-2113. [PMID: 37066613 DOI: 10.1039/d2ay01998a] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The spread of the monkeypox virus (MPXV) from Central and West Africa to previously non-endemic regions has caused a global panic. In this context, the rapid, specific, and ultrasensitive detection of MPXV is crucial to contain its spread, though such technology has seldom been reported. Herein, we proposed an MPXV assay combining recombinase-aided amplification (RAA) and CRISPR/Cas12a. This assay targeted the highly conserved MPXV F3L gene and demonstrates a low detection limit (LOD) of 101 copies per μL. By leveraging the high specificity nature of RAA and CRISPR/Cas12a, we rationally optimized probes and conditions to achieve high selectivity that differentiates MPXV from other orthopox viruses and current high-profile viruses. To facilitate on-site screening of potential MPXV carriers, a kit integrating lateral flow strips was developed, enabling naked-eye MPXV detection with a LOD of 104 copies per μL. Our RAA-Cas12a-MPXV assay was able to detect MPXV without the need for sophisticated operation and expensive equipment. We believe that this assay can be rapidly deployed in emerging viral outbreaks for on-site surveillance of MPXV.
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Affiliation(s)
- Furong Zhao
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Jiangsu, 210023, P.R. China.
| | - Pei Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Jiangsu, 210023, P.R. China.
| | - Haoxuan Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Jiangsu, 210023, P.R. China.
| | - Sirui Liu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Jiangsu, 210023, P.R. China.
| | - Muhammad Sohail
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Jiangsu, 210023, P.R. China.
| | - Xing Zhang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Jiangsu, 210023, P.R. China.
| | - Bingzhi Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Jiangsu, 210023, P.R. China.
| | - He Huang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Jiangsu, 210023, P.R. China.
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Monkeypox (mpox) virus: Classification, origin, transmission, genome organization, antiviral drugs, and molecular diagnosis. J Infect Public Health 2023; 16:531-541. [PMID: 36801633 PMCID: PMC9908738 DOI: 10.1016/j.jiph.2023.02.003] [Citation(s) in RCA: 44] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 01/22/2023] [Accepted: 02/05/2023] [Indexed: 02/11/2023] Open
Abstract
Monkeypox virus (MPXV) is a double-stranded DNA virus belonging to the Poxviridae family of the genus Orthopoxvirus with two different clades known as West African and Congo Basin. Monkeypox (MPX) is a zoonosis that arises from the MPXV and causes a smallpox-like disease. The endemic disease status of MPX was updated to an outbreak worldwide in 2022. Thus, the condition was declared a global health emergency independent of travel issues, accounting for the primary reason for its prevalence outside Africa. In addition to identified transmission mediators through animal-to-human and human-to-human, especially sexual transmission among men who have sex with men came to prominence in the 2022 global outbreak. Although the severity and prevalence of the disease differ depending on age and gender, some symptoms are commonly observed. Clinical signs such as fever, muscle and headache pain, swollen lymph nodes, and skin rashes in defined body regions are standard and an indicator for the first step of diagnosis. By following the clinical signs, laboratory diagnostic tests like conventional polymerase chain reaction (PCR) or real-time PCR (RT-PCR) are the most common and accurate diagnostic methods. Antiviral drugs such as tecovirimat, cidofovir, and brincidofovir are used for symptomatic treatment. There is no MPXV-specific vaccine; however, currently available vaccines against smallpox enhance the immunization rate. This comprehensive review covers the MPX disease history and the current state of knowledge by assessing broad topics and views related to disease origin, transmission, epidemiology, severity, genome organization and evolution, diagnosis, treatment, and prevention.
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Muñoz-Barrera A, Ciuffreda L, Alcoba-Florez J, Rubio-Rodríguez LA, Rodríguez-Pérez H, Gil-Campesino H, García-Martínez de Artola D, Salas-Hernández J, Rodríguez-Núñez J, Íñigo-Campos A, García-Olivares V, Díez-Gil O, González-Montelongo R, Valenzuela-Fernández A, Lorenzo-Salazar JM, Flores C. Bioinformatic approaches to draft the viral genome sequence of Canary Islands cases related to the multicountry mpox virus 2022-outbreak. Comput Struct Biotechnol J 2023; 21:2197-2203. [PMID: 36968018 PMCID: PMC10015108 DOI: 10.1016/j.csbj.2023.03.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 03/13/2023] [Accepted: 03/13/2023] [Indexed: 03/17/2023] Open
Abstract
On July 23, 2022, monkeypox disease (mpox) was declared a Public Emergency of International Concern (PHEIC) by the World Health Organization (WHO) due to a multicountry outbreak. In Europe, several cases of mpox virus (MPXV) infection related to this outbreak were detected in the Canary Islands (Spain). Here we describe the combination of viral DNA sequencing and bioinformatic approaches, including methods for de novo genome assembly and short- and long-read technologies, used to reconstruct the first MPXV genome isolated in the Canary Islands on the 31st of May 2022 from a male adult patient with mild symptoms. The same sequencing and bioinformatic approaches were then validated with three other positive cases of MPXV infection from the same mpox outbreak. We obtained the best results using a reference-based approach with short reads, evidencing 46-79 nucleotide variants against viral sequences from the 2018-2019 mpox outbreak and placing the viral sequences in the new B.1 sublineage of clade IIb of the MPXV classification. This study of MPXV demonstrates the potential of metagenomics sequencing for rapid and precise pathogen identification.
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Affiliation(s)
- Adrián Muñoz-Barrera
- Genomics Division, Instituto Tecnológico y de Energías Renovables, 38600 Santa Cruz de Tenerife, Spain
| | - Laura Ciuffreda
- Research Unit, Hospital Universitario Ntra. Sra. de Candelaria, 38010 Santa Cruz de Tenerife, Spain
| | - Julia Alcoba-Florez
- Servicio de Microbiología, Hospital Universitario Ntra. Sra. de Candelaria, 38010 Santa Cruz de Tenerife, Spain
| | - Luis A. Rubio-Rodríguez
- Genomics Division, Instituto Tecnológico y de Energías Renovables, 38600 Santa Cruz de Tenerife, Spain
| | - Héctor Rodríguez-Pérez
- Research Unit, Hospital Universitario Ntra. Sra. de Candelaria, 38010 Santa Cruz de Tenerife, Spain
| | - Helena Gil-Campesino
- Servicio de Microbiología, Hospital Universitario Ntra. Sra. de Candelaria, 38010 Santa Cruz de Tenerife, Spain
| | | | - Josmar Salas-Hernández
- Research Unit, Hospital Universitario Ntra. Sra. de Candelaria, 38010 Santa Cruz de Tenerife, Spain
| | - Julia Rodríguez-Núñez
- Research Unit, Hospital Universitario Ntra. Sra. de Candelaria, 38010 Santa Cruz de Tenerife, Spain
| | - Antonio Íñigo-Campos
- Genomics Division, Instituto Tecnológico y de Energías Renovables, 38600 Santa Cruz de Tenerife, Spain
| | - Víctor García-Olivares
- Genomics Division, Instituto Tecnológico y de Energías Renovables, 38600 Santa Cruz de Tenerife, Spain
| | - Oscar Díez-Gil
- Servicio de Microbiología, Hospital Universitario Ntra. Sra. de Candelaria, 38010 Santa Cruz de Tenerife, Spain
| | | | - Agustín Valenzuela-Fernández
- Laboratorio “Inmunología Celular y Viral”, Unidad de Farmacología, Sección de Medicina, Facultad de Ciencias de la Salud, Universidad de La Laguna, 38200 San Cristóbal de La Laguna, Spain
| | - José M. Lorenzo-Salazar
- Genomics Division, Instituto Tecnológico y de Energías Renovables, 38600 Santa Cruz de Tenerife, Spain
| | - Carlos Flores
- Genomics Division, Instituto Tecnológico y de Energías Renovables, 38600 Santa Cruz de Tenerife, Spain
- Research Unit, Hospital Universitario Ntra. Sra. de Candelaria, 38010 Santa Cruz de Tenerife, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Facultad de Ciencias de la Salud, Universidad Fernando Pessoa Canarias, 35450 Las Palmas de Gran Canaria, Spain
- Correspondence to: Unidad de Investigación, Hospital Universitario Nuestra Señora de Candelaria, Carretera del Rosario s/n, 38010 Santa Cruz de Tenerife, Spain.
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Mills MG, Juergens KB, Gov JP, McCormick CJ, Sampoleo R, Kachikis A, Amory JK, Fang FC, Pérez-Osorio AC, Lieberman NA, Greninger AL. Evaluation and clinical validation of monkeypox (mpox) virus real-time PCR assays. J Clin Virol 2023; 159:105373. [PMID: 36603329 PMCID: PMC9783225 DOI: 10.1016/j.jcv.2022.105373] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 12/15/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND In spring of 2022, an outbreak of monkeypox (mpox) spread worldwide. Here, we describe performance characteristics of monkeypox virus (MPXV)-specific and pan-orthopoxvirus qPCR assays for clinical use. METHODS We validated probe-based qPCR assays targeting MPXV-specific loci F3L and G2R (genes MPXVgp052/OPG065 and MPXVgp002 and gp190/OPG002, respectively) and a pan-orthopoxvirus assay targeting the E9L locus (MPXVgp057/OPG071). Clinical samples and synthetic controls were extracted using the Roche MP96 or Promega Maxwell 48 instrument. qPCR was performed on the AB7500 thermocycler. Synthetic control DNA and high concentration clinical samples were quantified by droplet PCR. Cross-reactivity was evaluated for camelpox and cowpox genomic DNA, vaccinia culture supernatant, and HSV- and VZV-positive clinical specimens. We also tested the performance of the F3L assay using dry swabs, Aptima vaginal and rectal swabs, nasopharyngeal, rectal, and oral swabs, cerebrospinal fluid, plasma, serum, whole blood, breastmilk, urine, saliva, and semen. RESULTS The MPXV-F3L assay is reproducible at a limit of detection (LoD) of 65.6 copies/mL of viral DNA in viral transport medium/universal transport medium (VTM/UTM), or 3.3 copies/PCR reaction. No cross-reactivity with herpesviruses or other poxviruses was observed. MPXV-F3L detects MPXV DNA in alternative specimen types, with an LoD ranging between 260-1000 copies/mL, or 5.7-10 copies/PCR reaction. In clinical swab VTM specimens, MPXV-F3L and MPXV-G2R assays outperformed OPXV-E9L by an average of 2.4 and 2.8 Cts, respectively. MPXV-G2R outperformed MPXV-F3L by 0.4 Cts, consistent with presence of two copies of G2R present in labile inverted terminal repeats (ITRs) of MPXV genome. CONCLUSIONS MPXV is readily detected by qPCR using three clinically validated assays.
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Affiliation(s)
- Margaret G. Mills
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, 98195, USA
| | - Kate B. Juergens
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, 98195, USA
| | - Jolene P. Gov
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, 98195, USA
| | - Carter J. McCormick
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, 98195, USA
| | - Reigran Sampoleo
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, 98195, USA
| | - Alisa Kachikis
- Department of Obstetrics and Gynecology, University of Washington, Seattle, WA, 98195, USA
| | - John K. Amory
- Department of Medicine, University of Washington, Seattle, WA, 98195, USA
| | - Ferric C. Fang
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, 98195, USA,Department of Medicine, University of Washington, Seattle, WA, 98195, USA
| | - Ailyn C. Pérez-Osorio
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, 98195, USA
| | - Nicole A.P. Lieberman
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, 98195, USA
| | - Alexander L. Greninger
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, 98195, USA,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA,Corresponding author
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