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Sene O, Sagne SN, Ngom D, Diagne MM, Badji A, Khoulé A, Ndiaye EH, Sankhe S, Loucoubar C, Diallo M, Weidmann M, Dia N, Simon-Lorière E, Sall Y, Diop B, Ndiaye M, Sakuntabhai A, Sall AA, Faye O, Faye O, Diallo D, Barry MA, Fall G. Emergence of Crimean-Congo Hemorrhagic Fever Virus in Eastern Senegal in 2022. Viruses 2024; 16:315. [PMID: 38400090 PMCID: PMC10891565 DOI: 10.3390/v16020315] [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: 12/01/2023] [Revised: 01/05/2024] [Accepted: 01/10/2024] [Indexed: 02/25/2024] Open
Abstract
Crimean-Congo hemorrhagic fever (CCHF), the most widespread tick-borne viral human infection, poses a threat to global health. In this study, clinical samples collected through national surveillance systems were screened for acute CCHF virus (CCHFV) infection using RT-PCR and for exposure using ELISA. For any CCHF-positive sample, livestock and tick samples were also collected in the neighborhood of the confirmed case and tested using ELISA and RT-PCR, respectively. Genome sequencing and phylogenetic analyses were also performed on samples with positive RT-PCR results. In Eastern Senegal, two human cases and one Hyalomma tick positive for CCHF were identified and a seroprevalence in livestock ranging from 9.33% to 45.26% was detected. Phylogenetic analyses revealed that the human strain belonged to genotype I based on the available L segment. However, the tick strain showed a reassortant profile, with the L and M segments belonging to genotype I and the S segment belonging to genotype III. Our data also showed that our strains clustered with strains isolated in different countries, including Mauritania. Therefore, our findings confirmed the high genetic variability inside the CCHF genotypes and their introduction to Senegal from other countries. They also indicate an increasing CCHF threat in Senegal and emphasize the need to reinforce surveillance using a one-health approach.
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Affiliation(s)
- Ousseynou Sene
- WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fevers, Virology Department, Pasteur Institute, Dakar 12900, Senegal; (O.S.); (M.M.D.); (S.S.); (N.D.); (A.A.S.); (O.F.); (O.F.)
| | - Samba Niang Sagne
- Epidemiology, Clinical Research & Data Science, Pasteur Institute, Dakar 12900, Senegal; (S.N.S.); (C.L.); (M.A.B.)
| | - Déthié Ngom
- Zoology Department, Pasteur Institute, Dakar 12900, Senegal; (D.N.); (A.B.); (A.K.); (E.H.N.); (M.D.); (D.D.)
| | - Moussa Moise Diagne
- WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fevers, Virology Department, Pasteur Institute, Dakar 12900, Senegal; (O.S.); (M.M.D.); (S.S.); (N.D.); (A.A.S.); (O.F.); (O.F.)
| | - Aminata Badji
- Zoology Department, Pasteur Institute, Dakar 12900, Senegal; (D.N.); (A.B.); (A.K.); (E.H.N.); (M.D.); (D.D.)
| | - Aliou Khoulé
- Zoology Department, Pasteur Institute, Dakar 12900, Senegal; (D.N.); (A.B.); (A.K.); (E.H.N.); (M.D.); (D.D.)
| | - El Hadji Ndiaye
- Zoology Department, Pasteur Institute, Dakar 12900, Senegal; (D.N.); (A.B.); (A.K.); (E.H.N.); (M.D.); (D.D.)
| | - Safietou Sankhe
- WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fevers, Virology Department, Pasteur Institute, Dakar 12900, Senegal; (O.S.); (M.M.D.); (S.S.); (N.D.); (A.A.S.); (O.F.); (O.F.)
| | - Cheikh Loucoubar
- Epidemiology, Clinical Research & Data Science, Pasteur Institute, Dakar 12900, Senegal; (S.N.S.); (C.L.); (M.A.B.)
| | - Mawlouth Diallo
- Zoology Department, Pasteur Institute, Dakar 12900, Senegal; (D.N.); (A.B.); (A.K.); (E.H.N.); (M.D.); (D.D.)
| | - Manfred Weidmann
- Institute of Microbiology and Virology, Brandenburg Medical School, 01968 Brandenburg, Germany;
| | - Ndongo Dia
- WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fevers, Virology Department, Pasteur Institute, Dakar 12900, Senegal; (O.S.); (M.M.D.); (S.S.); (N.D.); (A.A.S.); (O.F.); (O.F.)
| | | | - Yoro Sall
- Ministry of Health, Dakar 10700, Senegal; (Y.S.); (B.D.); (M.N.)
| | - Boly Diop
- Ministry of Health, Dakar 10700, Senegal; (Y.S.); (B.D.); (M.N.)
| | - Mamadou Ndiaye
- Ministry of Health, Dakar 10700, Senegal; (Y.S.); (B.D.); (M.N.)
| | - Anavaj Sakuntabhai
- Functional Genetics of Infectious Disease Unit, Pasteur Institute, 75015 Paris, France;
- Centre National de la Recherche Scientifique (CNRS), UMR2000, Department of Global Health, 75015 Paris, France
- International Vaccine Design Center (vDesC), The Institute of Medical Science, The University of Tokyo (IMSUT), Tokyo 108-8639, Japan
| | - Amadou Alpha Sall
- WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fevers, Virology Department, Pasteur Institute, Dakar 12900, Senegal; (O.S.); (M.M.D.); (S.S.); (N.D.); (A.A.S.); (O.F.); (O.F.)
| | - Ousmane Faye
- WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fevers, Virology Department, Pasteur Institute, Dakar 12900, Senegal; (O.S.); (M.M.D.); (S.S.); (N.D.); (A.A.S.); (O.F.); (O.F.)
| | - Oumar Faye
- WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fevers, Virology Department, Pasteur Institute, Dakar 12900, Senegal; (O.S.); (M.M.D.); (S.S.); (N.D.); (A.A.S.); (O.F.); (O.F.)
| | - Diawo Diallo
- Zoology Department, Pasteur Institute, Dakar 12900, Senegal; (D.N.); (A.B.); (A.K.); (E.H.N.); (M.D.); (D.D.)
| | - Mamadou Aliou Barry
- Epidemiology, Clinical Research & Data Science, Pasteur Institute, Dakar 12900, Senegal; (S.N.S.); (C.L.); (M.A.B.)
| | - Gamou Fall
- WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fevers, Virology Department, Pasteur Institute, Dakar 12900, Senegal; (O.S.); (M.M.D.); (S.S.); (N.D.); (A.A.S.); (O.F.); (O.F.)
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2
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Lind K, Mölsä M, Kalin-Mänttäri L, Hemmilä H, Voutilainen L, Nikkari S. Vacuum Oven Drying: A Cost-Effective Way of Producing Field-Deployable Reagents for In-house Real-Time PCR Methods. Mol Biotechnol 2023:10.1007/s12033-023-00999-2. [PMID: 38135831 DOI: 10.1007/s12033-023-00999-2] [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: 03/16/2023] [Accepted: 11/24/2023] [Indexed: 12/24/2023]
Abstract
The polymerase chain reaction (PCR), is a widely used, sensitive and reliable method for detecting pathogens. However, technical limitations may restrict its use outside sophisticated laboratories, e.g. for detecting pathogens at the site of a disease outbreak. In this study, real-time PCR reagents specific to four bacteria (Bacillus anthracis, Yersinia pestis, Francisella tularensis, and Brucella spp.) and to the Influenza A virus were dried using a vacuum oven drying method. The performance of the dried reagents stored at different temperatures, was monitored using both a standard-size and a portable real-time PCR instrument. The vacuum oven dried real-time PCR reagents were stable and retained the sensitivity for at least 14 months when stored in a refrigerator (+ 4 °C). When stored at room temperature, DNA assays remained stable for at least 10 weeks and Influenza A RNA assay for 3 weeks. These results demonstrate the feasibility of vacuum oven dried real-time PCR reagents and a portable thermocycler for the rapid and reliable detection of pathogens. The drying protocol presented here is cost-effective and easy to use, and could be applied to real-time PCR methods specific to other pathogens as well. In addition, this in-house drying protocol reduces reliance on commercial PCR tests during a time of shortage, such as that experienced during the Corovirus disease (COVID-19) crisis.
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Affiliation(s)
- Katja Lind
- Centre for Military Medicine, Finnish Defence Forces, P.O. Box 50, 00301, Helsinki, Finland.
- Finnish Institute for Health and Welfare, P.O. Box 30, 00271, Helsinki, Finland.
| | - Markos Mölsä
- Centre for Military Medicine, Finnish Defence Forces, P.O. Box 50, 00301, Helsinki, Finland
| | | | - Heidi Hemmilä
- Centre for Military Medicine, Finnish Defence Forces, P.O. Box 50, 00301, Helsinki, Finland
| | - Liina Voutilainen
- Finnish Institute for Health and Welfare, P.O. Box 30, 00271, Helsinki, Finland
| | - Simo Nikkari
- Centre for Military Medicine, Finnish Defence Forces, P.O. Box 50, 00301, Helsinki, Finland
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Mhamadi M, Mencattelli G, Gaye A, Ndiaye EH, Sow AA, Faye M, Ndione MHD, Diagne MM, Mhamadi M, Faye O, Weidmann M, Faye O, Diallo M, Diagne CT. Rapid On-Site Detection of Arboviruses by a Direct RT-qPCR Assay. BIOSENSORS 2023; 13:1035. [PMID: 38131795 PMCID: PMC10741549 DOI: 10.3390/bios13121035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 10/23/2023] [Accepted: 10/27/2023] [Indexed: 12/23/2023]
Abstract
Arthropod-borne diseases currently constitute a source of major health concerns worldwide. They account for about 50% of global infectious diseases and cause nearly 700,000 deaths every year. Their rapid increase and spread constitute a huge challenge for public health, highlighting the need for early detection during epidemics, to curtail the virus spread, and to enhance outbreak management. Here, we compared a standard quantitative polymerase chain reaction (RT-qPCR) and a direct RT-qPCR assay for the detection of Zika (ZIKV), Chikungunya (CHIKV), and Rift Valley Fever (RVFV) viruses from experimentally infected-mosquitoes. The direct RT-qPCR could be completed within 1.5 h and required 1 µL of viral supernatant from homogenized mosquito body pools. Results showed that the direct RT-qPCR can detect 85.71%, 89%, and 100% of CHIKV, RVFV, and ZIKV samples by direct amplifications compared to the standard method. The use of 1:10 diluted supernatant is suggested for CHIKV and RVFV direct RT-qPCR. Despite a slight drop in sensitivity for direct PCR, our technique is more affordable, less time-consuming, and provides a better option for qualitative field diagnosis during outbreak management. It represents an alternative when extraction and purification steps are not possible because of insufficient sample volume or biosecurity issues.
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Affiliation(s)
- Moufid Mhamadi
- Department of Virology, Fondation Institut Pasteur de Dakar 36, Avenue Pasteur, Dakar 220, Senegal; (G.M.); (A.A.S.); (M.F.); (M.H.D.N.); (M.M.D.); (O.F.); (O.F.)
| | - Giulia Mencattelli
- Department of Virology, Fondation Institut Pasteur de Dakar 36, Avenue Pasteur, Dakar 220, Senegal; (G.M.); (A.A.S.); (M.F.); (M.H.D.N.); (M.M.D.); (O.F.); (O.F.)
| | - Alioune Gaye
- Department of Medical Zoology, Fondation Institut Pasteur de Dakar 36, Avenue Pasteur, Dakar 220, Senegal; (A.G.); (E.H.N.)
| | - El Hadji Ndiaye
- Department of Medical Zoology, Fondation Institut Pasteur de Dakar 36, Avenue Pasteur, Dakar 220, Senegal; (A.G.); (E.H.N.)
| | - Aïssatou Aïcha Sow
- Department of Virology, Fondation Institut Pasteur de Dakar 36, Avenue Pasteur, Dakar 220, Senegal; (G.M.); (A.A.S.); (M.F.); (M.H.D.N.); (M.M.D.); (O.F.); (O.F.)
| | - Martin Faye
- Department of Virology, Fondation Institut Pasteur de Dakar 36, Avenue Pasteur, Dakar 220, Senegal; (G.M.); (A.A.S.); (M.F.); (M.H.D.N.); (M.M.D.); (O.F.); (O.F.)
| | - Marie Henriette Dior Ndione
- Department of Virology, Fondation Institut Pasteur de Dakar 36, Avenue Pasteur, Dakar 220, Senegal; (G.M.); (A.A.S.); (M.F.); (M.H.D.N.); (M.M.D.); (O.F.); (O.F.)
| | - Moussa Moïse Diagne
- Department of Virology, Fondation Institut Pasteur de Dakar 36, Avenue Pasteur, Dakar 220, Senegal; (G.M.); (A.A.S.); (M.F.); (M.H.D.N.); (M.M.D.); (O.F.); (O.F.)
| | - Moundhir Mhamadi
- DIATROPIX, Fondation Institut Pasteur de Dakar 36, Avenue Pasteur, Dakar 220, Senegal; (M.M.); (M.D.)
| | - Ousmane Faye
- Department of Virology, Fondation Institut Pasteur de Dakar 36, Avenue Pasteur, Dakar 220, Senegal; (G.M.); (A.A.S.); (M.F.); (M.H.D.N.); (M.M.D.); (O.F.); (O.F.)
| | - Manfred Weidmann
- Institute of Microbiology and Virology, Brandenburg Medical School Theodor Fontane, 01968 Senftenberg, Germany;
| | - Oumar Faye
- Department of Virology, Fondation Institut Pasteur de Dakar 36, Avenue Pasteur, Dakar 220, Senegal; (G.M.); (A.A.S.); (M.F.); (M.H.D.N.); (M.M.D.); (O.F.); (O.F.)
| | - Mawlouth Diallo
- DIATROPIX, Fondation Institut Pasteur de Dakar 36, Avenue Pasteur, Dakar 220, Senegal; (M.M.); (M.D.)
| | - Cheikh Tidiane Diagne
- Department of Virology, Fondation Institut Pasteur de Dakar 36, Avenue Pasteur, Dakar 220, Senegal; (G.M.); (A.A.S.); (M.F.); (M.H.D.N.); (M.M.D.); (O.F.); (O.F.)
- DIATROPIX, Fondation Institut Pasteur de Dakar 36, Avenue Pasteur, Dakar 220, Senegal; (M.M.); (M.D.)
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4
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Feng X, Liu Y, Zhao Y, Sun Z, Xu N, Zhao C, Xia W. Recombinase Polymerase Amplification-Based Biosensors for Rapid Zoonoses Screening. Int J Nanomedicine 2023; 18:6311-6331. [PMID: 37954459 PMCID: PMC10637217 DOI: 10.2147/ijn.s434197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Accepted: 10/21/2023] [Indexed: 11/14/2023] Open
Abstract
Recent, outbreaks of new emergency zoonotic diseases have prompted an urgent need to develop fast, accurate, and portable screening assays for pathogen infections. Recombinase polymerase amplification (RPA) is sensitive and specific and can be conducted at a constant low temperature with a short response time, making it especially suitable for on-site screening and making it a powerful tool for preventing or controlling the spread of zoonoses. This review summarizes the design principles of RPA-based biosensors as well as various signal output or readout technologies involved in fluorescence detection, lateral flow assays, enzymatic catalytic reactions, spectroscopic techniques, electrochemical techniques, chemiluminescence, nanopore sequencing technologies, microfluidic digital RPA, and clustered regularly interspaced short palindromic repeats/CRISPR-associated systems. The current status and prospects of the application of RPA-based biosensors in zoonoses screening are highlighted. RPA-based biosensors demonstrate the advantages of rapid response, easy-to-read result output, and easy implementation for on-site detection, enabling development toward greater portability, automation, and miniaturization. Although there are still problems such as high cost with unstable signal output, RPA-based biosensors are increasingly becoming one of the most important means of on-site pathogen screening in complex samples involving environmental, water, food, animal, and human samples for controlling the spread of zoonotic diseases.
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Affiliation(s)
- Xinrui Feng
- College of Public Health, Jilin Medical University, Jilin, 132013, People’s Republic of China
- Medical College, Yanbian University, Yanji, 136200, People’s Republic of China
| | - Yan Liu
- College of Public Health, Jilin Medical University, Jilin, 132013, People’s Republic of China
| | - Yang Zhao
- Department of Emergency and Intensive Medicine, No. 965 Hospital of PLA Joint Logistic Support Force, Jilin, 132013, People’s Republic of China
| | - Zhe Sun
- College of Public Health, Jilin Medical University, Jilin, 132013, People’s Republic of China
- College of Medical Technology, Beihua University, Jilin, 132013, People’s Republic of China
| | - Ning Xu
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, 130062, People’s Republic of China
| | - Chen Zhao
- College of Public Health, Jilin Medical University, Jilin, 132013, People’s Republic of China
| | - Wei Xia
- College of Medical Technology, Beihua University, Jilin, 132013, People’s Republic of China
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Reynes JM, Schaeffer L, Papadopoulos P, Ait-Ahmed M, Siby-Diakite D, Ripaux-Lefèvre M, Buivan TP, Lechat S, Vray M, Galempoix JM. Molecular Detection of Orthohantavirus puumalaense in Plasma and Urine Samples from Hospitalized Patients Presenting with a Serologically Confirmed Acute Hantavirus Infection in France. J Clin Microbiol 2023; 61:e0037223. [PMID: 37486218 PMCID: PMC10446862 DOI: 10.1128/jcm.00372-23] [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: 03/28/2023] [Accepted: 06/05/2023] [Indexed: 07/25/2023] Open
Abstract
Molecular detection of Orthohantavirus puumalaense (PUUV) RNA during the course of the disease has been studied in blood of patients in Sweden and Slovenia. The use of urine has been poorly investigated. The aims of this work were to study PUUV RNA detection in plasma from a cohort of patients in France where a different PUUV lineage circulates and to assess the use of urine instead of plasma. Matched plasma and urine samples were collected daily from hospitalized patients presenting with fever, pain, and thrombocytopenia within the last 8 days and testing positive for IgM and IgG against PUUV in serum collected at inclusion and/or approximately 1 month after release. RNA was extracted from samples, and PUUV RNA was detected using real-time reverse transcription-PCR for plasma and urine samples. Sixty-seven patients presented a serologically confirmed acute hantavirus infection. At inclusion, PUUV RNA was detected in plasma from 55 of 62 patients (88.7%) sampled within the first week after disease onset, whereas it was detected in 15 of 60 (25.0%) of matched urine samples. It was then detected from 33 (71.7%) and 2 (4.4%) of 46 patients discharged from the hospital during the second week after disease onset, in plasma and urine, respectively. When PUUV RNA was detected in urine it was also detected in plasma, and not vice versa. Detection of PUUV RNA in plasma from hospitalized patients in France is similar to that observed in Sweden and Slovenia. Urine is not an appropriate sample for this detection.
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Affiliation(s)
- Jean-Marc Reynes
- Institut Pasteur, Université Paris Cité, Unité Environnement et Risques Infectieux, Centre National de Référence Hantavirus, Paris, France
| | - Laura Schaeffer
- Institut Pasteur, Université Paris Cité, Unité Epidémiologie des Maladies Emergentes, Paris, France
| | - Pavlos Papadopoulos
- Institut Pasteur, Université Paris Cité, Unité Environnement et Risques Infectieux, Centre National de Référence Hantavirus, Paris, France
| | - Mohand Ait-Ahmed
- Institut Pasteur, Université Paris Cité, Centre de Recherche Translationnelle, Paris, France
| | - Dieyenaba Siby-Diakite
- Institut Pasteur, Université Paris Cité, Unité Environnement et Risques Infectieux, Centre National de Référence Hantavirus, Paris, France
| | - Maryline Ripaux-Lefèvre
- Institut Pasteur, Université Paris Cité, Unité Environnement et Risques Infectieux, Centre National de Référence Hantavirus, Paris, France
| | - Tan-Phuc Buivan
- Institut Pasteur, Université Paris Cité, Centre de Recherche Translationnelle, Paris, France
| | - Sylvie Lechat
- Centre Hospitalier Intercommunal nord Ardennes, Laboratoire de Biologie Médicale, Charleville- Mézières, France
| | - Muriel Vray
- Institut Pasteur, Université Paris Cité, Unité Epidémiologie des Maladies Emergentes, Paris, France
| | - Jean-Marc Galempoix
- Centre Hospitalier Intercommunal nord Ardennes, Service de Médecine Interne et Maladies Infectieuses, Charleville- Mézières, France
| | - for The HANTADIAG Study Group
- Institut Pasteur, Université Paris Cité, Unité Environnement et Risques Infectieux, Centre National de Référence Hantavirus, Paris, France
- Institut Pasteur, Université Paris Cité, Unité Epidémiologie des Maladies Emergentes, Paris, France
- Institut Pasteur, Université Paris Cité, Centre de Recherche Translationnelle, Paris, France
- Centre Hospitalier Intercommunal nord Ardennes, Laboratoire de Biologie Médicale, Charleville- Mézières, France
- Centre Hospitalier Intercommunal nord Ardennes, Service de Médecine Interne et Maladies Infectieuses, Charleville- Mézières, France
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6
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Crimean-Congo Hemorrhagic Fever Virus Survey in Humans, Ticks, and Livestock in Agnam (Northeastern Senegal) from February 2021 to March 2022. Trop Med Infect Dis 2022; 7:tropicalmed7100324. [PMID: 36288065 PMCID: PMC9610667 DOI: 10.3390/tropicalmed7100324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 10/14/2022] [Accepted: 10/15/2022] [Indexed: 11/16/2022] Open
Abstract
Crimean-Congo hemorrhagic fever virus (CCHFV) is widespread in Asia, Europe, and Africa. In Senegal, sporadic cases of CCHFV have been reported since 1960. Bordering Mauritania in northeastern Senegal, Agnam is an arid area in the region of Matam where CCHFV is endemic, which harbors a pastoralist community. Given the drought conditions of Agnam, inhabitants are in constant movement with their animals in search of pasture, which brings them into contact with pathogens such as arboviruses. To identify CCHFV in this area, we established a One Health site in order to analyze animal livestock, ticks and human samples collected over a one-year period by qRT-PCR and ELISA. Our analysis showed one (1/364) patient carried anti-CCHFV IgM and thirty-seven carried anti-CCHFV IgG (37/364). In livestock, anti-CCHFV IgG was detected in 13 (38.24%) of 34 sentinel sheep. The risk of CCHFV infection increased significatively with age in humans (p-value = 0.00117) and sheep (p-value = 1.18 × 10-11). Additional risk factors for CCHFV infection in sheep were dry seasons (p-value = 0.004) and time of exposure (p-value = 0.007). Furthermore, we detected a total of three samples with CCHFV RNA within Rhipicephalus evertsi evertsi and Rhipicephalus guilhoni tick species. Our results highlighted the usefulness of a One Health survey of CCHFV in pastoral communities at risk of arboviruses.
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7
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Mhamadi M, Badji A, Dieng I, Gaye A, Ndiaye EH, Ndiaye M, Mhamadi M, Toure CT, Barry A, Ndiaye O, Faye B, Ba FA, Diop B, Ndiaye M, Sagne SN, Fall G, Loucoubar C, Bovendo HF, Sall AA, Kobinger G, Faye O, Diallo M, Faye O. Multiple genotypes of Crimean-Congo Hemorrhagic Fever Virus detected in ticks during a one health survey in Agnam, Northeastern Senegal. Emerg Microbes Infect 2022; 11:2711-2714. [PMID: 36268900 DOI: 10.1080/22221751.2022.2136537] [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: 11/03/2022]
Abstract
A Crimean-Congo Hemorrhagic Fever Virus (CCHFV) survey in Agnam (North Senegal) permits the detection of 3 isolates in ticks. These isolates belong genetically to multiple genotypes (I, II, III) and clustered with strains from Uganda, Sudan, Mauritania and Senegal. The role of ticks in CCHF emergence and widespread is highlighted.
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Affiliation(s)
- Moufid Mhamadi
- Institut Pasteur de Dakar, virology department, Senegal.,Université Cheikh Anta Diop de Dakar, parasitology department, Senegal
| | - Aminata Badji
- Institut Pasteur de Dakar, medical zoology department, Senegal
| | - Idrissa Dieng
- Institut Pasteur de Dakar, virology department, Senegal
| | - Alioune Gaye
- Institut Pasteur de Dakar, medical zoology department, Senegal
| | - El Hadji Ndiaye
- Institut Pasteur de Dakar, medical zoology department, Senegal
| | | | | | | | - Aliou Barry
- Institut Pasteur de Dakar, Epidemiology, Clinical Research and Data Science department, Senegal
| | - Oumar Ndiaye
- Institut Pasteur de Dakar, virology department, Senegal.,Institut Pasteur de Dakar, DIATROPIX, Senegal
| | - Babacar Faye
- Université Cheikh Anta Diop de Dakar, parasitology department, Senegal
| | - Fatimata Amadou Ba
- Microbiology, Immunology and Infectious Pathology Service, Department of Public Health and Environment, EISMV of Dakar, Senegal
| | - Boly Diop
- Ministry of Health and Social Action
| | | | - Samba Niang Sagne
- Institut Pasteur de Dakar, Epidemiology, Clinical Research and Data Science department, Senegal
| | - Gamou Fall
- Institut Pasteur de Dakar, virology department, Senegal
| | - Cheikh Loucoubar
- Institut Pasteur de Dakar, Epidemiology, Clinical Research and Data Science department, Senegal
| | | | | | - Gary Kobinger
- University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Ousmane Faye
- Institut Pasteur de Dakar, virology department, Senegal
| | - Mawlouth Diallo
- Institut Pasteur de Dakar, medical zoology department, Senegal
| | - Oumar Faye
- Institut Pasteur de Dakar, virology department, Senegal
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8
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Yalley AK, Ahiatrogah S, Kafintu-Kwashie AA, Amegatcher G, Prah D, Botwe AK, Adusei-Poku MA, Obodai E, Nii-Trebi NI. A Systematic Review on Suitability of Molecular Techniques for Diagnosis and Research into Infectious Diseases of Concern in Resource-Limited Settings. Curr Issues Mol Biol 2022; 44:4367-4385. [PMID: 36286015 PMCID: PMC9601131 DOI: 10.3390/cimb44100300] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 09/15/2022] [Accepted: 09/16/2022] [Indexed: 11/16/2022] Open
Abstract
Infectious diseases significantly impact the health status of developing countries. Historically, infectious diseases of the tropics especially have received insufficient attention in worldwide public health initiatives, resulting in poor preventive and treatment options. Many molecular tests for human infections have been established since the 1980s, when polymerase chain reaction (PCR) testing was introduced. In spite of the substantial innovative advancements in PCR technology, which currently has found wide application in most viral pathogens of global concern, the development and application of molecular diagnostics, particularly in resource-limited settings, poses potential constraints. This review accessed data from sources including PubMed, Google Scholar, the Web of Knowledge, as well as reports from the World Health Organization’s Annual Meeting on infectious diseases and examined these for current molecular approaches used to identify, monitor, or investigate some neglected tropical infectious diseases. This review noted some growth efforts in the development of molecular techniques for diagnosis of pathogens that appear to be common in resource limited settings and identified gaps in the availability and applicability of most of these molecular diagnostics, which need to be addressed if the One Health goal is to be achieved.
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Affiliation(s)
- Akua K. Yalley
- Department of Medical Laboratory Sciences, School of Biomedical and Allied Health Sciences, University of Ghana, Accra P.O. Box KB 143, Ghana
| | - Selasie Ahiatrogah
- Department of Obstetrics and Gynaecology, College of Medicine, Pan African University of Life and Earth Sciences Institute, University of Ibadan, Ibadan P.O. Box 22133, Nigeria
| | - Anna A. Kafintu-Kwashie
- Department of Medical Microbiology, University of Ghana Medical School, Accra GA-221-1570, Ghana
| | - Gloria Amegatcher
- Department of Medical Laboratory Sciences, School of Biomedical and Allied Health Sciences, University of Ghana, Accra P.O. Box KB 143, Ghana
| | - Diana Prah
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra P.O. Box LG 54, Ghana
| | - Akua K. Botwe
- Molecular Biology Unit, Kintampo Health Research Centre, Ghana Health Service, Kintampo P.O. Box 200, Ghana
| | - Mildred A. Adusei-Poku
- Department of Medical Microbiology, University of Ghana Medical School, Accra GA-221-1570, Ghana
| | - Evangeline Obodai
- Department of Virology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra P.O. Box LG 581, Ghana
| | - Nicholas I. Nii-Trebi
- Department of Medical Laboratory Sciences, School of Biomedical and Allied Health Sciences, University of Ghana, Accra P.O. Box KB 143, Ghana
- Correspondence: ; Tel.: +233-54-827-6424
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9
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de Vries EM, Cogan NOI, Gubala AJ, Mee PT, O'Riley KJ, Rodoni BC, Lynch SE. Rapid, in-field deployable, avian influenza virus haemagglutinin characterisation tool using MinION technology. Sci Rep 2022; 12:11886. [PMID: 35831457 PMCID: PMC9279447 DOI: 10.1038/s41598-022-16048-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 07/04/2022] [Indexed: 11/29/2022] Open
Abstract
Outbreaks of avian influenza virus (AIV) from wild waterfowl into the poultry industry is of upmost significance and is an ongoing and constant threat to the industry. Accurate surveillance of AIV in wild waterfowl is critical in understanding viral diversity in the natural reservoir. Current surveillance methods for AIV involve collection of samples and transportation to a laboratory for molecular diagnostics. Processing of samples using this approach takes more than three days and may limit testing locations to those with practical access to laboratories. In potential outbreak situations, response times are critical, and delays have implications in terms of the spread of the virus that leads to increased economic cost. This study used nanopore sequencing technology for in-field sequencing and subtype characterisation of AIV strains collected from wild bird faeces and poultry. A custom in-field virus screening and sequencing protocol, including a targeted offline bioinformatic pipeline, was developed to accurately subtype AIV. Due to the lack of optimal diagnostic MinION packages for Australian AIV strains the bioinformatic pipeline was specifically targeted to confidently subtype local strains. The method presented eliminates the transportation of samples, dependence on internet access and delivers critical diagnostic information in a timely manner.
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Affiliation(s)
- Ellen M de Vries
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia. .,School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia.
| | - Noel O I Cogan
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia.,School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia
| | - Aneta J Gubala
- Land Division, Defence Science & Technology Group, Fishermans Bend, VIC, 3207, Australia
| | - Peter T Mee
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Kim J O'Riley
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Brendan C Rodoni
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia.,School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia
| | - Stacey E Lynch
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
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10
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Surveillance of Viral Encephalitis in the Context of COVID-19: A One-Year Observational Study among Hospitalized Patients in Dakar, Senegal. Viruses 2022; 14:v14050871. [PMID: 35632613 PMCID: PMC9145710 DOI: 10.3390/v14050871] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 04/20/2022] [Accepted: 04/20/2022] [Indexed: 02/05/2023] Open
Abstract
The burden of encephalitis and its associated viral etiology is poorly described in Africa. Moreover, neurological manifestations of COVID-19 are increasingly reported in many countries, but less so in Africa. Our prospective study aimed to characterize the main viral etiologies of patients hospitalized for encephalitis in two hospitals in Dakar. From January to December 2021, all adult patients that met the inclusion criteria for clinical infectious encephalitis were enrolled. Cerebrospinal fluids, blood, and nasopharyngeal swabs were taken and tested for 27 viruses. During the study period, 122 patients were enrolled. Viral etiology was confirmed or probable in 27 patients (22.1%), with SARS-CoV-2 (n = 8), HSV-1 (n = 7), HHV-7 (n = 5), and EBV (n = 4) being the most detected viruses. Age groups 40–49 was more likely to be positive for at least one virus with an odds ratio of 7.7. The mortality was high among infected patients, with 11 (41%) deaths notified during hospitalization. Interestingly, SARS-CoV-2 was the most prevalent virus in hospitalized patients presenting with encephalitis. Our results reveal the crucial need to establish a country-wide surveillance of encephalitis in Senegal to estimate the burden of this disease in our population and implement strategies to improve care and reduce mortality.
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11
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Goarant C, Dellagi K, Picardeau M. Ending the Neglect of Treatable Bacterial Zoonoses Responsible for Non-Malaria Fevers. THE YALE JOURNAL OF BIOLOGY AND MEDICINE 2021; 94:351-360. [PMID: 34211354 PMCID: PMC8223548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Bacterial zoonotic diseases such as leptospirosis, Q fever, melioidosis, spotted
fever group rickettsioses, and brucellosis are increasingly recognized causes of
non-malaria acute fevers. However, though readily treatable with antibiotics,
these diseases are commonly misdiagnosed resulting in poor outcomes in patients.
There is a considerable deficit in the understanding of basic aspects of the
epidemiology of these neglected diseases and diagnostic tests for these zoonotic
bacterial pathogens are not always available in resource-poor settings. Raising
awareness about these emerging bacterial zoonoses is directly beneficial to the
patients by allowing a test-and-treat approach and is essential to control these
life-threatening diseases.
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Affiliation(s)
- Cyrille Goarant
- Institut Pasteur de Nouvelle-Calédonie, Unité de Recherche et d'Expertise sur la Leptospirose, Nouméa, New Caledonia
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12
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Frimpong M, Amoako YA, Anim KB, Ahor HS, Yeboah R, Arthur J, Dakorah JS, Gborgblovor D, Akrofi S, Sekyi-Djan P, Owusu M, Sylverken AA, Binger T, Phillips RO. Diagnostics for COVID-19: A case for field-deployable, rapid molecular tests for community surveillance. Ghana Med J 2021; 54:71-76. [PMID: 33976444 PMCID: PMC8087371 DOI: 10.4314/gmj.v54i4s.11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Across the globe, the outbreak of the COVID-19 pandemic is causing distress with governments doing everything in their power to contain the spread of the novel coronavirus (SARS-CoV-2) to prevent morbidity and mortality. Actions are being implemented to keep health care systems from being overstretched and to curb the outbreak. Any policy responses aimed at slowing down the spread of the virus and mitigating its immediate effects on health care systems require a firm basis of information about the absolute number of currently infected people, growth rates, and locations/hotspots of infections. The only way to obtain this base of information is by conducting numerous tests in a targeted way. Currently, in Ghana, there is a centralized testing approach, that takes 4–5 days for samples to be shipped and tested at central reference laboratories with results communicated to the district, regional and national stakeholders. This delay in diagnosis increases the risk of ongoing transmission in communities and vulnerable institutions. We have validated, evaluated and deployed an innovative diagnostic tool on a mobile laboratory platform to accelerate the COVID-19 testing. A preliminary result of 74 samples from COVID-19 suspected cases has a positivity rate of 12% with a turn-around time of fewer than 3 hours from sample taking to reporting of results, significantly reducing the waiting time from days to hours, enabling expedient response by the health system for contact tracing to reduce transmission and additionally improving case management.
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Affiliation(s)
- Michael Frimpong
- Kumasi Centre for Collaborative Research, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana.,Department of Molecular Medicine, KNUST School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Yaw A Amoako
- Kumasi Centre for Collaborative Research, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana.,Department of Medicine, Komfo Anokye Teaching Hospital, Kumasi, Ghana
| | - Kwadwo B Anim
- AngloGold Ashanti Health Foundation, AngloGold Ashanti Obuasi Mine, Obuasi, Ghana.,Obuasi Health Directorates, Ghana Health Service, Obuasi, Ghana
| | - Hubert S Ahor
- Kumasi Centre for Collaborative Research, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana.,Department of Molecular Medicine, KNUST School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Richmond Yeboah
- Kumasi Centre for Collaborative Research, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Joshua Arthur
- Public Health, Komfo Anokye Teaching Hospital, Kumasi, Ghana
| | - Justin S Dakorah
- AngloGold Ashanti Health Foundation, AngloGold Ashanti Obuasi Mine, Obuasi, Ghana.,Obuasi Health Directorates, Ghana Health Service, Obuasi, Ghana
| | | | - Samuel Akrofi
- Customs Laboratory, Ghana Revenue Authority, Accra, Ghana
| | | | - Michael Owusu
- Kumasi Centre for Collaborative Research, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Augustina A Sylverken
- Kumasi Centre for Collaborative Research, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana.,Department of Theoretical and Applied Biology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Tabea Binger
- Kumasi Centre for Collaborative Research, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Richard O Phillips
- Kumasi Centre for Collaborative Research, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana.,Department of Medicine, Komfo Anokye Teaching Hospital, Kumasi, Ghana
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13
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Xing W, Wang J, Zhao C, Wang H, Bai L, Pan L, Li H, Wang H, Zhang Z, Lu Y, Chen X, Shan S, Wang D, Pan Y, Weng D, Zhou X, Huang R, He J, Jin R, Li W, Shang H, Zhong N, Cheng J. A Highly Automated Mobile Laboratory for On-site Molecular Diagnostics in the COVID-19 Pandemic. Clin Chem 2021; 67:672-683. [PMID: 33788940 PMCID: PMC8083610 DOI: 10.1093/clinchem/hvab027] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Accepted: 02/01/2021] [Indexed: 02/05/2023]
Abstract
BACKGROUND Infectious disease outbreaks such as the COVID-19 (coronavirus disease 2019) pandemic call for rapid response and complete screening of the suspected community population to identify potential carriers of pathogens. Central laboratories rely on time-consuming sample collection methods that are rarely available in resource-limited settings. METHODS We present a highly automated and fully integrated mobile laboratory for fast deployment in response to infectious disease outbreaks. The mobile laboratory was equipped with a 6-axis robot arm for automated oropharyngeal swab specimen collection; virus in the collected specimen was inactivated rapidly using an infrared heating module. Nucleic acid extraction and nested isothermal amplification were performed by a "sample in, answer out" laboratory-on-a-chip system, and the result was automatically reported by the onboard information platform. Each module was evaluated using pseudovirus or clinical samples. RESULTS The mobile laboratory was stand-alone and self-sustaining and capable of on-site specimen collection, inactivation, analysis, and reporting. The automated sampling robot arm achieved sampling efficiency comparable to manual collection. The collected samples were inactivated in as short as 12 min with efficiency comparable to a water bath without damage to nucleic acid integrity. The limit of detection of the integrated microfluidic nucleic acid analyzer reached 150 copies/mL within 45 min. Clinical evaluation of the onboard microfluidic nucleic acid analyzer demonstrated good consistency with reverse transcription quantitative PCR with a κ coefficient of 0.979. CONCLUSIONS The mobile laboratory provides a promising solution for fast deployment of medical diagnostic resources at critical junctions of infectious disease outbreaks and facilitates local containment of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) transmission.
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Affiliation(s)
- Wanli Xing
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing, China
- National Engineering Research Center for Beijing Biochip Technology, Beijing, China
- CapitalBio Technology, Beijing, China
| | - Jiadao Wang
- State Key Laboratory of Tribology, Tsinghua University, Beijing, China
| | - Chao Zhao
- Department of Industrial Design, Academy of Arts & Design, Tsinghua University, Beijing, China
| | - Han Wang
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing, China
| | - Liang Bai
- CapitalBio Technology, Beijing, China
| | - Liangbin Pan
- National Engineering Research Center for Beijing Biochip Technology, Beijing, China
- CapitalBio Technology, Beijing, China
| | - Hang Li
- National Engineering Research Center for Beijing Biochip Technology, Beijing, China
| | - Huili Wang
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing, China
| | - Zhi Zhang
- National Engineering Research Center for Beijing Biochip Technology, Beijing, China
| | - Ying Lu
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing, China
| | | | - Sisi Shan
- Center for Global Health and Infectious Diseases, Comprehensive AIDS Research Center, Beijing, Advanced Innovation Center for Structural Biology, School of Medicine, Tsinghua University, Beijing, China
| | - Dong Wang
- National Engineering Research Center for Beijing Biochip Technology, Beijing, China
| | - Yifei Pan
- National Engineering Research Center for Beijing Biochip Technology, Beijing, China
| | - Ding Weng
- State Key Laboratory of Tribology, Tsinghua University, Beijing, China
| | | | - Rudan Huang
- National Engineering Research Center for Beijing Biochip Technology, Beijing, China
| | - Jianxing He
- State Key Laboratory of Respiratory Disease and National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Ronghua Jin
- Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Weimin Li
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Hong Shang
- National Clinical Research Center for Laboratory Medicine, The First Affiliated Hospital of China Medical University, No 155, Nanjing North Street, Heping District, Shenyang, Liaoning Province, China
| | - Nanshan Zhong
- State Key Laboratory of Respiratory Disease/National Clinical Research Center for Respiratory Disease/National Center for Respiratory Medicine/Guangzhou Institute of Respiratory Health/The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jing Cheng
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing, China
- National Engineering Research Center for Beijing Biochip Technology, Beijing, China
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14
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Faye M, Abd El Wahed A, Faye O, Kissenkötter J, Hoffmann B, Sall AA, Faye O. A recombinase polymerase amplification assay for rapid detection of rabies virus. Sci Rep 2021; 11:3131. [PMID: 33542337 PMCID: PMC7862592 DOI: 10.1038/s41598-021-82479-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 01/13/2021] [Indexed: 11/09/2022] Open
Abstract
Rabies is a generally fatal encephalitis caused by a negative-sense single-stranded RNA lyssavirus transmitted to humans mainly from dog bite. Despite the recommendation by WHO and OIE to use the direct immunofluorescence test as standard method, molecular diagnostic assays like reverse transcription quantitative polymerase chain reaction (RT-qPCR) are increasing as a confirmatory method. However, both technologies are inaccessible in resource-limited settings. Moreover, the available point-of-need molecular assay is of poor detection limit for African strains. Herein, we developed a reverse transcription recombinase polymerase amplification (RT-RPA) assay as potential point-of-need diagnostic tool for rapid detection of various strains of rabies virus including locally isolated African strains. The sensitivity and specificity of the method was evaluated using a molecular RNA standard and different Rabies-related viruses belonging to the Rhabdoviridea family, respectively. The RABV-RPA performances were evaluated on isolates representative of the existing diversity and viral dilutions spiked in non-neural clinical specimen. The results were compared with RT-qPCR as a gold standard. The RABV-RPA detected down to 4 RNA molecules per reaction in 95% of the cases in less than 10 min. The RABV-RPA assay is highly specific as various RABV isolates were identified, but no amplification was observed for other member of the Rhabdoviridea family. The sample background did not affect the performance of the RABV-RPA as down to 11 RNA molecules were identified, which is similar to the RT-qPCR results. Our developed assay is suitable for use in low-resource settings as a promising alternative tool for ante-mortem rabies diagnosis in humans for facilitating timely control decisions.
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Affiliation(s)
- Martin Faye
- Virology Department, Institut Pasteur de Dakar, 36, Avenue Pasteur, 220, Dakar, Senegal.
| | - Ahmed Abd El Wahed
- Virology Lab, Division of Microbiology and Animal Hygiene, University of Göttingen, Göttingen, Germany.,Institute of Animal Hygiene and Veterinary Public Health, University of Leipzig, Leipzig, Germany
| | - Oumar Faye
- Virology Department, Institut Pasteur de Dakar, 36, Avenue Pasteur, 220, Dakar, Senegal
| | - Jonas Kissenkötter
- Virology Lab, Division of Microbiology and Animal Hygiene, University of Göttingen, Göttingen, Germany
| | - Bernd Hoffmann
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institute, Greifswald-Insel Riems, Germany
| | - Amadou Alpha Sall
- Virology Department, Institut Pasteur de Dakar, 36, Avenue Pasteur, 220, Dakar, Senegal
| | - Ousmane Faye
- Virology Department, Institut Pasteur de Dakar, 36, Avenue Pasteur, 220, Dakar, Senegal
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15
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El Wahed AA, Patel P, Maier M, Pietsch C, Rüster D, Böhlken-Fascher S, Kissenkötter J, Behrmann O, Frimpong M, Diagne MM, Faye M, Dia N, Shalaby MA, Amer H, Elgamal M, Zaki A, Ismail G, Kaiser M, Corman VM, Niedrig M, Landt O, Faye O, Sall AA, Hufert FT, Truyen U, Liebert UG, Weidmann M. Suitcase Lab for Rapid Detection of SARS-CoV-2 Based on Recombinase Polymerase Amplification Assay. Anal Chem 2021; 93:2627-2634. [PMID: 33471510 PMCID: PMC7839158 DOI: 10.1021/acs.analchem.0c04779] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 01/11/2021] [Indexed: 12/30/2022]
Abstract
In March 2020, the SARS-CoV-2 virus outbreak was declared as a world pandemic by the World Health Organization (WHO). The only measures for controlling the outbreak are testing and isolation of infected cases. Molecular real-time polymerase chain reaction (PCR) assays are very sensitive but require highly equipped laboratories and well-trained personnel. In this study, a rapid point-of-need detection method was developed to detect the RNA-dependent RNA polymerase (RdRP), envelope protein (E), and nucleocapsid protein (N) genes of SARS-CoV-2 based on the reverse transcription recombinase polymerase amplification (RT-RPA) assay. RdRP, E, and N RT-RPA assays required approximately 15 min to amplify 2, 15, and 15 RNA molecules of molecular standard/reaction, respectively. RdRP and E RT-RPA assays detected SARS-CoV-1 and 2 genomic RNA, whereas the N RT-RPA assay identified only SARS-CoV-2 RNA. All established assays did not cross-react with nucleic acids of other respiratory pathogens. The RT-RPA assay's clinical sensitivity and specificity in comparison to real-time RT-PCR (n = 36) were 94 and 100% for RdRP; 65 and 77% for E; and 83 and 94% for the N RT-RPA assay. The assays were deployed to the field, where the RdRP RT-RPA assays confirmed to produce the most accurate results in three different laboratories in Africa (n = 89). The RPA assays were run in a mobile suitcase laboratory to facilitate the deployment at point of need. The assays can contribute to speed up the control measures as well as assist in the detection of COVID-19 cases in low-resource settings.
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Affiliation(s)
- Ahmed Abd El Wahed
- Institute
of Animal Hygiene and Veterinary Public Health, University of Leipzig, 04103 Leipzig, Germany
- Division
of Microbiology and Animal Hygiene, Georg-August-University, 37077 Goettingen, Germany
| | - Pranav Patel
- Expert
Molecular Diagnostics, 82256Fürstenfeldbruck, Germany
| | - Melanie Maier
- Institute
of Medical Microbiology and VirologyLeipzig
University Hospital, 04103 Leipzig, Germany
| | - Corinna Pietsch
- Institute
of Medical Microbiology and VirologyLeipzig
University Hospital, 04103 Leipzig, Germany
| | - Dana Rüster
- Institute
of Animal Hygiene and Veterinary Public Health, University of Leipzig, 04103 Leipzig, Germany
| | - Susanne Böhlken-Fascher
- Division
of Microbiology and Animal Hygiene, Georg-August-University, 37077 Goettingen, Germany
| | - Jonas Kissenkötter
- Division
of Microbiology and Animal Hygiene, Georg-August-University, 37077 Goettingen, Germany
| | - Ole Behrmann
- Institute
of Microbiology & Virology, Brandenburg Medical School, 01968 Senftenberg, Germany
| | - Michael Frimpong
- Kumasi Centre
for Collaborative Research in Tropical Medicine, Department of Molecular
Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | | | - Martin Faye
- Virology
Department, Institute Pasteur de Dakar, BP 220, Dakar, Senegal
| | - Ndongo Dia
- Virology
Department, Institute Pasteur de Dakar, BP 220, Dakar, Senegal
| | - Mohamed A. Shalaby
- Virology
Department, Faculty of Veterinary Medicine, Cairo University, 12211 Giza, Egypt
| | - Haitham Amer
- Virology
Department, Faculty of Veterinary Medicine, Cairo University, 12211 Giza, Egypt
| | - Mahmoud Elgamal
- Virology
Department, Faculty of Veterinary Medicine, Cairo University, 12211 Giza, Egypt
| | - Ali Zaki
- Department
of Medical Microbiology and Immunology, Faculty of Medicine, Ain Shams University, 11591 Cairo, Egypt
| | - Ghada Ismail
- Department
of Clinical Pathology, Faculty of Medicine, Ain Shams University, 11591 Cairo, Egypt
| | - Marco Kaiser
- GenExpress Gesellschaft für Proteindesign, 12103 Berlin, Germany
| | - Victor M. Corman
- Charité−Universitätsmedizin
Berlin, Institute
of Virology, Berlin, Germany
- German Centre for Infection Research (DZIF), 10117 Berlin, Germany
| | | | | | - Ousmane Faye
- Virology
Department, Institute Pasteur de Dakar, BP 220, Dakar, Senegal
| | - Amadou A. Sall
- Virology
Department, Institute Pasteur de Dakar, BP 220, Dakar, Senegal
| | - Frank T. Hufert
- Institute
of Microbiology & Virology, Brandenburg Medical School, 01968 Senftenberg, Germany
| | - Uwe Truyen
- Institute
of Animal Hygiene and Veterinary Public Health, University of Leipzig, 04103 Leipzig, Germany
| | - Uwe G. Liebert
- Institute
of Medical Microbiology and VirologyLeipzig
University Hospital, 04103 Leipzig, Germany
| | - Manfred Weidmann
- Institute
of Microbiology & Virology, Brandenburg Medical School, 01968 Senftenberg, Germany
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16
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Frimpong M, Simpson SV, Ahor HS, Agbanyo A, Gyabaah S, Agbavor B, Amanor IB, Addo KK, Böhlken-Fascher S, Kissenkötter J, Wahed AAE, Phillips RO. Multiplex Recombinase Polymerase Amplification Assay for Simultaneous Detection of Treponema pallidum and Haemophilus ducreyi in Yaws-Like Lesions. Trop Med Infect Dis 2020; 5:tropicalmed5040157. [PMID: 33036234 PMCID: PMC7709673 DOI: 10.3390/tropicalmed5040157] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 09/28/2020] [Accepted: 09/29/2020] [Indexed: 11/22/2022] Open
Abstract
Yaws is a skin debilitating disease caused by Treponema pallidum subspecies pertenue with most cases reported in children. World Health Organization (WHO) aims at total eradication of this disease through mass treatment of suspected cases followed by an intensive follow-up program. However, effective diagnosis is pivotal in the successful implementation of this control program. Recombinase polymerase amplification (RPA), an isothermal nucleic acid amplification technique offers a wider range of differentiation of pathogens including those isolated from chronic skin ulcers with similar characteristics such as Haemophilus ducreyi (H. ducreyi). We have developed a RPA assay for the simultaneous detection of Treponema pallidum (T. pallidum) and H. ducreyi (TPHD-RPA). The assay demonstrated no cross-reaction with other pathogens and enable detection of T. pallidum and H. ducreyi within 15 min at 42 °C. The RPA assay was validated with 49 clinical samples from individuals confirmed to have yaws by serological tests. Comparing the developed assay with commercial multiplex real-time PCR, the assay demonstrated 94% and 95% sensitivity for T. pallidum and H. ducreyi, respectively and 100% specificity. This simple novel TPHD-RPA assay enables the rapid detection of both T. pallidum and H. ducreyi in yaws-like lesions. This test could support the yaws eradication efforts by ensuring reliable diagnosis, to enable monitoring of program success and planning of follow-up interventions at the community level.
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Affiliation(s)
- Michael Frimpong
- Department of Molecular Medicine, College of Health Sciences, Kwame Nkrumah University of Science and Technology, Kumasi AK-448, Ghana;
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi AK-312, Ghana; (A.A.); (S.G.); (B.A.); (R.O.P.)
- Correspondence:
| | - Shirley Victoria Simpson
- Bacteriology Department, Noguchi Memorial Institute of Medical Research, University of Ghana, Accra GA-337, Ghana; (S.V.S.); (I.B.A.); (K.K.A.)
| | - Hubert Senanu Ahor
- Department of Molecular Medicine, College of Health Sciences, Kwame Nkrumah University of Science and Technology, Kumasi AK-448, Ghana;
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi AK-312, Ghana; (A.A.); (S.G.); (B.A.); (R.O.P.)
| | - Abigail Agbanyo
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi AK-312, Ghana; (A.A.); (S.G.); (B.A.); (R.O.P.)
| | - Solomon Gyabaah
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi AK-312, Ghana; (A.A.); (S.G.); (B.A.); (R.O.P.)
| | - Bernadette Agbavor
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi AK-312, Ghana; (A.A.); (S.G.); (B.A.); (R.O.P.)
| | - Ivy Brago Amanor
- Bacteriology Department, Noguchi Memorial Institute of Medical Research, University of Ghana, Accra GA-337, Ghana; (S.V.S.); (I.B.A.); (K.K.A.)
| | - Kennedy Kwasi Addo
- Bacteriology Department, Noguchi Memorial Institute of Medical Research, University of Ghana, Accra GA-337, Ghana; (S.V.S.); (I.B.A.); (K.K.A.)
| | - Susanne Böhlken-Fascher
- Division of Microbiology and Animal Hygiene, Georg-August University, D-37077 Goettingen, Germany; (S.B.-F.); (J.K.); (A.A.E.W.)
| | - Jonas Kissenkötter
- Division of Microbiology and Animal Hygiene, Georg-August University, D-37077 Goettingen, Germany; (S.B.-F.); (J.K.); (A.A.E.W.)
| | - Ahmed Abd El Wahed
- Division of Microbiology and Animal Hygiene, Georg-August University, D-37077 Goettingen, Germany; (S.B.-F.); (J.K.); (A.A.E.W.)
- Institute of Animal Hygiene and Veterinary Public Health, University of Leipzig, D-04103 Leipzig, Germany
| | - Richard Odame Phillips
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi AK-312, Ghana; (A.A.); (S.G.); (B.A.); (R.O.P.)
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17
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Linster M, Ng B, Vijayan V. COVID-19 and Beyond: Safety and Design Considerations for the Development of a Mobile Biocontainment Laboratory. APPLIED BIOSAFETY 2020; 25:169-173. [DOI: 10.1177/1535676020943394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Martin Linster
- Duke-NUS Medical School, Emerging Infectious Diseases, Singapore
| | - Benson Ng
- Duke-NUS Medical School, Safety, Health, and Emergency Management, Singapore
| | - Viji Vijayan
- Duke-NUS Medical School, Safety, Health, and Emergency Management, Singapore
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Abstract
PURPOSE OF REVIEW Viral hemorrhagic fevers (VHF) encompass many organisms that have caused sporadic outbreaks with high case fatality rates. This article reviews VHF with reported human-to-human transmission and describes updates about personal protective equipment (PPE) for healthcare personnel (HCP) and others. We summarize existing information about appropriate PPE use, training, and compliance for care of VHF patients in endemic and nonendemic countries, as well as addresses the challenges HCP experience when using PPE. RECENT FINDINGS PPE is essential in protecting HCP from exposure to disease-causing pathogens. Recent evidence shows that anyone involved in care, management, and transport of certain VHF patients must use elements of PPE as part of appropriate infection prevention and control (IPC) practices. Strict adherence to standard precautions has effectively interrupted human-to-human transmission of a number of VHF. However, unclear protocols, inconsistent training, climate challenges, and cultural sensitivities impede proper PPE use. Appropriate PPE use can drastically reduce the risk of HCP exposure to VHF. SUMMARY Infections caused by certain VHFs can be highly pathogenic and associated with significant morbidity and mortality. Though it is well documented that use of PPE and good IPC practices are critical to reducing transmission, little conclusive evidence exists about the ideal PPE ensemble or components. Concerns with comfort, compliance, training, and usability may impede proper PPE use. Basic PPE elements, used appropriately as part of stringent IPC, must always form the foundation of care for HCP-treating patients with VHF. More research is required to identify the ideal PPE ensemble for caring for VHF patients in various settings.
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Dieng I, Hedible BG, Diagne MM, El Wahed AA, Diagne CT, Fall C, Richard V, Vray M, Weidmann M, Faye O, Sall AA, Faye O. Mobile Laboratory Reveals the Circulation of Dengue Virus Serotype I of Asian Origin in Medina Gounass (Guediawaye), Senegal. Diagnostics (Basel) 2020; 10:diagnostics10060408. [PMID: 32560073 PMCID: PMC7345902 DOI: 10.3390/diagnostics10060408] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 06/09/2020] [Accepted: 06/11/2020] [Indexed: 01/09/2023] Open
Abstract
With the growing success of controlling malaria in Sub-Saharan Africa, the incidence of fever due to malaria is in decline, whereas the proportion of patients with non-malaria febrile illness (NMFI) is increasing. Clinical diagnosis of NMFI is hampered by unspecific symptoms, but early diagnosis is a key factor for both better patient care and disease control. The aim of this study was to determine the arboviral aetiologies of NMFI in low resource settings, using a mobile laboratory based on recombinase polymerase amplification (RPA) assays. The panel of tests for this study was expanded to five arboviruses: dengue virus (DENV), zika virus (ZIKV), yellow fever virus (YFV), chikungunya virus (CHIKV), and rift valley fever virus (RVFV). One hundred and four children aged between one month and 115 months were enrolled and screened. Three of the 104 blood samples of children <10 years presented at an outpatient clinic tested positive for DENV. The results were confirmed by RT-PCR, partial sequencing, and non-structural protein 1 (NS1) antigen capture by ELISA (Biorad, France). Phylogenetic analysis of the derived DENV-1 sequences clustered them with sequences of DENV-1 isolated from Guangzhou, China, in 2014. In conclusion, this mobile setup proved reliable for the rapid identification of the causative agent of NMFI, with results consistent with those obtained in the reference laboratory’s settings.
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Affiliation(s)
- Idrissa Dieng
- Arboviruses and Hemorrhagic Fever Viruses Unit, Virology Department, Institut Pasteur de Dakar, BP220 Dakar, Senegal; (I.D.); (M.M.D.); (C.T.D.); (C.F.); (A.A.S.)
| | - Boris Gildas Hedible
- Epidemiology Unit, Institut Pasteur de Dakar, BP220 Dakar, Senegal; (B.G.H.); (V.R.); (M.V.)
| | - Moussa Moïse Diagne
- Arboviruses and Hemorrhagic Fever Viruses Unit, Virology Department, Institut Pasteur de Dakar, BP220 Dakar, Senegal; (I.D.); (M.M.D.); (C.T.D.); (C.F.); (A.A.S.)
| | - Ahmed Abd El Wahed
- Microbiology and Animal Hygiene, University of Goettingen, D-33077 Goettingen, Germany;
| | - Cheikh Tidiane Diagne
- Arboviruses and Hemorrhagic Fever Viruses Unit, Virology Department, Institut Pasteur de Dakar, BP220 Dakar, Senegal; (I.D.); (M.M.D.); (C.T.D.); (C.F.); (A.A.S.)
| | - Cheikh Fall
- Arboviruses and Hemorrhagic Fever Viruses Unit, Virology Department, Institut Pasteur de Dakar, BP220 Dakar, Senegal; (I.D.); (M.M.D.); (C.T.D.); (C.F.); (A.A.S.)
| | - Vicent Richard
- Epidemiology Unit, Institut Pasteur de Dakar, BP220 Dakar, Senegal; (B.G.H.); (V.R.); (M.V.)
| | - Muriel Vray
- Epidemiology Unit, Institut Pasteur de Dakar, BP220 Dakar, Senegal; (B.G.H.); (V.R.); (M.V.)
| | - Manfred Weidmann
- Institute of Aquaculture, University of Stirling, Scotland FK9 4LA, UK;
| | - Ousmane Faye
- Arboviruses and Hemorrhagic Fever Viruses Unit, Virology Department, Institut Pasteur de Dakar, BP220 Dakar, Senegal; (I.D.); (M.M.D.); (C.T.D.); (C.F.); (A.A.S.)
- Correspondence: (O.F.); (O.F.)
| | - Amadou Alpha Sall
- Arboviruses and Hemorrhagic Fever Viruses Unit, Virology Department, Institut Pasteur de Dakar, BP220 Dakar, Senegal; (I.D.); (M.M.D.); (C.T.D.); (C.F.); (A.A.S.)
| | - Oumar Faye
- Arboviruses and Hemorrhagic Fever Viruses Unit, Virology Department, Institut Pasteur de Dakar, BP220 Dakar, Senegal; (I.D.); (M.M.D.); (C.T.D.); (C.F.); (A.A.S.)
- Correspondence: (O.F.); (O.F.)
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20
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Kaestner L, Bianchi P. Trends in the Development of Diagnostic Tools for Red Blood Cell-Related Diseases and Anemias. Front Physiol 2020; 11:387. [PMID: 32528298 PMCID: PMC7264400 DOI: 10.3389/fphys.2020.00387] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 04/01/2020] [Indexed: 01/19/2023] Open
Abstract
In the recent years, the progress in genetic analysis and next-generation sequencing technologies have opened up exciting landscapes for diagnosis and study of molecular mechanisms, allowing the determination of a particular mutation for individual patients suffering from hereditary red blood cell-related diseases or anemia. However, the huge amount of data obtained makes the interpretation of the results and the identification of the pathogenetic variant responsible for the diseases sometime difficult. Moreover, there is increasing evidence that the same mutation can result in varying cellular properties and different symptoms of the disease. Even for the same patient, the phenotypic expression of the disorder can change over time. Therefore, on top of genetic analysis, there is a further request for functional tests that allow to confirm the pathogenicity of a molecular variant, possibly to predict prognosis and complications (e.g., vaso-occlusive pain crises or other thrombotic events) and, in the best case, to enable personalized theranostics (drug and/or dose) according to the disease state and progression. The mini-review will reflect recent and future directions in the development of diagnostic tools for red blood cell-related diseases and anemias. This includes point of care devices, new incarnations of well-known principles addressing physico-chemical properties, and interactions of red blood cells as well as high-tech screening equipment and mobile laboratories.
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Affiliation(s)
- Lars Kaestner
- Theoretical Medicine and Biosciences, Medical Faculty, Saarland University, Homburg, Germany.,Experimental Physics, Faculty of Natural Science and Technology, Saarland University, Saarbrücken, Germany
| | - Paola Bianchi
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico Milano, UOC Ematologia, UOS Fisiopatologia delle Anemie, Milan, Italy
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21
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Zidovec Lepej S, Poljak M. Portable molecular diagnostic instruments in microbiology: current status. Clin Microbiol Infect 2020; 26:411-420. [DOI: 10.1016/j.cmi.2019.09.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 09/16/2019] [Accepted: 09/17/2019] [Indexed: 12/25/2022]
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22
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Parra-Henao G, Oliveros H, Hotez PJ, Motoa G, Franco-Paredes C, Henao-Martínez AF. In Search of Congenital Chagas Disease in the Sierra Nevada de Santa Marta, Colombia. Am J Trop Med Hyg 2020; 101:482-483. [PMID: 31264558 DOI: 10.4269/ajtmh.19-0110] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Chagas disease remains a major impediment to sustainable socioeconomic development in Latin America. Transplacental transmission explains the persistence of transmission in urban areas, in non-endemic regions, and in areas with an established interrupted vectorial transmission. One of every five cases of congenital Chagas disease in the world occurs in Colombia and Venezuela. The massive migration of impoverished populations from neighboring Venezuela has worsened the situation creating a humanitarian crisis in Northeastern Colombia, including the Sierra Nevada de Santa Marta. The prevalence of Chagas infection among pregnant women in these areas is higher than the national average, and the public health resources are insufficient. This perspective discusses the associated increased morbidity and mortality of congenital Chagas in this region, where stigmatization contributes to the impression among health authorities and the general population that it affects indigenous communities only. The monitoring and control of congenital Chagas disease in the Sierra Nevada of Santa Marta is a public health necessity that demands urgent and effective interventions.
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Affiliation(s)
- Gabriel Parra-Henao
- Centro de Investigación en Salud para el Trópico (CIST), Universidad Cooperativa de Colombia, Santa Marta, Colombia
| | - Horacio Oliveros
- Centro de Investigación en Salud para el Trópico (CIST), Universidad Cooperativa de Colombia, Santa Marta, Colombia
| | - Peter J Hotez
- Department of Biology, Baylor University, Waco, Texas.,Department of Pediatrics, Texas Children's Hospital Center for Vaccine Development, National School of Tropical Medicine, Baylor College of Medicine, Houston, Texas
| | - Gabriel Motoa
- Division of Infectious Diseases, University of Colorado Denver, School of Medicine, Aurora, Colorado
| | - Carlos Franco-Paredes
- Hospital Infantil de México, Federico Gómez, México City, México.,Division of Infectious Diseases, University of Colorado Denver, School of Medicine, Aurora, Colorado
| | - Andrés F Henao-Martínez
- Division of Infectious Diseases, University of Colorado Denver, School of Medicine, Aurora, Colorado
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23
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Frimpong M, Ahor HS, Sakyi SA, Agbavor B, Akowuah E, Phillips RO. Rapid Extraction Method of Mycobacterium ulcerans DNA from Clinical Samples of Suspected Buruli Ulcer Patients. Diagnostics (Basel) 2019; 9:diagnostics9040204. [PMID: 31779247 PMCID: PMC6963521 DOI: 10.3390/diagnostics9040204] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 11/15/2019] [Accepted: 11/22/2019] [Indexed: 01/19/2023] Open
Abstract
Isothermal amplification techniques such as recombinase polymerase amplification (RPA) and loop-mediated isothermal amplification (LAMP) for diagnosing Buruli ulcer, a necrotic skin disease caused by Mycobacterium ulcerans, have renewed hope for the molecular diagnosis of clinically suspected Buruli ulcer cases in endemic districts. If these techniques are applied at district-level hospitals or clinics, they will help facilitate early case detection with prompt treatment, thereby reducing disability and associated costs of disease management. The accuracy as well as the application of these molecular techniques at point of need is dependent on simple and fast DNA extraction. We have modified and tested a rapid extraction protocol for use with an already developed recombinase polymerase amplification assay. The entire procedure from “sample in, extraction and DNA amplification” was conducted in a mobile suitcase laboratory within 40 min. The DNA extraction procedure was performed within 15 min, with only two manipulation/pipetting steps needed. The diagnostic sensitivity and specificity of this extraction protocol together with M. ulcerans RPA in comparison with standard DNA extraction with real-time PCR was 87% (n = 26) and 100% (n = 13), respectively. We have established a simple, fast and efficient protocol for the extraction and detection of M. ulcerans DNA in clinical samples that is adaptable to field conditions.
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Affiliation(s)
- Michael Frimpong
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi AK 312, Ghana; (H.S.A.); (B.A.); (E.A.); (R.O.P.)
- Correspondence: ; Tel.: +233-265940908
| | - Hubert Senanu Ahor
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi AK 312, Ghana; (H.S.A.); (B.A.); (E.A.); (R.O.P.)
- Department of Molecular Medicine, School of Medical Sciences, Kwame Nkrumah University of Science and Technology, Kumasi AK 312, Ghana;
| | - Samuel Asamoah Sakyi
- Department of Molecular Medicine, School of Medical Sciences, Kwame Nkrumah University of Science and Technology, Kumasi AK 312, Ghana;
| | - Bernadette Agbavor
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi AK 312, Ghana; (H.S.A.); (B.A.); (E.A.); (R.O.P.)
| | - Emmanuel Akowuah
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi AK 312, Ghana; (H.S.A.); (B.A.); (E.A.); (R.O.P.)
| | - Richard Odame Phillips
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi AK 312, Ghana; (H.S.A.); (B.A.); (E.A.); (R.O.P.)
- Department of Molecular Medicine, School of Medical Sciences, Kwame Nkrumah University of Science and Technology, Kumasi AK 312, Ghana;
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24
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Maehira Y, Spencer RC. Harmonization of Biosafety and Biosecurity Standards for High-Containment Facilities in Low- and Middle-Income Countries: An Approach From the Perspective of Occupational Safety and Health. Front Public Health 2019; 7:249. [PMID: 31572701 PMCID: PMC6751378 DOI: 10.3389/fpubh.2019.00249] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 08/19/2019] [Indexed: 01/10/2023] Open
Abstract
Following the global-level Ebola virus disease (EVD) outbreak during 2014–2016, international collaboration with multiorganizational participation has rapidly increased. Given the greater priorities for research and development (R&D) outcomes despite the quantitative and qualitative lack of high-containment laboratory facilities in low- and middle-income countries (LMICs), where biological targets for investigation are located near their natural habitats, occupational readiness for health workers' safety has not been well-addressed, where limited global expert human resources are being deployed to high-containment laboratories including biosafety level 4 (BSL-4) facilities for case management and medical investigations. Pursuing scientific and managerial success to make laboratories efficient and productive, most laboratory safety policies have focused on the functionality of technical skills or performance, procedural methodologies, and supervision over the employees to collaborate in LMICs. The experts dispatched from advanced countries bring a long list of scientific tasks with high-tech devices, supplies, and training programs to introduce their collaboration with local partners in LMICs. However, the dispatched experts would subsequently realize their list becomes endless to establish their basic functions required in high-containment laboratories to ensure qualified scientific outcomes in LMICs. Under such circumstances where dual or multiple policies and standards accommodated pose dilemmas for operational procedures to ensure biosafety and biosecurity, all the frontline experts from both LMICs and advanced countries may be exposed to significant risks of life-threating infection of highly pathogenic agents like EVD, without any pragmatic measures or road maps to establish valued international collaboration, pursuing its sustainability. Given the fact mentioned above, we conducted a quick review of the key biosafety and biosecurity management documents, relevant policy analyses, and research to understand the current status and, if any, measures to dissolve critical dilemmas mentioned above. As a result, we found that occupational safety and health (OSH) aspects had not been sufficiently addressed, particularly in the context of international BSL-4 collaboration in LMICs. Moreover, consideration of OSH can be one of the key drivers to make such collaborative interventions more pragmatic, safer to reorient, harness disease-based vertical approaches, and harmonize policies of biosafety and biosecurity, particularly for collaborations organized in resource-limited settings.
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Affiliation(s)
- Yuki Maehira
- Department of Emerging Infectious Diseases, Nagasaki University Institute of Tropical Medicine, Nagasaki, Japan
| | - Robert C Spencer
- Index Microbiology Ltd., School of Veterinary Science, University of Bristol, Bristol, United Kingdom
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25
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Mattiuzzo G, Bentley EM, Page M. The Role of Reference Materials in the Research and Development of Diagnostic Tools and Treatments for Haemorrhagic Fever Viruses. Viruses 2019; 11:E781. [PMID: 31450611 PMCID: PMC6783900 DOI: 10.3390/v11090781] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 08/15/2019] [Accepted: 08/21/2019] [Indexed: 11/16/2022] Open
Abstract
Following the Ebola outbreak in Western Africa in 2013-16, a global effort has taken place for preparedness for future outbreaks. As part of this response, the development of vaccines, treatments and diagnostic tools has been accelerated, especially towards pathogens listed as likely to cause an epidemic and for which there are no current treatments. Several of the priority pathogens identified by the World Health Organisation are haemorrhagic fever viruses. This review provides information on the role of reference materials as an enabling tool for the development and evaluation of assays, and ultimately vaccines and treatments. The types of standards available are described, along with how they can be applied for assay harmonisation through calibration as a relative potency to a common arbitrary unitage system (WHO International Unit). This assures that assay metrology is accurate and robust. We describe reference materials that have been or are being developed for haemorrhagic fever viruses and consider the issues surrounding their production, particularly that of biosafety where the viruses require specialised containment facilities. Finally, we advocate the use of reference materials at early stages, including research and development, as this helps produce reliable assays and can smooth the path to regulatory approval.
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MESH Headings
- Africa, Western/epidemiology
- Animals
- Antigens, Viral/blood
- Dengue Virus/immunology
- Dengue Virus/isolation & purification
- Dengue Virus/pathogenicity
- Diagnostic Techniques and Procedures
- Disease Outbreaks/prevention & control
- Ebolavirus/immunology
- Ebolavirus/isolation & purification
- Ebolavirus/pathogenicity
- Epidemics/prevention & control
- Hemorrhagic Fever Virus, Crimean-Congo/immunology
- Hemorrhagic Fever Virus, Crimean-Congo/isolation & purification
- Hemorrhagic Fever Virus, Crimean-Congo/pathogenicity
- Hemorrhagic Fever, Crimean/diagnosis
- Hemorrhagic Fever, Crimean/immunology
- Hemorrhagic Fever, Crimean/prevention & control
- Hemorrhagic Fever, Ebola/diagnosis
- Hemorrhagic Fever, Ebola/immunology
- Hemorrhagic Fever, Ebola/prevention & control
- Humans
- Information Services
- Lassa Fever/diagnosis
- Lassa Fever/immunology
- Lassa Fever/prevention & control
- Lassa virus/immunology
- Lassa virus/isolation & purification
- Lassa virus/pathogenicity
- Marburg Virus Disease/diagnosis
- Marburg Virus Disease/immunology
- Marburg Virus Disease/prevention & control
- Marburgvirus/immunology
- Marburgvirus/isolation & purification
- Marburgvirus/pathogenicity
- RNA Virus Infections/diagnosis
- RNA Virus Infections/immunology
- RNA Virus Infections/prevention & control
- RNA Viruses/immunology
- RNA Viruses/isolation & purification
- RNA Viruses/pathogenicity
- RNA, Viral/isolation & purification
- Rift Valley Fever/diagnosis
- Rift Valley Fever/immunology
- Rift Valley Fever/prevention & control
- Rift Valley fever virus/immunology
- Rift Valley fever virus/isolation & purification
- Rift Valley fever virus/pathogenicity
- Severe Dengue/diagnosis
- Severe Dengue/immunology
- Severe Dengue/prevention & control
- Vaccines/standards
- World Health Organization
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Affiliation(s)
- Giada Mattiuzzo
- Division of Virology, National Institute for Biological Standards and Control, Blanche Lane, South Mimms, Hertfordshire EN6 3QG, UK.
| | - Emma M Bentley
- Division of Virology, National Institute for Biological Standards and Control, Blanche Lane, South Mimms, Hertfordshire EN6 3QG, UK.
| | - Mark Page
- Division of Virology, National Institute for Biological Standards and Control, Blanche Lane, South Mimms, Hertfordshire EN6 3QG, UK.
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26
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Racine T, Kobinger GP. Challenges and perspectives on the use of mobile laboratories during outbreaks and their use for vaccine evaluation. Hum Vaccin Immunother 2019; 15:2264-2268. [PMID: 30893007 PMCID: PMC6816390 DOI: 10.1080/21645515.2019.1597595] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
Mobile laboratories provide diagnostic capabilities for routine surveillance and patient identification during an outbreak. In either situation, they face many challenges including identification of the appropriate assay(s) to employ, logistical arrangements, and providing for the health and safety of the laboratory staff. Great strides have been made over the last decade in the development of mobile laboratories with assays that require minimal infrastructure and technical experience. This knowledge and expertise have been developed in partnership with many researchers and public health officials who live in regions prone to infectious disease outbreaks. Mobile laboratories should now also be used in the evaluation of novel vaccines and therapeutics in remote locations. Clinical mobile laboratories will include similar diagnostic capabilities as outbreak response mobile labs, but will also include additional point-of-care instruments operated under Good Clinical Practice guidelines. They will also operate rigorous data management plans so that the data collected will satisfy regulatory agencies during the licensure process. Failure to deploy an adequate clinical mobile laboratory when administering a novel biological product in a remote location is a significant limitation to any collected scientific data that could ultimately undermine clinical development and availability of life-saving interventions.
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Affiliation(s)
- Trina Racine
- Department of Medical Microbiology, University of Manitoba , Winnipeg , Manitoba , Canada.,Centre de Recherche en Infectiologie, Centre Hospitalier Universitaire de Québec, Université Laval , Québec City , Québec , Canada
| | - Gary P Kobinger
- Department of Medical Microbiology, University of Manitoba , Winnipeg , Manitoba , Canada.,Centre de Recherche en Infectiologie, Centre Hospitalier Universitaire de Québec, Université Laval , Québec City , Québec , Canada.,Department of Immunology, University of Manitoba , Winnipeg , Manitoba , Canada.,Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine , Philadelphia , PA , USA
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27
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Development of Rapid Extraction Method of Mycobacterium avium Subspecies paratuberculosis DNA from Bovine Stool Samples. Diagnostics (Basel) 2019; 9:diagnostics9020036. [PMID: 30934956 PMCID: PMC6627389 DOI: 10.3390/diagnostics9020036] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 03/18/2019] [Accepted: 03/27/2019] [Indexed: 01/11/2023] Open
Abstract
The rapid identification of Mycobacterium avium subspecies paratuberculosis (MAP) infected animals within the herd is essential for preventing the spread of the disease as well as avoiding human exposure. Although culture is seen as the gold standard, there are various molecular assays available i.e., polymerase chain reaction (PCR) or isothermal amplification technique (recombinase polymerase amplification (RPA)) for the detection of MAP. The accuracy of the molecular assays is highly dependent on the DNA extraction method. In order to establish a rapid point of need system for the detection of MAP DNA from stool samples, we developed a rapid DNA extraction protocol (MAP DNA SpeedXtract) specified for use in combination with the RPA. The whole procedure from “sample in” to “result out” was conducted in a mobile suitcase laboratory. The DNA extraction is based on reverse purification by magnetic beads, which reduces the required technical demand. The MAP DNA SpeedXtract was performed within 25 min and only three pipetting steps were needed. The amplification and detection time were 20 min in RPA. The sensitivity and specificity of the developed protocol in comparison with the lab-based silica membrane column extraction and real-time PCR were 90.9% (n = 22) and 100% (n = 23), respectively. In conclusion, we established a rapid and reliable protocol for the extraction and detection of MAP DNA. All reagents are cold chain independent. The entire setup is ideal for point of need identification of MAP infected cases.
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