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2. A multi-country phase 2 study to evaluate the suitcase lab for rapid detection of SARS-CoV-2 in seven Sub-Saharan African countries: Lessons from the field

Author

Ceruti, Arianna, Dia, Ndongo, Bakarey, Adeleye Solomon, Ssekitoleko, Judah, Andriamandimby, Soa Fy, Malwengo-Kasongo, Padra, Ahmed, Rasheeda H.A., Kobialka, Rea Maja, Heraud, Jean Michel, Diagne, Moussa Moise, Dione, Marie Henriette Dior, Dieng, Idrissa, Faye, Martin, Faye, Ousmane, Rafisandratantsoa, Jean Théophile, Ravalohery, Jean-Pierre, Raharinandrasana, Claudio, Randriambolamanantsoa, Tsiry H., Razanajatovo, Norosoa, Razanatovo, Iony, Rabarison, Joelinotahina H., Dussart, Phillipe, Kyei-Tuffuor, Louis, Agbanyo, Abigail, Adewumi, Olubusuyi Moses, Fowotade, Adeola, Raifu, Muideen Kolawole, Okitale-Talunda, Patient, Kashitu-Mujinga, Gracia, Mbelu-Kabongo, Christelle, Ahuka-Mundeke, Steve, Makaka-Mutondo, Anguy, Abdalla, Enas M., Idris, Sanaa M., Elmagzoub, Wisal A., Ali, Rahma H., Nour, Eman O.M., Ebraheem, Rasha S.M., Ahmed, Huda H.H., Abdalla, Hamadelniel E., Elnegoumi, Musab, Mukhtar, Izdihar, Adam, Muatsim A.M., Mohamed, Nuha Y.I., Bedri, Shahinaz A., Hamdan, Hamdan Mustafa, Kisekka, Magid, Mpumwiire, Monica, Aloyo, Sharley Melissa, Wandera, Joanita Nabwire, Agaba, Andrew, Kamulegeya, Rogers, Kiprotich, Hosea, Kateete, David Patrick, Kadetz, Paul, Truyen, Uwe, Eltom, Kamal H., Sakuntabhai, Anavaj, Okuni, Julius Boniface, Makiala-Mandanda, Sheila, Lacoste, Vincent, Ademowo, George Olusegun, Frimpong, Michael, Sall, Amadou Alpha, Weidmann, Manfred, and Abd El Wahed, Ahmed

Published
2023
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4. Rapid detection of Ebolavirus using isothermal recombinase‐aided amplification.

Author

Ceruti, Arianna, Faye, Martin, Diagne, Moussa M., Kobialka, Rea M., Makiala‐Mandanda, Sheila, Faye, Ousmane, Faye, Oumar, El Wahed, Ahmed A., and Weidmann, Manfred

Subjects
EBOLA virus, RAPID diagnostic tests, HEALTH facilities, EBOLA virus disease, SENSITIVITY & specificity (Statistics)
Abstract

Ebolavirus disease (EVD) is an often‐lethal disease caused by the genus Ebolavirus (EBOV). Although vaccines are being developed and recently used, outbreak control still relies on a combination of various factors, including rapid identification of EVD cases. This allows rapid patient isolation and control measure implementation. Ebolavirus diagnosis is performed in treatment centers or reference laboratories, which usually takes a few hours to days to confirm the outbreak or deliver a clear result. A fast and field‐deployable molecular detection method, such as the isothermal amplification recombinase‐aided amplification (RAA), could significantly reduce sample‐to‐result time. In this study, a RT‐RAA assay was evaluated for EBOV detection. Various primer and probe combinations were screened; analytical sensitivity and cross‐specificity were tested. A total of 40 archived samples from the 2014 to 2016 Ebola outbreak in West Africa were tested with both the reference method real‐time RT‐PCR and the established RT‐RAA assay. The assay could detect down to 22.6 molecular copies per microliter. No other pathogens were detected with the Ebolavirus RT‐RAA assay. Testing 40 samples yield clinical sensitivity and specificity of 100% each. This rapid isothermal RT‐RAA assay can replace the previous RT‐RPA and continue to offer rapid EBOV diagnostics. [ABSTRACT FROM AUTHOR]

Published
2024
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5. Evolution of an Extended Pathogenicity Motif in VP2 of Infectious Pancreatic Necrosis Virus Isolates from Farmed Rainbow Trout in Turkey.

Author

Tamer, Cuneyt, Ulrich, Kristina, Di Paola, Nicholas, Kurucay, Hanne Nur, Albayrak, Harun, and Weidmann, Manfred

Subjects
RAINBOW trout, BLUETONGUE virus, WHOLE genome sequencing, NECROSIS, FOOT & mouth disease, DOUBLE-stranded RNA
Abstract

Infectious pancreatic necrosis virus (IPNV) causes economic losses with a highly variable mortality rate worldwide, especially in rainbow trout. The virus has a double-stranded bi-partite RNA genome designated segment A and B. New complete genome sequences of nine rainbow trout isolates from Turkey were determined and subjected to phylogenetic analysis, identifying all as genotype 5 (serotype Sp). A time-dependent change in the extended pathogenicity motif of VP2 from P217T221A247 (PTA) to PTE P217T221E247 over a period of 10 years was identified. A wider analysis of 99 IPNV sequences from Turkey and Iran revealed the emergence of the motif PTE from 2007 to 2017, inducing significant morbidity in fry by 2013. In fact, displacement of the PTA motif, by the PTE motif in IPNV isolates appeared to be connected to a production peak of rainbow trout in 2013. An additional CAI analysis provided more evidence, indicating that rainbow trout culture in Turkey has an influence on the evolution of IPNV. [ABSTRACT FROM AUTHOR]

Published
2024
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6. Emergence of Crimean–Congo Hemorrhagic Fever Virus in Eastern Senegal in 2022

Author

Sene, Ousseynou, primary, Sagne, Samba Niang, additional, Ngom, Déthié, additional, Diagne, Moussa Moise, additional, Badji, Aminata, additional, Khoulé, Aliou, additional, Ndiaye, El Hadji, additional, Sankhe, Safietou, additional, Loucoubar, Cheikh, additional, Diallo, Mawlouth, additional, Weidmann, Manfred, additional, Dia, Ndongo, additional, Simon-Lorière, Etienne, additional, Sall, Yoro, additional, Diop, Boly, additional, Ndiaye, Mamadou, additional, Sakuntabhai, Anavaj, additional, Sall, Amadou Alpha, additional, Faye, Ousmane, additional, Faye, Oumar, additional, Diallo, Diawo, additional, Barry, Mamadou Aliou, additional, and Fall, Gamou, additional

Published
2024
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13. Molecular Diagnostics of Ebola Patient Samples by Institut Pasteur de Dakar Mobile Laboratory in Guinea 2014–2016

Author

Faye, Oumar, primary, Tidiane Diagne, Cheikh, additional, Diallo, Amadou, additional, Meyer, Emily, additional, Soropogui, Barre, additional, Fall, Gamou, additional, Fall, Cheikh, additional, Magassouba, N’Faly, additional, Koivogui, Lamine, additional, Keita, Sakoba, additional, Loucoubar, Cheikh, additional, Diop, Mamadou, additional, Weidmann, Manfred, additional, Faye, Ousmane, additional, and Alpha Sall, Amadou, additional

Published
2020
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14. Comparative Analysis of Zika Virus Detection by RT-qPCR, RT-LAMP, and RT-RPA

Author

Diagne, Cheikh Tidiane, primary, Faye, Martin, additional, Lopez-Jimena, Benjamin, additional, Abd El Wahed, Ahmed, additional, Loucoubar, Cheikh, additional, Fall, Cheikh, additional, Mencatelli, Giulia, additional, Faye, Oumar, additional, Faye, Ousmane, additional, Weidmann, Manfred, additional, and Sall, Amadou Alpha, additional

Published
2020
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16. Zika Virus Amplification Using Strand Displacement Isothermal Method and Sequencing Using Nanopore Technology

Author

Hansen, Sören, primary, Faye, Oumar, additional, Sanabani, Sabri S., additional, Faye, Martin, additional, Böhlken-Fascher, Susanne, additional, Faye, Ousmane, additional, Sall, Amadou Alpha, additional, Bekaert, Michaël, additional, Weidmann, Manfred, additional, Czerny, Claus-Peter, additional, and Abd El Wahed, Ahmed, additional

Published
2020
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19. Rapid On-Site Detection of Arboviruses by a Direct RT-qPCR Assay.

Author

Mhamadi, Moufid, Mencattelli, Giulia, Gaye, Alioune, Ndiaye, El Hadji, Sow, Aïssatou Aïcha, Faye, Martin, Ndione, Marie Henriette Dior, Diagne, Moussa Moïse, Mhamadi, Moundhir, Faye, Ousmane, Weidmann, Manfred, Faye, Oumar, Diallo, Mawlouth, and Diagne, Cheikh Tidiane

Subjects
RIFT Valley fever, ARBOVIRUS diseases, ARBOVIRUSES, VIRAL transmission, POLYMERASE chain reaction, COMMUNICABLE diseases
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. [ABSTRACT FROM AUTHOR]

Published
2023
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20. Laboratory Evaluation and Field Testing of Dengue NS1 and IgM/IgG Rapid Diagnostic Tests in an Epidemic Context in Senegal

Author

Ndiaye, Oumar, primary, Woolston, Kevin, additional, Gaye, Aboubacry, additional, Loucoubar, Cheikh, additional, Cocozza, Michael, additional, Fall, Cheikh, additional, Dia, Fatou, additional, Adams, Emily R., additional, Samb, Marième, additional, Camara, Diogop, additional, Sadio, Bacary Djilocalisse, additional, Diagne, Cheikh T., additional, Faye, Oumar, additional, Weidmann, Manfred, additional, Fitchett, Joseph R. A., additional, Sall, Amadou Alpha, additional, and Diagne, Cheikh Tidiane, additional

Published
2023
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21. Rapid Isothermal Detection of Pathogenic Clostridioides difficileUsing Recombinase Polymerase Amplification

Author

Bachmann, Iris, Behrmann, Ole, Klingenberg-Ernst, Marcel, Rupnik, Maja, Hufert, Frank T., Dame, Gregory, and Weidmann, Manfred

Abstract

Nosocomial-associated diarrhea due to Clostridioides difficileinfection (CDI) is diagnosed after sample precultivation by the detection of the toxins in enzyme immunoassays or via toxin gene nucleic acid amplification. Rapid and direct diagnosis is important for targeted treatment to prevent severe cases and recurrence. We developed two singleplex and a one-pot duplex fluorescent 15 min isothermal recombinase polymerase amplification (RPA) assays targeting the toxin genes A and B (tcdAand tcdB). Furthermore, we adapted the singleplex RPA to a 3D-printed microreactor device. Analytical sensitivity was determined using a DNA standard and DNA extracts of 20 C. difficilestrains with different toxinotypes. Nineteen clostridial and gastrointestinal bacteria strains were used to determine analytical specificity. Adaptation of singleplex assays to duplex assays in a 50 μL volume required optimized primer and probe concentrations. A volume reduction by one-fourth (12.4 μL) was established for the 3D-printed microreactor. Mixing of RPA was confirmed as essential for optimal analytical sensitivity. Detection limits (LOD) ranging from 119 to 1411 DNA molecules detected were similar in the duplex tube format and in the singleplex 3D-printed microreactor format. The duplex RPA allows the simultaneous detection of both toxins important for the timely and reliable diagnosis of CDI. The 3D-printed reaction chamber can be developed into a microfluidic lab-on-a-chip system use at the point of care.

Published
2024
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22. Chikungunya Outbreak in Kedougou, Southeastern Senegal in 2009–2010

Author

Sow, Abdourahmane, Faye, Oumar, Diallo, Mawlouth, Diallo, Diawo, Chen, Rubing, Faye, Ousmane, Diagne, Cheikh T, Guerbois, Mathilde, Weidmann, Manfred, Ndiaye, Youssoupha, Senghor, Cheikh Sadibou, Faye, Abdourahmane, Diop, Ousmane M, Sadio, Bakary, Ndiaye, Oumar, Watts, Douglas, Hanley, Kathryn A, Dia, Anta T, Malvy, Denis, Weaver, Scott C, and Sall, Amadou Alpha

Published
2018
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24. Quantitative real time PCR detection of Saboya virus: A flavivirus member of yellow fever genetic group

Author

DIENG, Idrissa, primary, Ndiaye, Mignane, additional, Dia, Moussa, additional, Mhamadi, Moufid, additional, Toure, Cheikh Talibouya, additional, Gaye, Aboubacry, additional, Diagne, Cheikh Tidiane, additional, El Wahed, Ahmed, additional, Weidmann, Manfred, additional, Faye, Ousmane, additional, Sall, Amadou Alpha, additional, and Faye, Oumar, additional

Published
2023
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30. Institut Pasteur Dakar Mobile Lab: Part of the Solution to Tackle COVID Pandemic in Senegal, a Model to Be Exploited

Author

Fall, Amary, primary, Dieng, Idrissa, additional, Touré, Cheikh Talibouya, additional, Mhamadi, Moufid, additional, Sadio, Bacary Djilocalisse, additional, Ndione, Marie Henriette Dior, additional, Diagne, Moussa Moise, additional, Ndiaye, Mignane, additional, Barry, Mamadou Aliou, additional, Diaw, Yague, additional, Dieng, Allé Baba, additional, Diop, Ndeye Maguette, additional, Sankhe, Safietou, additional, Diop, Boly, additional, Ndiaye, Mamadou, additional, Diallo, Amadou, additional, Diop, Mamadou, additional, Dieng, Mamadou, additional, Cappuyns, Aurélie, additional, Pauwels, Steven, additional, Gning, Babacar, additional, Fall, Gamou, additional, Weidmann, Manfred, additional, Loucoubar, Cheikh, additional, Pauwels, Rudi, additional, Sall, Amadou Alpha, additional, Dia, Ndongo, additional, Faye, Ousmane, additional, and Faye, Oumar, additional

Published
2022
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32. Efficient Screening of Long Oligonucleotides Against Hundred Thousands of SARS-CoV-2 Genome Sequences

Author

Weidmann, Manfred, Graf, Elena, Lichterfeld, Daniel, Abd El Wahed, Ahmed, Bekaert, Michael, Weidmann, Manfred, Graf, Elena, Lichterfeld, Daniel, Abd El Wahed, Ahmed, and Bekaert, Michael

Abstract

An unprecedented use of high-throughput sequencing for routine monitoring of SARS-CoV-2 viruses in patient samples has created a dataset of over 6 million SARS-CoV-2 genomes. To monitor genomes, deposited in the GISAID database, and to track the continuous sequence evolution of molecular assay oligonucleotide target sequences. A simple pipeline tool for non-experts was developed to mine this database for nucleotide changes in oligonucleotides and tested with the long oligonucleotides of a Recombinase polymerase amplification (RPA) assay targeting the RNA-dependent RNA polymerase (RdRP) gene of the SARS-CoV-2. Results indicate the emergence of a single nucleotide change in the reverse oligonucleotide from 0.03 to 26.23% (January to May 2021) in Alpha variant genomes, which however reduced to 17.64% by September after which the Alpha variant was completely displaced by the Delta variant. For all other variants, no relevant nucleotide changes were observed. The oligonucleotide screening pipeline allows efficient screening of nucleotide changes in oligonucleotides of all sizes in minutes.

Published
2022

36. Development of Quantitative Rapid Isothermal Amplification Assay for Leishmania donovani

Author

Khan, Md Anik Ashfaq, Faisal, Khaledul, Chowdhury, Rajashree, Ghosh, Prakash, Hossain, Faria, Weidmann, Manfred, Mondal, Dinesh, and El Wahed, Ahmed Abd

Subjects
point-of-need testing, Medicine (General), R5-920, isothermal amplification, quantitative molecular assay, recombinase polymerase amplification, leishmaniasis, ddc:610, Article
Abstract

Quantification of pathogen load, although challenging, is of paramount importance for accurate diagnosis and clinical management of a range of infectious diseases in a point-of-need testing (PONT) scenario such as in resource-limited settings. We formulated a quantification approach to test the standard-curve based absolute quantification ability of isothermal recombinase polymerase amplification (RPA) assay. As a test of principle, a 10-fold dilution series of Leishmania donovani (LD) genomic DNA prepared in nuclease-free-water (NFW), and from culture-spiked-blood (CSB) were tested, and a 15 min assay was performed. A modified algorithm was formulated to derive the detection outcome. The threshold-record times (Tr) in seconds thus obtained were plotted against the initial load of parasite genomes for log-linear regression analysis. The quantitative RPA (Q-RPA) assay was further evaluated against a LD quantitative (q)-PCR assay with DNA extracted from visceral and post-Kala-azar dermal leishmaniasis case specimens and stratified into different ranges of threshold cycle (Ct). The best-fitted regression models were found linear with mean r2/root mean square error (RMSE) values of residual points (in seconds) estimated as 0.996/8.063 and 0.992/7.46 for replicated series of NFW and CSB, respectively. In both series, the lower limit of detection reached less than 0.1 parasite genome equivalent DNA. Absolute agreement between Q-RPA and LD-qPCR was found for test positivity, and strong positive correlations were observed between the Tr and Ct values (r = 0.89, p &lt, 0.0001) as well as between the absolute parasite loads (r = 0.87, 0.0001) quantified by respective assays. The findings in this very first Q-RPA assay for leishmaniasis are suggestive of its potential in monitoring LD load in clinical specimens, and the development of rapid Q-RPA assays for other infectious diseases.

Published
2021
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37. Virus nomenclature below the species level: a standardized nomenclature for filovirus strains and variants rescued from cDNA

Author

Kuhn, Jens H., Bào, Yīmíng, Bavari, Sina, Becker, Stephan, Bradfute, Steven, Brauburger, Kristina, Rodney Brister, J., Bukreyev, Alexander A., Caì, Yíngyún, Chandran, Kartik, Davey, Robert A., Dolnik, Olga, Dye, John M., Enterlein, Sven, Gonzalez, Jean-Paul, Formenty, Pierre, Freiberg, Alexander N., Hensley, Lisa E., Hoenen, Thomas, Honko, Anna N., Ignatyev, Georgy M., Jahrling, Peter B., Johnson, Karl M., Klenk, Hans-Dieter, Kobinger, Gary, Lackemeyer, Matthew G., Leroy, Eric M., Lever, Mark S., Mühlberger, Elke, Netesov, Sergey V., Olinger, Gene G., Palacios, Gustavo, Patterson, Jean L., Paweska, Janusz T., Pitt, Louise, Radoshitzky, Sheli R., Ryabchikova, Elena I., Saphire, Erica Ollmann, Shestopalov, Aleksandr M., Smither, Sophie J., Sullivan, Nancy J., Swanepoel, Robert, Takada, Ayato, Towner, Jonathan S., van der Groen, Guido, Volchkov, Viktor E., Volchkova, Valentina A., Wahl-Jensen, Victoria, Warren, Travis K., Warfield, Kelly L., Weidmann, Manfred, and Nichol, Stuart T.

Published
2014
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44. Virus nomenclature below the species level: a standardized nomenclature for laboratory animal-adapted strains and variants of viruses assigned to the family Filoviridae

Author

Kuhn, Jens H., Bao, Yiming, Bavari, Sina, Becker, Stephan, Bradfute, Steven, Brister, J. Rodney, Bukreyev, Alexander A., Caì, Yíngyún, Chandran, Kartik, Davey, Robert A., Dolnik, Olga, Dye, John M., Enterlein, Sven, Gonzalez, Jean-Paul, Formenty, Pierre, Freiberg, Alexander N., Hensley, Lisa E., Honko, Anna N., Ignatyev, Georgy M., Jahrling, Peter B., Johnson, Karl M., Klenk, Hans-Dieter, Kobinger, Gary, Lackemeyer, Matthew G., Leroy, Eric M., Lever, Mark S., Lofts, Loreen L., Mühlberger, Elke, Netesov, Sergey V., Olinger, Gene G., Palacios, Gustavo, Patterson, Jean L., Paweska, Janusz T., Pitt, Louise, Radoshitzky, Sheli R., Ryabchikova, Elena I., Saphire, Erica Ollmann, Shestopalov, Aleksandr M., Smither, Sophie J., Sullivan, Nancy J., Swanepoel, Robert, Takada, Ayato, Towner, Jonathan S., van der Groen, Guido, Volchkov, Viktor E., Wahl-Jensen, Victoria, Warren, Travis K., Warfield, Kelly L., Weidmann, Manfred, and Nichol, Stuart T.

Published
2013
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45. Virus nomenclature below the species level: a standardized nomenclature for natural variants of viruses assigned to the family Filoviridae

Author

Kuhn, Jens H., Bao, Yiming, Bavari, Sina, Becker, Stephan, Bradfute, Steven, Brister, J. Rodney, Bukreyev, Alexander A., Chandran, Kartik, Davey, Robert A., Dolnik, Olga, Dye, John M., Enterlein, Sven, Hensley, Lisa E., Honko, Anna N., Jahrling, Peter B., Johnson, Karl M., Kobinger, Gary, Leroy, Eric M., Lever, Mark S., Mühlberger, Elke, Netesov, Sergey V., Olinger, Gene G., Palacios, Gustavo, Patterson, Jean L., Paweska, Janusz T., Pitt, Louise, Radoshitzky, Sheli R., Saphire, Erica Ollmann, Smither, Sophie J., Swanepoel, Robert, Towner, Jonathan S., van der Groen, Guido, Volchkov, Viktor E., Wahl-Jensen, Victoria, Warren, Travis K., Weidmann, Manfred, and Nichol, Stuart T.

Published
2013
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50. Evaluation of Screening Tests in Bavarian Healthcare Facilities during the Second Wave of the SARS-CoV-2 Pandemic

Author

Tischer, Christina, primary, Stupp, Carolin, additional, Janson, Patrick, additional, Willeke, Kristina, additional, Hung, Chu-Wei, additional, Flöter, Jessica, additional, Kirchner, Anna, additional, Zink, Katharina, additional, Eder, Lisa, additional, Hackl, Christina, additional, Mühle, Ursula, additional, Weidmann, Manfred, additional, Nennstiel, Uta, additional, Kuhn, Joseph, additional, Weidner, Christian, additional, Liebl, Bernhard, additional, Wildner, Manfred, additional, and Keil, Thomas, additional

Published
2021
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