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The H9N2 subtype of avian influenza A virus (aIAV) is circulating among birds worldwide, leading to severe economic losses. H9N2 cocirculation with other highly pathogenic aIAVs has the potential to contribute to the rise of new strains with pandemic potential. Therefore, rapid detection of H9 aIAVs infection is crucial to control virus spread. A qualitative reverse transcription recombinase polymerase amplification (RT-RPA) assay for the detection of aIAV subtype H9N2 was developed. All results were compared to the gold standard (real-time reverse transcription polymerase chain reaction (RT-PCR)). The RT-RPA assay was designed to detect the hemagglutinin (HA) gene of H9N2 by testing three pairs of primers and a probe. A serial concentration between 106 and 100 EID50 (50% embryo infective dose)/mL was applied to calculate the analytical sensitivity. The H9 RT-RPA assay was highly sensitive as the lowest concentration point of a standard range at one EID50/mL was detected after 5 to 8 min. The H9N2 RT-RPA assay was highly specific as nucleic acid extracted from H9 negative samples and from other avian pathogens were not cross detected. The diagnostic sensitivity when testing clinical samples was 100% for RT-RPA and RT-PCR. In conclusion, H9N2 RT-RPA is a rapid sensitive and specific assay that easily operable in a portable device for field diagnosis of aIAV H9N2.
Nahed Yehia; Fatma Eldemery; Abdel-Satar Arafa; Ahmed Abd El Wahed; Ahmed El Sanousi; Manfred Weidmann; Mohamed Shalaby. Reverse Transcription Recombinase Polymerase Amplification Assay for Rapid Detection of Avian Influenza Virus H9N2 HA Gene. Veterinary Sciences 2021, 8, 134 .
AMA StyleNahed Yehia, Fatma Eldemery, Abdel-Satar Arafa, Ahmed Abd El Wahed, Ahmed El Sanousi, Manfred Weidmann, Mohamed Shalaby. Reverse Transcription Recombinase Polymerase Amplification Assay for Rapid Detection of Avian Influenza Virus H9N2 HA Gene. Veterinary Sciences. 2021; 8 (7):134.
Chicago/Turabian StyleNahed Yehia; Fatma Eldemery; Abdel-Satar Arafa; Ahmed Abd El Wahed; Ahmed El Sanousi; Manfred Weidmann; Mohamed Shalaby. 2021. "Reverse Transcription Recombinase Polymerase Amplification Assay for Rapid Detection of Avian Influenza Virus H9N2 HA Gene." Veterinary Sciences 8, no. 7: 134.
Due to the lack of data on asymptomatic SARS-CoV-2-positive persons in healthcare institutions, they represent an inestimable risk. Therefore, the aim of the current study was to evaluate the first 1,000,000 reported screening tests of asymptomatic staff, patients, residents, and visitors in hospitals and long-term care (LTC) facilities in the State of Bavaria over a period of seven months. Data were used from the online database BayCoRei (Bavarian Corona Screening Tests), established in July 2020. Descriptive analyses were performed, describing the temporal pattern of persons that tested positive for SARS-CoV-2 by real-time polymerase chain reaction (RT-PCR) or antigen tests, stratified by facility. Until 15 March 2021, this database had collected 1,038,146 test results of asymptomatic subjects in healthcare facilities (382,240 by RT-PCR, and 655,906 by antigen tests). Of the RT-PCR tests, 2.2% (n = 8380) were positive: 3.0% in LTC facilities, 2.2% in hospitals, and 1.2% in rehabilitation institutions. Of the antigen tests, 0.4% (n = 2327) were positive: 0.5% in LTC facilities, and 0.3% in both hospitals and rehabilitation institutions, respectively. In LTC facilities and hospitals, infection surveillance using RT-PCR tests, or the less expensive but less sensitive, faster antigen tests, could facilitate the long-term management of the healthcare workforce, patients, and residents.
Christina Tischer; Carolin Stupp; Patrick Janson; Kristina Willeke; Chu-Wei Hung; Jessica Flöter; Anna Kirchner; Katharina Zink; Lisa Eder; Christina Hackl; Ursula Mühle; Manfred Weidmann; Uta Nennstiel; Joseph Kuhn; Christian Weidner; Bernhard Liebl; Manfred Wildner; Thomas Keil. Evaluation of Screening Tests in Bavarian Healthcare Facilities during the Second Wave of the SARS-CoV-2 Pandemic. International Journal of Environmental Research and Public Health 2021, 18, 7371 .
AMA StyleChristina Tischer, Carolin Stupp, Patrick Janson, Kristina Willeke, Chu-Wei Hung, Jessica Flöter, Anna Kirchner, Katharina Zink, Lisa Eder, Christina Hackl, Ursula Mühle, Manfred Weidmann, Uta Nennstiel, Joseph Kuhn, Christian Weidner, Bernhard Liebl, Manfred Wildner, Thomas Keil. Evaluation of Screening Tests in Bavarian Healthcare Facilities during the Second Wave of the SARS-CoV-2 Pandemic. International Journal of Environmental Research and Public Health. 2021; 18 (14):7371.
Chicago/Turabian StyleChristina Tischer; Carolin Stupp; Patrick Janson; Kristina Willeke; Chu-Wei Hung; Jessica Flöter; Anna Kirchner; Katharina Zink; Lisa Eder; Christina Hackl; Ursula Mühle; Manfred Weidmann; Uta Nennstiel; Joseph Kuhn; Christian Weidner; Bernhard Liebl; Manfred Wildner; Thomas Keil. 2021. "Evaluation of Screening Tests in Bavarian Healthcare Facilities during the Second Wave of the SARS-CoV-2 Pandemic." International Journal of Environmental Research and Public Health 18, no. 14: 7371.
Assessment of seawater readiness of freshwater salmon smolts is a crucial husbandry step with economic implications in salmon aquaculture but current methods rely on delayed centralised enzymic activity measurement. The efficiency of a qRT-PCR assay for sodium potassium ATPase (NKA) α1a mRNA was tested in a 3-year study on 19 hatcheries across Scotland incorporating environmental factors such as temperature and metal contamination. The NKA qRT-PCR assay was transferred to a mobile laboratory and on-site testing was carried out at 3 hatchery sites. For the first two years standard enzymatic and gene expression assays had similar success rates in detecting smoltification (NKA activity 60%, qRT-PCR 57%). In the third year, all but one site were determined as sea water ready by qRT-PCR but only at 4 by enzymatic testing. On site testing with mobile qRT-PCR was successfully performed on four farm sites. Altogether, high sensitivity was shown for the in lab (98.9%, SE 0.24) and mobile (93.43%, SE 0.119) assays when tested using a quantitative RNA standard. Some indication for obscured smoltification assay results due to environmental increased heavy metal contamination was observed. Our results prove it is possible to test a smoltification marker on site and provide results on the day of testing during the smolt period allowing for informed decisions on seawater transfer.
Michael McGowan; Simon MacKenzie; Nikos Steiropoulos; Manfred Weidmann. Testing of NKA expression by mobile real time PCR is an efficient indicator of smoltification status of farmed Atlantic salmon. Aquaculture 2021, 544, 737085 .
AMA StyleMichael McGowan, Simon MacKenzie, Nikos Steiropoulos, Manfred Weidmann. Testing of NKA expression by mobile real time PCR is an efficient indicator of smoltification status of farmed Atlantic salmon. Aquaculture. 2021; 544 ():737085.
Chicago/Turabian StyleMichael McGowan; Simon MacKenzie; Nikos Steiropoulos; Manfred Weidmann. 2021. "Testing of NKA expression by mobile real time PCR is an efficient indicator of smoltification status of farmed Atlantic salmon." Aquaculture 544, no. : 737085.
The public health significance of plastics and microplastics in different environmental matrices has mainly focused on the toxicological effects of human ingestion. But these pollutants can also harbour pathogenic bacteria as the surfaces of plastics in the environment quickly become colonised by microbial biofilm. This novel microbial habitat has been termed the ‘plastisphere’ and could facilitate the survival and dissemination of important bacterial and fungal pathogens. Importantly, however, the role of plastic pollution as a secondary pathway for the transmission of human pathogenic viruses has never been addressed. Due to the high prevalence of both enteric and respiratory viruses in the population and in the environment, there is significant potential for human viruses to become associated with the plastisphere. In this review we critically evaluate current knowledge on the interaction of human enteric and respiratory viruses with plastic surfaces and identify the main environmental conditions and plastic characteristics that could affect virus survival and persistence in the environment. Our hypothesis is that the plastisphere can enhance the adhesion, survival and dissemination of human pathogenic viruses and potentially lead to more effective transfer and transmission of viral diseases within the environment. We identify key research questions needed to more fully assess the potential human health risks associated with viruses on plastic surfaces. These include understanding, (1) the mechanisms of viral attachment to either naked or biofilm-colonised plastic (2) how the structural characteristics of viruses (e.g., enveloped, or non-enveloped), affect their persistence in the plastisphere, (3) whether the plastisphere offers protection and increases the persistence of infectious viruses in soil, freshwater, and marine environments.
Vanessa Moresco; David M. Oliver; Manfred Weidmann; Sabine Matallana-Surget; Richard S. Quilliam. Survival of human enteric and respiratory viruses on plastics in soil, freshwater, and marine environments. Environmental Research 2021, 199, 111367 .
AMA StyleVanessa Moresco, David M. Oliver, Manfred Weidmann, Sabine Matallana-Surget, Richard S. Quilliam. Survival of human enteric and respiratory viruses on plastics in soil, freshwater, and marine environments. Environmental Research. 2021; 199 ():111367.
Chicago/Turabian StyleVanessa Moresco; David M. Oliver; Manfred Weidmann; Sabine Matallana-Surget; Richard S. Quilliam. 2021. "Survival of human enteric and respiratory viruses on plastics in soil, freshwater, and marine environments." Environmental Research 199, no. : 111367.
Novirhabdoviruses cause large epizootics and economic losses of farmed trout. In this study, we surveyed Viral hemorrhagic septicemia virus and Infectious hematopoietic and necrosis virus (VHSV and IHNV) through both monitoring and investigation of clinical outbreaks reported by farmers in the regions with major rainbow trout production in Iran from 2015 to 2019. RT-PCR assays of the kidney samples and cell culture (EPC/FHM cells) samples confirmed the presence of the viruses, with 9 VHSV and 4 IHNV isolates, in both endemic and new areas of Iran. Sequence analysis of the G gene revealed that VHSV isolates belonged to genogroup Ia, and IHNV isolates were clustered into genogroup E, both typical for isolates from European countries. A haplotype analysis based on non-homologous amino acids of the G gene supports the emergence of two lineages of IHNV from clade 1 (E-1), as well as VHSV clade 2 (Ia-2) of the European genogroups, confirming that VHSV and IHNV isolates in Iran, have originated from Europe possibly via imported eggs.
Sohrab Ahmadivand; Dušan Palić; Manfred Weidmann. Molecular Epidemiology of Novirhabdoviruses Emerging in Iranian Trout Farms. Viruses 2021, 13, 448 .
AMA StyleSohrab Ahmadivand, Dušan Palić, Manfred Weidmann. Molecular Epidemiology of Novirhabdoviruses Emerging in Iranian Trout Farms. Viruses. 2021; 13 (3):448.
Chicago/Turabian StyleSohrab Ahmadivand; Dušan Palić; Manfred Weidmann. 2021. "Molecular Epidemiology of Novirhabdoviruses Emerging in Iranian Trout Farms." Viruses 13, no. 3: 448.
The aquatic virus, infectious pancreatic necrosis virus (IPNV), is known to infect various farmed fish, in particular salmonids, and is responsible for large economic losses in the aquaculture industry. Common practices to detect the virus include qPCR tests based on specific primers and serum neutralization tests for virus serotyping. Following the potential presence of IPNV viruses in a fish farm in Scotland containing vaccinated and IPNV-resistant fish, the common serotyping of the IPNV isolates was not made possible. This led us to determine the complete genome of the new IPNV isolates in order to investigate the cause of the serotyping discrepancy. Next-generation sequencing using the Illumina technology along with the sequence-independent single primer amplification (SISPA) approach was conducted to fully characterize the new Scottish isolates. With this approach, the full genome of two isolates, V1810–4 and V1810–6, was determined and analyzed. The potential origin of the virus isolates was investigated by phylogenetic analyses along with tridimensional and secondary protein structure analyses. These revealed the emergence of a new variant from one of the main virus serotypes, probably caused by the presence of selective pressure exerted by the vaccinated IPNV-resistant farmed fish.
Jessica Benkaroun; Katherine Muir; Rosa Allshire; Cüneyt Tamer; Manfred Weidmann. Isolation of a New Infectious Pancreatic Necrosis Virus (IPNV) Variant from a Fish Farm in Scotland. Viruses 2021, 13, 385 .
AMA StyleJessica Benkaroun, Katherine Muir, Rosa Allshire, Cüneyt Tamer, Manfred Weidmann. Isolation of a New Infectious Pancreatic Necrosis Virus (IPNV) Variant from a Fish Farm in Scotland. Viruses. 2021; 13 (3):385.
Chicago/Turabian StyleJessica Benkaroun; Katherine Muir; Rosa Allshire; Cüneyt Tamer; Manfred Weidmann. 2021. "Isolation of a New Infectious Pancreatic Necrosis Virus (IPNV) Variant from a Fish Farm in Scotland." Viruses 13, no. 3: 385.
Background In this work, a platform was developed and tested to allow to detect a variety of candidate viral, bacterial and parasitic pathogens, for acute fever of unknown origin. The platform is based on a centrifugal microfluidic cartridge, the LabDisk (“FeverDisk” for the specific application), which integrates all necessary reagents for sample-to-answer analysis and is processed by a compact, point-of-care compatible device. Methodology/Principal findings A sample volume of 200 μL per FeverDisk was used. In situ extraction with pre-stored reagents was achieved by bind-wash-elute chemistry and magnetic particles. Enzymes for the loop-mediated isothermal amplification (LAMP) were pre-stored in lyopellet form providing stability and independence from the cold chain. The total time to result from sample inlet to read out was 2 h. The proof-of-principle was demonstrated in three small-scale feasibility studies: in Dakar, Senegal and Khartoum, Sudan we tested biobanked samples using 29 and 9 disks, respectively; in Reinfeld, Germany we tested spiked samples and analyzed the limit of detection using three bacteria simultaneously spiked in whole blood using 15 disks. Overall during the three studies, the FeverDisk detected dengue virus (different serotypes), chikungunya virus, Plasmodium falciparum, Salmonella enterica Typhi, Salmonella enterica Paratyphi A and Streptococcus pneumoniae. Conclusions/Significance The FeverDisk proved to be universally applicable as it successfully detected all different types of pathogens as single or co-infections, while it also managed to define the serotype of un-serotyped dengue samples. Thirty-eight FeverDisks at the two African sites provided 59 assay results, out of which 51 (86.4%) were confirmed with reference assay results. The results provide a promising outlook for future implementation of the platform in larger prospective clinical studies for defining its clinical sensitivity and specificity. The technology aims to provide multi-target diagnosis of the origins of fever, which will help fight lethal diseases and the incessant rise of antimicrobial resistance.
Sebastian Hin; Benjamin Lopez-Jimena; Mohammed Bakheit; Vanessa Klein; Seamus Stack; Cheikh Fall; Amadou Sall; Khalid Enan; Mohamed Mustafa; Liz Gillies; Viorel Rusu; Sven Goethel; Nils Paust; Roland Zengerle; Sieghard Frischmann; Manfred Weidmann; Konstantinos Mitsakakis. Fully automated point-of-care differential diagnosis of acute febrile illness. PLOS Neglected Tropical Diseases 2021, 15, e0009177 .
AMA StyleSebastian Hin, Benjamin Lopez-Jimena, Mohammed Bakheit, Vanessa Klein, Seamus Stack, Cheikh Fall, Amadou Sall, Khalid Enan, Mohamed Mustafa, Liz Gillies, Viorel Rusu, Sven Goethel, Nils Paust, Roland Zengerle, Sieghard Frischmann, Manfred Weidmann, Konstantinos Mitsakakis. Fully automated point-of-care differential diagnosis of acute febrile illness. PLOS Neglected Tropical Diseases. 2021; 15 (2):e0009177.
Chicago/Turabian StyleSebastian Hin; Benjamin Lopez-Jimena; Mohammed Bakheit; Vanessa Klein; Seamus Stack; Cheikh Fall; Amadou Sall; Khalid Enan; Mohamed Mustafa; Liz Gillies; Viorel Rusu; Sven Goethel; Nils Paust; Roland Zengerle; Sieghard Frischmann; Manfred Weidmann; Konstantinos Mitsakakis. 2021. "Fully automated point-of-care differential diagnosis of acute febrile illness." PLOS Neglected Tropical Diseases 15, no. 2: e0009177.
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.
Ahmed Abd El Wahed; Pranav Patel; Melanie Maier; Corinna Pietsch; Dana Rüster; Susanne Böhlken-Fascher; Jonas Kissenkötter; Ole Behrmann; Michael Frimpong; Moussa Moïse Diagne; Martin Faye; Ndongo Dia; Mohamed A. Shalaby; Haitham Amer; Mahmoud Elgamal; Ali Zaki; Ghada Ismail; Marco Kaiser; Victor M. Corman; Matthias Niedrig; Olfert Landt; Ousmane Faye; Amadou A. Sall; Frank T. Hufert; Uwe Truyen; Uwe G. Liebert; Manfred Weidmann. Suitcase Lab for Rapid Detection of SARS-CoV-2 Based on Recombinase Polymerase Amplification Assay. Analytical Chemistry 2021, 93, 2627 -2634.
AMA StyleAhmed Abd El Wahed, Pranav Patel, Melanie Maier, Corinna Pietsch, Dana Rüster, Susanne Böhlken-Fascher, Jonas Kissenkötter, Ole Behrmann, Michael Frimpong, Moussa Moïse Diagne, Martin Faye, Ndongo Dia, Mohamed A. Shalaby, Haitham Amer, Mahmoud Elgamal, Ali Zaki, Ghada Ismail, Marco Kaiser, Victor M. Corman, Matthias Niedrig, Olfert Landt, Ousmane Faye, Amadou A. Sall, Frank T. Hufert, Uwe Truyen, Uwe G. Liebert, Manfred Weidmann. Suitcase Lab for Rapid Detection of SARS-CoV-2 Based on Recombinase Polymerase Amplification Assay. Analytical Chemistry. 2021; 93 (4):2627-2634.
Chicago/Turabian StyleAhmed Abd El Wahed; Pranav Patel; Melanie Maier; Corinna Pietsch; Dana Rüster; Susanne Böhlken-Fascher; Jonas Kissenkötter; Ole Behrmann; Michael Frimpong; Moussa Moïse Diagne; Martin Faye; Ndongo Dia; Mohamed A. Shalaby; Haitham Amer; Mahmoud Elgamal; Ali Zaki; Ghada Ismail; Marco Kaiser; Victor M. Corman; Matthias Niedrig; Olfert Landt; Ousmane Faye; Amadou A. Sall; Frank T. Hufert; Uwe Truyen; Uwe G. Liebert; Manfred Weidmann. 2021. "Suitcase Lab for Rapid Detection of SARS-CoV-2 Based on Recombinase Polymerase Amplification Assay." Analytical Chemistry 93, no. 4: 2627-2634.
We investigated temporal trends of codon usage changes for different host species to determine their importance in Zika virus (ZIKV) evolution. Viral spillover resulting from the potential of codon adaptation to host genome was also assessed for the African genotype ZIKV in comparison to the Asian genotype. To improve our understanding on its zoonotic maintenance, we evaluated in vitro the biological properties of the African genotype ZIKV in vertebrate and mosquito cell lines. Analyses were performed in comparison to Yellow fever virus (YFV). Despite significantly lower codon adaptation index trends than YFV, ZIKV showed evident codon adaptation to vertebrate hosts, particularly for the green African monkey Chlorocebus aethiops. PCA and CAI analyses at the individual ZIKV gene level for both human and Aedes aegypti indicated a clear distinction between the two genotypes. African ZIKV isolates showed higher virulence in mosquito cells than in vertebrate cells. Their higher replication in mosquito cells than African YFV confirmed the role of mosquitoes in the natural maintenance of the African genotype ZIKV. An analysis of individual strain growth characteristics indicated that the widely used reference strain MR766 replicates poorly in comparison to African ZIKV isolates. The recombinant African Zika virus strain ArD128000*E/NS5 may be a good model to include in studies on the mechanism of host tropism, as it cannot replicate in the tested vertebrate cell line.
Martin Faye; Naimah Zein; Cheikh Loucoubar; Manfred Weidmann; Ousmane Faye; Marielton Dos Passos Cunha; Paolo Marinho De Andrade Zanotto; Amadou Alpha Sall; Oumar Faye. Biological Characteristics and Patterns of Codon Usage Evolution for the African Genotype Zika Virus. Viruses 2020, 12, 1306 .
AMA StyleMartin Faye, Naimah Zein, Cheikh Loucoubar, Manfred Weidmann, Ousmane Faye, Marielton Dos Passos Cunha, Paolo Marinho De Andrade Zanotto, Amadou Alpha Sall, Oumar Faye. Biological Characteristics and Patterns of Codon Usage Evolution for the African Genotype Zika Virus. Viruses. 2020; 12 (11):1306.
Chicago/Turabian StyleMartin Faye; Naimah Zein; Cheikh Loucoubar; Manfred Weidmann; Ousmane Faye; Marielton Dos Passos Cunha; Paolo Marinho De Andrade Zanotto; Amadou Alpha Sall; Oumar Faye. 2020. "Biological Characteristics and Patterns of Codon Usage Evolution for the African Genotype Zika Virus." Viruses 12, no. 11: 1306.
Infectious pancreatic necrosis (IPN), first described as acute viral catarrhal enteritis, is a highly contagious disease with variable pathogenicity that has been linked to genetic variation in the viral VP2 gene encoding the capsid protein. In this study, the IPN virus (IPNV) is isolated from the moribund fish from five of fourteen Iranian trout farms from 2015 to 2017. The affected fish showed mortality rates ranging from 20% to 60%, with the main clinical signs of exophthalmia, darkened skin, and mild abdominal distension, as well as yellow mucoid fluid in the intestine. Histopathological examination of intestinal sections confirmed acute catarrhal enteritis in all samples. RT-PCR assay of the kidney tissue and cell culture (CHSE-214) samples consistently confirmed the presence of the virus. The phylogenetic analysis of the partial VP2 sequence revealed that the detected isolates belong to genogroup 5, and are closely related to the Sp serotype strains of European origin. Characterization of VP2 of all isolates revealed the P217T221 motif that previously was associated with avirulence or low virulence, while all IPNV-positive fish in this study were clinically affected with moderate mortality. The IPNV isolates from Iran are associated with two lineages that appear to have originated from Europe, possibly via imported eggs.
Sohrab Ahmadivand; Manfred Weidmann; Mansour El-Matbouli; Hooman Rahmati-Holasoo. Low Pathogenic Strain of Infectious Pancreatic Necrosis Virus (IPNV) Associated with Recent Outbreaks in Iranian Trout Farms. Pathogens 2020, 9, 782 .
AMA StyleSohrab Ahmadivand, Manfred Weidmann, Mansour El-Matbouli, Hooman Rahmati-Holasoo. Low Pathogenic Strain of Infectious Pancreatic Necrosis Virus (IPNV) Associated with Recent Outbreaks in Iranian Trout Farms. Pathogens. 2020; 9 (10):782.
Chicago/Turabian StyleSohrab Ahmadivand; Manfred Weidmann; Mansour El-Matbouli; Hooman Rahmati-Holasoo. 2020. "Low Pathogenic Strain of Infectious Pancreatic Necrosis Virus (IPNV) Associated with Recent Outbreaks in Iranian Trout Farms." Pathogens 9, no. 10: 782.
The burden of disease is a major challenge in aquaculture production. The fish gill characterized with a large surface area and short route to the bloodstream is a major environmental interface and a significant portal of entry for pathogens. To investigate gill responses to viral infection the salmonid gill cell line RTgill-W1 was stimulated with synthetic dsRNA and the salmonid alphavirus subtype 2 (SAV-2). Epithelial integrity in polarized cells can be measured as transepithelial electrical resistance (TEER) which is defined as the electrical resistance across a cell monolayer. TEER is a widely accepted quantitative measure of cellular integrity of a cell monolayer. TEER increased immediately after stimulation with the synthetic dsRNA, polyinosinic:polycytidylic acid (poly(I:C)). In parallel, tight junction and gene expression of innate immune activation markers was modulated in response to poly(I:C). The SAV-2 virus was found to replicate at a low level in RTgill-W1 cells where TEER was disturbed at an early stage of infection, however, gene expression related to tight junction regulation was not modulated. A strong poly(I:C)-driven antiviral response was observed including increases of Rig-like receptors (RLRs) and interferon stimulating genes (ISGs) mRNAs. At the level of signal transduction, poly(I:C) stimulation was accompanied by the phosphorylation of 671 proteins, of which 390 were activated solely in response to the presence of poly(I:C). According to motif analysis, kinases in this group included MAPKs, Ca2+/calmodulin-dependent kinase (CaMK) and cAMP-dependent protein kinase (PKA), all reported to be activated in response to viral infection in mammals. Results also highlighted an activation of the cytoskeletal organization that could be mediated by members of the integrin family. While further work is needed to validate these results, our data indicate that salmonid gill epithelia has the ability to mount a significant response to viral infection which might be important in disease progression. In vitro cell culture can facilitate both a deeper understanding of the anti-viral response in fish and open novel therapeutic avenues for fish health management in aquaculture.
Shankar C. Mandal; Manfred Weidmann; Amaya Albalat; Emma Carrick; Bernat Morro; Simon MacKenzie. Polarized Trout Epithelial Cells Regulate Transepithelial Electrical Resistance, Gene Expression, and the Phosphoproteome in Response to Viral Infection. Frontiers in Immunology 2020, 11, 1809 .
AMA StyleShankar C. Mandal, Manfred Weidmann, Amaya Albalat, Emma Carrick, Bernat Morro, Simon MacKenzie. Polarized Trout Epithelial Cells Regulate Transepithelial Electrical Resistance, Gene Expression, and the Phosphoproteome in Response to Viral Infection. Frontiers in Immunology. 2020; 11 ():1809.
Chicago/Turabian StyleShankar C. Mandal; Manfred Weidmann; Amaya Albalat; Emma Carrick; Bernat Morro; Simon MacKenzie. 2020. "Polarized Trout Epithelial Cells Regulate Transepithelial Electrical Resistance, Gene Expression, and the Phosphoproteome in Response to Viral Infection." Frontiers in Immunology 11, no. : 1809.
In last five years, the Africa has faced two outbreaks of Zaire ebolavirus. These outbreaks have been the largest so far, and latest outbreak is still ongoing and affecting the Democratic Republic of the Congo. We tested in parallel three different Zaire ebolavirus (EBOV) realtime RT-PCRs targeting the nucleoprotein gene (EBOV NP-RT-qPCRs) described by Trombley et al. (2010), Huang et al. (2012) and Weidmann et al. (2004). These assays are used regularly in diagnostic laboratories. The limit of detection (LOD), intra-assay repeatability using different matrixes, sensitivity and specificity were determined. In addition, the primers and probes were aligned with the sequences available in ongoing and past outbreaks in order to check the mismatches. The specificity of all three EBOV NP-RT-qPCRs were excellent (100%), and LODs were under or 10 copies per PCR reaction. Intra-assay repeatability was good in all assays, however the Ct-values were bit higher using the EDTA-blood based matrix. All of the primers and probes in EBOV NP-RT-qPCR assays have one or more mismatches in the probes and primers when the 2267 Zaire EBOV NP sequences, including strains Ituri from DRC outbreak (year 2018), was aligned. The EBOV strain of Bikoro (year 2018) circulating in DRC was 100% match in Trombley and Weidmann assay, but had one mismatch in Huang assay.
Anne J Jääskeläinen; Tarja Sironen; Minttu Kaloinen; Laura Kakkola; Ilkka Julkunen; Roger Hewson; Manfred Weidmann; Ali Mirazimi; Robert Watson; Olli Vapalahti. Comparison of Zaire ebolavirus realtime RT-PCRs targeting the nucleoprotein gene. Journal of Virological Methods 2020, 284, 113941 .
AMA StyleAnne J Jääskeläinen, Tarja Sironen, Minttu Kaloinen, Laura Kakkola, Ilkka Julkunen, Roger Hewson, Manfred Weidmann, Ali Mirazimi, Robert Watson, Olli Vapalahti. Comparison of Zaire ebolavirus realtime RT-PCRs targeting the nucleoprotein gene. Journal of Virological Methods. 2020; 284 ():113941.
Chicago/Turabian StyleAnne J Jääskeläinen; Tarja Sironen; Minttu Kaloinen; Laura Kakkola; Ilkka Julkunen; Roger Hewson; Manfred Weidmann; Ali Mirazimi; Robert Watson; Olli Vapalahti. 2020. "Comparison of Zaire ebolavirus realtime RT-PCRs targeting the nucleoprotein gene." Journal of Virological Methods 284, no. : 113941.
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.
Idrissa Dieng; Boris Gildas Hedible; Moussa Moïse Diagne; Ahmed Abd El Wahed; Cheikh Tidiane Diagne; Cheikh Fall; Vicent Richard; Muriel Vray; Manfred Weidmann; Ousmane Faye; Amadou Alpha Sall; Oumar Faye. Mobile Laboratory Reveals the Circulation of Dengue Virus Serotype I of Asian Origin in Medina Gounass (Guediawaye), Senegal. Diagnostics 2020, 10, 408 .
AMA StyleIdrissa Dieng, Boris Gildas Hedible, Moussa Moïse Diagne, Ahmed Abd El Wahed, Cheikh Tidiane Diagne, Cheikh Fall, Vicent Richard, Muriel Vray, Manfred Weidmann, Ousmane Faye, Amadou Alpha Sall, Oumar Faye. Mobile Laboratory Reveals the Circulation of Dengue Virus Serotype I of Asian Origin in Medina Gounass (Guediawaye), Senegal. Diagnostics. 2020; 10 (6):408.
Chicago/Turabian StyleIdrissa Dieng; Boris Gildas Hedible; Moussa Moïse Diagne; Ahmed Abd El Wahed; Cheikh Tidiane Diagne; Cheikh Fall; Vicent Richard; Muriel Vray; Manfred Weidmann; Ousmane Faye; Amadou Alpha Sall; Oumar Faye. 2020. "Mobile Laboratory Reveals the Circulation of Dengue Virus Serotype I of Asian Origin in Medina Gounass (Guediawaye), Senegal." Diagnostics 10, no. 6: 408.
Richard S. Quilliam; Manfred Weidmann; Vanessa Moresco; Heather Purshouse; Zoe O'Hara; David M. Oliver. COVID-19: The environmental implications of shedding SARS-CoV-2 in human faeces. Environment International 2020, 140, 105790 -105790.
AMA StyleRichard S. Quilliam, Manfred Weidmann, Vanessa Moresco, Heather Purshouse, Zoe O'Hara, David M. Oliver. COVID-19: The environmental implications of shedding SARS-CoV-2 in human faeces. Environment International. 2020; 140 ():105790-105790.
Chicago/Turabian StyleRichard S. Quilliam; Manfred Weidmann; Vanessa Moresco; Heather Purshouse; Zoe O'Hara; David M. Oliver. 2020. "COVID-19: The environmental implications of shedding SARS-CoV-2 in human faeces." Environment International 140, no. : 105790-105790.
Molecular detection of Zika virus (ZIKV) is a key element of outbreak management. Multiple PCR and isothermal ZIKV assays targeting different ZIKV sequences have been published. In this study, we compared a qRT-PCR, 2 RT-LAMP assays (based on different primer design approaches), and an RT-RPA for the detection of African and Asian/American lineages of ZIKV isolates from human, mosquito, and monkey. Results showed that RT-LAMP detected 100% of samples with a time threshold (Tt) of 18.01 ± 11.71 min while qRT-PCR detected 88.88% of samples with a Tt of 58.30 ± 16.58 min and RT-RPA 50% of samples with a Tt of 3.70 ± 0.44 min.
Cheikh Tidiane Diagne; Martin Faye; Benjamin Lopez-Jimena; Ahmed Abd El Wahed; Cheikh Loucoubar; Cheikh Fall; Giulia Mencatelli; Oumar Faye; Ousmane Faye; Manfred Weidmann; Amadou Alpha Sall. Comparative Analysis of Zika Virus Detection by RT-qPCR, RT-LAMP, and RT-RPA. Methods in Molecular Biology 2020, 2142, 165 -179.
AMA StyleCheikh Tidiane Diagne, Martin Faye, Benjamin Lopez-Jimena, Ahmed Abd El Wahed, Cheikh Loucoubar, Cheikh Fall, Giulia Mencatelli, Oumar Faye, Ousmane Faye, Manfred Weidmann, Amadou Alpha Sall. Comparative Analysis of Zika Virus Detection by RT-qPCR, RT-LAMP, and RT-RPA. Methods in Molecular Biology. 2020; 2142 ():165-179.
Chicago/Turabian StyleCheikh Tidiane Diagne; Martin Faye; Benjamin Lopez-Jimena; Ahmed Abd El Wahed; Cheikh Loucoubar; Cheikh Fall; Giulia Mencatelli; Oumar Faye; Ousmane Faye; Manfred Weidmann; Amadou Alpha Sall. 2020. "Comparative Analysis of Zika Virus Detection by RT-qPCR, RT-LAMP, and RT-RPA." Methods in Molecular Biology 2142, no. : 165-179.
Two one-step real-time reverse transcription loop-mediated isothermal amplification (RT-LAMP) assays for the detection of Zika virus (ZIKV) were developed, based on two different primer design approaches: (1) open source, based on a combination of sequence diversity clustering (phylogeny and principal component analysis) and LAVA algorithm, using 45 whole genome ZIKV sequences retrieved from the National Center for Biotechnology Information (NCBI) database; (2) standard software for LAMP primer design (Primer Explorer V4), using 59 sequences of the ZIKV 3' UTR. The assays were firstly evaluated with External Quality Assessment panels from INSTAND e.V. (Germany) and EVD-LabNet (The Netherlands) including 4 and 12 unknown samples, respectively, and secondly, with 9 human, mosquito, and monkey ZIKV isolates from Africa (Senegal, Ivory Coast, and Uganda) and America (Brazil). The limit of detection as determined by probit analysis was 181 molecules for both RT-LAMP assays, and 100% reproducibility in the assays was obtained for 103 molecules (4/8 repetitions were positive for 102 molecules). Both assays were specific, amplifying only ZIKV RNA and not cross-detecting other arboviruses included in this study.
Benjamin Lopez-Jimena; Mohammed Bakheit; Michaël Bekaert; Graham Harold; Sieghard Frischmann; Cheikh Fall; Cheikh Tidiane Diagne; Oumar Faye; Ousmane Faye; Amadou Alpha Sall; Manfred Weidmann. Development and Validation of Real-Time RT-LAMP Assays for the Specific Detection of Zika Virus. Methods in Molecular Biology 2020, 2142, 147 -164.
AMA StyleBenjamin Lopez-Jimena, Mohammed Bakheit, Michaël Bekaert, Graham Harold, Sieghard Frischmann, Cheikh Fall, Cheikh Tidiane Diagne, Oumar Faye, Ousmane Faye, Amadou Alpha Sall, Manfred Weidmann. Development and Validation of Real-Time RT-LAMP Assays for the Specific Detection of Zika Virus. Methods in Molecular Biology. 2020; 2142 ():147-164.
Chicago/Turabian StyleBenjamin Lopez-Jimena; Mohammed Bakheit; Michaël Bekaert; Graham Harold; Sieghard Frischmann; Cheikh Fall; Cheikh Tidiane Diagne; Oumar Faye; Ousmane Faye; Amadou Alpha Sall; Manfred Weidmann. 2020. "Development and Validation of Real-Time RT-LAMP Assays for the Specific Detection of Zika Virus." Methods in Molecular Biology 2142, no. : 147-164.
Development of novel point of care diagnostic methods in order to help in implementing disease control program and identifying the causative agent of an outbreak is crucial. Classical diagnostic techniques, e.g., real-time polymerase chain reaction (PCR), rely on the presence of the nucleic acid sequence of the target in GenBank. In the case of an emerging new strain of a known or novel pathogen, false-negative results will be recorded by PCR. On the other hand, next-generation sequencing technologies allow rapid whole genome sequencing without previous knowledge of the target. One of these methods is the Oxford Nanopore sequencing technique, which utilizes a portable device named MinION and has a short run time. In this protocol, we describe the development of a novel nanopore sequencing protocol by combining random isothermal amplification technology and nanopore sequencing. The established protocol is rapid (<7 h) and sensitive as less than 4% of the sequenced RNA belonged to the target virus, Zika. Interestingly, we have established an offline BLAST search for the data analysis that facilitates the use of the whole protocol at remote settings without the need of an Internet connection.
Sören Hansen; Oumar Faye; Sabri S. Sanabani; Martin Faye; Susanne Böhlken-Fascher; Ousmane Faye; Amadou Alpha Sall; Michaël Bekaert; Manfred Weidmann; Claus-Peter Czerny; Ahmed Abd El Wahed. Zika Virus Amplification Using Strand Displacement Isothermal Method and Sequencing Using Nanopore Technology. Methods in Molecular Biology 2020, 2142, 123 -136.
AMA StyleSören Hansen, Oumar Faye, Sabri S. Sanabani, Martin Faye, Susanne Böhlken-Fascher, Ousmane Faye, Amadou Alpha Sall, Michaël Bekaert, Manfred Weidmann, Claus-Peter Czerny, Ahmed Abd El Wahed. Zika Virus Amplification Using Strand Displacement Isothermal Method and Sequencing Using Nanopore Technology. Methods in Molecular Biology. 2020; 2142 ():123-136.
Chicago/Turabian StyleSören Hansen; Oumar Faye; Sabri S. Sanabani; Martin Faye; Susanne Böhlken-Fascher; Ousmane Faye; Amadou Alpha Sall; Michaël Bekaert; Manfred Weidmann; Claus-Peter Czerny; Ahmed Abd El Wahed. 2020. "Zika Virus Amplification Using Strand Displacement Isothermal Method and Sequencing Using Nanopore Technology." Methods in Molecular Biology 2142, no. : 123-136.
As part of the laboratory response to the Ebola virus outbreak in Guinea, the Institut Pasteur de Dakar mobile laboratory (IPD-ML) was set up in Donka hospital from 2014 to 2016. EBOV suspected samples collected at Ebola Treatment Centers (ETC) and from community deaths were sent daily to IPD-ML. Analysis was performed using dried oligonucleotide mixes for real-time RT-PCR designed for field diagnostic. From March 2014 to May 2015, a total of 6055 patient samples suspected for EBOV collected from seven regions of Guinea were tested by real-time RT-PCR. These patients’ clinical included serum samples (n = 2537 samples) and swabs (n = 3518 samples) with positivity rates of 36.74 and 6.88% respectively. Females were significantly more affected than males with positivity rates of 22.39 and 17.22% respectively (p-value = 5.721e-7). All age groups were exposed to the virus with significant difference (p-value <= 2.2e-16). The IPD-ML contributed significantly to the surveillance and patient management during the EBOV outbreak in Guinea. Furthermore, dried reagents adapted for field diagnostic of EVD suspect cases could be useful for future outbreak preparedness and response.
Oumar Faye; Cheikh Tidiane Diagne; Amadou Diallo; Emily Meyer; Barre Soropogui; Gamou Fall; Cheikh Fall; N\'Faly Magassouba; Lamine Koivogui; Sakoba Keita; Cheikh Loucoubar; Mamadou Diop; Manfred Weidmann; Ousmane Faye; Amadou Alpha Sall. Molecular Diagnostics of Ebola Patient Samples by Institut Pasteur de Dakar Mobile Laboratory in Guinea 2014–2016. Emerging Challenges in Filovirus Infections 2020, 1 .
AMA StyleOumar Faye, Cheikh Tidiane Diagne, Amadou Diallo, Emily Meyer, Barre Soropogui, Gamou Fall, Cheikh Fall, N\'Faly Magassouba, Lamine Koivogui, Sakoba Keita, Cheikh Loucoubar, Mamadou Diop, Manfred Weidmann, Ousmane Faye, Amadou Alpha Sall. Molecular Diagnostics of Ebola Patient Samples by Institut Pasteur de Dakar Mobile Laboratory in Guinea 2014–2016. Emerging Challenges in Filovirus Infections. 2020; ():1.
Chicago/Turabian StyleOumar Faye; Cheikh Tidiane Diagne; Amadou Diallo; Emily Meyer; Barre Soropogui; Gamou Fall; Cheikh Fall; N\'Faly Magassouba; Lamine Koivogui; Sakoba Keita; Cheikh Loucoubar; Mamadou Diop; Manfred Weidmann; Ousmane Faye; Amadou Alpha Sall. 2020. "Molecular Diagnostics of Ebola Patient Samples by Institut Pasteur de Dakar Mobile Laboratory in Guinea 2014–2016." Emerging Challenges in Filovirus Infections , no. : 1.
Usutu virus (USUV) previously restricted to Africa where it caused mild infections, emerged in 2001 in Europe and caused more severe infections among birds and humans with neurological forms, suggesting an adaptation and increasing virulence. This evolution suggests the need to better understand USUV transmission patterns for assessing risks and to develop control strategies. Phylogenetic analysis conducted in Africa showed low genetic diversity of African USUV strains except for one human and the USUV subtype (USUVsub) strains, which exhibited a deletion in the 3′UTR and nucleotide substitutions throughout the genome. Here we analyzed their viral replication in vitro in mosquito and mammalian cells, and vector competence of Culex quinquefasciatus, compared to a reference strain. Growth kinetics of the different strains showed comparable replication rates however variations in replication and translation efficiency were observed. Vector competence analysis showed that all strains were able to infect Culex quinquefasciatus the main peridomestic Culex species in Africa, with detection of USUV viral genomes and infectious particles. Dissemination and transmission were observed only for USUVsub, but infectious particles were not detected in Culex quinquefasciatus saliva. Our findings suggest that genetic variability can affect USUV in vitro replication in a cell type-dependent manner and in vivo in mosquitoes. In addition, the results show that Culex quinquefasciatus is not competent for the USUV strains analyzed here and also suggest an aborted transmission process for the USUVsub, which requires further investigations.
Marie Henriette Dior Ndione; El Hadji Ndiaye; Marème Sèye Thiam; Manfred Weidmann; Martin Faye; Yamar Ba; Jessica Benkaroun; Oumar Faye; Cheikh Loucoubar; Pape Mbacké Sembène; Mawlouth Diallo; Amadou Alpha Sall; Ousmane Faye; Gamou Fall. Impact of genetic diversity on biological characteristics of Usutu virus strains in Africa. Virus Research 2019, 273, 197753 .
AMA StyleMarie Henriette Dior Ndione, El Hadji Ndiaye, Marème Sèye Thiam, Manfred Weidmann, Martin Faye, Yamar Ba, Jessica Benkaroun, Oumar Faye, Cheikh Loucoubar, Pape Mbacké Sembène, Mawlouth Diallo, Amadou Alpha Sall, Ousmane Faye, Gamou Fall. Impact of genetic diversity on biological characteristics of Usutu virus strains in Africa. Virus Research. 2019; 273 ():197753.
Chicago/Turabian StyleMarie Henriette Dior Ndione; El Hadji Ndiaye; Marème Sèye Thiam; Manfred Weidmann; Martin Faye; Yamar Ba; Jessica Benkaroun; Oumar Faye; Cheikh Loucoubar; Pape Mbacké Sembène; Mawlouth Diallo; Amadou Alpha Sall; Ousmane Faye; Gamou Fall. 2019. "Impact of genetic diversity on biological characteristics of Usutu virus strains in Africa." Virus Research 273, no. : 197753.
Polyarthritis and rash caused by Sindbis virus (SINV), was first recognised in northern Europe about 50 years ago and is known as Ockelbo disease in Sweden and Pogosta disease in Finland. This mosquito-borne virus occurs mainly in tropical and sub-tropical countries, and in northern Europe it is suggested to cause regularly reoccurring outbreaks. Here a seven-year cycle of SINV outbreaks has been referred to in scientific papers, although the hypothesis is based solely on reported human cases. In the search for a more objective outbreak signal, we evaluated mosquito abundance and SINV prevalence in vector mosquitoes from an endemic area in central Sweden. Vector mosquitoes collected in the River Dalälven floodplains during the years before, during, and after the hypothesised 2002 outbreak year were assayed for virus on cell culture. Obtained isolates were partially sequenced, and the nucleotide sequences analysed using Bayesian maximum clade credibility and median joining network analysis. Only one SINV strain was recovered in 2001, and 4 strains in 2003, while 15 strains were recovered in 2002 with significantly increased infection rates in both the enzootic and the bridge-vectors. In 2002, the Maximum Likelihood Estimated infection rates were 10.0/1000 in the enzootic vectors Culex torrentium/pipiens, and 0.62/1000 in the bridge-vector Aedes cinereus, compared to 4.9/1000 and 0.0/1000 in 2001 and 0.0/1000 and 0.32/1000 in 2003 Sequence analysis showed that all isolates belonged to the SINV genotype I (SINV-I). The genetic analysis revealed local maintenance of four SINV-I clades in the River Dalälven floodplains over the years. Our findings suggest that increased SINV-I prevalence in vector mosquitoes constitutes the most valuable outbreak marker for further scrutinising the hypothesized seven-year cycle of SINV-I outbreaks and the mechanisms behind.
Jan O. Lundström; Jenny C. Hesson; Martina L. Schäfer; Örjan Östman; Torsten Semmler; Michaël Bekaert; Manfred Weidmann; Åke Lundkvist; Martin Pfeffer. Sindbis virus polyarthritis outbreak signalled by virus prevalence in the mosquito vectors. PLoS Neglected Tropical Diseases 2019, 13, e0007702 .
AMA StyleJan O. Lundström, Jenny C. Hesson, Martina L. Schäfer, Örjan Östman, Torsten Semmler, Michaël Bekaert, Manfred Weidmann, Åke Lundkvist, Martin Pfeffer. Sindbis virus polyarthritis outbreak signalled by virus prevalence in the mosquito vectors. PLoS Neglected Tropical Diseases. 2019; 13 (8):e0007702.
Chicago/Turabian StyleJan O. Lundström; Jenny C. Hesson; Martina L. Schäfer; Örjan Östman; Torsten Semmler; Michaël Bekaert; Manfred Weidmann; Åke Lundkvist; Martin Pfeffer. 2019. "Sindbis virus polyarthritis outbreak signalled by virus prevalence in the mosquito vectors." PLoS Neglected Tropical Diseases 13, no. 8: e0007702.