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Sene O, Sagne SN, Bob NS, Mhamadi M, Dieng I, Gaye A, Ba H, Dia M, Faye ET, Diop SM, Sall Y, Diop B, Ndiaye M, Loucoubar C, Simon-Lorière E, Sakuntabhai A, Faye O, Sall AA, Diallo D, Dia N, Faye O, Diagne MM, Fall M, Ndione MHD, Barry MA, Fall G. Re-Emergence of Rift Valley Fever Virus Lineage H in Senegal in 2022: In Vitro Characterization and Impact on Its Global Emergence in West Africa. Viruses 2024; 16:1018. [PMID: 39066182 PMCID: PMC11281490 DOI: 10.3390/v16071018] [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: 03/31/2024] [Revised: 05/18/2024] [Accepted: 06/06/2024] [Indexed: 07/28/2024] Open
Abstract
Rift Valley fever (RVF) is a re-emerging vector-borne zoonosis with a high public health and veterinary impact. In West Africa, many lineages were previously detected, but since 2020, lineage H from South Africa has been the main cause of the outbreaks. In this study, clinical samples collected through national surveillance were screened for RVF virus (RVFV) acute infection by RT-PCR and IgM ELISA tests. Sequencing, genome mapping and in vitro phenotypic characterization in mammal cells were performed on RT-PCR positive samples in comparison with other epidemic lineages (G and C). Four RVFV human cases were detected in Senegal and the sequence analyses revealed that the strains belonged to lineage H. The in vitro kinetics and genome mapping showed different replication efficiency profiles for the tested RVFV lineages and non-conservative mutations, which were more common to lineage G or specific to lineage H. Our findings showed the re-emergence of lineage H in Senegal in 2022, its high viral replication efficiency in vitro and support the findings that genetic diversity affects viral replication. This study gives new insights into the biological properties of lineage H and calls for deeper studies to better assess its potential to cause a future threat in Senegal.
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Affiliation(s)
- Ousseynou Sene
- WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fevers, Virology Department, Pasteur Institute, Dakar 12900, Senegal; (N.S.B.); (I.D.); (H.B.); (M.D.); (E.T.F.); (S.M.D.); (O.F.); (A.A.S.); (N.D.); (O.F.); (M.M.D.); (M.H.D.N.); (G.F.)
| | - Samba Niang Sagne
- Epidemiology, Clinical Research & Data Science, Pasteur Institute, Dakar 12900, Senegal; (S.N.S.); (A.G.); (C.L.); (M.A.B.)
| | - Ndeye Sakha Bob
- WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fevers, Virology Department, Pasteur Institute, Dakar 12900, Senegal; (N.S.B.); (I.D.); (H.B.); (M.D.); (E.T.F.); (S.M.D.); (O.F.); (A.A.S.); (N.D.); (O.F.); (M.M.D.); (M.H.D.N.); (G.F.)
| | | | - Idrissa Dieng
- WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fevers, Virology Department, Pasteur Institute, Dakar 12900, Senegal; (N.S.B.); (I.D.); (H.B.); (M.D.); (E.T.F.); (S.M.D.); (O.F.); (A.A.S.); (N.D.); (O.F.); (M.M.D.); (M.H.D.N.); (G.F.)
| | - Aboubacry Gaye
- Epidemiology, Clinical Research & Data Science, Pasteur Institute, Dakar 12900, Senegal; (S.N.S.); (A.G.); (C.L.); (M.A.B.)
| | - Haoua Ba
- WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fevers, Virology Department, Pasteur Institute, Dakar 12900, Senegal; (N.S.B.); (I.D.); (H.B.); (M.D.); (E.T.F.); (S.M.D.); (O.F.); (A.A.S.); (N.D.); (O.F.); (M.M.D.); (M.H.D.N.); (G.F.)
| | - Moussa Dia
- WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fevers, Virology Department, Pasteur Institute, Dakar 12900, Senegal; (N.S.B.); (I.D.); (H.B.); (M.D.); (E.T.F.); (S.M.D.); (O.F.); (A.A.S.); (N.D.); (O.F.); (M.M.D.); (M.H.D.N.); (G.F.)
| | - Elisabeth Thérèse Faye
- WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fevers, Virology Department, Pasteur Institute, Dakar 12900, Senegal; (N.S.B.); (I.D.); (H.B.); (M.D.); (E.T.F.); (S.M.D.); (O.F.); (A.A.S.); (N.D.); (O.F.); (M.M.D.); (M.H.D.N.); (G.F.)
| | - Sokhna Mayemouna Diop
- WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fevers, Virology Department, Pasteur Institute, Dakar 12900, Senegal; (N.S.B.); (I.D.); (H.B.); (M.D.); (E.T.F.); (S.M.D.); (O.F.); (A.A.S.); (N.D.); (O.F.); (M.M.D.); (M.H.D.N.); (G.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.)
| | - Cheikh Loucoubar
- Epidemiology, Clinical Research & Data Science, Pasteur Institute, Dakar 12900, Senegal; (S.N.S.); (A.G.); (C.L.); (M.A.B.)
| | | | - 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, University of Tokyo (IMSUT), Tokyo 108-8639, Japan
| | - Ousmane Faye
- WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fevers, Virology Department, Pasteur Institute, Dakar 12900, Senegal; (N.S.B.); (I.D.); (H.B.); (M.D.); (E.T.F.); (S.M.D.); (O.F.); (A.A.S.); (N.D.); (O.F.); (M.M.D.); (M.H.D.N.); (G.F.)
| | - Amadou Alpha Sall
- WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fevers, Virology Department, Pasteur Institute, Dakar 12900, Senegal; (N.S.B.); (I.D.); (H.B.); (M.D.); (E.T.F.); (S.M.D.); (O.F.); (A.A.S.); (N.D.); (O.F.); (M.M.D.); (M.H.D.N.); (G.F.)
| | - Diawo Diallo
- Zoology Department, Pasteur Institute, Dakar 12900, Senegal;
| | - Ndongo Dia
- WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fevers, Virology Department, Pasteur Institute, Dakar 12900, Senegal; (N.S.B.); (I.D.); (H.B.); (M.D.); (E.T.F.); (S.M.D.); (O.F.); (A.A.S.); (N.D.); (O.F.); (M.M.D.); (M.H.D.N.); (G.F.)
| | - Oumar Faye
- WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fevers, Virology Department, Pasteur Institute, Dakar 12900, Senegal; (N.S.B.); (I.D.); (H.B.); (M.D.); (E.T.F.); (S.M.D.); (O.F.); (A.A.S.); (N.D.); (O.F.); (M.M.D.); (M.H.D.N.); (G.F.)
| | - Moussa Moise Diagne
- WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fevers, Virology Department, Pasteur Institute, Dakar 12900, Senegal; (N.S.B.); (I.D.); (H.B.); (M.D.); (E.T.F.); (S.M.D.); (O.F.); (A.A.S.); (N.D.); (O.F.); (M.M.D.); (M.H.D.N.); (G.F.)
| | - Malick Fall
- Animal Biology Department, Faculty of Sciences and Techniques, Cheikh Anta Diop University, Dakar 10700, Senegal;
| | - Marie Henriette Dior Ndione
- WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fevers, Virology Department, Pasteur Institute, Dakar 12900, Senegal; (N.S.B.); (I.D.); (H.B.); (M.D.); (E.T.F.); (S.M.D.); (O.F.); (A.A.S.); (N.D.); (O.F.); (M.M.D.); (M.H.D.N.); (G.F.)
| | - Mamadou Aliou Barry
- Epidemiology, Clinical Research & Data Science, Pasteur Institute, Dakar 12900, Senegal; (S.N.S.); (A.G.); (C.L.); (M.A.B.)
| | - Gamou Fall
- WHO Collaborating Centre for Arbovirus and Viral Hemorrhagic Fevers, Virology Department, Pasteur Institute, Dakar 12900, Senegal; (N.S.B.); (I.D.); (H.B.); (M.D.); (E.T.F.); (S.M.D.); (O.F.); (A.A.S.); (N.D.); (O.F.); (M.M.D.); (M.H.D.N.); (G.F.)
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2
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Huong TN, Lee ZQ, Lai SK, Lee HY, Tan BH, Sugrue RJ. Evidence that an interaction between the respiratory syncytial virus F and G proteins at the distal ends of virus filaments mediates efficient multiple cycle infection. Virology 2024; 591:109985. [PMID: 38227992 DOI: 10.1016/j.virol.2024.109985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 11/29/2023] [Accepted: 01/04/2024] [Indexed: 01/18/2024]
Abstract
Evidence for a stable interaction between the respiratory syncytial virus (RSV) F and G proteins on the surface of virus filaments was provided using antibody immunoprecipitation studies on purified RSV particles, and by the in situ analysis on the surface of RSV-infected cells using the proximity ligation assay. Imaging of the F and G protein distribution on virus filaments suggested that this protein complex was localised at the distal ends of the virus filaments, and suggested that this protein complex played a direct role in mediating efficient localised cell-to-cell virus transmission. G protein expression was required for efficient localised cell-to-cell transmission of RSV in cell monolayers which provided evidence that this protein complex mediates efficient multiple cycle infection. Collectively, these data provide evidence that F and G proteins form a complex on the surface of RSV particles, and that a role for this protein complex in promoting virus transmission is suggested.
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Affiliation(s)
- Tra Nguyen Huong
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Republic of Singapore
| | - Zhi Qi Lee
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Republic of Singapore
| | - Soak Kuan Lai
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Republic of Singapore
| | - Hsin Yee Lee
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Republic of Singapore
| | - Boon Huan Tan
- LKC School of Medicine, Nanyang Technological University, 11 Mandalay Road, Singapore, 308232, Republic of Singapore
| | - Richard J Sugrue
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Republic of Singapore.
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3
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D'Addiego J, Wand N, Afrough B, Fletcher T, Kurosaki Y, Leblebicioglu H, Hewson R. Recovery of complete genome sequences of Crimean-Congo haemorrhagic fever virus (CCHFV) directly from clinical samples: A comparative study between targeted enrichment and metagenomic approaches. J Virol Methods 2024; 323:114833. [PMID: 37879367 DOI: 10.1016/j.jviromet.2023.114833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 10/06/2023] [Accepted: 10/20/2023] [Indexed: 10/27/2023]
Abstract
Crimean-Congo haemorrhagic fever (CCHF) is the most prevalent human tick-borne viral disease, endemic to the Balkans, Africa, Middle East and Asia. There are currently no licensed vaccines or effective antivirals against CCHF. CCHF virus (CCHFV) has a negative sense segmented tripartite RNA genome consisting of the small (S), medium (M) and large (L) segments. Depending on the segment utilised for genetic affiliation, there are up to 7 circulating lineages of CCHFV. The current lack of geographical representation of CCHFV sequences in various repositories highlights a requirement for increased CCHFV sequencing capabilities in endemic regions. We have optimised and established a multiplex PCR tiling methodology for the targeted enrichment of complete genomes of Europe 1 CCHFV lineage directly from clinical samples and compared its performance to a non-targeted enrichment approach on both short-read and long-read sequencing platforms. We have found a statistically significant increase in mapped viral sequencing reads produced with our targeted enrichment approach. This has allowed us to recover near complete S segment sequences and above 90% of the M and L segment sequences for samples with Ct values as high as 31.3. This study demonstrates the superiority of a targeted enrichment approach for recovery of CCHFV genomic sequences from samples with low virus titre. CCHFV is an important vector-borne human pathogen with wide geographical distribution. The validated methodology reported here adds value to front-line public health laboratories employing genomic sequencing for CCHFV Europe 1 lineage surveillance, particularly in the Balkan and Middle Eastern territories currently monitoring the spread of the pathogen. Tracking the genomic evolution of the virus across regions improves risk assessment and directly informs the development of diagnostics, therapeutics, and vaccines.
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Affiliation(s)
- Jake D'Addiego
- UK Health Security Agency, Science Group, Porton Down, Salisbury, United Kingdom; Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom.
| | - Nadina Wand
- UK Health Security Agency, Science Group, Porton Down, Salisbury, United Kingdom
| | - Babak Afrough
- UK Health Security Agency, Science Group, Porton Down, Salisbury, United Kingdom
| | - Tom Fletcher
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Yohei Kurosaki
- National Research Centre for the Control and Prevention of Infectious Diseases, Nagasaki University, Japan
| | | | - Roger Hewson
- UK Health Security Agency, Science Group, Porton Down, Salisbury, United Kingdom; Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom; Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom; National Research Centre for the Control and Prevention of Infectious Diseases, Nagasaki University, Japan
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4
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Ebert CL, Söder L, Kubinski M, Glanz J, Gregersen E, Dümmer K, Grund D, Wöhler AS, Könenkamp L, Liebig K, Knoll S, Hellhammer F, Topp AK, Becher P, Springer A, Strube C, Nagel-Kohl U, Nordhoff M, Steffen I, Bauer BU, Ganter M, Feige K, Becker SC, Boelke M. Detection and Characterization of Alongshan Virus in Ticks and Tick Saliva from Lower Saxony, Germany with Serological Evidence for Viral Transmission to Game and Domestic Animals. Microorganisms 2023; 11:microorganisms11030543. [PMID: 36985117 PMCID: PMC10055853 DOI: 10.3390/microorganisms11030543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 02/15/2023] [Accepted: 02/17/2023] [Indexed: 02/25/2023] Open
Abstract
The newly discovered group of Jingmenviruses has been shown to infect a wide range of hosts and has been associated with febrile illness in humans. During a survey for Jingmenviruses in ticks from Lower Saxony, Germany, Alongshan virus (ALSV) was identified in Ixodes spp. ticks. Additional virus screenings revealed the presence of ALSV in the bodies and saliva of ticks collected at several locations in Lower Saxony. Vector competence studies that included Ixodes ricinus and Dermacentor reticulatus validated the replication of ALSV within those tick species. In vitro feeding experiments with ALSV-injected Ixodes ricinus demonstrated effective viral transmission during blood feeding. To evaluate the potential viral transmission during a natural blood meal, sera from wild game and domestic animals were investigated. One serum sample from a red deer was found to be positive for ALSV RNA, while serological screenings in game and domestic animals revealed the presence of ALSV-specific antibodies at different locations in Lower Saxony. Overall, those results demonstrate the broad distribution of ALSV in ticks in Lower Saxony and hypothesize frequent exposure to animals based on serological investigations. Hence, its potential risk to human and animal health requires further investigation.
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Affiliation(s)
- Cara Leonie Ebert
- Institute for Parasitology, Centre for Infection Medicine, University of Veterinary Medicine Hannover, Buenteweg 17, 30559 Hanover, Germany
- Research Center for Emerging Infections and Zoonoses, Buenteweg 17, 30559 Hanover, Germany
| | - Lars Söder
- Institute of Virology, Department of Infectious Diseases, University of Veterinary Medicine Hannover, Buenteweg 17, 30559 Hanover, Germany
| | - Mareike Kubinski
- Research Center for Emerging Infections and Zoonoses, Buenteweg 17, 30559 Hanover, Germany
| | - Julien Glanz
- Institute for Parasitology, Centre for Infection Medicine, University of Veterinary Medicine Hannover, Buenteweg 17, 30559 Hanover, Germany
- Research Center for Emerging Infections and Zoonoses, Buenteweg 17, 30559 Hanover, Germany
| | - Eva Gregersen
- Institute of Virology, Department of Infectious Diseases, University of Veterinary Medicine Hannover, Buenteweg 17, 30559 Hanover, Germany
| | - Katrin Dümmer
- Research Center for Emerging Infections and Zoonoses, Buenteweg 17, 30559 Hanover, Germany
| | - Domenic Grund
- Institute for Parasitology, Centre for Infection Medicine, University of Veterinary Medicine Hannover, Buenteweg 17, 30559 Hanover, Germany
- Research Center for Emerging Infections and Zoonoses, Buenteweg 17, 30559 Hanover, Germany
| | - Ann-Sophie Wöhler
- Institute for Parasitology, Centre for Infection Medicine, University of Veterinary Medicine Hannover, Buenteweg 17, 30559 Hanover, Germany
- Research Center for Emerging Infections and Zoonoses, Buenteweg 17, 30559 Hanover, Germany
| | - Laura Könenkamp
- Research Center for Emerging Infections and Zoonoses, Buenteweg 17, 30559 Hanover, Germany
- Institute for Biochemistry, University of Veterinary Medicine Hannover, Buenteweg 17, 30559 Hanover, Germany
| | - Katrin Liebig
- Institute for Parasitology, Centre for Infection Medicine, University of Veterinary Medicine Hannover, Buenteweg 17, 30559 Hanover, Germany
- Research Center for Emerging Infections and Zoonoses, Buenteweg 17, 30559 Hanover, Germany
| | - Steffen Knoll
- Institute for Parasitology, Centre for Infection Medicine, University of Veterinary Medicine Hannover, Buenteweg 17, 30559 Hanover, Germany
| | - Fanny Hellhammer
- Institute for Parasitology, Centre for Infection Medicine, University of Veterinary Medicine Hannover, Buenteweg 17, 30559 Hanover, Germany
- Research Center for Emerging Infections and Zoonoses, Buenteweg 17, 30559 Hanover, Germany
| | - Anna-Katharina Topp
- Institute for Parasitology, Centre for Infection Medicine, University of Veterinary Medicine Hannover, Buenteweg 17, 30559 Hanover, Germany
| | - Paul Becher
- Institute of Virology, Department of Infectious Diseases, University of Veterinary Medicine Hannover, Buenteweg 17, 30559 Hanover, Germany
| | - Andrea Springer
- Institute for Parasitology, Centre for Infection Medicine, University of Veterinary Medicine Hannover, Buenteweg 17, 30559 Hanover, Germany
| | - Christina Strube
- Institute for Parasitology, Centre for Infection Medicine, University of Veterinary Medicine Hannover, Buenteweg 17, 30559 Hanover, Germany
| | - Uschi Nagel-Kohl
- Lower Saxony State Office for Consumer Protection and Food Safety (LAVES), Food and Veterinary Institute Braunschweig/Hannover, Eintrachtweg 17, 30173 Hanover, Germany
| | - Marcel Nordhoff
- Lower Saxony State Office for Consumer Protection and Food Safety (LAVES), Food and Veterinary Institute Oldenburg, Philosophenweg 38, 26121 Oldenburg, Germany
| | - Imke Steffen
- Institute for Biochemistry, University of Veterinary Medicine Hannover, Buenteweg 17, 30559 Hanover, Germany
| | - Benjamin Ulrich Bauer
- Clinic for Swine and Small Ruminants, University of Veterinary Medicine Hannover, Bischofsholer Damm 15, 30173 Hanover, Germany
| | - Martin Ganter
- Clinic for Swine and Small Ruminants, University of Veterinary Medicine Hannover, Bischofsholer Damm 15, 30173 Hanover, Germany
| | - Karsten Feige
- Clinic for Horses, University of Veterinary Medicine Hannover, Buenteweg 9, 30559 Hanover, Germany
| | - Stefanie C. Becker
- Institute for Parasitology, Centre for Infection Medicine, University of Veterinary Medicine Hannover, Buenteweg 17, 30559 Hanover, Germany
- Research Center for Emerging Infections and Zoonoses, Buenteweg 17, 30559 Hanover, Germany
- Correspondence: (S.C.B.); (M.B.); Tel.: +49-511-953-8717 (S.C.B.)
| | - Mathias Boelke
- Institute for Parasitology, Centre for Infection Medicine, University of Veterinary Medicine Hannover, Buenteweg 17, 30559 Hanover, Germany
- Research Center for Emerging Infections and Zoonoses, Buenteweg 17, 30559 Hanover, Germany
- Correspondence: (S.C.B.); (M.B.); Tel.: +49-511-953-8717 (S.C.B.)
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Boshra H. An Overview of the Infectious Cycle of Bunyaviruses. Viruses 2022; 14:2139. [PMID: 36298693 PMCID: PMC9610998 DOI: 10.3390/v14102139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 09/19/2022] [Accepted: 09/26/2022] [Indexed: 11/17/2022] Open
Abstract
Bunyaviruses represent the largest group of RNA viruses and are the causative agent of a variety of febrile and hemorrhagic illnesses. Originally characterized as a single serotype in Africa, the number of described bunyaviruses now exceeds over 500, with its presence detected around the world. These predominantly tri-segmented, single-stranded RNA viruses are transmitted primarily through arthropod and rodent vectors and can infect a wide variety of animals and plants. Although encoding for a small number of proteins, these viruses can inflict potentially fatal disease outcomes and have even developed strategies to suppress the innate antiviral immune mechanisms of the infected host. This short review will attempt to provide an overall description of the order Bunyavirales, describing the mechanisms behind their infection, replication, and their evasion of the host immune response. Furthermore, the historical context of these viruses will be presented, starting from their original discovery almost 80 years ago to the most recent research pertaining to viral replication and host immune response.
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Affiliation(s)
- Hani Boshra
- Global Urgent and Advanced Research and Development (GUARD), 911 Rue Principale, Batiscan, QC G0X 1A0, Canada
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6
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Continuous Circulation of Yellow Fever among Rural Populations in the Central African Republic. Viruses 2022; 14:v14092014. [PMID: 36146820 PMCID: PMC9503741 DOI: 10.3390/v14092014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 09/05/2022] [Accepted: 09/06/2022] [Indexed: 11/16/2022] Open
Abstract
Yellow fever remains a public-health threat in remote regions of Africa. Here, we report the identification and genetic characterisation of one yellow-fever case observed during the investigation of a cluster of nine suspected haemorrhagic fever cases in a village in the Central African Republic. Samples were tested using real-time RT-PCR targeting the main African haemorrhagic fever viruses. Following negative results, we attempted virus isolation on VERO E6 cells and new-born mice and rescreened the samples using rRT-PCR. The whole viral genome was sequenced using an Illumina NovaSeq 6000 sequencer. Yellow-fever virus (YFV) was isolated from one woman who reported farming activities in a forest setting several days before disease onset. Phylogenetic analysis shows that this strain belongs to the East–Central African YFV genotype, with an estimated emergence some 63 years ago. Finally, five unique amino-acid changes are present in the capsid, envelop, NS1A, NS3, and NS4B proteins. More efforts are required to control yellow-fever re-emergence in resource-limited settings.
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Corona A, Fanunza E, Salata C, Morwitzer MJ, Distinto S, Zinzula L, Sanna C, Frau A, Daino GL, Quartu M, Taglialatela-Scafati O, Rigano D, Reid S, Mirazimi A, Tramontano E. Cynarin blocks Ebola virus replication by counteracting VP35 inhibition of interferon-beta production. Antiviral Res 2022; 198:105251. [DOI: 10.1016/j.antiviral.2022.105251] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 12/16/2021] [Accepted: 01/17/2022] [Indexed: 11/02/2022]
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8
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Dronina J, Samukaite-Bubniene U, Ramanavicius A. Advances and insights in the diagnosis of viral infections. J Nanobiotechnology 2021; 19:348. [PMID: 34717656 PMCID: PMC8556785 DOI: 10.1186/s12951-021-01081-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 10/11/2021] [Indexed: 12/15/2022] Open
Abstract
Viral infections are the most common among diseases that globally require around 60 percent of medical care. However, in the heat of the pandemic, there was a lack of medical equipment and inpatient facilities to provide all patients with viral infections. The detection of viral infections is possible in three general ways such as (i) direct virus detection, which is performed immediately 1-3 days after the infection, (ii) determination of antibodies against some virus proteins mainly observed during/after virus incubation period, (iii) detection of virus-induced disease when specific tissue changes in the organism. This review surveys some global pandemics from 1889 to 2020, virus types, which induced these pandemics, and symptoms of some viral diseases. Non-analytical methods such as radiology and microscopy also are overviewed. This review overlooks molecular analysis methods such as nucleic acid amplification, antibody-antigen complex determination, CRISPR-Cas system-based viral genome determination methods. Methods widely used in the certificated diagnostic laboratory for SARS-CoV-2, Influenza A, B, C, HIV, and other viruses during a viral pandemic are outlined. A comprehensive overview of molecular analytical methods has shown that the assay's sensitivity, accuracy, and suitability for virus detection depends on the choice of the number of regions in the viral open reading frame (ORF) genome sequence and the validity of the selected analytical method.
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Affiliation(s)
- Julija Dronina
- Laboratory of Nanotechnology, Department of Functional Materials and Electronics, Center for Physical Sciences and Technology, Sauletekio av. 3, Vilnius, Lithuania
- Department of Physical Chemistry, Faculty of Chemistry and Geoscience, Vilnius University, Naugarduko str. 24, 03225, Vilnius, Lithuania
| | - Urte Samukaite-Bubniene
- Department of Physical Chemistry, Faculty of Chemistry and Geoscience, Vilnius University, Naugarduko str. 24, 03225, Vilnius, Lithuania
| | - Arunas Ramanavicius
- Department of Physical Chemistry, Faculty of Chemistry and Geoscience, Vilnius University, Naugarduko str. 24, 03225, Vilnius, Lithuania.
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9
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Sánchez-González G, Belak ZR, Lozano L, Condé R. Probability of consolidation constrains novel serotype emergence in dengue fever virus. PLoS One 2021; 16:e0248765. [PMID: 33819302 PMCID: PMC8021166 DOI: 10.1371/journal.pone.0248765] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 03/05/2021] [Indexed: 12/30/2022] Open
Abstract
Since their first sequencing 40 years ago, Dengue virus (DENV) genotypes have shown extreme coherence regarding the serotype class they encode. Considering that DENV is a ribonucleic acid (RNA) virus with a high mutation rate, this behavior is intriguing. Here, we explore the effect of various parameters on likelihood of new serotype emergence. In order to determine the time scales of such an event, we used a Timed Markov Transmission Model to explore the influences of sylvatic versus peri-urban transmission, viral mutation rate, and vertical transmission on the probabilities of novel serotype emergence. We found that around 1 000 years are required for a new serotype to emerge, consistent with phylogenetic analysis of extant dengue serotypes. Furthermore, we show that likelihood of establishing chains of mosquito-human-mosquito infection, known as consolidation, is the primary factor which constrains novel serotype emergence. Our work illustrates the restrictions on and provides a mechanistic explanation for the low probability of novel dengue virus serotype emergence and the low number of observed DENV serotypes.
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Affiliation(s)
- Gilberto Sánchez-González
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, México
| | | | - Luis Lozano
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Renaud Condé
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, México
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10
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Bermúdez-Méndez E, Katrukha EA, Spruit CM, Kortekaas J, Wichgers Schreur PJ. Visualizing the ribonucleoprotein content of single bunyavirus virions reveals more efficient genome packaging in the arthropod host. Commun Biol 2021; 4:345. [PMID: 33753850 PMCID: PMC7985392 DOI: 10.1038/s42003-021-01821-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 02/09/2021] [Indexed: 01/31/2023] Open
Abstract
Bunyaviruses have a genome that is divided over multiple segments. Genome segmentation complicates the generation of progeny virus, since each newly formed virus particle should preferably contain a full set of genome segments in order to disseminate efficiently within and between hosts. Here, we combine immunofluorescence and fluorescence in situ hybridization techniques to simultaneously visualize bunyavirus progeny virions and their genomic content at single-molecule resolution in the context of singly infected cells. Using Rift Valley fever virus and Schmallenberg virus as prototype tri-segmented bunyaviruses, we show that bunyavirus genome packaging is influenced by the intracellular viral genome content of individual cells, which results in greatly variable packaging efficiencies within a cell population. We further show that bunyavirus genome packaging is more efficient in insect cells compared to mammalian cells and provide new insights on the possibility that incomplete particles may contribute to bunyavirus spread as well.
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Affiliation(s)
- Erick Bermúdez-Méndez
- Department of Virology, Wageningen Bioveterinary Research, Lelystad, The Netherlands
- Laboratory of Virology, Wageningen University, Wageningen, The Netherlands
| | - Eugene A Katrukha
- Cell Biology, Department of Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Cindy M Spruit
- Department of Virology, Wageningen Bioveterinary Research, Lelystad, The Netherlands
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Jeroen Kortekaas
- Department of Virology, Wageningen Bioveterinary Research, Lelystad, The Netherlands
- Laboratory of Virology, Wageningen University, Wageningen, The Netherlands
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11
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Tampere M, Pettke A, Salata C, Wallner O, Koolmeister T, Cazares-Körner A, Visnes T, Hesselman MC, Kunold E, Wiita E, Kalderén C, Lightowler M, Jemth AS, Lehtiö J, Rosenquist Å, Warpman-Berglund U, Helleday T, Mirazimi A, Jafari R, Puumalainen MR. Novel Broad-Spectrum Antiviral Inhibitors Targeting Host Factors Essential for Replication of Pathogenic RNA Viruses. Viruses 2020; 12:E1423. [PMID: 33322045 PMCID: PMC7762994 DOI: 10.3390/v12121423] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 11/26/2020] [Accepted: 12/07/2020] [Indexed: 12/14/2022] Open
Abstract
Recent RNA virus outbreaks such as Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and Ebola virus (EBOV) have caused worldwide health emergencies highlighting the urgent need for new antiviral strategies. Targeting host cell pathways supporting viral replication is an attractive approach for development of antiviral compounds, especially with new, unexplored viruses where knowledge of virus biology is limited. Here, we present a strategy to identify host-targeted small molecule inhibitors using an image-based phenotypic antiviral screening assay followed by extensive target identification efforts revealing altered cellular pathways upon antiviral compound treatment. The newly discovered antiviral compounds showed broad-range antiviral activity against pathogenic RNA viruses such as SARS-CoV-2, EBOV and Crimean-Congo hemorrhagic fever virus (CCHFV). Target identification of the antiviral compounds by thermal protein profiling revealed major effects on proteostasis pathways and disturbance in interactions between cellular HSP70 complex and viral proteins, illustrating the supportive role of HSP70 on many RNA viruses across virus families. Collectively, this strategy identifies new small molecule inhibitors with broad antiviral activity against pathogenic RNA viruses, but also uncovers novel virus biology urgently needed for design of new antiviral therapies.
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Affiliation(s)
- Marianna Tampere
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden; (M.T.); (A.P.); (O.W.); (T.K.); (A.C.-K.); (T.V.); (M.C.H.); (E.K.); (E.W.); (C.K.); (M.L.); (A.-S.J.); (J.L.); (Å.R.); (U.W.-B.); (T.H.); (R.J.)
- National Veterinary Institute, SE-756 51 Uppsala, Sweden;
| | - Aleksandra Pettke
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden; (M.T.); (A.P.); (O.W.); (T.K.); (A.C.-K.); (T.V.); (M.C.H.); (E.K.); (E.W.); (C.K.); (M.L.); (A.-S.J.); (J.L.); (Å.R.); (U.W.-B.); (T.H.); (R.J.)
| | - Cristiano Salata
- Department of Microbiology, Public Health Agency of Sweden, 171 65 Stockholm, Sweden;
- Department of Molecular Medicine, University of Padova, 35121 Padova, Italy
| | - Olov Wallner
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden; (M.T.); (A.P.); (O.W.); (T.K.); (A.C.-K.); (T.V.); (M.C.H.); (E.K.); (E.W.); (C.K.); (M.L.); (A.-S.J.); (J.L.); (Å.R.); (U.W.-B.); (T.H.); (R.J.)
| | - Tobias Koolmeister
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden; (M.T.); (A.P.); (O.W.); (T.K.); (A.C.-K.); (T.V.); (M.C.H.); (E.K.); (E.W.); (C.K.); (M.L.); (A.-S.J.); (J.L.); (Å.R.); (U.W.-B.); (T.H.); (R.J.)
| | - Armando Cazares-Körner
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden; (M.T.); (A.P.); (O.W.); (T.K.); (A.C.-K.); (T.V.); (M.C.H.); (E.K.); (E.W.); (C.K.); (M.L.); (A.-S.J.); (J.L.); (Å.R.); (U.W.-B.); (T.H.); (R.J.)
| | - Torkild Visnes
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden; (M.T.); (A.P.); (O.W.); (T.K.); (A.C.-K.); (T.V.); (M.C.H.); (E.K.); (E.W.); (C.K.); (M.L.); (A.-S.J.); (J.L.); (Å.R.); (U.W.-B.); (T.H.); (R.J.)
| | - Maria Carmen Hesselman
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden; (M.T.); (A.P.); (O.W.); (T.K.); (A.C.-K.); (T.V.); (M.C.H.); (E.K.); (E.W.); (C.K.); (M.L.); (A.-S.J.); (J.L.); (Å.R.); (U.W.-B.); (T.H.); (R.J.)
| | - Elena Kunold
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden; (M.T.); (A.P.); (O.W.); (T.K.); (A.C.-K.); (T.V.); (M.C.H.); (E.K.); (E.W.); (C.K.); (M.L.); (A.-S.J.); (J.L.); (Å.R.); (U.W.-B.); (T.H.); (R.J.)
| | - Elisee Wiita
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden; (M.T.); (A.P.); (O.W.); (T.K.); (A.C.-K.); (T.V.); (M.C.H.); (E.K.); (E.W.); (C.K.); (M.L.); (A.-S.J.); (J.L.); (Å.R.); (U.W.-B.); (T.H.); (R.J.)
| | - Christina Kalderén
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden; (M.T.); (A.P.); (O.W.); (T.K.); (A.C.-K.); (T.V.); (M.C.H.); (E.K.); (E.W.); (C.K.); (M.L.); (A.-S.J.); (J.L.); (Å.R.); (U.W.-B.); (T.H.); (R.J.)
| | - Molly Lightowler
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden; (M.T.); (A.P.); (O.W.); (T.K.); (A.C.-K.); (T.V.); (M.C.H.); (E.K.); (E.W.); (C.K.); (M.L.); (A.-S.J.); (J.L.); (Å.R.); (U.W.-B.); (T.H.); (R.J.)
| | - Ann-Sofie Jemth
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden; (M.T.); (A.P.); (O.W.); (T.K.); (A.C.-K.); (T.V.); (M.C.H.); (E.K.); (E.W.); (C.K.); (M.L.); (A.-S.J.); (J.L.); (Å.R.); (U.W.-B.); (T.H.); (R.J.)
| | - Janne Lehtiö
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden; (M.T.); (A.P.); (O.W.); (T.K.); (A.C.-K.); (T.V.); (M.C.H.); (E.K.); (E.W.); (C.K.); (M.L.); (A.-S.J.); (J.L.); (Å.R.); (U.W.-B.); (T.H.); (R.J.)
| | - Åsa Rosenquist
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden; (M.T.); (A.P.); (O.W.); (T.K.); (A.C.-K.); (T.V.); (M.C.H.); (E.K.); (E.W.); (C.K.); (M.L.); (A.-S.J.); (J.L.); (Å.R.); (U.W.-B.); (T.H.); (R.J.)
| | - Ulrika Warpman-Berglund
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden; (M.T.); (A.P.); (O.W.); (T.K.); (A.C.-K.); (T.V.); (M.C.H.); (E.K.); (E.W.); (C.K.); (M.L.); (A.-S.J.); (J.L.); (Å.R.); (U.W.-B.); (T.H.); (R.J.)
| | - Thomas Helleday
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden; (M.T.); (A.P.); (O.W.); (T.K.); (A.C.-K.); (T.V.); (M.C.H.); (E.K.); (E.W.); (C.K.); (M.L.); (A.-S.J.); (J.L.); (Å.R.); (U.W.-B.); (T.H.); (R.J.)
| | - Ali Mirazimi
- National Veterinary Institute, SE-756 51 Uppsala, Sweden;
- Unit of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute and Karolinska University Hospital, 17177 Stockholm, Sweden
| | - Rozbeh Jafari
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden; (M.T.); (A.P.); (O.W.); (T.K.); (A.C.-K.); (T.V.); (M.C.H.); (E.K.); (E.W.); (C.K.); (M.L.); (A.-S.J.); (J.L.); (Å.R.); (U.W.-B.); (T.H.); (R.J.)
| | - Marjo-Riitta Puumalainen
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden; (M.T.); (A.P.); (O.W.); (T.K.); (A.C.-K.); (T.V.); (M.C.H.); (E.K.); (E.W.); (C.K.); (M.L.); (A.-S.J.); (J.L.); (Å.R.); (U.W.-B.); (T.H.); (R.J.)
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12
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Relich RF, Feldmann H, Haddock E. Methanol Fixation, but not Giemsa Staining, Inactivates Ebola and Lassa Viruses in Peripheral Blood Smears Made on Plastic Microscope Slides. Am J Trop Med Hyg 2020; 103:2085-2090. [PMID: 32959767 DOI: 10.4269/ajtmh.19-0840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Diseases caused by many highly pathogenic viruses, including Ebola virus (EBOV) and Lassa virus (LASV), present with nonspecific signs and symptoms that overlap with common tropical diseases such as malaria. Initial diagnostic tests performed on patients under investigation for viral hemorrhagic fevers routinely include analysis of peripheral blood smears to detect and quantify Plasmodium species. In light of recent and ongoing Ebola virus disease and Lassa fever epidemics, clinical laboratories around the world require protocols for dealing with highly infectious specimens from patients with suspected or confirmed high-consequence diseases. Few validated protocols for safe analysis of peripheral blood smears are available, revealing a need for further research. In this study, we evaluated the performance of two plastic microscope slide types that offer safe alternatives to glass slides, determined the temporal parameters required to inactivate EBOV and LASV in thin blood smears by methanol fixation, and assessed the virucidal activity of Giemsa stain. Both types of plastic microscope slides performed optimally; there were no significant differences in blood cell morphology or tinctorial properties nor were differences noted in Plasmodium ovale morphology or staining, when compared with glass slides. For both EBOV and LASV, viable viruses were not detected in thin blood smears following fixation in absolute methanol for at least 2 minutes. By contrast, viable EBOV and LASV were recovered from all Giemsa-stained thick blood smears.
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Affiliation(s)
- Ryan F Relich
- Division of Clinical Microbiology, Department of Pathology and Laboratory Medicine, Indiana University Health, Indianapolis, Indiana.,Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, Indiana
| | - Heinz Feldmann
- Division of Intramural Research, Laboratory of Virology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana
| | - Elaine Haddock
- Division of Intramural Research, Laboratory of Virology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana
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13
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Mehta N, Perrais B, Martin K, Kumar A, Hobman TC, Cabalfin-Chua MN, Donaldo ME, Siose Painaga MS, Gaite JY, Tran V, Kain KC, Hawkes MT, Yanow SK. A Direct from Blood/Plasma Reverse Transcription-Polymerase Chain Reaction for Dengue Virus Detection in Point-of-Care Settings. Am J Trop Med Hyg 2020; 100:1534-1540. [PMID: 30994095 DOI: 10.4269/ajtmh.19-0138] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Infection with dengue virus (DENV) is widespread across tropical regions and can result in severe disease. Early diagnosis is important both for patient management and to differentiate infections that present with similar symptoms, such as malaria, chikungunya, and Zika. Rapid diagnostic tests that are used presently for point-of-care detection of DENV antigens lack the sensitivity of molecular diagnostics that detect viral RNA. However, no molecular diagnostic test for DENV is available for use in field settings. In this study, we developed and validated a reverse transcription-polymerase chain reaction (RT-PCR) for the detection of DENV adapted for use in field settings. Reverse transcription-polymerase chain reaction was performed directly from plasma samples without RNA extraction. The assay detected all four serotypes of DENV spiked into blood or plasma. Our RT-PCR does not cross-react with pathogens that cause symptoms that overlap with dengue infection. The test performed equally well in a conventional laboratory qPCR instrument and a small, low-cost portable instrument that can be used in a field setting. The lower limit of detection for the assay was 1 × 104 genome copy equivalents/mL in blood. Finally, we validated our test using 126 archived patient samples. The sensitivity of our RT-PCR was 76.7% (95% CI: 65.8-87.9%) on the conventional instrument, and 78.3% (95% CI: 65.8-87.9%) on the field instrument, when compared with the RealStar Dengue RT-PCR Kit 2.0. The molecular test described here is user-friendly, low-cost, and can be used in regions with limited laboratory capabilities.
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Affiliation(s)
- Ninad Mehta
- School of Public Health, University of Alberta, Edmonton, Canada
| | - Bastien Perrais
- School of Public Health, University of Alberta, Edmonton, Canada
| | - Kimberly Martin
- School of Public Health, University of Alberta, Edmonton, Canada
| | - Anil Kumar
- Department of Cell Biology, University of Alberta, Edmonton, Canada
| | - Tom C Hobman
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Canada.,Department of Cell Biology, University of Alberta, Edmonton, Canada
| | - Mary Noreen Cabalfin-Chua
- Section of Pediatric Infectious Diseases, Department of Pediatrics, Chong Hua Hospital, Cebu, Philippines
| | | | | | | | - Vanessa Tran
- Tropical Disease Unit, The University Health Network-Toronto General Hospital, University of Toronto, Toronto, Canada
| | - Kevin C Kain
- Tropical Disease Unit, The University Health Network-Toronto General Hospital, University of Toronto, Toronto, Canada
| | - Michael T Hawkes
- School of Public Health, University of Alberta, Edmonton, Canada.,Women and Children's Health Research Institute, Edmonton, Canada.,Stollery Science Lab, Edmonton, Canada.,Department of Pediatrics, University of Alberta, Edmonton, Canada
| | - Stephanie K Yanow
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Canada.,School of Public Health, University of Alberta, Edmonton, Canada
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14
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Impact of genetic diversity on biological characteristics of Usutu virus strains in Africa. Virus Res 2019; 273:197753. [PMID: 31521764 DOI: 10.1016/j.virusres.2019.197753] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 09/09/2019] [Accepted: 09/10/2019] [Indexed: 11/20/2022]
Abstract
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.
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15
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Yue C, Teitz S, Miyabashi T, Boller K, Lewis-Ximenez LL, Baylis SA, Blümel J. Inactivation and Removal of Chikungunya Virus and Mayaro Virus from Plasma-derived Medicinal Products. Viruses 2019; 11:v11030234. [PMID: 30866548 PMCID: PMC6466239 DOI: 10.3390/v11030234] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 03/01/2019] [Accepted: 03/04/2019] [Indexed: 12/21/2022] Open
Abstract
Background: Chikungunya virus (CHIKV) and Mayaro virus (MAYV) are closely related members of the Semliki Forest complex within the genus alphavirus and are transmitted by arthropods, causing acute febrile illness in humans. CHIKV has spread to almost all continents, whereas autochthonous MAYV infections have been reported in South America and in the Caribbean. Nevertheless, there was concern about potential spread of MAYV to other regions similar to CHIKV in the past. The risk for transmission of emerging viruses by blood transfusion and the safety of plasma-derived medicinal products (PDMPs) are constant concerns. The manufacturing processes of PDMPs include procedures to inactivate/remove viruses. Methods: In this study, we investigated the reduction of MAYV and CHIKV by heat inactivation in various matrices, solvent/detergent treatment and nanofiltration. Results: Unexpectedly, MAYV was significantly more resistant to heat and solvent/detergent treatment compared to CHIKV. However, being similar in size, both MAYV and CHIKV were removed below the detection limit by 35 nm virus filters. Conclusions: The inactivation profiles of different alphavirus members vary considerably, even within the Semliki Forest Complex. However, robust dedicated viral inactivation/removal procedures commonly used in the plasma product industry are effective in inactivating or removing MAYV and CHIKV.
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Affiliation(s)
- Constanze Yue
- Department of Virology, Paul-Ehrlich-Institut, 63225 Langen, Germany.
| | | | | | - Klaus Boller
- Department of Virology, Paul-Ehrlich-Institut, 63225 Langen, Germany.
| | | | - Sally A Baylis
- Department of Virology, Paul-Ehrlich-Institut, 63225 Langen, Germany.
| | - Johannes Blümel
- Department of Virology, Paul-Ehrlich-Institut, 63225 Langen, Germany.
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16
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Banadyga L, Schiffman Z, He S, Qiu X. Virus inoculation and treatment regimens for evaluating anti-filovirus monoclonal antibody efficacy in vivo. BIOSAFETY AND HEALTH 2019; 1:6-13. [PMID: 32835206 PMCID: PMC7347303 DOI: 10.1016/j.bsheal.2019.02.004] [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: 11/12/2018] [Revised: 01/07/2019] [Accepted: 02/21/2019] [Indexed: 01/05/2023] Open
Abstract
The development of monoclonal antibodies to treat disease caused by filoviruses, particularly Ebola virus, has risen steeply in recent years thanks to several key studies demonstrating their remarkable therapeutic potential. The increased drive to develop new and better monoclonal antibodies has necessarily seen an increase in animal model efficacy testing, which is critical to the pre-clinical development of any novel countermeasure. Primary and secondary efficacy testing against filoviruses typically makes use of one or more rodent models (mice, guinea pigs, and occasionally hamsters) or the more recently described ferret model, although the exact choice of model depends on the specific filovirus being evaluated. Indeed, no single small animal model exists for all filoviruses, and the use of any given model must consider the nature of that model as well as the nature of the therapeutic and the experimental objectives. Confirmatory evaluation, on the other hand, is performed in nonhuman primates (rhesus or cynomolgus macaques) regardless of the filovirus. In light of the number of different animal models that are currently used in monoclonal antibody efficacy testing, we sought to better understand how these efficacy tests are being performed by numerous different laboratories around the world. To this end, we review the animal models that are being used for antibody efficacy testing against filoviruses, and we highlight the challenge doses and routes of infection that are used. We also describe the various antibody treatment regimens, including antibody dose, route, and schedule of administration, that are used in these model systems. We do not identify any single best model or treatment regimen, and we do not advocate for field-wide protocol standardization. Instead, we hope to provide a comprehensive resource that will facilitate and enhance the continued pre-clinical development of novel monoclonal antibody therapeutics.
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Affiliation(s)
- Logan Banadyga
- Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada
| | - Zachary Schiffman
- Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada.,Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Shihua He
- Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada
| | - Xiangguo Qiu
- Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada.,Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
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17
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Ackermann-Gäumann R, Siegrist D, Züst R, Signer J, Lenz N, Engler O. Standardized focus assay protocol for biosafety level four viruses. J Virol Methods 2018; 264:51-54. [PMID: 30513365 DOI: 10.1016/j.jviromet.2018.12.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 11/18/2018] [Accepted: 12/01/2018] [Indexed: 10/27/2022]
Abstract
Working in accordance with biosafety level four practices is highly complex and time-consuming. Therefore, the respective laboratory protocols should be as uniform as possible, simple to perform and straightforward in readout. Here we describe the successful application of a standardized 24-well plate focus assay protocol for the titration of Zaire ebolavirus (two isolates), Marburg virus (three isolates), Lassa virus (two isolates), Crimean Congo hemorrhagic fever virus (one isolate), and tick-borne encephalitis virus (two isolates). Viral titers are determined based on a simple visual readout. The protocol exhibits high precision, with coefficients of variation for interassay variability ranging between 0.05 and 0.21 and those for intraassay variability between 0.08 and 0.23. All reagents required for the test, including primary and secondary antibodies, are commercially available, facilitating the establishment of the protocol in other laboratories.
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Affiliation(s)
| | - Denise Siegrist
- Spiez Laboratory, Federal Office for Civil Protection, Austrasse, 3700, Spiez, Switzerland.
| | - Roland Züst
- Spiez Laboratory, Federal Office for Civil Protection, Austrasse, 3700, Spiez, Switzerland.
| | - Johanna Signer
- Spiez Laboratory, Federal Office for Civil Protection, Austrasse, 3700, Spiez, Switzerland.
| | - Nicole Lenz
- Spiez Laboratory, Federal Office for Civil Protection, Austrasse, 3700, Spiez, Switzerland.
| | - Olivier Engler
- Spiez Laboratory, Federal Office for Civil Protection, Austrasse, 3700, Spiez, Switzerland.
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18
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Zapata JC, Medina-Moreno S, Guzmán-Cardozo C, Salvato MS. Improving the Breadth of the Host's Immune Response to Lassa Virus. Pathogens 2018; 7:E84. [PMID: 30373278 PMCID: PMC6313495 DOI: 10.3390/pathogens7040084] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 10/20/2018] [Accepted: 10/24/2018] [Indexed: 12/21/2022] Open
Abstract
In 2017, the global Coalition for Epidemic Preparedness (CEPI) declared Lassa virus disease to be one of the world's foremost biothreats. In January 2018, World Health Organization experts met to address the Lassa biothreat. It was commonly recognized that the diversity of Lassa virus (LASV) isolated from West African patient samples was far greater than that of the Ebola isolates from the West African epidemic of 2013⁻2016. Thus, vaccines produced against Lassa virus disease face the added challenge that they must be broadly-protective against a wide variety of LASV. In this review, we discuss what is known about the immune response to Lassa infection. We also discuss the approaches used to make broadly-protective influenza vaccines and how they could be applied to developing broad vaccine coverage against LASV disease. Recent advances in AIDS research are also potentially applicable to the design of broadly-protective medical countermeasures against LASV disease.
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Affiliation(s)
- Juan Carlos Zapata
- Institute of Human Virology, School of Medicine, University of Maryland, Baltimore, MD 21201, USA.
| | - Sandra Medina-Moreno
- Institute of Human Virology, School of Medicine, University of Maryland, Baltimore, MD 21201, USA.
| | - Camila Guzmán-Cardozo
- Institute of Human Virology, School of Medicine, University of Maryland, Baltimore, MD 21201, USA.
| | - Maria S Salvato
- Institute of Human Virology, School of Medicine, University of Maryland, Baltimore, MD 21201, USA.
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19
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Wichgers Schreur PJ, Kormelink R, Kortekaas J. Genome packaging of the Bunyavirales. Curr Opin Virol 2018; 33:151-155. [PMID: 30227361 DOI: 10.1016/j.coviro.2018.08.011] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Revised: 08/17/2018] [Accepted: 08/28/2018] [Indexed: 11/18/2022]
Abstract
The order Bunyavirales comprises nine families of enveloped, negative-strand RNA viruses. Depending on the family and genus, bunyaviruses (i.e. now referring to all members of the Bunyavirales) contain genomes consisting of two to six segments. Each genome segment is encapsidated by multiple copies of the nucleocapsid (N) protein and one or a few molecules of the viral polymerase, forming so-called ribonucleoproteins (RNPs). Incorporation of RNPs into virions is mediated by the interaction of N with the cytoplasmic tails of the structural glycoproteins. Although some selectivity exists in the packaging of RNPs into virions, which seems to be driven by the 5' and 3'-untranslated regions of the genomic RNA segments, evidence is accumulating that bunyavirus genome packaging is a stochastic process.
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Affiliation(s)
| | - Richard Kormelink
- Laboratory of Virology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Jeroen Kortekaas
- Wageningen Bioveterinary Research, Houtribweg 39, 8221 RA Lelystad, The Netherlands; Laboratory of Virology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
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20
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Lopez-Jimena B, Bekaert M, Bakheit M, Frischmann S, Patel P, Simon-Loriere E, Lambrechts L, Duong V, Dussart P, Harold G, Fall C, Faye O, Sall AA, Weidmann M. Development and validation of four one-step real-time RT-LAMP assays for specific detection of each dengue virus serotype. PLoS Negl Trop Dis 2018; 12:e0006381. [PMID: 29813062 PMCID: PMC5973574 DOI: 10.1371/journal.pntd.0006381] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 03/12/2018] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND 4 one-step, real-time, reverse transcription loop-mediated isothermal amplification (RT-LAMP) assays were developed for the detection of dengue virus (DENV) serotypes by considering 2,056 full genome DENV sequences. DENV1 and DENV2 RT-LAMP assays were validated with 31 blood and 11 serum samples from Tanzania, Senegal, Sudan and Mauritania. DENV3 and DENV4 RT-LAMP assays were validated with 25 serum samples from Cambodia. METHODOLOGY/PRINCIPAL FINDINGS 4 final reaction primer mixes were obtained by using a combination of Principal Component Analysis of the full DENV genome sequences, and LAMP primer design based on sequence alignments using the LAVA software. These mixes contained 14 (DENV1), 12 (DENV2), 8 (DENV3) and 3 (DENV4) LAMP primer sets. The assays were evaluated with an External Quality Assessment panel from Quality Control for Molecular Diagnostics. The assays were serotype-specific and did not cross-detect with other flaviviruses. The limits of detection, with 95% probability, were 22 (DENV1), 542 (DENV2), 197 (DENV3) and 641 (DENV4) RNA molecules, and 100% reproducibility in the assays was obtained with up to 102 (DENV1) and 103 RNA molecules (DENV2, DENV3 and DENV4). Validation of the DENV2 assay with blood samples from Tanzania resulted in 23 samples detected by RT-LAMP, demonstrating that the assay is 100% specific and 95.8% sensitive (positive predictive value of 100% and a negative predictive value of 85.7%). All serum samples from Senegal, Sudan and Mauritania were detected and 3 untyped as DENV1. The sensitivity of RT-LAMP for DENV4 samples from Cambodia did not quite match qRT-PCR. CONCLUSIONS/SIGNIFICANCE We have shown a novel approach to design LAMP primers that makes use of fast growing sequence databases. The DENV1 and DENV2 assays were validated with viral RNA extracted clinical samples, showing very good performance parameters.
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Affiliation(s)
- Benjamin Lopez-Jimena
- Institute of Aquaculture, University of Stirling, Stirling, Scotland, United Kingdom
| | - Michaël Bekaert
- Institute of Aquaculture, University of Stirling, Stirling, Scotland, United Kingdom
| | | | | | - Pranav Patel
- Robert Koch Institute, Centre for biological security 1 (ZBS1), Berlin, Germany
| | - Etienne Simon-Loriere
- Functional Genetics of Infectious Diseases Unit, Department of Genomes and Genetics, Institut Pasteur, Paris, France
- Centre National de la Recherche Scientifique, Unité de Recherche Associée, Paris, France
| | - Louis Lambrechts
- Centre National de la Recherche Scientifique, Unité de Recherche Associée, Paris, France
- Insect-Virus Interactions Group, Department of Genomes and Genetics, Institut Pasteur, Paris, France
| | - Veasna Duong
- Virology Unit, Institut Pasteur du Cambodge, Institut Pasteur International Network, Phnom Penh, Cambodia
| | - Philippe Dussart
- Virology Unit, Institut Pasteur du Cambodge, Institut Pasteur International Network, Phnom Penh, Cambodia
| | - Graham Harold
- Institute of Aquaculture, University of Stirling, Stirling, Scotland, United Kingdom
| | - Cheikh Fall
- Arbovirus and viral haemorrhagic fever unit, Institut Pasteur de Dakar, Institut Pasteur International Network, Dakar, Senegal
| | - Oumar Faye
- Arbovirus and viral haemorrhagic fever unit, Institut Pasteur de Dakar, Institut Pasteur International Network, Dakar, Senegal
| | - Amadou Alpha Sall
- Arbovirus and viral haemorrhagic fever unit, Institut Pasteur de Dakar, Institut Pasteur International Network, Dakar, Senegal
| | - Manfred Weidmann
- Institute of Aquaculture, University of Stirling, Stirling, Scotland, United Kingdom
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21
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Shah K, Bentley E, Tyler A, Richards KSR, Wright E, Easterbrook L, Lee D, Cleaver C, Usher L, Burton JE, Pitman JK, Bruce CB, Edge D, Lee M, Nazareth N, Norwood DA, Moschos SA. Field-deployable, quantitative, rapid identification of active Ebola virus infection in unprocessed blood. Chem Sci 2017; 8:7780-7797. [PMID: 29163915 PMCID: PMC5694917 DOI: 10.1039/c7sc03281a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 09/20/2017] [Indexed: 01/01/2023] Open
Abstract
The West African Ebola virus outbreak underlined the importance of delivering mass diagnostic capability outside the clinical or primary care setting in effectively containing public health emergencies caused by infectious disease. Yet, to date, there is no solution for reliably deploying at the point of need the gold standard diagnostic method, real time quantitative reverse transcription polymerase chain reaction (RT-qPCR), in a laboratory infrastructure-free manner. In this proof of principle work, we demonstrate direct performance of RT-qPCR on fresh blood using far-red fluorophores to resolve fluorogenic signal inhibition and controlled, rapid freeze/thawing to achieve viral genome extraction in a single reaction chamber assay. The resulting process is entirely free of manual or automated sample pre-processing, requires no microfluidics or magnetic/mechanical sample handling and thus utilizes low cost consumables. This enables a fast, laboratory infrastructure-free, minimal risk and simple standard operating procedure suited to frontline, field use. Developing this novel approach on recombinant bacteriophage and recombinant human immunodeficiency virus (HIV; Lentivirus), we demonstrate clinical utility in symptomatic EBOV patient screening using live, infectious Filoviruses and surrogate patient samples. Moreover, we evidence assay co-linearity independent of viral particle structure that may enable viral load quantification through pre-calibration, with no loss of specificity across an 8 log-linear maximum dynamic range. The resulting quantitative rapid identification (QuRapID) molecular diagnostic platform, openly accessible for assay development, meets the requirements of resource-limited countries and provides a fast response solution for mass public health screening against emerging biosecurity threats.
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Affiliation(s)
- Kavit Shah
- Westminster Genomic Services , Department of Biomedical Sciences , Faculty of Science and Technology , University of Westminster , 115 New Cavendish Str , London W1W 6UW , UK
- BGResearch Ltd. , 6 The Business Centre, Harvard Way, Harvard Industrial Estate , Kimbolton , Huntingdon PE28 0NJ , UK
| | - Emma Bentley
- Department of Biomedical Sciences , Faculty of Science and Technology , University of Westminster , 115 New Cavendish Str , London W1W 6UW , UK
| | - Adam Tyler
- BioGene Ltd. , 8 The Business Centre, Harvard Way, Harvard Industrial Estate , Kimbolton , Huntingdon PE28 0NJ , UK
| | - Kevin S R Richards
- Public Health England , National Infection Service , High Containment Microbiology Department , Porton Down , Salisbury , Wiltshire SP4 0JG , UK
| | - Edward Wright
- Department of Biomedical Sciences , Faculty of Science and Technology , University of Westminster , 115 New Cavendish Str , London W1W 6UW , UK
| | - Linda Easterbrook
- Public Health England , National Infection Service , High Containment Microbiology Department , Porton Down , Salisbury , Wiltshire SP4 0JG , UK
| | - Diane Lee
- Fluorogenics LIMITED , Building 227, Tetricus Science Park, Dstl Porton Down , Salisbury , Wiltshire SP4 0JQ , UK
| | - Claire Cleaver
- Fluorogenics LIMITED , Building 227, Tetricus Science Park, Dstl Porton Down , Salisbury , Wiltshire SP4 0JQ , UK
| | - Louise Usher
- Westminster Genomic Services , Department of Biomedical Sciences , Faculty of Science and Technology , University of Westminster , 115 New Cavendish Str , London W1W 6UW , UK
| | - Jane E Burton
- Public Health England , National Infection Service , High Containment Microbiology Department , Porton Down , Salisbury , Wiltshire SP4 0JG , UK
| | - James K Pitman
- Public Health England , National Infection Service , High Containment Microbiology Department , Porton Down , Salisbury , Wiltshire SP4 0JG , UK
| | - Christine B Bruce
- Public Health England , National Infection Service , High Containment Microbiology Department , Porton Down , Salisbury , Wiltshire SP4 0JG , UK
| | - David Edge
- BioGene Ltd. , 8 The Business Centre, Harvard Way, Harvard Industrial Estate , Kimbolton , Huntingdon PE28 0NJ , UK
| | - Martin Lee
- Fluorogenics LIMITED , Building 227, Tetricus Science Park, Dstl Porton Down , Salisbury , Wiltshire SP4 0JQ , UK
| | - Nelson Nazareth
- BioGene Ltd. , 8 The Business Centre, Harvard Way, Harvard Industrial Estate , Kimbolton , Huntingdon PE28 0NJ , UK
| | - David A Norwood
- Diagnostic Systems Division and Virology Division , United States Army Medical Research Institute of Infectious Diseases , Fort Detrick , MD 21701-5011 , USA
| | - Sterghios A Moschos
- Westminster Genomic Services , Department of Biomedical Sciences , Faculty of Science and Technology , University of Westminster , 115 New Cavendish Str , London W1W 6UW , UK
- Department of Biomedical Sciences , Faculty of Science and Technology , University of Westminster , 115 New Cavendish Str , London W1W 6UW , UK
- Department of Applied Sciences , Faculty of Health and Life Sciences , Northumbria University , C4.03 Ellison Building, Ellison Place , Newcastle Upon Tyne , Tyne and Wear NE1 8ST , UK . ; Tel: +44(0) 191 215 6623
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22
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Bob NS, Bâ H, Fall G, Ishagh E, Diallo MY, Sow A, Sembene PM, Faye O, El Kouri B, Sidi ML, Sall AA. Detection of the Northeastern African Rift Valley Fever Virus Lineage During the 2015 Outbreak in Mauritania. Open Forum Infect Dis 2017. [PMID: 28638845 PMCID: PMC5473438 DOI: 10.1093/ofid/ofx087] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Background Rift Valley fever (RVF) is an acute viral anthropozoonosis that causes epizootics and epidemics among livestock population and humans. Multiple emergences and reemergences of the virus have occurred in Mauritania over the last decade. This article describes the outbreak that occurred in 2015 in Mauritania and reports the results of serological and molecular investigations of blood samples collected from suspected RVF patients. Methods An RVF outbreak was reported from 14 September to 26 November 2015 in Mauritania. Overall, 184 suspected cases from different localities were identified by 26 health facilities. Blood samples were collected and tested by enzyme-linked immunosorbent assay (ELISA) and real-time reverse-transcription polymerase chain reaction (RT-PCR) at the Institut Pasteur de Dakar (IPD). Sequencing of partial genomes and phylogenetic analyses were performed on RT-PCR–positive samples. As part of routine surveillance at IPD, samples were also screened for dengue, yellow fever, West Nile, Crimean Congo hemorrhagic fever, Zika, and Chikungunya viruses by ELISA and RT-PCR. Results Of the 184 suspected cases, there were 57 confirmed cases and 12 deaths. Phylogenetic analysis of the sequences indicated an emergence of a virus that originated from Northeastern Africa. Our results show co-circulation of other arboviruses in Mauritania—dengue, Crimean Congo hemorrhagic fever, and West Nile viruses. Conclusion The Northeastern Africa lineage of RVF was responsible for the outbreak in Mauritania in 2015. Co-circulation of multiples arboviruses was detected. This calls for systematic differential diagnosis and highlights the need to strengthen arbovirus surveillance in Africa.
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Affiliation(s)
- Ndeye Sakha Bob
- Pole of Virology, Arbovirus and Viral Hemorrhagic Fevers Unit, Pasteur Institute of Dakar, Senegal
| | - Hampâté Bâ
- Viral Hemorrhagic Fevers Diagnostics Unit, National Institute of Public Health Research, Nouakchott, Mauritania
| | - Gamou Fall
- Pole of Virology, Arbovirus and Viral Hemorrhagic Fevers Unit, Pasteur Institute of Dakar, Senegal
| | - Elkhalil Ishagh
- Department of Epidemiological Surveillance, Ministry of Health, Islamic Republic of Mauritania, Nouakchott
| | - Mamadou Y Diallo
- Health Securities and Emergency, World Health Organization,Mauritania
| | - Abdourahmane Sow
- Pole of Virology, Arbovirus and Viral Hemorrhagic Fevers Unit, Pasteur Institute of Dakar, Senegal.,West African Health Organization, Ouagadougou, Burkina Fasso
| | | | - Ousmane Faye
- Pole of Virology, Arbovirus and Viral Hemorrhagic Fevers Unit, Pasteur Institute of Dakar, Senegal
| | - Brahim El Kouri
- Viral Hemorrhagic Fevers Diagnostics Unit, National Institute of Public Health Research, Nouakchott, Mauritania
| | - Mohamed Lemine Sidi
- Direction of Diseases Control, Ministry of Health, Islamic Republic of Mauritania, Nouakchott
| | - Amadou Alpha Sall
- Pole of Virology, Arbovirus and Viral Hemorrhagic Fevers Unit, Pasteur Institute of Dakar, Senegal
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23
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Hoferer M, Braun A, Sting R. Creation of a bovine herpes virus 1 (BoHV-1) quantitative particle standard by transmission electron microscopy and comparison with established standards for use in real-time PCR. Biologicals 2017; 48:121-125. [PMID: 28456444 DOI: 10.1016/j.biologicals.2017.03.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 02/01/2017] [Accepted: 03/20/2017] [Indexed: 11/29/2022] Open
Abstract
Standards are pivotal for pathogen quantification by real-time PCR (qPCR); however, the creation of a complete and universally applicable virus particle standard is challenging. In the present study a procedure based on purification of bovine herpes virus type 1 (BoHV-1) and subsequent quantification by transmission electron microscopy (TEM) is described. Accompanying quantitative quality controls of the TEM preparation procedure using qPCR yielded recovery rates of more than 95% of the BoHV-1 virus particles on the grid used for virus counting, which was attributed to pre-treatment of the grid with 5% bovine albumin. To compare the value of the new virus particle standard for use in qPCR, virus counter based quantification and established pure DNA standards represented by a plasmid and an oligonucleotide were included. It could be shown that the numbers of virus particles, plasmid and oligonucleotide equivalents were within one log10 range determined on the basis of standard curves indicating that different approaches provide comparable quantitative values. However, only virus particles represent a complete, universally applicable quantitative virus standard that meets the high requirements of an RNA and DNA virus gold standard. In contrast, standards based on pure DNA have to be considered as sub-standard due to limited applications.
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Affiliation(s)
- Marc Hoferer
- Chemisches und Veterinäruntersuchungsamt Stuttgart (Chemical and Veterinary Investigations Office Stuttgart), Schaflandstrasse 3/3, 70736 Fellbach, Germany
| | - Anne Braun
- Chemisches und Veterinäruntersuchungsamt Stuttgart (Chemical and Veterinary Investigations Office Stuttgart), Schaflandstrasse 3/3, 70736 Fellbach, Germany
| | - Reinhard Sting
- Chemisches und Veterinäruntersuchungsamt Stuttgart (Chemical and Veterinary Investigations Office Stuttgart), Schaflandstrasse 3/3, 70736 Fellbach, Germany.
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24
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Mikel P, Vasickova P, Tesarik R, Malenovska H, Kulich P, Vesely T, Kralik P. Preparation of MS2 Phage-Like Particles and Their Use As Potential Process Control Viruses for Detection and Quantification of Enteric RNA Viruses in Different Matrices. Front Microbiol 2016; 7:1911. [PMID: 28133456 PMCID: PMC5234545 DOI: 10.3389/fmicb.2016.01911] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 11/15/2016] [Indexed: 01/26/2023] Open
Abstract
The detection and quantification of enteric RNA viruses is based on isolation of viral RNA from the sample followed by quantitative reverse transcription polymerase chain reaction (RT-qPCR). To control the whole process of analysis and in order to guarantee the validity and reliability of results, process control viruses (PCV) are used. The present article describes the process of preparation and use of such PCV– MS2 phage-like particles (MS2 PLP) – in RT-qPCR detection and quantification of enteric RNA viruses. The MS2 PLP were derived from bacteriophage MS2 carrying a unique and specific de novo-constructed RNA target sequence originating from the DNA of two extinct species. The amount of prepared MS2 particles was quantified using four independent methods – UV spectrophotometry, fluorimetry, transmission electron microscopy and a specifically developed duplex RT-qPCR. To evaluate the usefulness of MS2 PLP in routine diagnostics different matrices known to harbor enteric RNA viruses (swab samples, liver tissue, serum, feces, and vegetables) were artificially contaminated with specific amounts of MS2 PLP. The extraction efficiencies were calculated for each individual matrix. The prepared particles fulfill all requirements for PCV – they are very stable, non-infectious, and are genetically distinct from the target RNA viruses. Due to these properties they represent a good morphological and physiochemical model. The use of MS2 PLP as a PCV in detection and quantification of enteric RNA viruses was evaluated in different types of matrices.
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Affiliation(s)
- Pavel Mikel
- Veterinary Research Institute, Department of Food and Feed SafetyBrno, Czechia; Department of Experimental Biology, Faculty of Science, Masaryk UniversityBrno, Czechia
| | - Petra Vasickova
- Veterinary Research Institute, Department of Food and Feed Safety Brno, Czechia
| | - Radek Tesarik
- Veterinary Research Institute, Department of Food and Feed Safety Brno, Czechia
| | - Hana Malenovska
- Veterinary Research Institute, Department of Food and Feed Safety Brno, Czechia
| | - Pavel Kulich
- Veterinary Research Institute, Department of Food and Feed Safety Brno, Czechia
| | - Tomas Vesely
- Veterinary Research Institute, Department of Food and Feed Safety Brno, Czechia
| | - Petr Kralik
- Veterinary Research Institute, Department of Food and Feed Safety Brno, Czechia
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25
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Xia H, Beck AS, Gargili A, Forrester N, Barrett ADT, Bente DA. Transstadial Transmission and Long-term Association of Crimean-Congo Hemorrhagic Fever Virus in Ticks Shapes Genome Plasticity. Sci Rep 2016; 6:35819. [PMID: 27775001 PMCID: PMC5075774 DOI: 10.1038/srep35819] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 10/04/2016] [Indexed: 02/05/2023] Open
Abstract
The trade-off hypothesis, the current paradigm of arbovirus evolution, proposes that cycling between vertebrate and invertebrate hosts presents significant constraints on genetic change of arboviruses. Studying these constraints in mosquito-borne viruses has led to a new understanding of epizootics. The trade-off hypothesis is assumed to be applicable to tick-borne viruses too, although studies are lacking. Tick-borne Crimean-Congo hemorrhagic fever virus (CCHFV), a member of the family Bunyaviridae, is a major cause of severe human disease worldwide and shows an extraordinary amount of genetic diversity compared to other arboviruses, which has been linked to increased virulence and emergence in new environments. Using a transmission model for CCHFV, utilizing the main vector tick species and mice plus next generation sequencing, we detected a substantial number of consensus-level mutations in CCHFV recovered from ticks after only a single transstadial transmission, whereas none were detected in CCHFV obtained from the mammalian host. Furthermore, greater viral intra-host diversity was detected in the tick compared to the vertebrate host. Long-term association of CCHFV with its tick host for 1 year demonstrated mutations in the viral genome become fixed over time. These findings suggest that the trade-off hypothesis may not be accurate for all arboviruses.
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Affiliation(s)
- Han Xia
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA.,Galveston National Laboratory, Galveston TX, USA.,Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Andrew S Beck
- Department of Pathology, and Sealy Center for Vaccine Development, University of Texas Medical Branch, Galveston, TX, USA
| | | | - Naomi Forrester
- Department of Pathology, and Sealy Center for Vaccine Development, University of Texas Medical Branch, Galveston, TX, USA
| | - Alan D T Barrett
- Department of Pathology, and Sealy Center for Vaccine Development, University of Texas Medical Branch, Galveston, TX, USA
| | - Dennis A Bente
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA.,Galveston National Laboratory, Galveston TX, USA
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26
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Fall G, Faye M, Weidmann M, Kaiser M, Dupressoir A, Ndiaye EH, Ba Y, Diallo M, Faye O, Sall AA. Real-Time RT-PCR Assays for Detection and Genotyping of West Nile Virus Lineages Circulating in Africa. Vector Borne Zoonotic Dis 2016; 16:781-789. [PMID: 27710313 DOI: 10.1089/vbz.2016.1967] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
West Nile virus (WNV) is an emerging arbovirus, circulating worldwide between birds and mosquitoes, which impacts human and animal health. Since the mid-1990s, WNV outbreaks have emerged in Europe and America and represent currently the primary cause of encephalitis in the United States. WNV exhibits a great genetic diversity with at least eight different lineages circulating in the world, and four (1, 2, Koutango, and putative new) are present in Africa. These different WNV lineages are not readily differentiated by serology, and thus, rapid molecular tools are required for diagnostic. We developed here real-time RT-PCR assays for detection and genotyping of African WNV lineages. The specificity of the assays was tested using other flaviviruses circulating in Africa. The sensitivity was determined by testing serial 10-fold dilutions of viruses and RNA standards. The assays provided good specificity and sensitivity and the analytical detection limit was 10 copies/reaction. The RT-PCR assays allowed the detection and genotyping of all WNV isolates in culture medium, human serum, and vertebrate tissues, as well as in field and experimental mosquito samples. Comparing the ratios of genome copy number/infectious virion (plaque-forming units), our study finally revealed new insight on the replication of these different WNV lineages in mosquito cells. Our RT-PCR assays are the first ones allowing the genotyping of all WNV African variants, and this may have important applications in surveillance and epidemiology in Africa and also for monitoring of their emergence in Europe and other continents.
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Affiliation(s)
- Gamou Fall
- 1 Unité des Arbovirus et Virus de Fièvres Hémorragiques, Institut Pasteur de Dakar , Dakar, Senegal
| | - Martin Faye
- 1 Unité des Arbovirus et Virus de Fièvres Hémorragiques, Institut Pasteur de Dakar , Dakar, Senegal
| | - Manfred Weidmann
- 2 Institute of Aquaculture, University of Stirling , Stirling, Scotland
| | | | - Anne Dupressoir
- 1 Unité des Arbovirus et Virus de Fièvres Hémorragiques, Institut Pasteur de Dakar , Dakar, Senegal
| | - El Hadj Ndiaye
- 4 Unité d'Entomologie Médicale, Institut Pasteur de Dakar , Dakar, Senegal
| | - Yamar Ba
- 4 Unité d'Entomologie Médicale, Institut Pasteur de Dakar , Dakar, Senegal
| | - Mawlouth Diallo
- 4 Unité d'Entomologie Médicale, Institut Pasteur de Dakar , Dakar, Senegal
| | - Ousmane Faye
- 1 Unité des Arbovirus et Virus de Fièvres Hémorragiques, Institut Pasteur de Dakar , Dakar, Senegal
| | - Amadou Alpha Sall
- 1 Unité des Arbovirus et Virus de Fièvres Hémorragiques, Institut Pasteur de Dakar , Dakar, Senegal
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27
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Wichgers Schreur PJ, Kortekaas J. Single-Molecule FISH Reveals Non-selective Packaging of Rift Valley Fever Virus Genome Segments. PLoS Pathog 2016; 12:e1005800. [PMID: 27548280 PMCID: PMC4993503 DOI: 10.1371/journal.ppat.1005800] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 07/09/2016] [Indexed: 12/28/2022] Open
Abstract
The bunyavirus genome comprises a small (S), medium (M), and large (L) RNA segment of negative polarity. Although genome segmentation confers evolutionary advantages by enabling genome reassortment events with related viruses, genome segmentation also complicates genome replication and packaging. Accumulating evidence suggests that genomes of viruses with eight or more genome segments are incorporated into virions by highly selective processes. Remarkably, little is known about the genome packaging process of the tri-segmented bunyaviruses. Here, we evaluated, by single-molecule RNA fluorescence in situ hybridization (FISH), the intracellular spatio-temporal distribution and replication kinetics of the Rift Valley fever virus (RVFV) genome and determined the segment composition of mature virions. The results reveal that the RVFV genome segments start to replicate near the site of infection before spreading and replicating throughout the cytoplasm followed by translocation to the virion assembly site at the Golgi network. Despite the average intracellular S, M and L genome segments approached a 1:1:1 ratio, major differences in genome segment ratios were observed among cells. We also observed a significant amount of cells lacking evidence of M-segment replication. Analysis of two-segmented replicons and four-segmented viruses subsequently confirmed the previous notion that Golgi recruitment is mediated by the Gn glycoprotein. The absence of colocalization of the different segments in the cytoplasm and the successful rescue of a tri-segmented variant with a codon shuffled M-segment suggested that inter-segment interactions are unlikely to drive the copackaging of the different segments into a single virion. The latter was confirmed by direct visualization of RNPs inside mature virions which showed that the majority of virions lack one or more genome segments. Altogether, this study suggests that RVFV genome packaging is a non-selective process. The bunyavirus family is one of the largest virus families on Earth, of which several members cause severe disease in humans, animals or plants. Little is known about the mechanisms that facilitate the production of infectious bunyavirus virions, which should contain at least one copy of the small (S), medium (M) and large (L) genome segment. In this study, we investigated the genome packaging process of the Rift Valley fever virus (RVFV) by visualizing individual genome segments inside infected cells and virions. Experiments performed with wild-type virus, two- and four-segmented variants, and a variant with a codon-shuffled M segment showed that the production of infectious virions is a non-selective process and is unlikely to involve the formation of a supramolecular viral RNA complex. These observations have broad implications for understanding the bunyavirus replication cycle and may facilitate the development of new vaccines and the identification of novel antiviral targets.
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Affiliation(s)
- Paul J Wichgers Schreur
- Department of Virology, Central Veterinary Institute, part of Wageningen University and Research Centre, Lelystad, The Netherlands
| | - Jeroen Kortekaas
- Department of Virology, Central Veterinary Institute, part of Wageningen University and Research Centre, Lelystad, The Netherlands
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Rapid Bedside Inactivation of Ebola Virus for Safe Nucleic Acid Tests. J Clin Microbiol 2016; 54:2521-9. [PMID: 27466385 DOI: 10.1128/jcm.00346-16] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 07/11/2016] [Indexed: 11/20/2022] Open
Abstract
Rapid bedside inactivation of Ebola virus would be a solution for the safety of medical and technical staff, risk containment, sample transport, and high-throughput or rapid diagnostic testing during an outbreak. We show that the commercially available Magna Pure lysis/binding buffer used for nucleic acid extraction inactivates Ebola virus. A rapid bedside inactivation method for nucleic acid tests is obtained by simply adding Magna Pure lysis/binding buffer directly into vacuum blood collection EDTA tubes using a thin needle and syringe prior to sampling. The ready-to-use inactivation vacuum tubes are stable for more than 4 months, and Ebola virus RNA is preserved in the Magna Pure lysis/binding buffer for at least 5 weeks independent of the storage temperature. We also show that Ebola virus RNA can be manually extracted from Magna Pure lysis/binding buffer-inactivated samples using the QIAamp viral RNA minikit. We present an easy and convenient method for bedside inactivation using available blood collection vacuum tubes and reagents. We propose to use this simple method for fast, safe, and easy bedside inactivation of Ebola virus for safe transport and routine nucleic acid detection.
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Maat DS, van Bleijswijk JDL, Witte HJ, Brussaard CPD. Virus production in phosphorus-limitedMicromonas pusillastimulated by a supply of naturally low concentrations of different phosphorus sources, far into the lytic cycle. FEMS Microbiol Ecol 2016; 92:fiw136. [DOI: 10.1093/femsec/fiw136] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/12/2016] [Indexed: 11/13/2022] Open
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Abstract
During virus entry, the surface glycoprotein of Ebola virus (EBOV) undergoes a complex set of transformations within the endosomal network. Tools to study EBOV entry have been limited to static immunofluorescence or biochemical and functional analysis. In a recent article in mBio, Spence et al. reported a novel, live-cell-imaging method that tracks this transformational journey of EBOV in real time [J. S. Spence, T. B. Krause, E. Mittler, R. K. Jangra, and K. Chandran, mBio 7(1):e01857-15, 2016, http://dx.doi.org/10.1128/mBio.01857-15]. The assay validates known mechanisms of EBOV entry and sheds light on some novel intricacies. Direct evidence supports the hypothesis that fusion is a rare event that starts in maturing early endosomes, is completed in late endosomes, and occurs entirely in Niemann-Pick C1 (NPC1)-positive (NPC1+) compartments. The study demonstrated that lipid mixing and productive fusion are temporally decoupled, with different energetic barriers and a protease-dependent step between the two events. Analysis of the mechanism of action of an important class of EBOV neutralizing antibodies, such as KZ52 and ZMapp, provides direct evidence that these antibodies act by inhibiting the membrane fusion.
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31
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Herath TK, Ferguson HW, Weidmann MW, Bron JE, Thompson KD, Adams A, Muir KF, Richards RH. Pathogenesis of experimental salmonid alphavirus infection in vivo: an ultrastructural insight. Vet Res 2016; 47:7. [PMID: 26743442 PMCID: PMC4705579 DOI: 10.1186/s13567-015-0300-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Accepted: 05/23/2015] [Indexed: 12/27/2022] Open
Abstract
Salmonid alphavirus (SAV) is an enveloped, single-stranded,
positive sense RNA virus belonging to the family Togaviridae. It causes economically devastating disease in cultured salmonids. The characteristic features of SAV infection include severe histopathological changes in the heart, pancreas and skeletal muscles of diseased fish. Although the presence of virus has been reported in a wider range of tissues, the mechanisms responsible for viral tissue tropism and for lesion development during the disease are not clearly described or understood. Previously, we have described membrane-dependent morphogenesis of SAV and associated apoptosis-mediated cell death in vitro. The aims of the present study were to explore ultrastructural changes associated with SAV infection in vivo. Cytolytic changes were observed in heart, but not in gill and head-kidney of virus-infected fish, although they still exhibited signs of SAV morphogenesis. Ultrastructural changes associated with virus replication were also noted in leukocytes in the head kidney of virus-infected fish. These results further describe the presence of degenerative lesions in the heart as expected, but not in the gills and in the kidney.
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Affiliation(s)
- Tharangani K Herath
- Institute of Aquaculture, School of Natural Sciences, University of Stirling, Stirling, UK.
| | - Hugh W Ferguson
- School of Veterinary Medicine, St George's University, St. George, Grenada, West Indies.
| | - Manfred W Weidmann
- Institute of Aquaculture, School of Natural Sciences, University of Stirling, Stirling, UK.
| | - James E Bron
- Institute of Aquaculture, School of Natural Sciences, University of Stirling, Stirling, UK.
| | - Kimberly D Thompson
- Institute of Aquaculture, School of Natural Sciences, University of Stirling, Stirling, UK. .,Moredun Research Institute, Pentlands Science Park, Bush Loan Penicuik, Edinburgh, UK.
| | - Alexandra Adams
- Institute of Aquaculture, School of Natural Sciences, University of Stirling, Stirling, UK.
| | - Katherine F Muir
- Institute of Aquaculture, School of Natural Sciences, University of Stirling, Stirling, UK.
| | - Randolph H Richards
- Institute of Aquaculture, School of Natural Sciences, University of Stirling, Stirling, UK.
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Abalone Hemocyanin Blocks the Entry of Herpes Simplex Virus 1 into Cells: a Potential New Antiviral Strategy. Antimicrob Agents Chemother 2015; 60:1003-12. [PMID: 26643336 DOI: 10.1128/aac.01738-15] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 11/22/2015] [Indexed: 02/07/2023] Open
Abstract
A marine-derived compound, abalone hemocyanin, from Haliotis rubra was shown to have a unique mechanism of antiviral activity against herpes simplex virus 1 (HSV-1) infections. In vitro assays demonstrated the dose-dependent and inhibitory effect of purified hemocyanin against HSV-1 infection in Vero cells with a 50% effective dose (ED50) of 40 to 50 nM and no significant toxicity. In addition, hemocyanin specifically inhibited viral attachment and entry by binding selectively to the viral surface glycoproteins gD, gB, and gC, probably by mimicking their receptors. However, hemocyanin had no effect on postentry events and did not block infection by binding to cellular receptors for HSV. By the use of different mutants of gD and gB and a competitive heparin binding assay, both protein charge and conformation were shown to be the driving forces of the interaction between hemocyanin and viral glycoproteins. These findings also suggested that hemocyanin may have different motifs for binding to each of the viral glycoproteins B and D. The dimer subunit of hemocyanin with a 10-fold-smaller molecular mass exhibited similar binding to viral surface glycoproteins, showing that the observed inhibition did not require the entire multimer. Therefore, a small hemocyanin analogue could serve as a new antiviral candidate for HSV infections.
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Salata C, Munegato D, Piccoli E, Calistri A, Parolin C, Mirazimi A, Baritussio A, Palù G. Amiodarone increases positive-strand RNA virus replication in vitro: implications for its use in patients with viral infections. J Antimicrob Chemother 2015; 71:280-1. [PMID: 26429565 DOI: 10.1093/jac/dkv305] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Affiliation(s)
- Cristiano Salata
- Department of Molecular Medicine, University of Padova, Padova, Italy Department of Microbiology, Public Health Agency of Sweden, Solna, Sweden
| | - Denis Munegato
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Elena Piccoli
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Arianna Calistri
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Cristina Parolin
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Ali Mirazimi
- Department of Microbiology, Public Health Agency of Sweden, Solna, Sweden Department for Laboratory Medicine, Karolinska Institute, Huddinge/Stockholm, Sweden National Veterinary Institute, Uppsala, Sweden
| | - Aldo Baritussio
- Clinica Medica 1, Department of Medicine, University of Padova, Padova, Italy
| | - Giorgio Palù
- Department of Molecular Medicine, University of Padova, Padova, Italy
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Rougemont B, Simon R, Carrière R, Biarc J, Fonbonne C, Salvador A, Huillet C, Berard Y, Adam O, Manin C, Lemoine J. Absolute quantification of dengue virus serotype 4 chimera vaccine candidate in Vero cell culture by targeted mass spectrometry. Proteomics 2015. [DOI: 10.1002/pmic.201500101] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Blandine Rougemont
- Institut des Sciences Analytiques; UMR 5280 CNRS Université Lyon 1; Université de Lyon; Villeurbanne France
| | - Romain Simon
- Institut des Sciences Analytiques; UMR 5280 CNRS Université Lyon 1; Université de Lyon; Villeurbanne France
| | - Romain Carrière
- Institut des Sciences Analytiques; UMR 5280 CNRS Université Lyon 1; Université de Lyon; Villeurbanne France
| | - Jordane Biarc
- Institut des Sciences Analytiques; UMR 5280 CNRS Université Lyon 1; Université de Lyon; Villeurbanne France
| | - Catherine Fonbonne
- Institut des Sciences Analytiques; UMR 5280 CNRS Université Lyon 1; Université de Lyon; Villeurbanne France
| | - Arnaud Salvador
- Institut des Sciences Analytiques; UMR 5280 CNRS Université Lyon 1; Université de Lyon; Villeurbanne France
| | - Céline Huillet
- Sanofi Pasteur; 1541 av. Marcel Mérieux Marcy l’étoile France
| | - Yves Berard
- Sanofi Pasteur; 1541 av. Marcel Mérieux Marcy l’étoile France
| | - Olivier Adam
- Sanofi Pasteur; 1541 av. Marcel Mérieux Marcy l’étoile France
| | - Catherine Manin
- Sanofi Pasteur; 1541 av. Marcel Mérieux Marcy l’étoile France
| | - Jérôme Lemoine
- Institut des Sciences Analytiques; UMR 5280 CNRS Université Lyon 1; Université de Lyon; Villeurbanne France
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Alfson KJ, Avena LE, Beadles MW, Staples H, Nunneley JW, Ticer A, Dick EJ, Owston MA, Reed C, Patterson JL, Carrion R, Griffiths A. Particle-to-PFU ratio of Ebola virus influences disease course and survival in cynomolgus macaques. J Virol 2015; 89:6773-81. [PMID: 25903348 PMCID: PMC4468478 DOI: 10.1128/jvi.00649-15] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 04/08/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED This study addresses the role of Ebola virus (EBOV) specific infectivity in virulence. Filoviruses are highly lethal, enveloped, single-stranded negative-sense RNA viruses that can cause hemorrhagic fever. No approved vaccines or therapies exist for filovirus infections, and infectious virus must be handled in maximum containment. Efficacy testing of countermeasures, in addition to investigations of pathogenicity and immune response, often requires a well-characterized animal model. For EBOV, an obstacle in performing accurate disease modeling is a poor understanding of what constitutes an infectious dose in animal models. One well-recognized consequence of viral passage in cell culture is a change in specific infectivity, often measured as a particle-to-PFU ratio. Here, we report that serial passages of EBOV in cell culture resulted in a decrease in particle-to-PFU ratio. Notably, this correlated with decreased potency in a lethal cynomolgus macaque (Macaca fascicularis) model of infection; animals were infected with the same viral dose as determined by plaque assay, but animals that received more virus particles exhibited increased disease. This suggests that some particles are unable to form a plaque in a cell culture assay but are able to result in lethal disease in vivo. These results have a significant impact on how future studies are designed to model EBOV disease and test countermeasures. IMPORTANCE Ebola virus (EBOV) can cause severe hemorrhagic disease with a high case-fatality rate, and there are no approved vaccines or therapies. Specific infectivity can be considered the total number of viral particles per PFU, and its impact on disease is poorly understood. In stocks of most mammalian viruses, there are particles that are unable to complete an infectious cycle or unable to cause cell pathology in cultured cells. We asked if these particles cause disease in nonhuman primates by infecting monkeys with equal infectious doses of genetically identical stocks possessing either high or low specific infectivities. Interestingly, some particles that did not yield plaques in cell culture assays were able to result in lethal disease in vivo. Furthermore, the number of PFU needed to induce lethal disease in animals was very low. Our results have a significant impact on how future studies are designed to model EBOV disease and test countermeasures.
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Affiliation(s)
- Kendra J. Alfson
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, Texas, USA
- Department of Microbiology and Immunology, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Laura E. Avena
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Michael W. Beadles
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Hilary Staples
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Jerritt W. Nunneley
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Anysha Ticer
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Edward J. Dick
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Michael A. Owston
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Christopher Reed
- Division of Virology, U.S. Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, USA
| | - Jean L. Patterson
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Ricardo Carrion
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Anthony Griffiths
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, Texas, USA
- Department of Microbiology and Immunology, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
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36
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Salata C, Baritussio A, Munegato D, Calistri A, Ha HR, Bigler L, Fabris F, Parolin C, Palù G, Mirazimi A. Amiodarone and metabolite MDEA inhibit Ebola virus infection by interfering with the viral entry process. Pathog Dis 2015; 73:ftv032. [PMID: 25933611 PMCID: PMC7108539 DOI: 10.1093/femspd/ftv032] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/22/2015] [Indexed: 12/15/2022] Open
Abstract
Ebola virus disease (EVD) is one of the most lethal transmissible infections characterized by a high fatality rate, and a treatment has not been developed yet. Recently, it has been shown that cationic amphiphiles, among them the antiarrhythmic drug amiodarone, inhibit filovirus infection. In the present work, we investigated how amiodarone interferes with Ebola virus infection. Wild-type Sudan ebolavirus and recombinant vesicular stomatitis virus, pseudotyped with the Zaire ebolavirus glycoprotein, were used to gain further insight into the ability of amiodarone to affect Ebola virus infection. We show that amiodarone decreases Ebola virus infection at concentrations close to those found in the sera of patients treated for arrhythmias. The drug acts by interfering with the fusion of the viral envelope with the endosomal membrane. We also show that MDEA, the main amiodarone metabolite, contributes to the antiviral activity. Finally, studies with amiodarone analogues indicate that the antiviral activity is correlated with drug ability to accumulate into and interfere with the endocytic pathway. Considering that it is well tolerated, especially in the acute setting, amiodarone appears to deserve consideration for clinical use in EVD. The anti-arrhythmic drug amiodarone, and one of its active metabolites interfere with the early steps of Ebola virus life cycle by blocking the fusion step between the viral envelope and the endosomal membrane.
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Affiliation(s)
- Cristiano Salata
- Department of Molecular Medicine, University of Padova, Padova 35121, Italy Department of Microbiology, The Public Health Agency of Sweden, Solna 171 82, Sweden
| | - Aldo Baritussio
- Clinica Medica 1, Department of Medicine, University of Padova, Padova 35128, Italy
| | - Denis Munegato
- Department of Molecular Medicine, University of Padova, Padova 35121, Italy
| | - Arianna Calistri
- Department of Molecular Medicine, University of Padova, Padova 35121, Italy
| | - Huy Riem Ha
- Cardiovascular Therapy Research Laboratory, Clinical Research Center, University Hospital, Zurich 8091, Switzerland
| | - Laurent Bigler
- Department of Chemistry, University of Zurich, Zurich 8057, Switzerland
| | - Fabrizio Fabris
- Clinica Medica 1, Department of Medicine, University of Padova, Padova 35128, Italy
| | - Cristina Parolin
- Department of Molecular Medicine, University of Padova, Padova 35121, Italy
| | - Giorgio Palù
- Department of Molecular Medicine, University of Padova, Padova 35121, Italy
| | - Ali Mirazimi
- Department of Microbiology, The Public Health Agency of Sweden, Solna 171 82, Sweden Department for Laboratory Medicine, Karolinska Institute, Huddinge/Stockholm 141 83, Sweden National Veterinary Institute, Uppsala 751 89, Sweden
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37
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Rossi CA, Kearney BJ, Olschner SP, Williams PL, Robinson CG, Heinrich ML, Zovanyi AM, Ingram MF, Norwood DA, Schoepp RJ. Evaluation of ViroCyt® Virus Counter for rapid filovirus quantitation. Viruses 2015; 7:857-72. [PMID: 25710889 PMCID: PMC4379551 DOI: 10.3390/v7030857] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 02/06/2015] [Accepted: 02/16/2015] [Indexed: 11/16/2022] Open
Abstract
Development and evaluation of medical countermeasures for diagnostics, vaccines, and therapeutics requires production of standardized, reproducible, and well characterized virus preparations. For filoviruses this includes plaque assay for quantitation of infectious virus, transmission electron microscopy (TEM) for morphology and quantitation of virus particles, and real-time reverse transcription PCR for quantitation of viral RNA (qRT-PCR). The ViroCyt® Virus Counter (VC) 2100 (ViroCyt, Boulder, CO, USA) is a flow-based instrument capable of quantifying virus particles in solution. Using a proprietary combination of fluorescent dyes that stain both nucleic acid and protein in a single 30 min step, rapid, reproducible, and cost-effective quantification of filovirus particles was demonstrated. Using a seed stock of Ebola virus variant Kikwit, the linear range of the instrument was determined to be 2.8E+06 to 1.0E+09 virus particles per mL with coefficient of variation ranging from 9.4% to 31.5% for samples tested in triplicate. VC particle counts for various filovirus stocks were within one log of TEM particle counts. A linear relationship was established between the plaque assay, qRT-PCR, and the VC. VC results significantly correlated with both plaque assay and qRT-PCR. These results demonstrated that the VC is an easy, fast, and consistent method to quantify filoviruses in stock preparations.
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Affiliation(s)
- Cynthia A Rossi
- Diagnostic Systems Division, US Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA.
| | - Brian J Kearney
- Diagnostic Systems Division, US Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA.
| | - Scott P Olschner
- Diagnostic Systems Division, US Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA.
| | - Priscilla L Williams
- Diagnostic Systems Division, US Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA.
| | - Camenzind G Robinson
- Pathology Division, US Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA.
| | - Megan L Heinrich
- Diagnostic Systems Division, US Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA.
| | - Ashley M Zovanyi
- Diagnostic Systems Division, US Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA.
| | - Michael F Ingram
- Diagnostic Systems Division, US Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA.
| | - David A Norwood
- Diagnostic Systems Division, US Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA.
| | - Randal J Schoepp
- Diagnostic Systems Division, US Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA.
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Sting R, Molz K, Hoferer M. Creating standards for absolute quantification of Coxiella burnetii in real-time PCR--a comparative study based on transmission electron microscopy. Biologicals 2014; 43:18-22. [PMID: 25465354 DOI: 10.1016/j.biologicals.2014.10.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Revised: 08/02/2014] [Accepted: 10/31/2014] [Indexed: 10/24/2022] Open
Abstract
Quantitative standards are a prerequisite for quality control and quantification of pathogens. In this study the creation of quantitative standards for use in qPCR is described using the pathogen Coxiella burnetii. Quantification of Coxiella burnetii particles by transmission electron microscopy (TEM) was used as primary standard and compared with data obtained by light microscopy as well as genome equivalents (GE) and plasmid units (recombinant plasmid). Based on pathogen quantification using TEM and light microscopy, pathogen detection limits of 6 and 2 C. burnetii particles could be determined per com1 qPCR reaction, respectively. In comparison, the detection limits were 17 and 13 pathogen units using GE and plasmid units, respectively. The standard generated by TEM can be used as gold standard for universal application due to high accuracy, quantitative control of the producing process and supplying intact pathogen particles.
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Affiliation(s)
- Reinhard Sting
- Chemisches und Veterinäruntersuchungsamt Stuttgart (Chemical and Veterinary Investigations Office Stuttgart), Schaflandstrasse 3/3, 70736 Fellbach, Germany.
| | - Kerstin Molz
- Chemisches und Veterinäruntersuchungsamt Stuttgart (Chemical and Veterinary Investigations Office Stuttgart), Schaflandstrasse 3/3, 70736 Fellbach, Germany
| | - Marc Hoferer
- Chemisches und Veterinäruntersuchungsamt Stuttgart (Chemical and Veterinary Investigations Office Stuttgart), Schaflandstrasse 3/3, 70736 Fellbach, Germany
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Rosenstierne MW, McLoughlin KS, Olesen ML, Papa A, Gardner SN, Engler O, Plumet S, Mirazimi A, Weidmann M, Niedrig M, Fomsgaard A, Erlandsson L. The microbial detection array for detection of emerging viruses in clinical samples--a useful panmicrobial diagnostic tool. PLoS One 2014; 9:e100813. [PMID: 24963710 PMCID: PMC4070998 DOI: 10.1371/journal.pone.0100813] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Accepted: 05/29/2014] [Indexed: 11/30/2022] Open
Abstract
Emerging viruses are usually endemic to tropical and sub-tropical regions of the world, but increased global travel, climate change and changes in lifestyle are believed to contribute to the spread of these viruses into new regions. Many of these viruses cause similar disease symptoms as other emerging viruses or common infections, making these unexpected pathogens difficult to diagnose. Broad-spectrum pathogen detection microarrays containing probes for all sequenced viruses and bacteria can provide rapid identification of viruses, guiding decisions about treatment and appropriate case management. We report a modified Whole Transcriptome Amplification (WTA) method that increases unbiased amplification, particular of RNA viruses. Using this modified WTA method, we tested the specificity and sensitivity of the Lawrence Livermore Microbial Detection Array (LLMDA) against a wide range of emerging viruses present in both non-clinical and clinical samples using two different microarray data analysis methods.
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Affiliation(s)
- Maiken W. Rosenstierne
- Department of Microbiological Diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark
- * E-mail:
| | - Kevin S. McLoughlin
- Global Security, Lawrence Livermore National Laboratory, Livermore, California, United States of America
| | - Majken Lindholm Olesen
- Department of Microbiological Diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark
| | - Anna Papa
- Department of Microbiology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Shea N. Gardner
- Global Security, Lawrence Livermore National Laboratory, Livermore, California, United States of America
| | - Olivier Engler
- Spiez Laboratory, Federal Office for Civil Protection, Spiez, Switzerland
| | - Sebastien Plumet
- Virology department, French Army Forces Biomedical Institute (IRBA), Marseille, France
| | - Ali Mirazimi
- Swedish Institute for Communicable Disease Control, Solna, Sweden
- National Veterinary Institute (SVA), Uppsala, Sweden
- Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Manfred Weidmann
- Institute of Aquaculture, University of Stirling, Stirling, United Kingdom
| | | | - Anders Fomsgaard
- Department of Microbiological Diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark
- Institute of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Lena Erlandsson
- Department of Microbiological Diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark
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Martínez-Betancur V, Marín-Villa M, Martínez-Gutierrez M. Infection of epithelial cells with dengue virus promotes the expression of proteins favoring the replication of certain viral strains. J Med Virol 2013; 86:1448-58. [PMID: 24374781 DOI: 10.1002/jmv.23857] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/30/2013] [Indexed: 11/12/2022]
Abstract
Dengue virus (DENV) is the causative agent of dengue and severe dengue. To understand better the dengue virus-host interaction, it is important to determine how the expression of cellular proteins is modified due to infection. Therefore, a comparison of protein expression was conducted in Vero cells infected with two different DENV strains, both serotype 2: DENV-2/NG (associated with dengue) and DENV-2/16681 (associated with severe dengue). The viability of the infected cells was determined, and neither strain induced cell death at 48 hr. In addition, the viral genomes and infectious viral particles were quantified, and the genome of the DENV-2/16681 strain was determined to have a higher replication rate compared with the DENV-2/NG strain. Finally, the proteins from infected and uninfected cultures were separated using two-dimensional gel electrophoresis, and the differentially expressed proteins were identified by mass spectrometry. Compared with the uninfected controls, the DENV-2/NG- and DENV-2/16681-infected cultures had five and six differentially expressed proteins, respectively. The most important results were observed when the infected cultures were compared to each other (DENV-2/NG vs. DENV-2/16681), and 18 differentially expressed proteins were identified. Based on their cellular functions, many of these proteins were linked to the increase in the replication efficiency of DENV. Among the proteins were calreticulin, acetyl coenzyme A, acetyl transferase, and fatty acid-binding protein. It was concluded that the infection of Vero cells with DENV-2/NG or DENV-2/16681 differentially modifies the expression of certain proteins, which can, in turn, facilitate infection.
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Affiliation(s)
- Viviana Martínez-Betancur
- Programa de Estudio y Control de Enfermedades Tropicales-PECET, Universidad de Antioquia, Medellin, Colombia
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Comparison of the plaque assay and 50% tissue culture infectious dose assay as methods for measuring filovirus infectivity. J Virol Methods 2013; 193:565-71. [DOI: 10.1016/j.jviromet.2013.05.015] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Revised: 05/15/2013] [Accepted: 05/28/2013] [Indexed: 11/23/2022]
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Malenovska H. Virus quantitation by transmission electron microscopy, TCID₅₀, and the role of timing virus harvesting: a case study of three animal viruses. J Virol Methods 2013; 191:136-40. [PMID: 23603437 DOI: 10.1016/j.jviromet.2013.04.008] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Revised: 03/24/2013] [Accepted: 04/04/2013] [Indexed: 12/13/2022]
Abstract
Quantitation of viruses is practised widely in both basic and applied virology. Infectious titration in cell cultures, the most common approach to it, is quite labour-intensive and alternative protocols are therefore sought. One of the alternatives is transmission electron microscope (TEM) quantitation using latex particles at a known concentration as a reference for counting virus particles. If virus TCID₅₀ is determined in parallel, the ratio of infectious to non-infectious virus particles may be established. This study employs such an approach to compute the number of virus particles and TCID₅₀, and establish their correlation for three viruses: Canine adenovirus 1 (CAdV-1), Feline calicivirus (FCV) and Bovine herpesvirus 1 (BoHV-1). Each of the viruses was grown in five replicates until complete cytopathology was recorded (time 0), then frozen. They were thawed, filter-sterilised and left for additional periods of 16, 32 and 48 h at 37°C. At each time point, the infectious ability of the virus was characterised by TCID50 and the number of virions quantified by TEM, in order to evaluate the influence of timing on virus harvest. The virus particle count determined by TEM did not change for any of the viruses throughout the experiment. The relationship between virus particle counts with TCID₅₀ at time 0 showed good linearity response; their ratio was almost constant. The virus particle-to-TCID₅₀ ratio varied between 146 and 426 (mean±SD: 282±103) for CAdV-1, between 36 and 79 (57±18) for FCV and between 110 and 249 (167±53) for BoHV-1. The proportion of non-infectious particles did not change throughout the experiment for either CAdV-1 or BoHV-1. However, a decrease in virus infectious ability disclosed by TCID₅₀ indicated that the fraction of non-infectious particles in FCV increased 300,000 times when time 0 and 48 h were compared. The quantitation of viruses with TEM is a simple and rapid protocol for virus quantitation but account must be taken of the type of virus and harvesting time as virus counts need not necessarily correlate with virus infectious ability.
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Affiliation(s)
- Hana Malenovska
- Collection of Animal Pathogenic Microorganisms, Veterinary Research Institute, Hudcova 70, 62100 Brno, Czech Republic.
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Sherwood LJ, Hayhurst A. Ebolavirus nucleoprotein C-termini potently attract single domain antibodies enabling monoclonal affinity reagent sandwich assay (MARSA) formulation. PLoS One 2013; 8:e61232. [PMID: 23577211 PMCID: PMC3618483 DOI: 10.1371/journal.pone.0061232] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2012] [Accepted: 03/06/2013] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Antigen detection assays can play an important part in environmental surveillance and diagnostics for emerging threats. We are interested in accelerating assay formulation; targeting the agents themselves to bypass requirements for a priori genome information or surrogates. Previously, using in vitro affinity reagent selection on Marburg virus we rapidly established monoclonal affinity reagent sandwich assay (MARSA) where one recombinant antibody clone was both captor and tracer for polyvalent nucleoprotein (NP). Hypothesizing that the closely related Ebolavirus genus may share the same Achilles' heel, we redirected the scheme to see whether similar assays could be delivered and began to explore their mechanism. METHODS AND FINDINGS In parallel we selected panels of llama single domain antibodies (sdAb) from a semi-synthetic library against Zaire, Sudan, Ivory Coast, and Reston Ebola viruses. Each could perform as both captor and tracer in the same antigen sandwich capture assay thereby forming MARSAs. All sdAb were specific for NP and those tested required the C-terminal domain for recognition. Several clones were cross-reactive, indicating epitope conservation across the Ebolavirus genus. Analysis of two immune shark sdAb revealed they also targeted the C-terminal domain, and could be similarly employed, yet were less sensitive than a comparable llama sdAb despite stemming from immune selections. CONCLUSIONS The C-terminal domain of Ebolavirus NP is a strong attractant for antibodies and enables sensitive sandwich immunoassays to be rapidly generated using a single antibody clone. The polyvalent nature of nucleocapsid borne NP and display of the C-terminal region likely serves as a bountiful affinity sink during selections, and a highly avid target for subsequent immunoassay capture. Combined with the high degree of amino acid conservation through 37 years and across wide geographies, this domain makes an ideal handle for monoclonal affinity reagent driven antigen sandwich assays for the Ebolavirus genus.
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Affiliation(s)
- Laura J. Sherwood
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, Texas, United States of America
| | - Andrew Hayhurst
- Department of Virology and Immunology, Texas Biomedical Research Institute, San Antonio, Texas, United States of America
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Fajs L, Durmiši E, Knap N, Strle F, Avšič-Županc T. Phylogeographic characterization of tick-borne encephalitis virus from patients, rodents and ticks in Slovenia. PLoS One 2012. [PMID: 23185257 PMCID: PMC3502456 DOI: 10.1371/journal.pone.0048420] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Tick-borne encephalitis virus (TBEV) is the most important arboviral agent causing infections of the central nervous system in central Europe. Previous studies have shown that TBEV exhibits pronounced genetic variability, which is often correlated to the geographical origin of TBEV. Genetic variability of TBEV has previously been studied predominantly in rodents and ticks, while information about the variability in patients is scarce. In order to understand the molecular relationships of TBEV between natural hosts, vectors and humans, as well as correlation between phylogenetic and geographical clustering, sequences of TBEV E and NS5 protein genes, were obtained by direct sequencing of RT-PCR products from TBE-confirmed patients as well as from rodents and ticks collected from TBE-endemic regions in Slovenia. A total of 27 partial E protein gene sequences representing 15 human, 4 rodent and 8 tick samples and 30 partial NS5 protein gene sequences representing 17 human, 5 rodent and 8 tick samples were obtained. The complete genome sequence of TBEV strain Ljubljana I was simultaneously obtained. Phylogenetic analysis of the E and NS5 protein gene sequences revealed a high degree of TBEV variability in patients, ticks and rodents. Furthermore, an evident correlation between geographical and phylogenetic clustering was shown that was independent of the TBEV host. Moreover, we show the presence of a possible recombination event in the TBEV genome obtained from a patient sample, which was supported with multiple recombination event detection methods. This is the first study that simultaneously analyzed the genetic relationships of directly sequenced TBEV samples from patients, ticks and rodents and provides the largest set of patient-derived TBEV sequences up to date. In addition, we have confirmed the geographical clustering of TBEV sequences in Slovenia and have provided evidence of a possible recombination event in the TBEV genome, obtained from a patient.
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Affiliation(s)
- Luka Fajs
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Emina Durmiši
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Nataša Knap
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Franc Strle
- Department of Infectious Diseases, University Medical Center Ljubljana, Ljubljana, Slovenia
| | - Tatjana Avšič-Županc
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
- * E-mail:
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Hysom DA, Naraghi-Arani P, Elsheikh M, Carrillo AC, Williams PL, Gardner SN. Skip the alignment: degenerate, multiplex primer and probe design using K-mer matching instead of alignments. PLoS One 2012; 7:e34560. [PMID: 22485178 PMCID: PMC3317645 DOI: 10.1371/journal.pone.0034560] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2011] [Accepted: 03/05/2012] [Indexed: 11/18/2022] Open
Abstract
PriMux is a new software package for selecting multiplex compatible, degenerate primers and probes to detect diverse targets such as viruses. It requires no multiple sequence alignment, instead applying k-mer algorithms, hence it scales well for large target sets and saves user effort from curating sequences into alignable groups. PriMux has the capability to predict degenerate primers as well as probes suitable for TaqMan or other primer/probe triplet assay formats, or simply probes for microarray or other single-oligo assay formats. PriMux employs suffix array methods for efficient calculations on oligos 10-~100 nt in length. TaqMan® primers and probes for each segment of Rift Valley fever virus were designed using PriMux, and lab testing comparing signatures designed using PriMux versus those designed using traditional methods demonstrated equivalent or better sensitivity for the PriMux-designed signatures compared to traditional signatures. In addition, we used PriMux to design TaqMan® primers and probes for unalignable or poorly alignable groups of targets: that is, all segments of Rift Valley fever virus analyzed as a single target set of 198 sequences, or all 2863 Dengue virus genomes for all four serotypes available at the time of our analysis. The PriMux software is available as open source from http://sourceforge.net/projects/PriMux.
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Affiliation(s)
- David A. Hysom
- Computations, Lawrence Livermore National Laboratory, Livermore, California, United States of America
| | - Pejman Naraghi-Arani
- Physics and Life Sciences, Lawrence Livermore National Laboratory, Livermore, California, United States of America
| | - Maher Elsheikh
- Physics and Life Sciences, Lawrence Livermore National Laboratory, Livermore, California, United States of America
| | - A. Celena Carrillo
- Physics and Life Sciences, Lawrence Livermore National Laboratory, Livermore, California, United States of America
| | - Peter L. Williams
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Walnut Creek, California, United States of America
| | - Shea N. Gardner
- Computations, Lawrence Livermore National Laboratory, Livermore, California, United States of America
- * E-mail:
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Kuhn JH, Dodd LE, Wahl-Jensen V, Radoshitzky SR, Bavari S, Jahrling PB. Evaluation of perceived threat differences posed by filovirus variants. Biosecur Bioterror 2011; 9:361-71. [PMID: 22070137 DOI: 10.1089/bsp.2011.0051] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
In the United States, filoviruses (ebolaviruses and marburgviruses) are listed as National Institute of Allergy and Infectious Diseases (NIAID) Category A Priority Pathogens, Select Agents, and Centers for Disease Control and Prevention (CDC) Category A Bioterrorism Agents. In recent months, U.S. biodefense professionals and policy experts have initiated discussions on how to optimize filovirus research in regard to medical countermeasure (ie, diagnostics, antiviral, and vaccine) development. Standardized procedures and reagents could accelerate the independent verification of research results across government agencies and establish baselines for the development of animal models acceptable to regulatory entities, such as the Food and Drug Administration (FDA), while being fiscally responsible. At the root of standardization lies the question of which filovirus strains, variants, or isolates ought to be the prototypes for product development, evaluation, and validation. Here we discuss a rationale for their selection. We conclude that, based on currently available data, filovirus biodefense research ought to focus on the classical taxonomic filovirus prototypes: Marburg virus Musoke in the case of marburgviruses and Ebola virus Mayinga in the case of Zaire ebolaviruses. Arguments have been made in various committees in favor of other variants, such as Marburg virus Angola, Ci67 or Popp, or Ebola virus Kikwit, but these rationales seem to be largely based on anecdotal or unpublished and unverified data, or they may reflect a lack of awareness of important facts about the variants' isolation history and genomic properties.
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Affiliation(s)
- Jens H Kuhn
- National Institutes of Health, National Institute of Allergy and Infectious Diseases, Division of Clinical Research, Integrated Research Facility at Fort Detrick, Frederick, Maryland, USA
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Carrion R, Ro Y, Hoosien K, Ticer A, Brasky K, de la Garza M, Mansfield K, Patterson JL. A small nonhuman primate model for filovirus-induced disease. Virology 2011; 420:117-24. [PMID: 21959017 PMCID: PMC3195836 DOI: 10.1016/j.virol.2011.08.022] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2011] [Revised: 07/21/2011] [Accepted: 08/29/2011] [Indexed: 01/02/2023]
Abstract
Ebolavirus and Marburgvirus are members of the filovirus family and induce a fatal hemorrhagic disease in humans and nonhuman primates with 90% case fatality. To develop a small nonhuman primate model for filovirus disease, common marmosets (Callithrix jacchus) were intramuscularly inoculated with wild type Marburgvirus Musoke or Ebolavirus Zaire. The infection resulted in a systemic fatal disease with clinical and morphological features closely resembling human infection. Animals experienced weight loss, fever, high virus titers in tissue, thrombocytopenia, neutrophilia, high liver transaminases and phosphatases and disseminated intravascular coagulation. Evidence of a severe disseminated viral infection characterized principally by multifocal to coalescing hepatic necrosis was seen in EBOV animals. MARV-infected animals displayed only moderate fibrin deposition in the spleen. Lymphoid necrosis and lymphocytic depletion observed in spleen. These findings provide support for the use of the common marmoset as a small nonhuman primate model for filovirus induced hemorrhagic fever.
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Affiliation(s)
- Ricardo Carrion
- Department of Virology and Immunology, Texas Biomedical Research Institute, 7620 NW Loop 410, San Antonio, TX 78227, USA.
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