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Whole-Genome Sequencing of Six Neglected Arboviruses Circulating in Africa Using Sequence-Independent Single Primer Amplification (SISPA) and MinION Nanopore Technologies. Pathogens 2022; 11:pathogens11121502. [PMID: 36558837 PMCID: PMC9781818 DOI: 10.3390/pathogens11121502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/30/2022] [Accepted: 12/02/2022] [Indexed: 12/13/2022] Open
Abstract
On the African continent, a large number of arthropod-borne viruses (arboviruses) with zoonotic potential have been described, and yet little is known of most of these pathogens, including their actual distribution or genetic diversity. In this study, we evaluated as a proof-of-concept the effectiveness of the nonspecific sequencing technique sequence-independent single primer amplification (SISPA) on third-generation sequencing techniques (MinION sequencing, Oxford Nanopore Technologies, Oxford, UK) by comparing the sequencing results from six different samples of arboviruses known to be circulating in Africa (Crimean-Congo hemorrhagic fever virus (CCHFV), Rift Valley fever virus (RVFV), Dugbe virus (DUGV), Nairobi sheep disease virus (NSDV), Middleburg virus (MIDV) and Wesselsbron virus (WSLV)). All sequenced samples were derived either from previous field studies or animal infection trials. Using this approach, we were able to generate complete genomes for all six viruses without the need for virus-specific whole-genome PCRs. Higher Cq values in diagnostic RT-qPCRs and the origin of the samples (from cell culture or animal origin) along with their quality were found to be factors affecting the success of the sequencing run. The results of this study may stimulate the use of metagenomic sequencing approaches, contributing to a better understanding of the genetic diversity of neglected arboviruses.
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Belij-Rammerstorfer S, Limon G, Maze EA, Hannant K, Hughes E, Tchakarova SR, Alexandrov T, Mmbaga BT, Willett B, Booth G, Lyons NA, Baker N, Thomas KM, Wright D, Saunders J, Browning C, Wilsden G, Carroll M, Hewson R, Charleston B, Lambe T, Ludi AB. Development of anti-Crimean-Congo hemorrhagic fever virus Gc and NP-specific ELISA for detection of antibodies in domestic animal sera. Front Vet Sci 2022; 9:913046. [PMID: 36090164 PMCID: PMC9454098 DOI: 10.3389/fvets.2022.913046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 07/20/2022] [Indexed: 11/21/2022] Open
Abstract
Crimean-Congo hemorrhagic fever (CCHF) is a priority emerging disease. CCHF, caused by the CCHF virus (CCHFV), can lead to hemorrhagic fever in humans with severe cases often having fatal outcomes. CCHFV is maintained within a tick-vertebrate-tick cycle, which includes domestic animals. Domestic animals infected with CCHFV do not show clinical signs of the disease and the presence of antibodies in the serum can provide evidence of their exposure to the virus. Current serological tests are specific to either one CCHFV antigen or the whole virus antigen. Here, we present the development of two in-house ELISAs for the detection of serum IgG that is specific for two different CCHFV antigens: glycoprotein Gc (CCHFV Gc) and nucleoprotein (CCHFV NP). We demonstrate that these two assays were able to detect anti-CCHFV Gc-specific and anti-CCHFV NP-specific IgG in sheep from endemic CCHFV areas with high specificity, providing new insight into the heterogeneity of the immune response induced by natural infection with CCHFV in domestic animals.
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Affiliation(s)
| | | | | | | | - Ellen Hughes
- Medical Research Council (MRC)-University of Glasgow Centre for Virus Research (CRV), Glasgow, United Kingdom
| | | | | | - Blandina T. Mmbaga
- Kilimanjaro Clinical Research Institute (KCRI), Kilimanjaro Christian Medical Centre, Moshi, Tanzania
- Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Brian Willett
- Medical Research Council (MRC)-University of Glasgow Centre for Virus Research (CRV), Glasgow, United Kingdom
| | | | | | - Natalie Baker
- Research and Evaluation, UK Health Security Agency, Porton Down, United Kingdom
| | - Kelly M. Thomas
- Research and Evaluation, UK Health Security Agency, Porton Down, United Kingdom
| | - Daniel Wright
- Nuffield Department of Medicine, The Jenner Institute, University of Oxford, Oxford, United Kingdom
| | - Jack Saunders
- Nuffield Department of Medicine, The Jenner Institute, University of Oxford, Oxford, United Kingdom
| | | | | | - Miles Carroll
- Pandemic Science Institute, Wellcome Centre for Human Genetics, Nuffield Department of Medicine, Oxford University, Oxford, United Kingdom
| | - Roger Hewson
- Research and Evaluation, UK Health Security Agency, Porton Down, United Kingdom
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | | | - Teresa Lambe
- Nuffield Department of Medicine, The Jenner Institute, University of Oxford, Oxford, United Kingdom
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Daodu OB, Eisenbarth A, Schulz A, Hartlaub J, Olopade JO, Oluwayelu DO, Groschup MH. Molecular detection of dugbe orthonairovirus in cattle and their infesting ticks (Amblyomma and Rhipicephalus (Boophilus)) in Nigeria. PLoS Negl Trop Dis 2021; 15:e0009905. [PMID: 34788303 PMCID: PMC8598060 DOI: 10.1371/journal.pntd.0009905] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 10/12/2021] [Indexed: 11/27/2022] Open
Abstract
Dugbe orthonairovirus (DUGV), a tick-borne zoonotic arbovirus, was first isolated in 1964 in Nigeria. For over four decades, no active surveillance was conducted to monitor the spread and genetic variation of DUGV. This study detected and genetically characterized DUGV circulating in cattle and their infesting ticks (Amblyomma and Rhipicephalus (Boophilus)) in Kwara State, North-Central Nigeria. Blood and or ticks were collected from 1051 cattle at 31 sampling sites (abattoirs and farms) across 10 local government areas of the State. DUGV detection was carried out by RT-qPCR, and positive samples sequenced and phylogenetically analysed. A total of 11824 ticks, mostly A. variegatum (36.0%) and R. (B.) microplus (63.9%), were obtained with mean tick burden of 12 ticks/cattle. Thirty-four (32 A. variegatum and two R. (B.) microplus) of 4644 examined ticks were DUGV-positive, whereas all of the cattle sera tested negative for DUGV genome. Whole genome sequence (S, M and L segments) and phylogenetic analyses indicate that the positive samples shared up to 99.88% nucleotide identity with and clustered around the Nigerian DUGV prototype strain IbAr 1792. Hence, DUGV with high similarity to the previously characterised strain has been detected in Nigeria. To our knowledge, this is the first report of DUGV in North-Central Nigeria and the most recent information after its last surveillance in 1974.
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Affiliation(s)
- Oluwafemi Babatunde Daodu
- Department of Veterinary Microbiology, Faculty of Veterinary Medicine, University of Ilorin, Ilorin, Nigeria
| | - Albert Eisenbarth
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Greifswald–Insel Riems, Germany
- Bundeswehr Hospital Hamburg, Branch Tropical Microbiology and Entomology, Hamburg, Germany
| | - Ansgar Schulz
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Greifswald–Insel Riems, Germany
| | - Julia Hartlaub
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Greifswald–Insel Riems, Germany
| | - James Olukayode Olopade
- Department of Veterinary Anatomy, Faculty of Veterinary Medicine, University of Ibadan, Ibadan, Nigeria
| | - Daniel Oladimeji Oluwayelu
- Department of Veterinary Microbiology, Faculty of Veterinary Medicine, University of Ibadan, Ibadan, Nigeria
- Center for Control and Prevention of Zoonoses, Faculty of Veterinary Medicine, University of Ibadan, Ibadan, Nigeria
| | - Martin H. Groschup
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Greifswald–Insel Riems, Germany
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Hartlaub J, Daodu OB, Sadeghi B, Keller M, Olopade J, Oluwayelu D, Groschup MH. Cross-Reaction or Co-Infection? Serological Discrimination of Antibodies Directed against Dugbe and Crimean-Congo Hemorrhagic Fever Orthonairovirus in Nigerian Cattle. Viruses 2021; 13:1398. [PMID: 34372604 PMCID: PMC8310240 DOI: 10.3390/v13071398] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 07/14/2021] [Accepted: 07/15/2021] [Indexed: 11/16/2022] Open
Abstract
Dugbe orthonairovirus (DUGV) and Crimean-Congo hemorrhagic fever orthonairovirus (CCHFV) are tick-borne arboviruses within the order Bunyavirales. Both viruses are endemic in several African countries and can induce mild (DUGV, BSL 3) or fatal (CCHFV, BSL 4) disease in humans. Ruminants play a major role in their natural transmission cycle. Therefore, they are considered as suitable indicator animals for serological monitoring studies to assess the risk for human infections. Although both viruses do not actually belong to the same serogroup, cross-reactivities have already been reported earlier-hence, the correct serological discrimination of DUGV and CCHFV antibodies is crucial. In this study, 300 Nigerian cattle sera (150 CCHFV seropositive and seronegative samples, respectively) were screened for DUGV antibodies via N protein-based ELISA, indirect immunofluorescence (iIFA) and neutralization assays. Whereas no correlation between the CCHFV antibody status and DUGV seroprevalence data could be demonstrated with a newly established DUGV ELISA, significant cross-reactivities were observed in an immunofluorescence assay. Moreover, DUGV seropositive samples did also cross-react in a species-adapted commercial CCHFV iIFA. Therefore, ELISAs seem to be able to reliably differentiate between DUGV and CCHFV antibodies and should preferentially be used for monitoring studies. Positive iIFA results should always be confirmed by ELISAs.
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Affiliation(s)
- Julia Hartlaub
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Suedufer 10, 17489 Greifswald–Insel Riems, Germany; (J.H.); (B.S.); (M.K.)
| | - Oluwafemi B. Daodu
- Department of Veterinary Microbiology, University of Ilorin, Ilorin 240103, Nigeria;
| | - Balal Sadeghi
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Suedufer 10, 17489 Greifswald–Insel Riems, Germany; (J.H.); (B.S.); (M.K.)
| | - Markus Keller
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Suedufer 10, 17489 Greifswald–Insel Riems, Germany; (J.H.); (B.S.); (M.K.)
| | - James Olopade
- Department of Veterinary Anatomy, University of Ibadan, Ibadan 200284, Nigeria;
| | - Daniel Oluwayelu
- Department of Veterinary Microbiology, University of Ibadan, Ibadan 200281, Nigeria;
| | - Martin H. Groschup
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Suedufer 10, 17489 Greifswald–Insel Riems, Germany; (J.H.); (B.S.); (M.K.)
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Hartlaub J, Keller M, Groschup MH. Deciphering Antibody Responses to Orthonairoviruses in Ruminants. Microorganisms 2021; 9:1493. [PMID: 34361926 PMCID: PMC8303759 DOI: 10.3390/microorganisms9071493] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/08/2021] [Accepted: 07/09/2021] [Indexed: 11/17/2022] Open
Abstract
Antibody cross-reactivities between related viruses are common diagnostic challenges, resulting in reduced diagnostic specificities and sensitivities. In this study, antibody cross-reactions between neglected members of the genus Orthonairovirus-Hazara (HAZV), Dugbe (DUGV), and Nairobi sheep disease orthonairovirus (NSDV)-were investigated. Mono-specific ovine and bovine sera following experimental infections as well immunization trials with HAZV, DUGV, and NSDV were tested in homologous and heterologous virus-specific assays, namely indirect ELISAs based on recombinant N protein, indirect immunofluorescence assays (iIFA), and two neutralization test formats (plaque reduction neutralization test (PRNT) and micro-virus neutralization test (mVNT)). The highest specificities were achieved with the ELISAs, followed by the mVNT, iIFA, and PRNT. Cross-reactivities were mainly observed within the Nairobi sheep disease serogroup-but surprisingly, HAZV antibodies in PRNT did also neutralize NSDV and DUGV. In conclusion, we recommend ELISAs and mVNTs for a discriminative diagnostic approach to differentiate between these antibodies. NSDV antisera were also used in serological assays for the detection of antibodies against the human pathogen Crimean-Congo hemorrhagic fever orthonairovirus (CCHFV). Interestingly, all CCHFV ELISAs (In-house and commercial) achieved high diagnostic specificities, whereas significant cross-reactivities were observed in a CCHFV iIFA. Previously, similar results were obtained when analyzing the HAZV and DUGV antisera.
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Affiliation(s)
| | | | - Martin H. Groschup
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Suedufer 10, 17489 Greifswald, Insel Riems, Germany; (J.H.); (M.K.)
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Diagnosis and Pathogenesis of Nairobi Sheep Disease Orthonairovirus Infections in Sheep and Cattle. Viruses 2021; 13:v13071250. [PMID: 34199054 PMCID: PMC8310034 DOI: 10.3390/v13071250] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 06/18/2021] [Accepted: 06/22/2021] [Indexed: 12/13/2022] Open
Abstract
Nairobi sheep disease orthonairovirus (NSDV) is a zoonotic tick-borne arbovirus, which causes severe gastroenteritis in small ruminants. To date, the virus is prevalent in East Africa and Asia. However, due to climate change, including the spread of transmitting tick vectors and increased animal movements, it is likely that the distribution range of NSDV is enlarging. In this project, sheep and cattle (hitherto classified as resistant to NSDV) were experimentally infected with NSDV for a comparative study of the species-specific pathogenesis. For this purpose, several new diagnostic assays (RT-qPCR, ELISA, iIFA, mVNT, PRNT) were developed, which will also be useful for future epidemiological investigations. All challenged sheep (three different doses groups) developed characteristic clinical signs, transient viremia and virus shedding—almost independent on the applied virus dose. Half of the sheep had to be euthanized due to severe clinical signs, including hemorrhagic diarrhea. In contrast, the course of infection in cattle was only subclinical. However, all ruminants showed seroconversion—implying that, indeed, both species are susceptible for NSDV. Hence, not only sheep but also cattle sera can be included in serological monitoring programs for the surveillance of NSDV occurrence and spread in the future.
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