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Hakizimana JN, Yona C, Makange MR, Kasisi EA, Netherton CL, Nauwynck H, Misinzo G. Complete genome analysis of African swine fever virus genotypes II, IX and XV from domestic pigs in Tanzania. Sci Rep 2023; 13:5318. [PMID: 37002287 PMCID: PMC10066019 DOI: 10.1038/s41598-023-32625-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 03/30/2023] [Indexed: 04/03/2023] Open
Abstract
African swine fever (ASF) caused by ASF virus (ASFV) is an infectious transboundary animal disease notifiable to the World Organization for Animal Health causing high mortality in domestic pigs and wild boars threatening the global domestic pig industry. To date, twenty-four ASFV genotypes have been described and currently genotypes II, IX, X, XV and XVI are known to be circulating in Tanzania. Despite the endemic status of ASF in Tanzania, only one complete genome of ASFV from the country has been described. This study describes the first complete genome sequence of ASFV genotype XV. In addition, the first Tanzanian complete genome of ASFV genotype IX and three ASFV strains belonging to genotype II collected during ASF outbreaks in domestic pigs in Tanzania were determined in this study using Illumina sequencing and comparative genomics analysis. The generated ASFV complete genome sequences ranged from 171,004 to 184,521 base pairs in length with an average GC content of 38.53% and encoded 152 to 187 open reading frames. The results of this study provide insights into the genomic structure of ASFV and can be used to monitor changes within the ASFV genome and improve our understanding of ASF transmission dynamics.
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Affiliation(s)
- Jean N Hakizimana
- OR Tambo Africa Research Chair for Viral Epidemics, SACIDS Foundation for One Health, Sokoine University of Agriculture, PO Box 3297, Morogoro, Tanzania
| | - Clara Yona
- OR Tambo Africa Research Chair for Viral Epidemics, SACIDS Foundation for One Health, Sokoine University of Agriculture, PO Box 3297, Morogoro, Tanzania
- Department of Biosciences, Solomon Mahlangu College of Natural and Applied Sciences, Sokoine University of Agriculture, PO Box 3038, Morogoro, Tanzania
| | - Mariam R Makange
- OR Tambo Africa Research Chair for Viral Epidemics, SACIDS Foundation for One Health, Sokoine University of Agriculture, PO Box 3297, Morogoro, Tanzania
- SACIDS Africa Centre of Excellence for Infectious Diseases, SACIDS Foundation for One Health, Sokoine University of Agriculture, PO Box 3297, Morogoro, Tanzania
| | - Ester A Kasisi
- OR Tambo Africa Research Chair for Viral Epidemics, SACIDS Foundation for One Health, Sokoine University of Agriculture, PO Box 3297, Morogoro, Tanzania
| | - Christopher L Netherton
- African Swine Fever Vaccinology Group, The Pirbright Institute, Ash Road, Pirbright, Woking, GU24 0NF, Surrey, UK
| | - Hans Nauwynck
- Laboratory of Virology, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium
| | - Gerald Misinzo
- OR Tambo Africa Research Chair for Viral Epidemics, SACIDS Foundation for One Health, Sokoine University of Agriculture, PO Box 3297, Morogoro, Tanzania.
- SACIDS Africa Centre of Excellence for Infectious Diseases, SACIDS Foundation for One Health, Sokoine University of Agriculture, PO Box 3297, Morogoro, Tanzania.
- Department of Veterinary Microbiology, Parasitology and Biotechnology, College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, PO Box 3019, Morogoro, Tanzania.
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Ngingo BL, Mboera LEG, Chengula A, Machelle I, Makange MR, Msolla M, Mwanyika GO, Rugarabamu S, Misinzo G. Aedes aegypti abundance, larval indices and risk for dengue virus transmission in Kinondoni district, Tanzania. Trop Med Health 2022; 50:1. [PMID: 34980286 PMCID: PMC8725502 DOI: 10.1186/s41182-021-00395-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 12/27/2021] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Tanzania has experienced periodic dengue outbreaks with increased incidence since 2010. However, there is limited information on vector dynamics and transmission risk in most parts of the country. This study was conducted to determine Aedes mosquito abundance, larval indices and dengue virus infection rate as risk indicators for DENV transmission in Kinondoni district, Dar es Salaam, Tanzania. METHODS A cross-sectional study was conducted in three wards of Kinondoni district in Tanzania between December 2019 and January 2020. In each ward, three streets were randomly selected for adult and immature mosquito sampling. The adult mosquitoes were collected using Mosquito Magnet traps, while mosquito larvae and pupae were inspected in water-holding containers in the selected household compounds. The detection of dengue virus (DENV) in female Aedes mosquitoes was done using a one-step reverse transcription-polymerase chain reaction (RT-PCR) method. RESULTS Of the 1416 adult female mosquitoes collected, Ae. aegypti accounted for 16.8% (n = 238). A total of 333 water-holding containers were inspected and 201 (60.4%) had at least an Aedes larvae or pupae. Water-holding containers supporting the breeding of Aedes larvae and pupae included discarded car tires, flowerpots and small and large plastic containers. The overall House Index, Container Index and Breteau Index were 55.1%, 60.4% and 114.2, respectively. None of the 763 female Aedes mosquitoes tested by RT-PCR was found to be infected with DENV. CONCLUSION The presence and abundance Ae. aegypti mosquitoes and the large proportion of water-holding containers infested with the mosquito larvae and pupae put residents of Kinondoni district at high risk of DENV transmission. Our findings emphasize the need for continuous mosquito vector surveillance and control to prevent the possibility of future DENV outbreaks in Tanzania.
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Affiliation(s)
- Baraka L Ngingo
- Department of Veterinary Microbiology, Parasitology and Biotechnology, Sokoine University of Agriculture, Morogoro, Tanzania.
- SACIDS Foundation for One Health, Sokoine University of Agriculture, Morogoro, Tanzania.
- Faculty of Natural and Applied Sciences, St John's University of Tanzania, Dodoma, Tanzania.
| | - Leonard E G Mboera
- SACIDS Foundation for One Health, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Augustino Chengula
- Department of Veterinary Microbiology, Parasitology and Biotechnology, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Ines Machelle
- Department of Veterinary Microbiology, Parasitology and Biotechnology, Sokoine University of Agriculture, Morogoro, Tanzania
- SACIDS Foundation for One Health, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Mariam R Makange
- Department of Veterinary Microbiology, Parasitology and Biotechnology, Sokoine University of Agriculture, Morogoro, Tanzania
- SACIDS Foundation for One Health, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Michael Msolla
- Department of Veterinary Microbiology, Parasitology and Biotechnology, Sokoine University of Agriculture, Morogoro, Tanzania
- SACIDS Foundation for One Health, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Gaspary O Mwanyika
- Department of Veterinary Microbiology, Parasitology and Biotechnology, Sokoine University of Agriculture, Morogoro, Tanzania
- SACIDS Foundation for One Health, Sokoine University of Agriculture, Morogoro, Tanzania
- Department of Medical Sciences and Technology, Mbeya University of Science and Technology, Mbeya, Tanzania
| | - Sima Rugarabamu
- Department of Veterinary Microbiology, Parasitology and Biotechnology, Sokoine University of Agriculture, Morogoro, Tanzania
- SACIDS Foundation for One Health, Sokoine University of Agriculture, Morogoro, Tanzania
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Gerald Misinzo
- Department of Veterinary Microbiology, Parasitology and Biotechnology, Sokoine University of Agriculture, Morogoro, Tanzania
- SACIDS Foundation for One Health, Sokoine University of Agriculture, Morogoro, Tanzania
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Kinimi E, Mahapatra M, Kgotlele T, Makange MR, Tennakoon C, Njeumi F, Odongo S, Muyldermans S, Kock R, Parida S, Rweyemamu M, Misinzo G. Complete Genome Sequencing of Field Isolates of Peste des Petits Ruminants Virus from Tanzania Revealed a High Nucleotide Identity with Lineage III PPR Viruses. Animals (Basel) 2021; 11:2976. [PMID: 34679994 PMCID: PMC8532778 DOI: 10.3390/ani11102976] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/10/2021] [Accepted: 10/12/2021] [Indexed: 01/30/2023] Open
Abstract
Peste des petits ruminants virus (PPRV) causes a highly devastating disease of sheep and goats that threatens food security, small ruminant production and susceptible endangered wild ruminants. With policy directed towards achieving global PPR eradication, the establishment of cost-effective genomic surveillance tools is critical where PPR is endemic. Genomic data can provide sufficient in-depth information to identify the pockets of endemicity responsible for PPRV persistence and viral evolution, and direct an appropriate vaccination response. Yet, access to the required sequencing technology is low in resource-limited settings and is compounded by the difficulty of transporting clinical samples from wildlife across international borders due to the Convention on International Trade in Endangered Species (CITES) of Wild Fauna and Flora, and Nagoya Protocol regulations. Oxford nanopore MinION sequencing technology has recently demonstrated an extraordinary performance in the sequencing of PPRV due to its rapidity, utility in endemic countries and comparatively low cost per sample when compared to other whole-genome (WGS) sequencing platforms. In the present study, Oxford nanopore MinION sequencing was utilised to generate complete genomes of PPRV isolates collected from infected goats in Ngorongoro and Momba districts in the northern and southern highlands of Tanzania during 2016 and 2018, respectively. The tiling multiplex polymerase chain reaction (PCR) was carried out with twenty-five pairs of long-read primers. The resulting PCR amplicons were used for nanopore library preparation and sequencing. The analysis of output data was complete genomes of PPRV, produced within four hours of sequencing (accession numbers: MW960272 and MZ322753). Phylogenetic analysis of the complete genomes revealed a high nucleotide identity, between 96.19 and 99.24% with lineage III PPRV currently circulating in East Africa, indicating a common origin. The Oxford nanopore MinION sequencer can be deployed to overcome diagnostic and surveillance challenges in the PPR Global Control and Eradication program. However, the coverage depth was uneven across the genome and amplicon dropout was observed mainly in the GC-rich region between the matrix (M) and fusion (F) genes of PPRV. Thus, larger field studies are needed to allow the collection of sufficient data to assess the robustness of nanopore sequencing technology.
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Affiliation(s)
- Edson Kinimi
- SACIDS Africa Centre of Excellence for Infectious Diseases, SACIDS Foundation for One Health, Sokoine University of Agriculture, P.O. Box 3297, Morogoro 67125, Tanzania; (S.P.); (M.R.)
- Department of Veterinary Physiology, Biochemistry and Pharmacology, College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, P.O. Box 3017, Morogoro 67125, Tanzania
- Department of Veterinary Microbiology, Parasitology and Biotechnology, College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, P.O. Box 3019, Morogoro 67125, Tanzania; (T.K.); (M.R.M.)
| | - Mana Mahapatra
- The Pirbright Institute, Ash Road, Pirbright, Woking GU24 0NF, UK; (M.M.); (C.T.)
| | - Tebogo Kgotlele
- Department of Veterinary Microbiology, Parasitology and Biotechnology, College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, P.O. Box 3019, Morogoro 67125, Tanzania; (T.K.); (M.R.M.)
| | - Mariam R. Makange
- Department of Veterinary Microbiology, Parasitology and Biotechnology, College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, P.O. Box 3019, Morogoro 67125, Tanzania; (T.K.); (M.R.M.)
| | - Chandana Tennakoon
- The Pirbright Institute, Ash Road, Pirbright, Woking GU24 0NF, UK; (M.M.); (C.T.)
| | - Felix Njeumi
- Food and Agriculture Organization of the United Nations (FAO), Viale delle Terme di Caracalla, 00153 Rome, Italy;
| | - Steven Odongo
- Department of Biotechnical and Diagnostic Sciences, College of Veterinary Medicine, Animal Resources and Biosecurity (COVAB), Makerere University, Kampala P.O. Box 7062, Uganda;
| | - Serge Muyldermans
- Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium;
| | - Richard Kock
- The Royal Veterinary College, University of London, Hawkshead Lane, North Mymms, Hertfordshire, Hatfield AL9 7TA, UK;
| | - Satya Parida
- SACIDS Africa Centre of Excellence for Infectious Diseases, SACIDS Foundation for One Health, Sokoine University of Agriculture, P.O. Box 3297, Morogoro 67125, Tanzania; (S.P.); (M.R.)
- The Pirbright Institute, Ash Road, Pirbright, Woking GU24 0NF, UK; (M.M.); (C.T.)
- Food and Agriculture Organization of the United Nations (FAO), Viale delle Terme di Caracalla, 00153 Rome, Italy;
| | - Mark Rweyemamu
- SACIDS Africa Centre of Excellence for Infectious Diseases, SACIDS Foundation for One Health, Sokoine University of Agriculture, P.O. Box 3297, Morogoro 67125, Tanzania; (S.P.); (M.R.)
| | - Gerald Misinzo
- SACIDS Africa Centre of Excellence for Infectious Diseases, SACIDS Foundation for One Health, Sokoine University of Agriculture, P.O. Box 3297, Morogoro 67125, Tanzania; (S.P.); (M.R.)
- Department of Veterinary Microbiology, Parasitology and Biotechnology, College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, P.O. Box 3019, Morogoro 67125, Tanzania; (T.K.); (M.R.M.)
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Mboera LEG, Mweya CN, Rumisha SF, Tungu PK, Stanley G, Makange MR, Misinzo G, De Nardo P, Vairo F, Oriyo NM. The Risk of Dengue Virus Transmission in Dar es Salaam, Tanzania during an Epidemic Period of 2014. PLoS Negl Trop Dis 2016; 10:e0004313. [PMID: 26812489 PMCID: PMC4728062 DOI: 10.1371/journal.pntd.0004313] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 11/30/2015] [Indexed: 01/29/2023] Open
Abstract
Background In 2010, 2012, 2013 and 2014 dengue outbreaks have been reported in Dar es Salaam, Tanzania. However, there is no comprehensive data on the risk of transmission of dengue in the country. The objective of this study was to assess the risk of transmission of dengue in Dar es Salaam during the 2014 epidemic. Methodology/Principal Findings This cross-sectional study was conducted in Dar es Salaam, Tanzania during the dengue outbreak of 2014. The study involved Ilala, Kinondoni and Temeke districts. Adult mosquitoes were collected using carbon dioxide-propane powered Mosquito Magnet Liberty Plus traps. In each household compound, water-holding containers were examined for mosquito larvae and pupae. Dengue virus infection of mosquitoes was determined using real-time reverse transcription polymerase chain reaction (qRT-PCR). Partial amplification and sequencing of dengue virus genome in infected mosquitoes was performed. A total of 1,000 adult mosquitoes were collected. Over half (59.9%) of the adult mosquitoes were collected in Kinondoni. Aedes aegypti accounted for 17.2% of the mosquitoes of which 90.6% were from Kinondoni. Of a total of 796 houses inspected, 38.3% had water-holding containers in their premises. Kinondoni had the largest proportion of water-holding containers (57.7%), followed by Temeke (31.4%) and Ilala (23.4%). The most common breeding containers for the Aedes mosquitoes were discarded plastic containers and tires. High Aedes infestation indices were observed for all districts and sites, with a house index of 18.1% in Ilala, 25.5% in Temeke and 35.3% in Kinondoni. The respective container indices were 77.4%, 65.2% and 80.2%. Of the reared larvae and pupae, 5,250 adult mosquitoes emerged, of which 61.9% were Ae. aegypti. Overall, 27 (8.18) of the 330 pools of Ae. aegypti were positive for dengue virus. On average, the overall maximum likelihood estimate (MLE) indicates pooled infection rate of 8.49 per 1,000 mosquitoes (95%CI = 5.72–12.16). There was no significant difference in pooled infection rates between the districts. Dengue viruses in the tested mosquitoes clustered into serotype 2 cosmopolitan genotype. Conclusions/Significance Ae. aegypti is the main vector of dengue in Dar es Salaam and breeds mainly in medium size plastic containers and tires. The Aedes house indices were high, indicating that the three districts were at high risk of dengue transmission. The 2014 dengue outbreak was caused by Dengue virus serotype 2. The high mosquito larval and pupal indices in the area require intensification of vector surveillance along with source reduction and health education. Until 2010, little was known about Dengue in Tanzania. Since then, four outbreaks have been reported in Dar es Salaam City. This study was therefore carried out to assess the risk of transmission of dengue in Dar es Salaam during an outbreak in 2014. In this study adult mosquitoes were collected using carbon dioxide-propane powered traps. In addition, household compounds were visited and all water-holding containers examined for presence of mosquito larvae and pupae. Mosquito virus infection was determined using real-time reverse transcription polymerase chain reaction (qRT-PCR). Of the total of 1,000 adult mosquitoes collected, Aedes aegypti accounted for 17.2%. A total of 796 houses were inspected and 38.3% had water-holding containers in their premises. The most common breeding containers for the Aedes mosquitoes were discarded plastic containers and tires. High Aedes infestation indices were observed for all districts and sites, with a house and container indices ranging from 18.1–25.5% and 65.2–80.2%, respectively. The Breteaux indices were 30.6, 20.8 and 25.3 in Ilala, Kinondoni and Temeke, respectively. An overall 8.18% of mosquito pools were infected with dengue virus serotype 2. The overall maximum likelihood estimate of pooled infection rate of 8.49 per 1,000 mosquitoes was observed. This information is useful for the design of appropriate vector surveillance and control strategies in the City of Dar es Salaam.
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Affiliation(s)
| | - Clement N. Mweya
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Susan F. Rumisha
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Patrick K. Tungu
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Grades Stanley
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Mariam R. Makange
- Department of Veterinary Microbiology and Parasitology, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Gerald Misinzo
- Department of Veterinary Microbiology and Parasitology, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Pasquale De Nardo
- National Institute for Infectious Diseases, "L. Spallanzani", Rome, Italy
| | - Francesco Vairo
- National Institute for Infectious Diseases, "L. Spallanzani", Rome, Italy
| | - Ndekya M. Oriyo
- National Institute for Medical Research, Dar es Salaam, Tanzania
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