Complete genome analysis of African swine fever virus genotypes II, IX and XV from domestic pigs in Tanzania.

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.

Aedes aegypti abundance, larval indices and risk for dengue virus transmission in Kinondoni district, Tanzania.

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.

Complete Genome Sequencing of Field Isolates of Peste des Petits Ruminants Virus from Tanzania Revealed a High Nucleotide Identity with Lineage III PPR Viruses.

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.

Peste des Petits Ruminants Virus Infection at the Wildlife-Livestock Interface in the Greater Serengeti Ecosystem, 2015-2019.

Peste des petits ruminants (PPR) is a viral disease of goats and sheep that occurs in Africa, the Middle East and Asia with a severe impact on livelihoods and livestock trade. Many wild artiodactyls are susceptible to PPR virus (PPRV) infection, and some outbreaks have threatened endangered wild populations. The role of wild species in PPRV epidemiology is unclear, which is a knowledge gap for the Global Strategy for the Control and Eradication of PPR. These studies aimed to investigate PPRV infection in wild artiodactyls in the Greater Serengeti and Amboseli ecosystems of Kenya and Tanzania. Out of 132 animals purposively sampled in 2015-2016, 19.7% were PPRV seropositive by ID Screen PPR competition enzyme-linked immunosorbent assay (cELISA; IDvet, France) from the following species: African buffalo, wildebeest, topi, kongoni, Grant's gazelle, impala, Thomson's gazelle, warthog and gerenuk, while waterbuck and lesser kudu were seronegative. In 2018-2019, a cross-sectional survey of randomly selected African buffalo and Grant's gazelle herds was conducted. The weighted estimate of PPRV seroprevalence was 12.0% out of 191 African buffalo and 1.1% out of 139 Grant's gazelles. All ocular and nasal swabs and faeces were negative by PPRV real-time reverse transcription-polymerase chain reaction (RT-qPCR). Investigations of a PPR-like disease in sheep and goats confirmed PPRV circulation in the area by rapid detection test and/or RT-qPCR. These results demonstrated serological evidence of PPRV infection in wild artiodactyl species at the wildlife-livestock interface in this ecosystem where PPRV is endemic in domestic small ruminants. Exposure to PPRV could be via spillover from infected small ruminants or from transmission between wild animals, while the relatively low seroprevalence suggests that sustained transmission is unlikely. Further studies of other major wild artiodactyls in this ecosystem are required, such as impala, Thomson's gazelle and wildebeest.

The Risk of Dengue Virus Transmission in Dar es Salaam, Tanzania during an Epidemic Period of 2014.

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.