Theses and Dissertations Collection

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    Species composition and genetic stock structure of elasmobranchs in the Indo - West Pacific Ocean
    (Sokoine University of Agriculture, 2022) Simwanza, Rehema Joseph
    Although Tanzania has prohibited the capture and sale of endangered elasmobranchs, there is a chance that the fish are traded in processed form because fish products in the country are traded in such forms. Therefore, this study used DNA barcoding to assess the composition and conservation status of elasmobranchs landed and traded in Tanzanian fish markets. Fin tissues of 102 elasmobranchs were collected from fish markets in Tanga, Dar es Salaam, Nungwi, Kilwa and Mtwara between 2020 and 2022. Fragments of the Cytochrome Oxidase Subunit 1 gene were amplified and sequenced from the DNA extracts of each sample. The results showed that 23 different species of elasmobranch are landed and traded in Tanzanian fish markets. However, 50% of the traded species are listed as either endangered or critically endangered on the IUCN Red List, and 49% of them are CITES protected. This indicates that although Tanzania prohibited fishing and trade in endangered elasmobranchs; many of these species are still fished and sold in local markets. This shows that the ban on endangered elasmobranchs is not being effectively enforced and that fishing activities continue to endanger the protected species. Therefore, the DNA based approach is suggested to be used by authorities to identify threatened and protected species of elasmobranch. Measures should be taken to strengthen enforcement of the fisheries regulations 13 (11) and 67 (2) of 2009 at landing sites and fish markets in the country. Similarly, efforts should be taken to raise fishers’ awareness of the protected elasmobranchs.
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    The prospective of using plants with antifertility effects in controlling the rodent pest, mastomys natalensis
    (Sokoine university of agriculture, 2022) Mwangengwa, Lusekelo Msomba
    The prolific nature of some rodents has been a significant threat to the livelihood and public health in sub-Saharan Africa escalating the use of rodenticides. Regrettably, rodent pests are increasingly becoming resistant to rodenticides due to bait shyness or resisting death. Also, the rodenticidal poison has been killing other untargeted species of animals. Thus, alternative methods of rodent control including the use of birth control methods are increasingly being explored. So, the current study investigated the antifertility potential of Acacia nilotica pods and Albizzia lebbeck stem bark extracts in the Mastomys natalensis. Specifically, the study was done to investigate the effect of the plant's extracts on the fertility success rate of female and male M. natalensis, to evaluate the effect of the plant's extracts on follicular and corpora lutea counts in the female rat’s ovaries, to explore the effect of the plant’s extracts on the sperm cells parameters and histomorphology of the testes in the male rats and to determine the phytochemical constituents of the two plants. Pods of A. nilotica were collected from Kilwa and stem barks of A. lebbeck were collected from Morogoro urban, in Tanzania. The M. natalensis were collected from Sokoine University of Agriculture (SUA) owned farms. Experiments and Laboratory works were done at the College of Veterinary Medicine and Biomedical Sciences (CVBMS) at SUA. This thesis contains the research works done in the current study and is divided into three sections. Section one comprises introduction and literature review, problem statement, objectives, the rationale of the study, scope and limitations of the study. Section two encompasses the three manuscripts describing the research work done. The third section consists of the general conclusion and recommendation of the study. The first manuscript assesses the pathophysiological significance of A. nilotica pods aqueous extract and A. lebbeck stem bark methanolic extract on the reproductive system of female M. natalensis. A total of 60 sexually mature rats were randomized into a 2 x 3 factorial design for treatments (Control A. nilotica, and A. lebbeck) and treatment duration (7 or 14 days). Control rats consumed basal feed, treated rats consumed feed with 2% w/w of either of the plant extracts. At the end of treatment duration, treated female rats were cohabited with males for 16 days and sacrificed 20 days after the first day of cohabitation. Parameters assessed at necropsy included the pregnancy rates, number of fetal implantations, possible resorption sites, and fetal litter size. Other evaluated parameters included the ovarian weights, follicular and corpora lutea numbers, and general histopathology of ovaries. Results showed that pregnancy percentages, the number of fetal implantations, and fetal litter size were significantly reduced (p< 0.01) in rats under the A. nilotica and A. lebbeck extract treatments relative to the control. The ovarian weights of rats receiving the extracts did not differ significantly from the control (p > 0.05). However, the number of corpora lutea of pregnancy was significantly reduced (p < 0.001) in the ovaries of rats under extract treatments than in the control. Instead, the ovaries of rats receiving the two extracts contained a larger number of atretic follicles, signifying halted ovulatory and conception activities. In conclusion, the study demonstrated that dietary inclusion of crude extracts from A. nilotica pods and A. lebbeck stem bark can lead to decreased fertility success rates in M. natalensis female rats through suppression of ovulatory activities and induction of follicular atresia. The second manuscript evaluated the contraceptive potential of the methanolic extracts from A. nilotica pods and A. lebbeck stem bark in male M. natalensis. A total of 90 rats were randomized into a 3 x 3 factorial design for treatment (control, A. lebbeck and A. nilotica) (n = 10) and treatment durations (15, 30, or 60 days). Control rats consumed plain feed. Treated rats consumed feed with 2% w/w of either of the plant extract. Following treatment, male rats were mated to untreated females before sedation in ether and sacrification. Assessments were done on fertility success rates (number of impregnated females), weights of testes and reproductive glands, sperm cell parameters, and testes histopathology. Results revealed that the fertility success rate was reduced to 0% in the A. nilotica treated rats at all the treatment durations and in the A. lebbeck treated rats after 60 days of treatment. Moreover, the extract-treated rats revealed a significant reduction in the testes, seminal vesicles, and epididymides weights. Also, sperm cell density and the proportions of live and progressively motile spermatozoa were significantly reduced and there were numerous seminiferous tubules with damaged and thinned germinal epithelium and widened empty lumen in the extract-treated rats. In conclusion, treatment with A. nilotica or A. lebbeck extract in male rats reduced their fertility success rates through distortion of testicular structure and disruption of spermatogenesis. The third manuscript evaluated the phytochemical constituents of raw grounded materials and methanolic extracts of A. nilotica pods and A. lebbeck stem bark extracts and the potential effects the methanolic extracts may have on spermatozoa morphologies in the male M. natalensis. A portion of the grounded materials from each plant was extracted in 70% methanol. Both the grounded materials and corresponding methanolic extracts were assessed for the presence of phytochemicals with antifertility potentials. A total of 90 male rats were randomized into 9 groups based on treatment (control, A. lebbeck and A. nilotica) (n = 10) and extract treatment durations (15, 30, or 60 days). Results indicated that flavonoids, tannins, saponins, steroids, terpenoids and plant phenols were all present in the powdered raw materials and their corresponding extracts of both plants. However, saponin was shown to be more intensely present in the powdered and methanolic extracts of the A. lebbeck compared to those of A. nilotica while the reverse was true for flavonoids and tannins. Spermatozoa with normal head-abnormal tail, normal head-tailless, abnormal head-normal tail, both abnormal head and tail spermatozoa were more revealed in extracts treated rats relative to the control. In conclusion, the studied pods of A. nilotica and the Stem bark of A. lebbeck are rich in flavonoids, tannins, saponins, steroids, terpenoids and plant phenols which possess some antifertility properties explaining the adverse effects of the plant’s extracts on spermatozoa morphologies. The research information contained in this thesis contributes significantly to the limited available knowledge on the antifertility efficacies of medicinal herbal extracts in the wild rodents, more particularly the M. natalensis.
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    Development and evaluation of a reverse transcription loop-mediated isothermal amplification assay for rapid typing of serotype “o” foot-and-mouth disease virus in endemic settings of Tanzania
    (Sokoine University of Agriculture, 2021) Njeru, Sarah Mueni
    The foot-and-mouth disease (FMD) is an economically important transboundary animal disease (TADs) affecting all cloven-hoofed animals. It is caused by foot-and- mouth disease virus (FMDV), which has seven antigenically distinct serotypes. FMD is endemic in Tanzania, with outbreaks caused by predominantly five serotypes. In order to improve the control of this disease, for instance using serotype-specific vaccines, rapid detection and identification of circulating FMDV strains is of paramount importance. This study describes the development and evaluation of a reverse transcription loop- mediated isothermal amplification (RT-LAMP) assay for diagnosis of serotype ‘O’ FMDV in endemic settings in Tanzania. A retrospective study design was employed for this research whereby a total of forty-four (n=44) archived epithelial tissue samples were analyzed by RNA extraction, reverse transcription polymerase chain reaction (RT-PCR), RT-LAMP and DNA sequencing. Primers for RT-LAMP targeting serotype ‘O’ FMDV isolates in Tanzania were developed and found to optimally amplify the targeted gene at 65.0 ̊C for 45 minutes in the presence of both Avian Myeloblastosis Virus (AMV) reverse transcriptase enzyme and loop primers. The results indicated that RT-LAMP assay could amplify the viral protein 1 (VP1) gene of serotype ‘O’ FMDV within a range of 13 to 26 minutes, with annealing temperatures of between 70.0 and 89.0°C. The findings indicate that RT-LAMP assay is highly specific as no cross- reactivity occurred between serotype ‘O’ primers with any of the other serotypes. The sensitivity as indicated by the detection limit of the assay was deduced to be 3.78 ×10 -2 ng/μl. This study concludes that RT-LAMP assay could be used to rapidly and accurately detect VP1 gene of serotype ‘O’ FMDV from Tanzania. It is advisable that further studiesare required to evaluate the comparative sensitivity of the assay and check whether the assay is field deployable. Further evaluation is also needed to determine whether the assay would be useful for detecting serotype ‘O’ FMDV strains circulating in other regions in Tanzania.
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    Effect of women empowerment on sustainable household food security: a case of Monduli district in Tanzania
    (Sokoine University of Agriculture, 2022) Muhoze, Linda-Darlene
    Food security exists when all people, at all times, have physical and economic access to sufficient, safe, and nutritious food that meets their dietary needs and food preferences for active and healthy life. Food insecurity continues to be a significant problem for public health nutrition in developing and developed countries, and women are the most affected. Similarly, women's empowerment has been used as a strategy to improve household food security and nutrition. Women invest in household food needs, increase household consumption, and improve children's nutritional status compared to men. The objective of this study was to determine the effect of women empowerment on sustainable household food security in Monduli District in Tanzania. A cross-sectional study was conducted between March 2021 and April 2021. A total of 245 households and 491 women between 15 and 49 years of age fully participated in household survey using questionnaire about household food security and women empowerment. Data were analyzed using SPSS for windows (Version 21.0. SPSS Inc., Chicago, IL, USA). The Household Food Insecurity Access Scale (HFIAS) and Minimum Dietary Diversity-Women(MDD-W) revealed that most households were food insecure (73%) and did not reach minimum dietary diversity (95.7%). Women’s Empowerment in Agriculture Index (WEAI) only categorized (16.9%) as empowered women. The low status of women’s empowerment was expressed by their non-involvement in household decision matters, less control over resources, and a low level of education. The positive effect of women empowerment on sustainable household food security in Monduli District (OR=3.15; 95% CI: 1.93-5.13, p<0.05) was determined by using multivariate logistic regression and backward Wald methods. Government policies reienforcement on social mechanisms that allows higher percentage of women to be enrolled in education, gender equality promotion, land ownership, decision- making ,involvement in leadership and programs that access women's participation in off- farm income-generating activities will reduce and prevent household food insecurity in Monduli.
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    The evolutionary dynamics of genetic determinants of plasmodium falciparum resistance to sulfadoxine/pyrimethamine (sp) in South Eastern Tanzania
    (Sokoine University of Agriculture, 2008) Malisa, Allen Lewis
    This study reports a systematic follow up of genetic changes in the genes encoding the dihydrofolate reductase (DHFR) and dihydropteroate synthase (DHPS) enzymes of Plasmodium falciparum, in isolates from three rural districts of South-eastern Tanzania. The enzymes are the target of antimalarial drug, sulphadoxine- pyrimethamine (SP). The population-wide analysis of resistance mutations in the dhfr and dhps genes was applied to examine the influence of different drug use policies and their potential for the selection for SP resistance. A total of 47 244 bloodspot filter paper samples were collected from all individuals of all ages in randomly selected households in a series of annual surveys conducted between 2000 - 2006. Twenty percent (9 662) of all samples were found positive for P. falciparum infection on microscopy and hence were used for the genetic studies. DNA was extracted from P. falciparum-positxvz samples and dhfr and dhps genes were amplified by a nested polymerase chain reaction (PCR) and resistance conferring point mutations determined. Size polymorphisms at three sets of microsatellite loci linked to dhfr and three other sets of unlinked microsatellite loci were analysed by PCR amplification and electrophoresis on an automated sequencer. The influence of National treatment policy on the parasite reservoir was profound. The change of first line therapy from CQ to SP brought about highly significant increase of the frequencies of dhfr triple and dhps double mutants. Artemisinin-based combination therapy (ACT- SP+Artesunate) in Rufiji had a small and non-significant impact on the frequency of dhps double and dhfr triple mutant alleles, but significantly disrupted their association. Z)A/r-l inked microsatellites revealed high diversity around the dhfr sensitive alleles and significantly reduced diversity around mutant dhfr alleles. The majority of triple mutant alleles had one flanking microsatellite haplotype which has previously been shown to be derived from Southeast Asia, while the double mutant alleles had multiple haplotypes which were independently derived. Distribution of major lineages indicates that there is extensive genetic exchange among the geographic regions. Unlinked microsatellites confirmed the extent of allele sharing among the regions and revealed a major trend for reduced transmission intensity, which was apparently independent of the ACT intervention.
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    Assessment of pesticide residues in harvested tomato fruits at Makambako town council in Njombe Region, Tanzania.
    (Sokoine University of Agriculture, 2021) Bilaro, Jansen Stanslaus
    In modern agriculture, pest infestation has posed a great challenge to farmers. The use of pesticide has eventually become an important tool to ensure quality and quantity of crop yields. However, such chemicals might have residual impacts to consumers. This study was conducted to assess the extent of pesticide residues in harvested tomato fruits at Makambako Town Council in Njombe region, Tanzania. Specifically the study aimed at: (i) investigating adherence to recommended manufacturer’s instructions on pesticide application among tomato farmers (ii) determining level and frequency of occurrence of selected pesticide residues in tomato fruits and (iii) characterizing dietary risks associated with consumption of fresh tomato fruits containing pesticide residues. Forty seven (47) farmers were interviewed on pesticide types and their application using structured questionnaire. Forty two (42) fresh tomato fruits for laboratory analysis were sampled from interviewed farmers who were at harvesting season. QuEChERS (CEN) Method 15662.5 was employed for pesticide extraction and analyzed by Gas Chromatography Mass Spectrometer. It was found that all respondents mixed more than one pesticide in a single spray tank without adhering to recommended mixing procedures. The average withholding period was 5 days, below the recommended 7 days for mixture of mancozeb and metalaxyl which were commonly used fungicides at the study area. Eighty three percent of the respondents exceeded the mixing concentration of pesticide above the recommended mixing ratios. Residues of chlorpyrifos, profenofos, gamma cyhalothrin and cypermethrin were alternatingly detected in 78.51 % of analyzed samples. The average concentrations of residues were 0.014, 0.056, 0.003 and 0.2 mg/kg for chlorpyrifos, profenofos, gamma cyhalothrin and cypermethrin, and were all below Codex MRLs of 1, 10, 0.3 and 0.2 mg/kg respectively, as per FAO/WHO guidelines. The maximum residue concentration was 0.718 mg/kg for cypermethrin, which was above the Codex MRL of 0.2 mg/kg. Profenofos was the most frequently detected pesticide, occurring in 60 % of samples. The hazard indices for the selected pesticide indicate no potential health hazards to general population due to lifetime consumption of fresh tomato fruits from the study area. The study recommend regular training to farmers on good agricultural practices through extension officers and pesticide regulatory authority. Further research on pesticide residues and dietary risk assessment is recommended for other pesticide commonly used at the study area.
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    Establishment of long-read nanopore sequencing and proficient nanobodies against peste des petits ruminants virus on the road to develop diagnostic and therapeutic tools
    (Sokoine University of Agriculture, 2022) Kinimi, Edson
    Peste des petits ruminants virus (PPRV) causes a highly devastating disease of sheep and goats, peste des petits ruminants (PPR), that threatens food security, animal production and the conservation of wild small ruminants. Growing body of evidence suggests that multiple wildlife and atypical host species can be infected with PPRV, posing a serological diagnostic challenge in multi-host environment. Recent studies confirmed that single- domain antigen binding fragments (nanobodies) derived from heavy-chain-only camelid antibodies and nanopore sequencing have proven to be powerful technologies for the development of cost-effective and robust therapeutic and diagnostic tools, respectively. Therefore, the main objective of this study was to generate PPRV-reactive nanobodies in order to set pace for the development of diagnostic and possible therapeutic nanobodies in the future, alongside with establishment of rapid complete genome nanopore sequencing of PPRV. Firstly, a strategy was developed to generate nanobodies against PPRV, whereby an alpaca (Vicugna pacos) was immunized with live attenuated vaccine strain (PPRV/Nigeria/75/1) to raise an affinity-matured immune response in the heavy-chain- only antibody classes. An immune nanobody library with approximately 64 million independent transformants was engineered, of which 100% contained an insert with the proper size of nanobody gene. Following phage display and in vitro affinity selection (biopanning), nine nanobodies that specifically recognise PPRV were identified on enzyme-linked immunosorbent assay. They showed superb potency in identifying rapidly PPRV, which is likely to open a new perspective in the diagnosis and possible treatment of PPRV infection. Secondly, prior to the full genome sequencing of PPRV, nanopore sequencing protocol was tested for amplification and sequencing of PPRV. With this protocol, there were no DNA fragments and nucleotide sequences in the GC-rich region between matrix (M) and fusion (F) genes at the genome position between 4,444 and 5,526. Thus, a tiling multiplex polymerase chain reaction method was developed to amplify the missing DNA fragments. Following redesigning of three pairs of overlapping long read primers and cascade of optimization, the GC rich region was successfully amplified and sequenced (accession numbers: MW580394, MW580395 and MW580396). These three pairs of primers targeting the GC-rich region were used along with other 22 pairs of primers in tiling multiplex PCR for complete PPRV genome sequencing. The resulting PCR amplicons were used for nanopore library preparation and ultimate sequencing. This method has resulted into complete genomes of PPRV, with 15,948 nucleotides long for both isolates that were 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 PPR viruses currently circulating in East Africa indicating a common origin. The nanopore sequencing platform can be deployed to overcome PPR diagnostic and surveillance challenges, unanticipated variations in virus pathogenicity, circulation of disease in wildlife populations and to service remote and nomadic communities with challenging geographical landscapes. However, further investigations are recommended for PPRV reactive nanobodies especially on diagnostic and therapeutic applications. Once validated, these technologies have great potential for use in the field as rapid and cost-effective tools in context of planned PPR Global Control and Eradication Programme.
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    Viral genetic diversity, risk factors and socio-economic impact of African swine fever from selected parts of Tanzania, 2019 and 2022
    (Sokoine University of Agriculture, 2022) Kivumbi, Clementina Clement
    African swine fever virus (ASFV) is a double stranded DNA virus of the family Asfaviridae and genus Asfivirus that causes African swine fever (ASF). The disease can lead up to 100% mortality of infected domestic pigs causing farmers to incur enormous losses as a result of pig mortalities and loss of market for pigs and pig products. The disease is one of the major pig diseases in Tanzania, with outbreaks reported in different regions including Kigoma, Arusha, Dar es Salaam, Dodoma and Mbeya. Twenty-four (I-XXIV) p72 genotypes have been described so far in Sub-Saharan Africa. Previous studies have reported ASFV genotypes II, IX, X, XV and XVI to be associated with ASF outbreaks in Tanzania. Major factors responsible for the spread of ASF in Tanzania include illegal movement of pigs and swill feeding. This present study was conducted to: (i) diagnose and genotype ASFV from the 2019 ASF Ngara district outbreak western Tanzania, (ii) genotype different ASFV trains in ASF outbreaks between march 2021 and march 2022 located un Lake Zone (Kahama, Geita), northern (Mwanza and Katavi) and central Tanzania (Mpwapwa, Kongwa) and Morogoro in eastern Tanzania, and to (iii) determine the Ngara ASF outbreak related risk factors and socio-economic impact. Spleen, lymph nodes, tonsils and liver were collected from the outbreaks from pigs with ASF clinical signs including hyperthermia, sternal recumbence and cutaneous congestion on the limbs, abdomen and outer side of the pinna. Postmortem findings on affected pigs included splenomegaly, enteritis, and severe hemorrhages of gastrohepatic and mesenteric lymph nodes. Polymerase chain reaction (PCR) using peste porcina Africana (PPA 1/2) primers targeting the conserved part of B646L gene (coding for the p72 capsid protein) that generates a 257 base pairs amplicon was used for ASF diagnosis. Genotyping was done by nucleotide sequence analysis of the variable 3’ end of the B646L gene. African swine fever was confirmed in dead pigs by PCR. Phylogenetic analysis found ASFV genotype II of ASFV in pigs samples from Kongwa (TAN/2021/Kongwa), Mpwapwa (TAN/2021/Mpwapwa) and Morogoro (TAN/2022/ Morogoro) districts. Genotype X was found in domestic pigs samples from Kahama (TAN/2021/Kahama), Geita (TAN/2021/Geita) and Katavi (TAN/2022/Katavi) districts and genotype IX was found in Mwanza (TAN/2022/Mwanza). Phylogenetic analysis clustered ASFV from Ngara into genotype X. Presence of these genotypes indicate their relation with previous outbreaks in Tanzania indicating persistent circulation of the viruses. Feeding pigs of uncooked swill was shown to be significantly associated with the Ngara ASF transmission (OR=3.08, C.I.95%=1.06-8.99, P=0.0009). Occurrence of ASF outbreak resulted into loss of income and investment as most farmers kept pigs for the purpose of income generation. Food security was disturbed due to high pig mortality following occurrence of ASF outbreak. A total of 93 630 000 Tanzanian shillings (approximately 41 065 USD) was estimated to be lost as a result of pigs’ mortality in 219 households. This calls for the need to educate farmers on the methods for effective control of disease and for the veterinary services to enforce regulation on movement of pigs and pig products between regions so as to prevent disease spread.
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    Phenotypic and molecular evaluation of lines developed for multiple disease resistance in common bean (phaseolus vulgaris l.)
    (Sokoine University of Agriculture, 2021) Mlemba, Sylvia Adam
    Common bean (Phaseolus vulgaris L.) is the most important grain legume serving as a key source of protein and vital micronutrients for human beings worldwide. In Tanzania common bean yield average is 1 metric tons (MT) per hectare while the potential yield is reported to be 1.5 to 3 MT per hectare. The low yield among other factors is largely contributed by occurrence of foliar diseases caused by fungi, viruses, and bacteria. In this context, breeding common beans for multiple disease resistance in adapted genotypes is proposed as the most economical and environmentally safe approach for control of these diseases. Experiments were conducted on seventeen common bean genotypes for evaluation of resistance to four major foliar diseases viz., angular leaf spot, common mosaic virus disease, common bacterial blight, and anthracnose under natural infection. Phenotypic evaluation was conducted at Tanzania Agriculture Research Institute – Selian center (TARI–Selian) during the main bean growing season (March to July 2020). Experiment was laid in a randomized complete block design (RCBD) with three replications. Data were collected six weeks after planting and then after every fourteen days, three times by using the CIAT 1-9 disease rating scale. The mean disease scores were analyzed using GenStat software 15 th version. Polymerase chain reaction (PCR) was performed using four gene specific primers to screen for specific disease resistant genes. Phenotypic results showed significant variation in disease reaction and yield (P< 0.001). Genotype Mex 54 had the highest yield (2888.89kg/ha) while improved genotype S-3 recorded the lowest yield (280.44kg/ha). Molecular results indicated that 17.4% of the genotypes contained all four genes while 7.9% lacked any gene for disease resistance. Positive correlation between disease severity scores and molecular marker scores were observed (r = 0.106; P < 0.05). This suggests that genotypes confirmed as resistant for both phenotypic and molecular evaluations can be recommended as promising materials for advancement and release as resistant common bean varieties for use by farmers in Tanzania.
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    Prevalence, characterisation and antimicrobial resistance profiles of salmonella isolates from healthy broiler and indigenous free range chickens in Morogoro, Tanzania
    (Sokoine University of Agriculture, 2021) Munuo, Lidia Abiael
    The study was conducted to determine prevalence, biochemical profiles and antimicrobial susceptibility profiles of non typhoidal salmonella (NTS) in indigenous free range and broiler chickens in Morogoro Municipality. Between November 2019 and May 2020, a total of 384 cloaca swab samples from Magadu, Mzinga and Bigwa wards were collected. Identification was done by standard bacteriological methods, serotyping and genetically confirmed by PCR using Salmonella specific primers pair and Salmonella enterica primer pair (invA and iroB gene primers). Antimicrobial sensitivity tests were done using Ampicillin, Cefaclor, Imipenem, Gentamycin, Ciprofloxacin, Sulfamethaxazole- Trimethoprim and Tetracycline antimicrobial discs. Out of 384 samples, 11 (2.9%) samples confirmed to be Salmonella of which 8(4%) were from broilers and 3(1.6%) were from free range chickens. Of the 11 isolates 8 were from group B and 3 isolates were from group D. Bigwa ward showed high prevalence (5.2%) of Salmonella than the other wards, broilers being the more prevalent in Salmonella than free range chickens. Antimicrobial susceptibility results showed variable level of sensitivity to majority of antimicrobial tested, however, variable level of resistance were also found with 7 isolates resistant to Ampicillin, 4 isolates resistant to Sulfamethoxazole-Trimethoprim and 3 isolates resistant to Tetracycline. Screening for resistant genes detected three isolates with Sulfamethaxole (sulII) resistant gene and none for Tetracycline and Ampicillin. This study revealed the presence of Salmonella carriers among chicken kept in Morogoro Municipal with antimicrobial resistances from both free range and broilers chickens. The results underline the importance of the biosecurity measures in the production and processing of chicken for human consumption, Similarly improvement of management is recommended to stop transmission of Salmonella from natural carriers to chickens as indicated by faecal carriers found. Contamination or spread from rats that are natural carriers to poultry needs to be further investigated.
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    Molecular detection and evolutionary characteristics of recently recovered serotypes a and o foot-and-mouth disease viruses in selected areas of Tanzania
    (Sokoine University of Agriculture, 2020) Julieth, E.
    Foot-and-mouth disease (FMD) is a highly contagious disease that infects cloven hoofed animals. FMD is caused by FMD virus (FMDV), a picornavirus with a positive sense single stranded RNA genome of about 8.5 kb in size. FMD is endemic in East African countries including Tanzania. The general objective of this study was to determine the genetic characteristics of recently circulated serotypes O and A FMDV field strains in selected regions of Tanzania in 2019. A total of 36 (four serotype O and 22 serotype A) archived epithelial samples collected from cattle and pig in Kibaha, Morogoro, Sengerema, Butiama and Musoma were used in this study. The laboratory analysis of the samples was performed by reverse transcription polymerase chain reaction (RT-PCR) targeting the 3D and VP1 coding regions, VP1 sequencing and phylogeny. The RT-PCR results revealed that 72% of samples (n= 26) were positive for FMDV genome. Molecular typing of the FMDV genome positive samples was achieved by using serotype specific primers of which serotypes A were 85 % (n= 22) and O were 15 % (n= 4). Phylogenetic reconstructions were determined by neighbour-joining methods. Phylogenetic analysis of VP1 showed genetic diversity among the circulating viruses and their molecular relatedness with previously recorded sequences from East Africa, particularly Kenya and Tanzania. These findings indicate that the 2019 FMDV types A and O responsible for the disease outbreaks in Tanzania were the East Africa 2 (EA-2) and genotype I (GI) which showed a very closely evolutionary relatedness with previous strains collected in Kenya and Tanzania. Further studies are required to design new vaccine strains so as to prevent upcoming outbreaks.
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    Toxoplasma gondii infection among outpatients attending Dodoma regional referral hospital in central Tanzania: prevalence and associated risk factors in central Tanzania
    (Sokoine University of Agriculture, 2020) Lema, G. B
    Toxoplasmosis is a parasitic zoonotic disease caused by coccidian intracellular protozoan parasite, Toxoplasma gondii. The parasite is ubiquitous and infects almost all warm blooded animals including humans. Primary infection in human is usually asymtomatic or manifest with febrile illness characterized by headache, sore throat, muscle pain and swollen lymph nodes. Clinical implication of the disease is more on pregnant women and immunocompromised individuals. The overall objective of this study was to determine the prevalence and associated factors to toxoplasmosis among patients attending Dodoma Regional Referral Hospital (DRRH) in Central Tanzania. In this cross-sectional study, a total of 395 outpatients attending DRRH between December 2019 and February 2020 were enrolled. Blood was collected from consenting patients. A structured questionnaire with simple, open and closed ended questions was administered to study subjects to collect information on knowledge of infectious agent, transmission mode and information regarding risk of exposures. Of 395 subjects enrolled in this study, 2% were infected with T. gondii after screening using polymerase chain reaction. There was no statistical relationship between disease diagnosis and risk of exposures. Only 1.3% of the participants had good knowledge towards toxoplasmosis. Majority (88.4%) of the enrolled participants showed good practises towards toxoplasmosis. The results indicate that T. gondii is prevalent among individuals in Dodoma Region and a very low proportion of them had knowledge of the disease. The results suggest the need of health education toward toxoplasmosis among residents of Dodoma. It is important that the health care system diagnostic capacity is enhanced to provide routine diagnosis of T. gondii and promote an interdisciplinary collaboration in its risk management.
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    Indiscriminate use of agro-verinary pesticides and susceptibility status of xenopsylla cheopis (family: pulicidae) in plague endemic foci in Tanzania
    (Sokoine University of Agriculture, 2020) Rugalema, G. P
    The control of rodent-borne fleas, which play major role in the transmission of plague, is the mainstay of plague control. The application of chemical insecticides forms the most powerful and widely used control measure. The reliability and continued use of this approach however is threatened by the development of resistance. The excessive use of agro-veterinary pesticides is increasingly associated with the development of resistance in different arthropods; however, such possibility has not been explored in flea vectors of plague in Tanzania. This study identified injudicious uses and/or malpractices which potentially enhance exposure of flea vectors to agro-veterinary insecticides and emergence of resistance thereof. Furthermore, the study assessed susceptibility status of major plague flea vector, Xenopsylla cheopis, to commonly used agro-veterinary and public health pesticides. The study was conducted in Lushoto and Mbulu districts, northern Tanzania, both of which are active plague foci. About 91% of the respondents in Lushoto and 93% respondents in Mbulu reported using agricultural pesticides during the cropping season. Excessive and injudicious use of agricultural and veterinary pesticides was common across the study districts. Most of the farmers reported applying agricultural pesticides for up to four times per a cropping season. The three out of fourteen most commonly used agricultural pesticides in Lushoto were master kinga72WP (mancozeb 640g/kg+ cymoxanil 80g/kg) (44%), suracron720EC (profenos 500g/l EC) (25.3%) and Sumo 5EC (lambda-cyhalothrin) (18.7%). The three out of seventeen most commonly used agricultural pesticides in Mbulu were Dursban 50W (Chlorpyrifos) (29%), Duduban 450EC (Cypermethrin 10g/lt+chloropyrifos 35g/lt) (18%) and Dursban+farmerzeb (Chlorpyrifos 48%, Mancozeb 80%WP). Cybadip (Cypermethrin) (≥45%) and paranex (alphacypermethrin) (≥13%) were the two most commonly used veterinary pesticides across the districts. Moreover, the susceptibility of Xenopsylla cheopis, originating from wild population in Mbulu was assessed against nine different agro-veterinary and public health pesticides via contact bioassays. The percentage mortality after exposure to recommended doses of eight insecticides tested was strongly suggestive of resistance (100% 24 h mortality, 93 - 96%). The fleas confirmed resistance to lambdacyhalothrin and carbaryl, with 90% mortality. The reference ‘susceptible’ colony Xenopsylla Cheopis was fully susceptible (100% 24 h mortality) to all tested insecticides. Similarly, the field Xenopsylla Cheopis was fully susceptible (100% 24 h mortality) to 5× and 10× the recommended doses of all insecticides indicating low resistance intensity. Conclusively, this study identified a suite of injudicious uses and/or malpractices; excessive use of agricultural chemicals, maluse of agro-veterinary chemicals as well as poor adherence to the application and safety procedures, all of which potentiate contamination of environments/surfaces and exposure of the chemicals to fleas thereof. Furthermore, the study indicates resistance in the wild population of Xenopsylla cheopis from Mbulu district. As such, flea vector populations across Lushoto and Mbulu districts are putatively under intense risk of resistance development, thus warranting further studies across plague endemic areas in country to understand distribution of the resistance, involved resistance mechanisms; and confirm the contribution of agro-veterinary insecticides
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    Arbovirus infections in aedes mosquitoes at the interface of human-livestock-wildlife ecosystem in Kilosa district, Tanzania
    (Sokoine University of Agriculture, 2020) Machelle, I. S
    Arboviruses refer to a group of viruses, which are transmitted by arthropods including mosquitoes and ticks. The objective of this study was to determine mosquito transmission potential of arboviruses at the interface of human-livestock-wildlife ecosystem in Kilosa district, Tanzania. Adult mosquitoes were collected using Mosquito Magnet® Liberty Plus traps. Reverse transcription polymerase chain reaction assay was performed on pooled adult Aedes mosquitoes to detect the presence of Dengue virus (DENV), Chikungunya virus (CHIKV), Rift Valley fever virus (RVFV) and Yellow fever virus (YFV). A total of 1340 mosquitoes belonging to four genera (Aedes, Anopheles, Culex and Mansonia) and 6 species were collected. Culex accounted for the largest (48.06%; n= 644) proportion of the mosquitoes while Anopheles for the lowest proportion (2.54%; n=34). Of the total mosquitoes collected, Aedes aegypti accounted for the majority of mosquito species (46%; n=613), followed by Culex quinquefasciatus (44.1%; n=591). Of the 36 Ae. aegypti pools tested for arbovirus 10 (28%) pools were positive. Dengue virus was detected in 3% (1/ 36) pools and CHIKV in 25% (9/ 36) pools. One pool that was positive for DENV also tested positive for CHIKV indicating the possibility of co-infection whereby, individuals may become infected by more than one arbovirus at a time thus risk of co-transmission to human and livestock. Nucleotide sequencing of polymerase chain reaction (PCR) products of the structural polyprotein region of DENV produced 511 bp fragment. Basic Local Alignment Search tool for nucleotides (BLASTn) and phylogenetic analysis showed that the (DENV3/TAN/Mikumi/2020 strain) (Accession number MW133786) obtained from this study clustered with DENV-3 strains reported in China and Kenya. This information is important as it gives knowledge on areas at high risk for arboviral disease outbreaks. The findings indicate that the presence of various mosquito vectors and detection of arboviruses in wild-caught Aedes mosquitoes leave the population of Kilosa district at a higher risk of transmission of DENV and CHIKV
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    Morphological and molecular diversity of stinging nettle (Urtica simensis) from northern Ethiopia
    (Sokoine University of Agriculture, 2020) Abdulkadir, B. E
    Urtica simensis is an erect perennial herb among the species of nettle which belongs to the family Urticaceae that is endemic to Ethiopia and locally known as Samma. It is cooked and consumed as vegetable in some parts of Ethiopia. It has medicinal properties where traditionally people use it in treating different types of diseases, including infectious diseases like allergies, diabetes and Malaria. This study was conducted to evaluate the diversity of Urtica simensis to address and fill the gap on its genetic variability and distribution using morphological characters and ISSR DNA markers. A total 133 plant samples were collected from Northern growing areas of Ethiopia (Gondar and Mekelle), based on variations in morphological characters. Morphological characterization was conducted on six morphological traits which demonstrated variation based on PCA and correlation matrix analysis. Molecular characterization was carried out using ISSR markers where, only 5 were selected out of 16 ISSR primers that produced a total of 445 scorable bands and 30 polymorphic loci, 100% of polymorphic bands, 1.88 genetic diversity and 2.75 Shannon index from a collection of 133 plant samples. Highest genetic diversity (H) was found to be 0.4286 and Shannon Information index (I) was 0.6197. The highest genetic diversity was indicated in plant samples from Mekelle compared to samples from Gondar (0.3462 and 0.3152 respectively). The Dendrogram based on Jaccard’s similarity coefficients generated by UPGMA cluster analysis using morphological and ISSR data shows major and minor clusters with broad distribution of Urtica simensis individuals over the entire tree which indicates the low divergence in morphological appearance among populations from both study areas. Based on the results of this study, morphological and ISSR markers were effective in studying genetic diversity of Urtica simensis demonstrated by variations in terms of morphological appearances and genetic variability. These results have valuable effect on characterization of Urtica simensis genetic resources in different parts of Ethiopia for conservation purposes.
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    Mosquito species composition, abundance and transmission Risk of dengue in Kinondoni district, Dar es salaam, Tanzania
    (Sokoine University of Agriculture, 2020) Ngingo, B. L
    Dar es Salaam city of Tanzania has experienced continued Dengue outbreaks with increased incidence since 2010. However, there is inadequate evidence of vector dynamics and transmission risk in the region. This study aimed to determine mosquito species composition, abundance and transmission risk of Dengue in Kinondoni district, Dar es Salaam, Tanzania. Specifically, this study aimed to: (i) determine mosquito species composition and abundance in Kinondoni district; (ii) examine Aedes mosquito breeding sites and establish container productivity rates; (iii) determine Dengue virus (DENV) infection rate and genetically characterize DENV in mosquito vectors. This cross-sectional study was conducted in Kinondoni district, Dar es salaam, Tanzania. Three wards: Mikocheni, Mwananyamala and Mzimuni were purposively selected. In each ward, three streets were randomly selected as sampling sites. The study involved sampling adult and immature mosquitoes, morphological identification and screening for DENV in collected female Aedes mosquitoes using a one-step reverse transcription polymerase chain reaction (RT-PCR). Three mosquito species were identified in 2001 collected mosquitoes namely Culex quinquefasciatus (53.1%), Aedes aegypti (23.2%) and Mansonia mosquitoes (23.6%) of which Culex quinquefasciatus was observed to be the most abundant species in Kinondoni district. The common water-holding containers observed to be breeding sites of Aedes mosquitoes included used car tires, flowerpots and plastic water buckets. The overall House Index (HI), Container Index (CI) and Breteaux Index (BI) of Kinondoni district were 55.1%, 60.4% and 114.2, respectively. DENV was not detected in all collected female Aedes Mosquitoes. Generally, Kinondoni district continues to be at risk of transmission of Dengue as Aedes aegypti, a DENV vector was observed to be present. Although DENV was not detected in mosquito vectors, the presence of potential breeding sites around Kinondoni district and higher Aedes HI, CI and BI put Kinondoni at risk of DENV transmission. Vector control interventions specifically integrated mosquito control approaches are recommended to be directed towards the elimination of breeding sites and adult mosquitoes.
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    Seroprevalence and molecular detection of chikungunyaVirus among febrile outpatients seeking health care in Mzuzu city, Malawi
    (Sokoine University of Agriculture, 2020) Kawonga, F.
    Chikungunya is a viral disease caused by Chikungunya virus (CHIKV) that is transmitted to humans by infected Aedes aegypti and Ae. albopictus mosquitoes. The objective of this study was to determine the seroprevalence of Chikungunya infection among febrile patients seeking healthcare in Mzuzu City, Malawi. Blood samples were collected during 2019 from outpatients attending Mzuzu Central Hospital who presented with fever but who were malaria and sepsis negative. Sera from outpatients were transported to the University of Malawi for analysis of the presence or absence of CHIKV specific immunoglobulin M (IgM) antibodies and CHIKV ribonucleic acid (RNA). Enzyme- linked immunosorbent assay (ELISA) was used to detect anti-CHIKV IgM antibodies while one step reverse transcription-polymerase chain reaction (RT-PCR) was conducted in IgM positive sera in order detect the presence of CHIKV RNA. Out of 119 CHIKV-suspected samples, 73 (61.3%) tested positive for anti-CHIKV IgM antibodies by ELISA. When 14 of the IgM seropositive sera were randomly selected and screened using RT-PCR, they were all positive for CHIKV RNA. This study has therefore provided an insight of current seroprevalence of Chikungunya and circulation of CHIKV among the human population in Mzuzu city, Malawi. These results suggest an active circulation of CHIKV in the population, therefore accurate laboratory assays are highly recommended for CHIKV diagnosis and appropriate management of febrile patients.
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    Molecular characterization of foot-and-mouth disease Virus recently recovered in Zambezi region, Namibia
    (Sokoine University of Agriculture, 2020) Lukas, S. S
    Foot-and-mouth disease (FMD) is a severe highly contagious viral disease of clovenhoofed animals that has significant economic impacts. FMD causes significant economic loss in Namibia in which the molecular epidemiology of FMD virus (FMDV) responsible for the outbreaks has not been consistently studied. The general objective of this study was to determine molecular characteristics of FMD viruses of 2019 outbreak in Zambezi region, Namibia. A total of 11 epithelial tissue samples collected from cattle showing FMD clinical signs were used in this study. The RNA extraction and detection of FMDV genome was done by One-step Reverse Transcription Polymerase Chain Reaction (RT-PCR) of 5’ untranslated region (5’UTR) using universal primers. Typing and sequencing was performed using serotype-specific oligonucleotide primers. Phylogenetic analysis was performed using distance matrix neighbour joining method employing the Kimura-2- parameter option. The findings indicated that all 8 sequenced viruses revealed 100% nucleotide identity among themselves. Phylogenetic analysis of 36 sequences including 8 sequences of this study, 7 from publication and other sequences from GenBank revealed that the 2019 isolates clustered together with historic Namibian isolates and those from neighbouring countries. In-depth typing and phylogeny proved that SAT3 viruses of topotype II were responsible for 2019 outbreak. Further analysis revealed that the 2019 isolates closely related to isolates from Botswana, some isolates from Zimbabwe and Kenya but were distantly related to isolates from Zambia and South Africa and no genetic linkage with isolate from Uganda. These findings indicate that topotype II SAT 3 FMD viruses were involved in the 2019 FMD outbreak in Zambezi region, Namibia. Further indepth studies are required to elucidate transmission dynamics and factors associated with the outbreaks so that appropriate FMD control measure (s) in Namibia can be recommended.
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    Influenza virus infections among outpatients seeking health care at selected hospitals in Morogoro, Mbeya and Zanzibar, Tanzania
    (Sokoine University of Agriculture, 2020) Mjema, Flora Alfred
    Respiratory infections cause significant morbidity and mortality worldwide and are the second leading causes of death in Tanzania. Several studies involving national sentinel surveillance for influenza and epidemiology of influenza have been conducted in Tanzania. However, there is dearth in the information on the aetiology of respiratory diseases. This study screened for influenza viruses in subject with influenza-like illnesses in selected areas of Tanzania. A total of 735 subjects were recruited at hospitals in Morogoro, Mbeya and Zanzibar and the collected sample were screened for influenza viruses using reverse transcription polymerase chain reaction (RT-PCR). Out of the tested samples, 13% (93/735) were positive for influenza virus. Influenza A accounted for 56% (52/93) of the detected viruses. Majority of positive cases (19/93; 20%) were from individuals <9 years and 20 to 35 years old categories. There was a significant difference in the proportion of influenza positive sample by month (χ2=67.9 p<0.05). Two peaks of infection were observed from March to May and from November to January. Four representative influenza isolates were sequenced and genetically characterized. The BLAST search showed that A/Tanzania/BMH1674/2019 isolate from Zanzibar had 99.86% nucleotide identity with Texas/109/2019 strain from Texas in United States. All of the three influenza B viruses from Zanzibar and Morogoro were 100% identical and belong to the influenza B victoria lineage. This study have revealed that influenza A virus was the most prevalent in 2019 and most of the isolates in our study are not independent evolution variants, as they shared high nucleotide similarity with characterized reference strains from the neighbouring countries and other part of the world.
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    Assessment of illegal bushmeat using high thoroughput molecular tools in transboundary villages bordering Serengeti ecosystem in Tarime District, Tanzania
    (Sokoine University of Agriculture, 2018) Kilwanila, S. I.
    Detection of illegal bush-meat in Africa has over the years relied on morphological identification technique, which is less effective due to post-hunting procedures. Therefore, the current study aimed at assessing bush-meat dynamics in trans-boundary areas of Tanzania and Kenya in the western part of Serengeti ecosystem. A cross-sectional design with two different methodologies was used. First, semi-structured questionnaires were administered to collect information on socio-demographic and other social factors leading to illegal bush-meat hunting, preference and consumption. Secondly, to augment the information obtained from the questionnaire, qPCR-HRM analysis was employed by using three different molecular markers 16s, Cytb and COI for molecular identification of assumed 138 collected sundried bush-meat samples. The results indicated that hunting occurs mostly in the dry season primarily using snares, and wildebeest was revealed to be the most hunted. Furthermore, young demonstrated high bush-meat consumption whereas immigrants showed high bush-meat preference. Likewise, highly educated young respondents indicated to have a high consumption and preference than less educated old respondents. Regarding molecular identification, 20 species were identified altogether, with zebra constituting the majority (n=51, 49.5%). It is recommended that high surveillance against poaching is needed by wildlife authorities during dry season; proper disposal of the unworthy wire cables by TANESCO; sensitization of both primary and secondary school students on legal harvesting of wildlife were made. Other recommendations focused on the need for proper execution of HRM procedures for bush- meat identification; and that for bush-meat samples to be accepted in court of law as exhibits should be analyzed using molecular procedures that proved to be reliable.