Incidence of porcine circovirus type 2 and porcine parvoviruses in swine herds of some communities in Eastern Cape, South Africa
- Authors: Afolabi, Kayode Olayinka
- Date: 2018
- Subjects: Swine -- Diseases Swine -- South Africa -- Eastern Cape
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10353/9691 , vital:34820
- Description: Porcine circovirus type 2 (PCV2) is one of the swine pathogens of global economic importance. Since its first detection in early 1990s as the main etiologic agent of porcine multisystemic wasting syndrome (PMWS) and many other porcine circovirus-associated diseases (PCVAD), the virus has been extensively studied and has been found to be present in virtually all the pig producing countries of the world. As a viral pathogen that brings about clinical diseases aided by co-infecting pathogens, the involvement of many other viral agents including porcine parvoviruses (PPVs) have caught the attention of stakeholders worldwide. However, no surveillance study of the viral pathogens has been carried out in South Africa as there are little or no information on their prevalence in the swine herds of the country. This present study therefore aimed at detection and molecular characterization of PCV2 and PPVs in swine herds of some selected communities in Eastern Cape Province, South Africa. A total of 375 field samples were collected from seven commercial and communal farms from three District Municipalities of Eastern Cape, South Africa between 2015 and 2016. Structured questionnaires were also administered to each farm at the time of sample collection to obtain some important information relating to health status and farm management practices in the sampled farms. With the aid of conventional PCR method, 339 samples were initially screened for the presence of PCV2; positive amplicons were sequenced and obtained partial genomes of the virus were preliminarily analyzed. In order to obtain the complete genomes of the virus, four overlapping primer pairs were used to amplify the full-genome of PCV2 from the initial positive samples; amplified genomes were sequenced using the Sanger methods, sequenced PCV2 genomes were assembled and characterized. Furthermore, the prevalences of some designated PPVs in the sampled farms were obtained using 110 samples randomly selected from the previously archived samples and screened with 6 different primer pairs specific for the detection of 7 PPVs. All the amplified parvoviruses’ genomes were sequenced; their sequenced partial genomes were subsequently base-culled and analysed. The data obtained revealed that 54/339 (15.93 percent) samples from the swine herds were positive for PCV2; whereas the degree of occurrence of the viral pathogen as observed at farm level ranges from approximately 5.6 to 60 percent. The majority 15/17 (88 percent) of the analyzed partial sequences were found clustering with other PCV2b strains in the phylogenetic analysis. More interestingly, two other sequences obtained were also found clustering within PCV2d genotype in the initial screening and analysis. Furthermore, 15 complete PCV2 genomes were successfully amplified, sequenced and assembled. NJ and ML phylogenetic analysis of the complete ORF2 gene and full genomes unanimously showed 11 of the assembled genomes belonging to genotype PCV2b. Another 3 of the characterized sequences formed clade with other reference mutant PCV2b and PCV2b subtype 1C (PCV2d) strains from different parts of the world. The last sequence however, clustered with other reference strains belonging to PCV2 intermediate clade 2 (PCV2-IM2) recently identified in a global PCV2 strains phylogenetic analysis. Other genetic analyses including multiple sequence alignment and p-distance analysis also confirmed the outcomes of the phylogenetic analyses of the complete capsid gene and fullgenomes of the virus. On the other hand, the findings of the molecular profiling for PPVs showed that all the screened parvoviruses were present in the study area, having prevalence of 29.1 percent (PPV1), 21.8 percent (PPV2), 5.5 percent (PPV3), 43.6 percent (PPV4), 21.8 percent (PBo-likeV) and 44.6 percent for PBoV1 and PBoV2. Double infection of the screened PPVs was observed to be very rampant among the pigs as high as 20/110 (18.2 percent) for PPV2/PPV4 and PPV4/PBoV; followed by 19/110 (17.3 percent) of the samples for PPV1/PPV4 and PPV1/PBoV. Three of the viruses were found simultaneously in 19 of the screened samples representing 17.3 percent, whereas 8 (7.3 percent) samples were positive for four of the viruses. Phylogenetic analyses of PPV1, PPV2 and PBoVs 1 and 2 were conducted with two major clades homologous for each of them. This is the first report of PCV2 in swine herds of the Province and the first detection of PCV2b, PCV2d and PCV2-IM2 strains in South African swine herds. It follows the first reported case of PCV2a in an outbreak of porcine multisystemic wasting syndrome (PMWS) in Gauteng Province, South Africa over two decades ago. Also, this is the first major epidemiologic study on PPVs in the country following the initial case study of 1975. These findings confirmed the presence of the allimportant viral pathogens among pigs and also give preliminary insights into the possibility of co-infections of the pathogens in the studied area. This could however result in a serious large scale outbreak of devastating disease(s) associated with the viral pathogens, thereby ultimately resulting in huge economic losses if no appropriate measures are taken to effectively curb their spread across the country.
- Full Text:
- Authors: Afolabi, Kayode Olayinka
- Date: 2018
- Subjects: Swine -- Diseases Swine -- South Africa -- Eastern Cape
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10353/9691 , vital:34820
- Description: Porcine circovirus type 2 (PCV2) is one of the swine pathogens of global economic importance. Since its first detection in early 1990s as the main etiologic agent of porcine multisystemic wasting syndrome (PMWS) and many other porcine circovirus-associated diseases (PCVAD), the virus has been extensively studied and has been found to be present in virtually all the pig producing countries of the world. As a viral pathogen that brings about clinical diseases aided by co-infecting pathogens, the involvement of many other viral agents including porcine parvoviruses (PPVs) have caught the attention of stakeholders worldwide. However, no surveillance study of the viral pathogens has been carried out in South Africa as there are little or no information on their prevalence in the swine herds of the country. This present study therefore aimed at detection and molecular characterization of PCV2 and PPVs in swine herds of some selected communities in Eastern Cape Province, South Africa. A total of 375 field samples were collected from seven commercial and communal farms from three District Municipalities of Eastern Cape, South Africa between 2015 and 2016. Structured questionnaires were also administered to each farm at the time of sample collection to obtain some important information relating to health status and farm management practices in the sampled farms. With the aid of conventional PCR method, 339 samples were initially screened for the presence of PCV2; positive amplicons were sequenced and obtained partial genomes of the virus were preliminarily analyzed. In order to obtain the complete genomes of the virus, four overlapping primer pairs were used to amplify the full-genome of PCV2 from the initial positive samples; amplified genomes were sequenced using the Sanger methods, sequenced PCV2 genomes were assembled and characterized. Furthermore, the prevalences of some designated PPVs in the sampled farms were obtained using 110 samples randomly selected from the previously archived samples and screened with 6 different primer pairs specific for the detection of 7 PPVs. All the amplified parvoviruses’ genomes were sequenced; their sequenced partial genomes were subsequently base-culled and analysed. The data obtained revealed that 54/339 (15.93 percent) samples from the swine herds were positive for PCV2; whereas the degree of occurrence of the viral pathogen as observed at farm level ranges from approximately 5.6 to 60 percent. The majority 15/17 (88 percent) of the analyzed partial sequences were found clustering with other PCV2b strains in the phylogenetic analysis. More interestingly, two other sequences obtained were also found clustering within PCV2d genotype in the initial screening and analysis. Furthermore, 15 complete PCV2 genomes were successfully amplified, sequenced and assembled. NJ and ML phylogenetic analysis of the complete ORF2 gene and full genomes unanimously showed 11 of the assembled genomes belonging to genotype PCV2b. Another 3 of the characterized sequences formed clade with other reference mutant PCV2b and PCV2b subtype 1C (PCV2d) strains from different parts of the world. The last sequence however, clustered with other reference strains belonging to PCV2 intermediate clade 2 (PCV2-IM2) recently identified in a global PCV2 strains phylogenetic analysis. Other genetic analyses including multiple sequence alignment and p-distance analysis also confirmed the outcomes of the phylogenetic analyses of the complete capsid gene and fullgenomes of the virus. On the other hand, the findings of the molecular profiling for PPVs showed that all the screened parvoviruses were present in the study area, having prevalence of 29.1 percent (PPV1), 21.8 percent (PPV2), 5.5 percent (PPV3), 43.6 percent (PPV4), 21.8 percent (PBo-likeV) and 44.6 percent for PBoV1 and PBoV2. Double infection of the screened PPVs was observed to be very rampant among the pigs as high as 20/110 (18.2 percent) for PPV2/PPV4 and PPV4/PBoV; followed by 19/110 (17.3 percent) of the samples for PPV1/PPV4 and PPV1/PBoV. Three of the viruses were found simultaneously in 19 of the screened samples representing 17.3 percent, whereas 8 (7.3 percent) samples were positive for four of the viruses. Phylogenetic analyses of PPV1, PPV2 and PBoVs 1 and 2 were conducted with two major clades homologous for each of them. This is the first report of PCV2 in swine herds of the Province and the first detection of PCV2b, PCV2d and PCV2-IM2 strains in South African swine herds. It follows the first reported case of PCV2a in an outbreak of porcine multisystemic wasting syndrome (PMWS) in Gauteng Province, South Africa over two decades ago. Also, this is the first major epidemiologic study on PPVs in the country following the initial case study of 1975. These findings confirmed the presence of the allimportant viral pathogens among pigs and also give preliminary insights into the possibility of co-infections of the pathogens in the studied area. This could however result in a serious large scale outbreak of devastating disease(s) associated with the viral pathogens, thereby ultimately resulting in huge economic losses if no appropriate measures are taken to effectively curb their spread across the country.
- Full Text:
Community policing and partnership policing : a case study of shared responsibilities between the police and Alice community
- Authors: Manganyi, Foster Mzamani
- Date: 2017
- Subjects: Police-community relations -- South Africa -- Eastern Cape
- Language: English
- Type: Thesis , Masters , DPhil
- Identifier: http://hdl.handle.net/10353/8386 , vital:32558
- Description: The purpose of this study was to explore the shared responsibilities between the police and the community on crime prevention. Various authorities such as Sir Robert Peel (1829), Sower (1957), William and Kelling (1982), Roelofse (2007), to mention a few, had been advocating community policing as an essential component of democratic policing. In an attempt to understand the shared responsibilities between the police and the community, a thorough literature review had been presented in chapter two. Through the intertwined approach of secondary data, explorations had been noted on the shared responsibility between the police and the community. Literature and theoretical review had been presented in the thesis to clarify critical aspects of the topic. Triangulation approach was adopted for the purpose of this study. The researcher triangulated, methodologies, sampling methods, data collection methods as well as data analysis methods. Using qualitative approach in Phase A, data was collected through structured interview, observation and content analysis which was thematically presented. The quantitative data (Phase B) was collected through structured questionnaire. In case of codding and analysis SPSS was utilised. The findings of the study in chapter six shows the shared responsibilities between the police and the community exist within Alice. Moreover, the findings shows that there is a need for community empowerment on human rights and its applicability.
- Full Text:
- Authors: Manganyi, Foster Mzamani
- Date: 2017
- Subjects: Police-community relations -- South Africa -- Eastern Cape
- Language: English
- Type: Thesis , Masters , DPhil
- Identifier: http://hdl.handle.net/10353/8386 , vital:32558
- Description: The purpose of this study was to explore the shared responsibilities between the police and the community on crime prevention. Various authorities such as Sir Robert Peel (1829), Sower (1957), William and Kelling (1982), Roelofse (2007), to mention a few, had been advocating community policing as an essential component of democratic policing. In an attempt to understand the shared responsibilities between the police and the community, a thorough literature review had been presented in chapter two. Through the intertwined approach of secondary data, explorations had been noted on the shared responsibility between the police and the community. Literature and theoretical review had been presented in the thesis to clarify critical aspects of the topic. Triangulation approach was adopted for the purpose of this study. The researcher triangulated, methodologies, sampling methods, data collection methods as well as data analysis methods. Using qualitative approach in Phase A, data was collected through structured interview, observation and content analysis which was thematically presented. The quantitative data (Phase B) was collected through structured questionnaire. In case of codding and analysis SPSS was utilised. The findings of the study in chapter six shows the shared responsibilities between the police and the community exist within Alice. Moreover, the findings shows that there is a need for community empowerment on human rights and its applicability.
- Full Text:
The effects of Real Exchange Rate (RER) on the export competitiveness of South African fruit industry
- Authors: Peter, Bathathu
- Date: 2017
- Subjects: Foreign exchange rates -- South Africa Free trade -- South Africa
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10353/15732 , vital:40514
- Description: South Africa has diverse climatic conditions that allow it to grow and produce various fruit cultivars across the country. Limpopo, Western Cape, Mpumalanga, Eastern Cape, KwaZulu-Natal, and Northern Cape are South Africa’s main fruit production regions. In 2015, fruits ranked the 7th largest sector on exports and the largest in South Africa’s agricultural exports. South Africa’s major export partners for fruit in the same year were Netherlands, United Kingdom, Russian Federation, United Arab Emirate, and Hong Kong China. Correspondingly, exports to non-traditional markets such as India and China have increased rapidly. South Africa has prioritized exports as the engine for economic growth and job creation. The country has two major export destinations namely; the high income countries of Europe and North America, and the low-income markets of Africa, especially Southern African Customs Union (SADC) countries. South Africa’s Real Exchange Rates (RER) fluctuated widely since early 1970’s. This occurred after the collapse of the Bretton Woods system of fixed exchange rates in 1973. South Africa’s RER has been depreciating since then. Consequently, there has been a proliferation of debates on the relationship between the RER and exports performance. The most commonly held belief is that the RER depresses trade thereby increasing riskiness of trading activity. The South African fruit industry has been operating in the background of the depreciating RER. A high degree of RER volatility has posed a serious challenge to policy making environment because the magnitude of its impacts on trade flows is still unknown. The policy making environment becomes stagnant. Policy makers and researchers continue to examine the effects of RER on trade for an indefinite period. The South African fruit producers are unable to anticipate income earnings from trade due to increased risks associated with RER. South Africa’s agricultural sector encompasses the Historically Disadvantaged Individuals (HDI) which the country wants to prioritise and give them opportunities to participate in trade. The risks associated with the RER impair the development of the HDIs. The Thesis seeks to examine South Africa’s trade performance and the competitiveness of South African fruit industry as well as the effects of the RER. Specifically, the Thesis examines South Africa’s global fruit trade performance, explores the export competitiveness of South African fruit industry, and estimates the export demand equation for South African fruit exports to the world. The Thesis used the data obtained from the Department of Agriculture, Forestry and Fisheries (DAFF) for the period of 1080 to 2015 to estimate the export demand equation. The data from the International Trade Centre (ITC) for the period of 2001 to 2015 was used to examine South Africa’s global trade performance and competitiveness. The analytical framework followed incorporates the South Africa’s fruit Trade Performance Index (TPI) and the effects of RER on South African fruit industry. The TPI presents South Africa’s global fruit trade and its competitiveness using Trade Map, while the effects of RER are investigated on local fruit sales and on exports using the regression model. The Trade Map is the dominant trade analysis tool increasingly being used by the researchers and policy makers to make informed decisions on trade issues. The Thesis also made use of the Trade Map tools to examine South Africa’s global fruit trade performance and its competitiveness. The market analysis tools developed by the International Trade Centre (ITC) are: Trade Map, Market Access Map, Investment Map, Trade Competitiveness Map, Standard Map, and the Procurement Map. Trade Map, Trade Competitiveness Map, and the Market Access Map are used. Subsequently, the Thesis applied econometric techniques to examine the effects of RER on South Africa’s fruit exports and on fruit sales on local markets using the regression model. In this regard, the Thesis followed the export demand equation used by Todani and Munyama (2005). De Vita & Abbott (2004), and Tandra-Ragoobur & Emamdy (2011). Todani & Munyama (2005), to estimate the relationship between exchange rate volatility and South African export. Real exports and the exchange rate volatility were the main variables used in the model. The relative prices and the income of South Africa’s trading partner were also included in the model. The results show that South Africa was the 11th largest fruit exporter after Viet Nam and Spain in 2015. During the same year, the U.S. was the largest exporter of fruit with 14percent in the world, followed by Spain and Netherlands with 9percent and 6percent, respectively. The fruit industry ranked 8th largest exporter and the largest in agricultural sectors in 2015. Its exports totaled R 37 133 million in 2015, from R 30 566 million in 2014. South Africa’s total fruit exports accounted for a 33percent share on total agricultural exports and 4percent on South Africa’s total exports in 2015. The coefficients of the regression model were all statistically significant. Most importantly, an inverse relationship between the relative price and South Africa’s real fruit exports was established. Moreover, the RER had a significant negative effect on the South Africa’s fruit export competitiveness. This imposes more pain on the development of the HDIs in South Africa’s agricultural sector. South Africa has desire to move away from the export of raw materials and traditional export commodities and promote the export of value added products, including the agro processing products. Accordingly, this affects the entire value chain of the agricultural sector, since trade cannot be anticipated. On the basis of the regression results shown by the variables included in the model, the objectives of the study were accomplished. South Africa’s fruit exports are said to be more competitive to the European markets as a result of the weaker rand relative to other countries. The overview of South Africa’s fruit trade shows that South African fruit exports are more competitive across the globe. This is probably because the South Africa’s fruit exports for the top ten commodities are ranked almost the first five in the European markets and the first ten for the world. The results are supported by previous documented research, which emphasised that the weaker rand leads to more South African fruit produce being absorbed by the international markets. The evidence from the results shows that the RER stimulates the fruit export competitiveness.
- Full Text:
- Authors: Peter, Bathathu
- Date: 2017
- Subjects: Foreign exchange rates -- South Africa Free trade -- South Africa
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10353/15732 , vital:40514
- Description: South Africa has diverse climatic conditions that allow it to grow and produce various fruit cultivars across the country. Limpopo, Western Cape, Mpumalanga, Eastern Cape, KwaZulu-Natal, and Northern Cape are South Africa’s main fruit production regions. In 2015, fruits ranked the 7th largest sector on exports and the largest in South Africa’s agricultural exports. South Africa’s major export partners for fruit in the same year were Netherlands, United Kingdom, Russian Federation, United Arab Emirate, and Hong Kong China. Correspondingly, exports to non-traditional markets such as India and China have increased rapidly. South Africa has prioritized exports as the engine for economic growth and job creation. The country has two major export destinations namely; the high income countries of Europe and North America, and the low-income markets of Africa, especially Southern African Customs Union (SADC) countries. South Africa’s Real Exchange Rates (RER) fluctuated widely since early 1970’s. This occurred after the collapse of the Bretton Woods system of fixed exchange rates in 1973. South Africa’s RER has been depreciating since then. Consequently, there has been a proliferation of debates on the relationship between the RER and exports performance. The most commonly held belief is that the RER depresses trade thereby increasing riskiness of trading activity. The South African fruit industry has been operating in the background of the depreciating RER. A high degree of RER volatility has posed a serious challenge to policy making environment because the magnitude of its impacts on trade flows is still unknown. The policy making environment becomes stagnant. Policy makers and researchers continue to examine the effects of RER on trade for an indefinite period. The South African fruit producers are unable to anticipate income earnings from trade due to increased risks associated with RER. South Africa’s agricultural sector encompasses the Historically Disadvantaged Individuals (HDI) which the country wants to prioritise and give them opportunities to participate in trade. The risks associated with the RER impair the development of the HDIs. The Thesis seeks to examine South Africa’s trade performance and the competitiveness of South African fruit industry as well as the effects of the RER. Specifically, the Thesis examines South Africa’s global fruit trade performance, explores the export competitiveness of South African fruit industry, and estimates the export demand equation for South African fruit exports to the world. The Thesis used the data obtained from the Department of Agriculture, Forestry and Fisheries (DAFF) for the period of 1080 to 2015 to estimate the export demand equation. The data from the International Trade Centre (ITC) for the period of 2001 to 2015 was used to examine South Africa’s global trade performance and competitiveness. The analytical framework followed incorporates the South Africa’s fruit Trade Performance Index (TPI) and the effects of RER on South African fruit industry. The TPI presents South Africa’s global fruit trade and its competitiveness using Trade Map, while the effects of RER are investigated on local fruit sales and on exports using the regression model. The Trade Map is the dominant trade analysis tool increasingly being used by the researchers and policy makers to make informed decisions on trade issues. The Thesis also made use of the Trade Map tools to examine South Africa’s global fruit trade performance and its competitiveness. The market analysis tools developed by the International Trade Centre (ITC) are: Trade Map, Market Access Map, Investment Map, Trade Competitiveness Map, Standard Map, and the Procurement Map. Trade Map, Trade Competitiveness Map, and the Market Access Map are used. Subsequently, the Thesis applied econometric techniques to examine the effects of RER on South Africa’s fruit exports and on fruit sales on local markets using the regression model. In this regard, the Thesis followed the export demand equation used by Todani and Munyama (2005). De Vita & Abbott (2004), and Tandra-Ragoobur & Emamdy (2011). Todani & Munyama (2005), to estimate the relationship between exchange rate volatility and South African export. Real exports and the exchange rate volatility were the main variables used in the model. The relative prices and the income of South Africa’s trading partner were also included in the model. The results show that South Africa was the 11th largest fruit exporter after Viet Nam and Spain in 2015. During the same year, the U.S. was the largest exporter of fruit with 14percent in the world, followed by Spain and Netherlands with 9percent and 6percent, respectively. The fruit industry ranked 8th largest exporter and the largest in agricultural sectors in 2015. Its exports totaled R 37 133 million in 2015, from R 30 566 million in 2014. South Africa’s total fruit exports accounted for a 33percent share on total agricultural exports and 4percent on South Africa’s total exports in 2015. The coefficients of the regression model were all statistically significant. Most importantly, an inverse relationship between the relative price and South Africa’s real fruit exports was established. Moreover, the RER had a significant negative effect on the South Africa’s fruit export competitiveness. This imposes more pain on the development of the HDIs in South Africa’s agricultural sector. South Africa has desire to move away from the export of raw materials and traditional export commodities and promote the export of value added products, including the agro processing products. Accordingly, this affects the entire value chain of the agricultural sector, since trade cannot be anticipated. On the basis of the regression results shown by the variables included in the model, the objectives of the study were accomplished. South Africa’s fruit exports are said to be more competitive to the European markets as a result of the weaker rand relative to other countries. The overview of South Africa’s fruit trade shows that South African fruit exports are more competitive across the globe. This is probably because the South Africa’s fruit exports for the top ten commodities are ranked almost the first five in the European markets and the first ten for the world. The results are supported by previous documented research, which emphasised that the weaker rand leads to more South African fruit produce being absorbed by the international markets. The evidence from the results shows that the RER stimulates the fruit export competitiveness.
- Full Text:
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