Honey bee population worldwide is dwindling due to a number of interrelated factors among them pa... more Honey bee population worldwide is dwindling due to a number of interrelated factors among them pathogens such as viruses, bacteria, fungi and metazoan parasites. These factors negatively affect agricultural production as well as the apiculture industry which is dependent on a seasonal abundance of honey bees year-round. As a result, food security and livelihood is compromised due to loss of pollinators. Majority of viruses infecting honey bees are positive-sense single-stranded RNA viruses of the order Picornavirales. The economically important viruses of bees in this order belong to family Dicistroviridae and Iflaviridae. Paenibacillus larvae and Melisococcus plutonius are bacteria known to cause bee brood diseases. This study aimed at identifying the viruses circulating in Kenyan honey bee colonies using next generation sequencing. Ribonucleic acid (RNA) was extracted from sixteen libraries and was used in cDNA synthesis using superscript II. The cDNA converted to dsDNA using Klenow reaction and used in amplification. 454 pyro sequencing was performed on genome sequencer FLX system. The resultant single reads were analyzed using CLC Genomic workbench. The reads were mapped on the full genomes of the identified viruses and then de novo assembled. The resultant contigs were interrogated using basic alignment search tool (BLAST) on national center for biotechnology information (NCBI) database. The contigs were exported to MEGA6 and used in phylogenetic analysis. The viruses identified belonged to family Iflaviridae and included deformed wing virus, Kakugo virus and Varroa destructor virus-1. Melissococcus plutonius and Enterococcus faecalis were also detected. Of the sixteen libraries sequenced, two libraries; Busia_adult and Siaya_brood reported the incidences of iflaviruses while five libraries had reads matching with M. plutonius and E. faecalis. There is need for a strategy in place for the management of bee diseases to enhance bee health and quality of hive products.
Key words: Bee viruses, Paenibacillus larvae, Melissococcus plutonius, Iflavirus, Next generation sequencing R Skilton2, S Muya3, G Michuki2, S Kabochi1, H Kutima3 and M Kasina4
Description: List of Bird Species captured in Tana River County, Kenya. Title: Frequency table of... more Description: List of Bird Species captured in Tana River County, Kenya. Title: Frequency table of sampled bird species. (DOCX 18 kb)
Confirmation of the presence of Aphid lethal paralysis virus (ALPV) and a Big Sioux River-like vi... more Confirmation of the presence of Aphid lethal paralysis virus (ALPV) and a Big Sioux River-like virus. (PDF 1.5 MB)
RT-PCR confirmation of Rhopalosiphum padi virus in maize samples collected from Kitui County. (PD... more RT-PCR confirmation of Rhopalosiphum padi virus in maize samples collected from Kitui County. (PDF 84 kb)
A summary of the C. imicola markers designed to the flanking regions of the microsatellite repeat... more A summary of the C. imicola markers designed to the flanking regions of the microsatellite repeats with the type of repeats. The table provides a list of a total of 169 primer pairs predicted to anneal to a unique single pair read. The motif type that the primer represents is also indicated (XLS 41 kb)
A table of estimates of genetic diversity of the microsatellite markers per population. The table... more A table of estimates of genetic diversity of the microsatellite markers per population. The table describes the genetic diversity of the markers. Significant Hardy-Weinberg equilibrium (P
Mosquito ecology is influenced by wetness in the environment. In 2011-2014, a rise in waters of L... more Mosquito ecology is influenced by wetness in the environment. In 2011-2014, a rise in waters of Lake Baringo resulted in unprecedented flooding that inundated over 88km of the shoreline. A longitudinal study carried out from October 2012-October 2013 assessed mosquito abundance and diversity in two habitats. A total of 386,624 mosquitoes were captured, 89% from flooded shoreline and 11% from swampy habitat. Family Culicinae constituted 10 genera. Mansonia dominated the catches with 98% from flooded shoreline and swampy habitat 2%. Genetic sequences of Aedes albopictus species was identified and reported for the first time in the basin. Diversity index was higher in swampy habitat (Simpson Diversity Index=0.56), compared to flooded shoreline (Simpson diversity index =0.13). Future recurring floods will result in drastic changes of the ecology and could lead to emergence and reemergence of more species.
Mosquitoes’ ecology and associated arboviruses are heavily influenced by precipitation and retent... more Mosquitoes’ ecology and associated arboviruses are heavily influenced by precipitation and retention of water in the environment. In 2011 and 2014, unprecedented floods occurred in the Lake Baringo basin inundating approximately 88 km2 of the shoreline land. This caused abrupt environmental changes raising fears of an outbreak of Rift Valley Fever (RVF) disease. This study was carried out to determine the situation of RVF disease in livestock from diverse habitats during the extreme unprecedented flooding phenomenon that occurred in the Lake Baringo basin, in 2012-2013. Blood was drawn from the ear vein of livestock selected randomly from the three study areas (lakeshore land, swamp marshy, and dry rangeland habitats). Mosquitoes were trapped using CDC light traps and identified morphologically. From a total of 77 blood samples, eight were positive for RVF virus (RVFV) representing an overall infection of 12%. RVF prevalence from livestock residents in flooded lakeshore land habitat...
Rift Valley fever (RVF) is a re-emerging zoonotic disease responsible for major losses in livesto... more Rift Valley fever (RVF) is a re-emerging zoonotic disease responsible for major losses in livestock production, with negative impact on the livelihoods of both commercial and resource-poor farmers in sub-Sahara African countries. The disease remains a threat in countries where its mosquito vectors thrives. Outbreaks of RVF usually follow weather conditions which favour increase in mosquito populations. Such outbreaks are usually cyclical, occurring every 10-15 years. Recent outbreaks of the disease in South Africa have occurred unpredictably and with increased frequency. In 2008 outbreaks were reported in Mpumalanga, Limpopo and Gauteng provinces, followed by a 2009 outbreak in KwaZulu-Natal, Mpumalanga and Northern Cape provinces and in 2010 in the Eastern Cape, Northern Cape, Western Cape, North West, Free State and Mpumalanga provinces. By August 2010, 232 confirmed infections had been reported in humans, with 26 confirmed deaths. To investigate the evolutionary dynamics of RVF v...
Aphids are major vectors of plant viruses. Common bean (Phaseolus vulgaris L.) and maize (Zea may... more Aphids are major vectors of plant viruses. Common bean (Phaseolus vulgaris L.) and maize (Zea mays L.) are important crops that are vulnerable to aphid herbivory and aphid-transmitted viruses. In East and Central Africa, common bean is frequently intercropped by smallholder farmers to provide fixed nitrogen for cultivation of starch crops such as maize. We used a PCR-based technique to identify aphids prevalent in smallholder bean farms and next generation sequencing shotgun metagenomics to examine the diversity of viruses present in aphids and in maize leaf samples. Samples were collected from farms in Kenya in a range of agro-ecological zones. Cytochrome oxidase 1 (CO1) gene sequencing showed that Aphis fabae was the sole aphid species present in bean plots in the farms visited. Sequencing of total RNA from aphids using the Illumina platform detected three dicistroviruses. Maize leaf RNA was also analysed. Identification of Aphid lethal paralysis virus (ALPV), Rhopalosiphum padi v...
Water is essential for sustainable development. in Kenya, 43% of the population does not have acc... more Water is essential for sustainable development. in Kenya, 43% of the population does not have access to clean water. to fetch water, women are sometimes required to walk long distances using jerry cans. use of the jerry can has been associated with musculoskeletal pains and microbial contaminations. the water backpack has been designed as a suitable alternative to the use of jerry cans. this study was conducted to assess the extent of proper utilisation of the backpacks previously distributed in Embu, machakos, Kilifi (Watamu) and Kiambu (limuru) counties of Kenya. observation and structured questionnaires were used to collect data. study participants consisted of 403 volunteers selected randomly from the study locations. data was analysed using r?? and descriptive statistics were used to present the data. from the study, 86% of all study participants demonstrated proper usage of the water backpack. in addition there was a significant association between the use of the backpack and various water treatment methods. in machakos and Kilifi counties, over 67% reported a marked reduction of musculoskeletal pains associated with use of the water backpack. in conclusion, there was strong evidence of many health and related benefits associated with proper usage of the water backpacks in the counties. IntroductIon Water is life and it is at the core of any development. it is a finite resource under a growing pressure of demand. according to united nations Water development report 2015 (WWap, 2015), 748 million people today still do not have access to an improved source of drinking water. this situation is bound to get worse since the demand for water in manufacturing is expected to increase by 400 per cent between 2000 and 2050 globally. in africa, only 5% of potential water resources are developed. there are a myriad of challenges with access to water in africa as articulated at the 9th african union general assembly of the african ministers council of Water (amcoW) in 2014. these include water infrastructure deficit, protection of the sanctity of the water sources and resources, water governance and management systems, water supply and distribution, financing and a lack of knowledge, and water information (WWap, 2015). for instance, compared to north america’s average per capita water storage of 6,000 m3, africa has measly average per capita water storage of 200 m3. poor water and sanitation facilities in africa have resulted in waterborne illnesses. for instance, diarrhea is the third biggest killer of children under five in sub-saharan africa. in Kenya, 43% of the population has no access to clean water (marshall, 2011). the water scarcity in Kenya has been attributed to global warming (leading to years of recurrent droughts), challenges with water management, low investment in the water sector, contamination of available water resources and an increase in demand for water due to the population growth and industrialisation. ISSN 2206-1991 Volume 2 No 2 2017 https://doi.org/10.21139/wej.2017.020 Water transport and storage using a water backpack
Honey bee population worldwide is dwindling due to a number of interrelated factors among them pa... more Honey bee population worldwide is dwindling due to a number of interrelated factors among them pathogens such as viruses, bacteria, fungi and metazoan parasites. These factors negatively affect agricultural production as well as the apiculture industry which is dependent on a seasonal abundance of honey bees year-round. As a result, food security and livelihood is compromised due to loss of pollinators. Majority of viruses infecting honey bees are positive-sense single-stranded RNA viruses of the order Picornavirales. The economically important viruses of bees in this order belong to family Dicistroviridae and Iflaviridae. Paenibacillus larvae and Melisococcus plutonius are bacteria known to cause bee brood diseases. This study aimed at identifying the viruses circulating in Kenyan honey bee colonies using next generation sequencing. Ribonucleic acid (RNA) was extracted from sixteen libraries and was used in cDNA synthesis using superscript II. The cDNA converted to dsDNA using Klenow reaction and used in amplification. 454 pyro sequencing was performed on genome sequencer FLX system. The resultant single reads were analyzed using CLC Genomic workbench. The reads were mapped on the full genomes of the identified viruses and then de novo assembled. The resultant contigs were interrogated using basic alignment search tool (BLAST) on national center for biotechnology information (NCBI) database. The contigs were exported to MEGA6 and used in phylogenetic analysis. The viruses identified belonged to family Iflaviridae and included deformed wing virus, Kakugo virus and Varroa destructor virus-1. Melissococcus plutonius and Enterococcus faecalis were also detected. Of the sixteen libraries sequenced, two libraries; Busia_adult and Siaya_brood reported the incidences of iflaviruses while five libraries had reads matching with M. plutonius and E. faecalis. There is need for a strategy in place for the management of bee diseases to enhance bee health and quality of hive products.
Key words: Bee viruses, Paenibacillus larvae, Melissococcus plutonius, Iflavirus, Next generation sequencing R Skilton2, S Muya3, G Michuki2, S Kabochi1, H Kutima3 and M Kasina4
Description: List of Bird Species captured in Tana River County, Kenya. Title: Frequency table of... more Description: List of Bird Species captured in Tana River County, Kenya. Title: Frequency table of sampled bird species. (DOCX 18 kb)
Confirmation of the presence of Aphid lethal paralysis virus (ALPV) and a Big Sioux River-like vi... more Confirmation of the presence of Aphid lethal paralysis virus (ALPV) and a Big Sioux River-like virus. (PDF 1.5 MB)
RT-PCR confirmation of Rhopalosiphum padi virus in maize samples collected from Kitui County. (PD... more RT-PCR confirmation of Rhopalosiphum padi virus in maize samples collected from Kitui County. (PDF 84 kb)
A summary of the C. imicola markers designed to the flanking regions of the microsatellite repeat... more A summary of the C. imicola markers designed to the flanking regions of the microsatellite repeats with the type of repeats. The table provides a list of a total of 169 primer pairs predicted to anneal to a unique single pair read. The motif type that the primer represents is also indicated (XLS 41 kb)
A table of estimates of genetic diversity of the microsatellite markers per population. The table... more A table of estimates of genetic diversity of the microsatellite markers per population. The table describes the genetic diversity of the markers. Significant Hardy-Weinberg equilibrium (P
Mosquito ecology is influenced by wetness in the environment. In 2011-2014, a rise in waters of L... more Mosquito ecology is influenced by wetness in the environment. In 2011-2014, a rise in waters of Lake Baringo resulted in unprecedented flooding that inundated over 88km of the shoreline. A longitudinal study carried out from October 2012-October 2013 assessed mosquito abundance and diversity in two habitats. A total of 386,624 mosquitoes were captured, 89% from flooded shoreline and 11% from swampy habitat. Family Culicinae constituted 10 genera. Mansonia dominated the catches with 98% from flooded shoreline and swampy habitat 2%. Genetic sequences of Aedes albopictus species was identified and reported for the first time in the basin. Diversity index was higher in swampy habitat (Simpson Diversity Index=0.56), compared to flooded shoreline (Simpson diversity index =0.13). Future recurring floods will result in drastic changes of the ecology and could lead to emergence and reemergence of more species.
Mosquitoes’ ecology and associated arboviruses are heavily influenced by precipitation and retent... more Mosquitoes’ ecology and associated arboviruses are heavily influenced by precipitation and retention of water in the environment. In 2011 and 2014, unprecedented floods occurred in the Lake Baringo basin inundating approximately 88 km2 of the shoreline land. This caused abrupt environmental changes raising fears of an outbreak of Rift Valley Fever (RVF) disease. This study was carried out to determine the situation of RVF disease in livestock from diverse habitats during the extreme unprecedented flooding phenomenon that occurred in the Lake Baringo basin, in 2012-2013. Blood was drawn from the ear vein of livestock selected randomly from the three study areas (lakeshore land, swamp marshy, and dry rangeland habitats). Mosquitoes were trapped using CDC light traps and identified morphologically. From a total of 77 blood samples, eight were positive for RVF virus (RVFV) representing an overall infection of 12%. RVF prevalence from livestock residents in flooded lakeshore land habitat...
Rift Valley fever (RVF) is a re-emerging zoonotic disease responsible for major losses in livesto... more Rift Valley fever (RVF) is a re-emerging zoonotic disease responsible for major losses in livestock production, with negative impact on the livelihoods of both commercial and resource-poor farmers in sub-Sahara African countries. The disease remains a threat in countries where its mosquito vectors thrives. Outbreaks of RVF usually follow weather conditions which favour increase in mosquito populations. Such outbreaks are usually cyclical, occurring every 10-15 years. Recent outbreaks of the disease in South Africa have occurred unpredictably and with increased frequency. In 2008 outbreaks were reported in Mpumalanga, Limpopo and Gauteng provinces, followed by a 2009 outbreak in KwaZulu-Natal, Mpumalanga and Northern Cape provinces and in 2010 in the Eastern Cape, Northern Cape, Western Cape, North West, Free State and Mpumalanga provinces. By August 2010, 232 confirmed infections had been reported in humans, with 26 confirmed deaths. To investigate the evolutionary dynamics of RVF v...
Aphids are major vectors of plant viruses. Common bean (Phaseolus vulgaris L.) and maize (Zea may... more Aphids are major vectors of plant viruses. Common bean (Phaseolus vulgaris L.) and maize (Zea mays L.) are important crops that are vulnerable to aphid herbivory and aphid-transmitted viruses. In East and Central Africa, common bean is frequently intercropped by smallholder farmers to provide fixed nitrogen for cultivation of starch crops such as maize. We used a PCR-based technique to identify aphids prevalent in smallholder bean farms and next generation sequencing shotgun metagenomics to examine the diversity of viruses present in aphids and in maize leaf samples. Samples were collected from farms in Kenya in a range of agro-ecological zones. Cytochrome oxidase 1 (CO1) gene sequencing showed that Aphis fabae was the sole aphid species present in bean plots in the farms visited. Sequencing of total RNA from aphids using the Illumina platform detected three dicistroviruses. Maize leaf RNA was also analysed. Identification of Aphid lethal paralysis virus (ALPV), Rhopalosiphum padi v...
Water is essential for sustainable development. in Kenya, 43% of the population does not have acc... more Water is essential for sustainable development. in Kenya, 43% of the population does not have access to clean water. to fetch water, women are sometimes required to walk long distances using jerry cans. use of the jerry can has been associated with musculoskeletal pains and microbial contaminations. the water backpack has been designed as a suitable alternative to the use of jerry cans. this study was conducted to assess the extent of proper utilisation of the backpacks previously distributed in Embu, machakos, Kilifi (Watamu) and Kiambu (limuru) counties of Kenya. observation and structured questionnaires were used to collect data. study participants consisted of 403 volunteers selected randomly from the study locations. data was analysed using r?? and descriptive statistics were used to present the data. from the study, 86% of all study participants demonstrated proper usage of the water backpack. in addition there was a significant association between the use of the backpack and various water treatment methods. in machakos and Kilifi counties, over 67% reported a marked reduction of musculoskeletal pains associated with use of the water backpack. in conclusion, there was strong evidence of many health and related benefits associated with proper usage of the water backpacks in the counties. IntroductIon Water is life and it is at the core of any development. it is a finite resource under a growing pressure of demand. according to united nations Water development report 2015 (WWap, 2015), 748 million people today still do not have access to an improved source of drinking water. this situation is bound to get worse since the demand for water in manufacturing is expected to increase by 400 per cent between 2000 and 2050 globally. in africa, only 5% of potential water resources are developed. there are a myriad of challenges with access to water in africa as articulated at the 9th african union general assembly of the african ministers council of Water (amcoW) in 2014. these include water infrastructure deficit, protection of the sanctity of the water sources and resources, water governance and management systems, water supply and distribution, financing and a lack of knowledge, and water information (WWap, 2015). for instance, compared to north america’s average per capita water storage of 6,000 m3, africa has measly average per capita water storage of 200 m3. poor water and sanitation facilities in africa have resulted in waterborne illnesses. for instance, diarrhea is the third biggest killer of children under five in sub-saharan africa. in Kenya, 43% of the population has no access to clean water (marshall, 2011). the water scarcity in Kenya has been attributed to global warming (leading to years of recurrent droughts), challenges with water management, low investment in the water sector, contamination of available water resources and an increase in demand for water due to the population growth and industrialisation. ISSN 2206-1991 Volume 2 No 2 2017 https://doi.org/10.21139/wej.2017.020 Water transport and storage using a water backpack
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Conference Presentations by George Michuki
Key words: Bee viruses, Paenibacillus larvae, Melissococcus plutonius, Iflavirus, Next generation sequencing
R Skilton2, S Muya3, G Michuki2, S Kabochi1, H Kutima3 and M Kasina4
Papers by George Michuki
Key words: Bee viruses, Paenibacillus larvae, Melissococcus plutonius, Iflavirus, Next generation sequencing
R Skilton2, S Muya3, G Michuki2, S Kabochi1, H Kutima3 and M Kasina4