Exploring the phylodynamics, genetic reassortment and RNA secondary structure formation patterns of orthomyxoviruses by comparative sequence analysis

RNA viruses are among the most virulent microorganisms that threaten the health of humans and livestock. Among the most socio-economically important of the known RNA viruses are those found in the family Orthomyxovirus. In this era of rapid low-cost genome sequencing and advancements in computational biology techniques, many previously difficult research questions relating to the molecular epidemiology and evolutionary dynamics of these viruses can now be answered with ease. Using sequence data together with associated meta-data, in chapter two of this dissertation I tested the hypothesis that the Influenza A/H1N1 2009 pandemic virus was introduced multiple times into Africa, and subsequently dispersed heterogeneously across the continent. I further tested to what degree factors such as road distances and air travel distances impacted the observed pattern of spread of this virus in Africa using a generalised linear modelbased approach. The results suggested that their were multiple simultaneous introductions of 2009 pandemic A/H1N1 into Africa, and geographical distance and human mobility through air travel played an important role towards dissemination. In chapter three, I set out to test two hypotheses: (1) that there is no difference in the frequency of reassortments among the segments that constitute influenza virus genomes; and (2) that there is epochal temporal reassortment among influenza viruses and that all geographical regions are equally likely sources of epidemiologically important influenza virus reassortant lineages. The findings suggested that surface segments are more frequently exchanges than internal genes and that North America/Asia, Oceania, and Asia could be the most likely source locations for reassortant Influenza A, B and C virus lineages respectively. In chapter four of this thesis, I explored the formation of RNA secondary structures within the genomes of orthomyxoviruses belonging to five genera: Influenza A, B and C, Infectious Salmon Anaemia Virus and Thogotovirus using in silico RNA folding predictions and additional molecular evolution and phylogenetic tests to show that structured regions may be biologically functional. The presence of some conserved structures across the five genera is likely a reflection of the biological importance of these structures, warranting further investigation regarding their role in the evolution and possible development of antiviral resistance. The studies herein demonstrate that pathogen genomics-based analytical approaches are useful both for understanding the mechanisms that drive the evolution and spread of rapidly evolving viral pathogens such as orthomyxoviruses, and for illuminating how these approaches could be leveraged to improve the management of these pathogens

Pathways out of Poverty in Western Kenya and the Role of Livestock

The objectives of the study were to obtain a better understanding of households' pathways into, and out of, poverty, with poverty defined from the communities' own perspective. The authors used a community-based methodology called the 'stages of progress' approach to assess household poverty dynamics in 20 communities and for over 1,700 households representing two different ethnic groups in Western Kenya. The proportion of households that had managed to escape poverty over the last 25 years was ascertained, as well as the proportion of households that had fallen into poverty during the same period. The major reasons for movements into or out of poverty were elicited at both the community and household-level, and in particular, the role that livestock play in the different pathways was examined. The results show considerable movement over the last 2½ decades by households in the study region both into and out of poverty, and the main reasons behind households' escape from poverty are completely different (i.e. not merely the opposite) from the reasons for descent into poverty, and hence have different policy implications in terms of what has been referred to as 'cargo net' versus 'safety net' interventions. Cargo nets help poor people climb out of poverty; safety nets stop people from falling into poverty. Redistributive programs to build up the assets of poor people (such as giving heifers to poor households) may be effective in achieving long-term reductions in chronic poverty, but will have to be complemented by safety net policies.Poverty, livestock, Western Kenya, Vihiga District, Siaya District, stages of progress, Food Security and Poverty, Livestock Production/Industries,

Socioeconomic and Environmental Impacts of the Fall Armyworm and The Striga Weed at Three Stages of the Maize (Corn) Value Chains in Kenya: A Review

Global food security faces increasing threats from climate change, leading to diseases, pests, drought, water salinity, and rising temperatures. The study broadly addresses global food security challenges, focusing on two pests. The purpose of the study was to assess the socioeconomic and environmental impacts of the fall armyworm and the Striga weed at three stages of maize (corn) value chains in Kenya. The methodology used encompassed a desk review of relevant research and current literature. The results indicated that the Fall Armyworm (FAW) and the Striga weed significantly impact maize (corn) production. The FAW and the Striga weed cause losses in yield, reduce the ability of agricultural lands to respond to shocks, and financially increase the cost of production resulting from the quest to deal with the pests mentioned above

Phylogenetic exploration of nosocomial transmission chains of 2009 influenza A/H1N1 among children admitted at Red Cross War Memorial Children's Hospital, Cape Town, South Africa in 2011

Traditional modes of investigating influenza nosocomial transmission have entailed a combination of confirmatory molecular diagnostic testing and epidemiological investigation. Common hospital-acquired infections like influenza require a discerning ability to distinguish between viral isolates to accurately identify patient transmission chains. We assessed whether influenza hemagglutinin sequence phylogenies can be used to enrich epidemiological data when investigating the extent of nosocomial transmission over a four-month period within a paediatric Hospital in Cape Town South Africa. Possible transmission chains/channels were initially determined through basic patient admission data combined with Maximum likelihood and time-scaled Bayesian phylogenetic analyses. These analyses suggested that most instances of potential hospital-acquired infections resulted from multiple introductions of Influenza A into the hospital, which included instances where virus hemagglutinin sequences were identical between different patients. Furthermore, a general inability to establish epidemiological transmission linkage of patients/viral isolates implied that identified isolates could have originated from asymptomatic hospital patients, visitors or hospital staff. In contrast, a traditional epidemiological investigation that used no viral phylogenetic analyses, based on patient co-admission into specific wards during a particular time-frame, suggested that multiple hospital acquired infection instances may have stemmed from a limited number of identifiable index viral isolates/patients. This traditional epidemiological analysis by itself could incorrectly suggest linkage between unrelated cases, underestimate the number of unique infections and may overlook the possible diffuse nature of hospital transmission, which was suggested by sequencing data to be caused by multiple unique introductions of influenza A isolates into individual hospital wards. We have demonstrated a functional role for viral sequence data in nosocomial transmission investigation through its ability to enrich traditional, non-molecular observational epidemiological investigation by teasing out possible transmission pathways and working toward more accurately enumerating the number of possible transmission events

STUDI TEMPORAL KOMUNITAS IKAN KARANG (2014-2018) PADA PERAIRAN KECAMATAN MESJID RAYA DAN PEUKAN BADA, KABUPATEN ACEH BESAR

Ikan karang merupakan ikan yang memanfaatkan ekosistem terumbu karang sebagai tempat tinggal, mencari makan, memijah dan pengasuhan. Penelitian ini bertujuan untuk mengetahui komunitas ikan karang melalui pendekatan kelimpahan, keanekaragaman, keseragaman dan dominansi ikan karang pada tahun 2014-2018 di perairan Kecamatan Mesjid Raya dan Peukan Bada, Kabupaten Aceh Besar. Penelitian ini dilaksanakan dari tahun 2014 hingga tahun 2018, dengan lokasi penelitian ada 8 lokasi. Pengambilan data ikan karang dilakukan dengan menggunakan metode underwater visual cencus (UVC). Total spesies ikan karang yang ditemukan selama tahun 2014 dan 2018 adalah sebanyak 115 spesies dari 39 famili. Perairan Kecamatan Mesjid Raya memiliki nilai kelimpahan ikan karang terendah sejumlah 128 ind/ha pada pengamatan tahun 2014 di perairan Lhok Mee dan kelimpahan ikan tertinggi sejumlah 796 ind/ha di perairan Benteng Inong Balee tahun 2017. Sedangkan perairan Kecamatan Peukan Bada memiliki kelimpahan ikan karang dengan nilai terendah sejumlah 96 ind/ha pada pengamatan tahun 2014 di perairan Lhok Mata Ie dan mencapai nilai tertinggi sejumlah 2401,70 ind/ha di perairan yang sama tahun 2018. Hasil rata-rata nilai indeks ekologi ikan karang di Kecamatan Mesjid Raya dan Peukan Bada tahun 2014-2018 tidak memiliki perbedaan yang signifikan.Reef fishes are the group of fish that have a high association with the coral reef ecosystem as spawning, nursery, and feeding grounds. This study aims to determine the reef fish community through the approach of abundance, diversity, uniformity, and dominance of reef fish in 2014-2018 in the waters of the Mesjid Raya Sub-district and Peukan Bada, Aceh Besar District. This research was carried out from 2014 to 2018, with research locations, there are 8 locations. Reef fish data collection was carried out using the underwater visual census (UVC). The total species of reef fish found during 2014-2018 were 115 species from 39 families. The waters of Mesjid Raya sub-district have the lowest abundance of reef fish with a number of 128 ind/ha in 2014 observations in Lhok Mee waters and the highest abundance of fish as much as 80 ind/ha in the waters of Fort Inong Balee in 2017. It is different from sub-district waters Peukan Bada has an abundance of reef fish with the lowest value of 96 ind/ha in 2014 observations in the waters of Lhok Mata Ie and reached the highest value of 2401.70 ind/ha in the same waters in 2018. Results of the average ecological index value Reef fish in the District of Mesjid Raya and Peukan Bada in 2014-2018 did not have a significant difference

Pathways out of poverty in western Kenya and the role of livestock

A community-based methodology called the ‘stages of progress’ approach was used to assess household poverty dynamics in 20 communities and for over 1,700 households representing two different ethnic groups in Western Kenya. The objectives of the study were to obtain a better understanding of households’ pathways into, and out of, poverty, with poverty defined from the communities’ own perspective. The proportion of households that have managed to escape poverty over the last 25 years was ascertained, as well as the proportion of households that have fallen into poverty during the same period. The major reasons for movements into or out of poverty were elicited at both the community and household-level, and in particular, the role that livestock play in the different pathways was examined.Ten communities in Vihiga District and ten in Siaya District were included in the study. Vihiga District (Western Province), with an extremely high population density of 886 persons per square km, has seen average farm sizes steadily declining to a current 0.5 ha. Poverty rates here are amongst the highest in Kenya, rising from 53 percent in 1994 to 58 percent in 1999. HIV prevalence rates rose from 12 percent in 1994 to 25 percent in 2000. In Siaya District (Nyanza Province), with a lower population density of 316 persons per square km, 47 percent of the population fell below the rural poverty line in 1994, increasing to 64 percent in 1999. While average farm sizes are higher in Siaya, most of them are located on lower potential agricultural land than that found in Vihiga. Most of Siaya’s population depends on small-scale agriculture (mainly subsistence crop farming), local businesses, livestock production and fishing. Siaya has the highest levels of HIV prevalence and HIVrelated sickness and death rates in Kenya, rising from 14 percent in 1994 to 27 percent in 2000. Key to the approach used was to define with the participating communities a common understanding of poverty. What, for example, does an extremely poor household do when a little bit of money becomes available to the household? Which expenses are usually the first to be incurred? As a little more money flows in, what does this household do in the second stage? The third stage? And so on. Discussions of these questions provoked lively debate among assembled villagers followed by high levels of consensus as to the successive stages of household progress from acute poverty to economic self-reliance. Most interesting was the broad agreement across nearly all villages on the sequence of these stages. The results show that households, as they climb out of poverty, typically first acquire food, then (in the following order) clothes, shelter, primary education for their children, and small animals including chickens, sheep and goats. Beyond these initial stages of progress, households are no longer considered poor. A remarkably similar understanding of poverty exists within the different villages and across the two main ethnic groups found in Vihiga and Siaya Districts of western Kenya. In almost all the villages, purchasing local cattle came in the first stage beyond the poverty threshold drawn by the villagers. Community members were then asked to describe each current household in the village in terms of whether they were above or below that poverty line 25 years ago (a full generation) and today. The Pathways out of Poverty in Western Kenya and the Role of Livestock 2 reasons why particular households had moved into or out of poverty were discussed at the community-level and followed up in more detail with individual households. The field researchers conducting this study received considerable facilitation training towards delving in detail into the reasons, many of which are ‘nested’ or linked, for household movements into and out of poverty. The results show considerable movement over the last 2½ decades by households in this region both into and out of poverty, and the main reasons behind households’ escape from poverty are completely different (i.e. not merely the opposite) from the reasons for descent into poverty, and hence have different policy implications. In Vihiga District, 27 percent of households managed to escape from poverty in the last 25 years, while 11 percent fell into poverty at the same time. In Siaya District, only 8 percent of households managed to climb out of poverty, while 29 percent became impoverished during the same period. A similar set of reasons for these movements, while varying slightly from village to village, was found to be broadly shared among all the study villages. Most households (73 percent) in both districts that escaped poverty over the last 25 years did so because they diversified their income sources when a household member obtained a job in the urban formal or informal sector. Over 80 percent of these jobs (accounting for a total of 61 percent of successful escapes) were found within the private sector. Of the households that escaped poverty, a major reason for 57 percent of those that did so was by diversifying on-farm income through cash crop production. These households were able to produce and consistently sell either surplus food crops (sorghum, maize, bananas) or cash crops (tea, sugarcane, rice). In 42 percent of the cases, households that had escaped poverty diversified their on-farm incomes through livestock, ranging from poultry to dairy animals. Diversification of income sources through livestock farming emerged as a particularly important strategy for escaping poverty in Vihiga District. Poor health and health-related expenses were the principal reasons overwhelmingly cited as responsible for households declining into poverty in both Districts (cited by 73 percent of households that had fallen into poverty). Following these were heavy funeral expenses, particularly the slaughter of a household’s livestock assets, mentioned in 63 percent of the cases. Over half of households cited low levels of education within the household as another critical factor in explaining why they became poor. The striking importance of health and health-related problems and expenses in poverty status is also seen in India and in other areas of western Kenya and Tanzania. The devastating loss of livestock assets due to funerals is also found in other African countries such as Madagascar and Zambia. And the critical importance of non-farm income diversification in pathways out of poverty has been highlighted in many other studies across Africa. The findings of this study have implications in terms of what has been referred to as ‘cargo net’ versus ‘safety net’ interventions. Cargo nets help poor people climb out of poverty; safety nets stop people from falling into poverty. Redistributive programs to build up the assets of poor people (such as giving heifers to poor households) may be effective in achieving long-term reductions in chronic poverty, but will have to be complemented by safety net policies. The results of the study suggest that the most important safety nets required by poor households in western Kenya are those that help protect the health and improve the education of community members. This study has highlighted the key role that livestock play in both pathways into and out of poverty. On-farm diversification of income sources away from a sole reliance on crops through investment in chickens, sheep, goats and/or cattle helped many of the households in the study escape poverty. Given that investment in large animal stock is typically beyond the means of the poorest households, this finding suggests that projects that provide a heifer or a loan to buy a sheep or goat, for example, could provide a one-time transfer sufficiently substantial to help households lift themselves out of poverty. Such livestock acquisitions, however, must be accompanied by policies and interventions that reduce the risks associated with keeping farm animals alive and productive in Pathways out of Poverty in Western Kenya and the Role of Livestock 3 harsh environments. And without safety net strategies aimed at the huge health and education constraints facing these communities, livestock-related investment strategies may well fail. To open up opportunities for poor households to benefit from livestock even more than they do now, problems of poor roads and market infrastructure, widespread insecurity and high and multiple animal disease risks will have to be addressed. The potential for dairy enterprises in particular would be much larger if some of these risks were lowered. These are areas where local, regional and national authorities have an obvious role to play. Improving access to appropriate information regarding livestock management and disease strategies is an area where research organisations can help

A laminated polymer film formulation for enteric delivery of live vaccine and probiotic bacteria

Live bacterial cells (LBC) are administered orally as attenuated vaccines, to deliver biopharmaceutical agents, and as probiotics to improve gastrointestinal health. However, LBC present unique formulation challenges and must survive gastrointestinal antimicrobial defenses including gastric acid after administration. We present a simple new formulation concept, termed Polymer Film Laminate (PFL). LBC are ambient dried onto cast acid-resistant enteric polymer films that are then laminated together to produce a solid oral dosage form. LBC of a model live bacterial vaccine and a probiotic were dried directly onto a cast film of enteric polymer. The effectiveness at protecting dried cells in a simulated gastric fluid (pH 2.0) depended on the composition of enteric polymer film used, with a blend of ethylcellulose plus Eudragit L100 55 providing greater protection from acid than Eudragit alone. However, although PFL made from blended polymers films completely released low molecular weight dye into intestinal conditions (pH 7.0), they failed to release LBC. In contrast, PFL made from Eudragit alone successfully protected dried probiotic or vaccine LBC from simulated gastric fluid for 2h, and subsequently released all viable cells within 60min of transfer into simulated intestinal fluid. Release kinetics could be controlled by modifying the lamination method

Whole genome phylogenetic investigation of a West Nile virus strain isolated from a tick sampled from livestock in north eastern Kenya

BACKGROUND:West Nile virus (WNV) has a wide geographical distribution and has been associated to cause neurological disease in humans and horses. Mosquitoes are the traditional vectors for WNV; however, the virus has also been isolated from tick species in North Africa and Europe which could be a means of introduction and spread of the virus over long distances through migratory birds. Although WNV has been isolated in mosquitoes in Kenya, paucity of genetic and pathogenicity data exists. We previously reported the isolation of WNV from ticks collected from livestock and wildlife in Ijara District of Kenya, a hotspot for arbovirus activity. Here we report the full genome sequence and phylogenetic investigation of their origin and relation to strains from other regions. METHODS: A total of 10,488 ticks were sampled from animal hosts, classified to species and processed in pools of up to eight ticks per pool. Virus screening was performed by cell culture, RT-PCR and sequencing. Phylogenetic analysis was carried out to determine the evolutionary relationships of our isolate. RESULTS: Among other viruses, WNV was isolated from a pool of Rhipicephalus pulchellus sampled from cattle, sequenced and submitted to GenBank (Accession number: KC243146). Comparative analysis with 27 different strains revealed that our isolate belongs to lineage 1 and clustered relatively closely to isolates from North Africa and Europe, Russia and the United States. Overall, Bayesian analysis based on nucleotide sequences showed that lineage 1 strains including the Kenyan strain had diverged 200years ago from lineage 2 strains of southern Africa. Ijara strain collected from a tick sampled on livestock was closest to another Kenyan strain and had diverged 20years ago from strains detected in Morocco and Europe and 30years ago from strains identified in the USA. CONCLUSION: To our knowledge, this is the first characterized WNV strain isolated from R. pulchellus. The epidemiological role of this tick in WNV transmission and dissemination remains equivocal but presents tick verses mosquito virus transmission has been neglected. Genetic data of this strain suggest that lineage 1 strains from Africa could be dispersed through tick vectors by wild migratory birds to Europe and beyond