Genetic and potential antigenic evolution of influenza A(H1N1)pdm09 viruses circulating in Kenya during 2009-2018 influenza seasons

Influenza viruses undergo rapid evolutionary changes, which requires continuous surveillance to monitor for genetic and potential antigenic changes in circulating viruses that can guide control and prevention decision making. We sequenced and phylogenetically analyzed A(H1N1)pdm09 virus genome sequences obtained from specimens collected from hospitalized patients of all ages with or without pneumonia between 2009 and 2018 from seven sentinel surveillance sites across Kenya. We compared these sequences with recommended vaccine strains during the study period to infer genetic and potential antigenic changes in circulating viruses and associations of clinical outcome. We generated and analyzed a total of 383 A(H1N1)pdm09 virus genome sequences. Phylogenetic analyses of HA protein revealed that multiple genetic groups (clades, subclades, and subgroups) of A(H1N1)pdm09 virus circulated in Kenya over the study period; these evolved away from their vaccine strain, forming clades 7 and 6, subclades 6C, 6B, and 6B.1, and subgroups 6B.1A and 6B.1A1 through acquisition of additional substitutions. Several amino acid substitutions among circulating viruses were associated with continued evolution of the viruses, especially in antigenic epitopes and receptor binding sites (RBS) of circulating viruses. Disease severity declined with an increase in age among children aged < 5 years. Our study highlights the necessity of timely genomic surveillance to monitor the evolutionary changes of influenza viruses. Routine influenza surveillance with broad geographic representation and whole genome sequencing capacity to inform on prioritization of antigenic analysis and the severity of circulating strains are critical to improved selection of influenza strains for inclusion in vaccines

Natural selection on cork oak: allele frequency reveals divergent selection in cork oak populations along a temperature cline

A recent study of population divergence at neutral markers and adaptive traits in cork oak has observed an association between genetic distances at locus QpZAG46 and genetic distances for leaf size and growth. In that study it was proposed that certain loci could be linked to genes encoding for adaptive traits in cork oak and, thus, could be used in adaptation studies. In order to investigate this hypothesis, here we (1) looked for associations between molecular markers and a set of adaptive traits in cork oak, and (2) explored the effects of the climate on among-population patterns in adaptive traits and molecular markers. For this purpose, we chose 9-year-old plants originating from thirteen populations spanning a broad range of climatic conditions. Plants established in a common garden site were genotyped at six nuclear microsatellites and phenotypically characterized for six functional traits potentially related to plant performance. Our results supported the proposed linkage between locus QpZAG46 and genes encoding for leaf size and growth. Temperature caused adaptive population divergence in leaf size and growth, which was expressed as differences in the frequencies of the alleles at locus QpZAG46

Valorizing the 'Irulas' traditional knowledge of medicinal plants in the Kodiakkarai Reserve Forest, India

A mounting body of critical research is raising the credibility of Traditional Knowledge (TK) in scientific studies. These studies have gained credibility because their claims are supported by methods that are repeatable and provide data for quantitative analyses that can be used to assess confidence in the results. The theoretical importance of our study is to test consensus (reliability/replicable) of TK within one ancient culture; the Irulas of the Kodiakkarai Reserve Forest (KRF), India. We calculated relative frequency (RF) and consensus factor (Fic) of TK from 120 Irulas informants knowledgeable of medicinal plants. Our research indicates a high consensus of the Irulas TK concerning medicinal plants. The Irulas revealed a diversity of plants that have medicinal and nutritional utility in their culture and specific ethnotaxa used to treat a variety of illnesses and promote general good health in their communities. Throughout history aboriginal people have been the custodians of bio-diversity and have sustained healthy life-styles in an environmentally sustainable manner. However this knowledge has not been transferred to modern society. We suggest this may be due to the asymmetry between scientific and TK, which demands a new approach that considers the assemblage of TK and scientific knowledge. A greater understanding of TK is beginning to emerge based on our research with both the Irulas and Malasars; they believe that a healthy lifestyle is founded on a healthy environment. These aboriginal groups chose to share this knowledge with society-at-large in order to promote a global lifestyle of health and environmental sustainability

Urban agriculture, dietary diversity and child health in a sample of Tanzanian town folk

Undernutrition and micronutrient deficiency continue to be two of the major health burdens in less developed economies. In this study, we explore the link between urban agriculture, dietary diversity and child health, using weight-for-age and height-for-age Z-scores. The study makes use of two rounds of observational data for urban Tanzania and employs an instrumental variables estimation approach. We show that practising urban agriculture leads to the consumption of a greater variety of food items and the health status of urban children living in households practising urban agriculture significantly improves in the short and, more importantly, long term

The effect of economic crisis on youth precariousness in Nairobi - An analysis of itinerary to adulthood of three generations of men and women

Depuis l’analyse pionnière sur le marché de l’emploi menée par le BIT au début des années 1970, le NUrIP, qui a recueilli près de 1.600 biographies auprès d’un échantillon de la population adulte de Nairobi, est la première opération à offrir une vue globale de l’emploi et de la situation sociodémographique à Nairobi. Les analyses dressent l’image d’une surprenante stabilité du processus d’entrée dans la vie adulte à Nairobi. Le calendrier des évènements reste le même et le retard peut être expliqué essentiellement par la crise économique des années 1990. La ville de Nairobi joue d’abord et avant tout le rôle du principal marché de l’emploi formel au Kenya. Cette caractéristique, qui remonte aux temps coloniaux, influence considérablement le modèle de migration circulaire entre la ville et l’intérieur du pays, ainsi que la formation des ménages et la constitution de la famille. Alors que l’emploi est clairement la clé d’entrée dans la vie adulte pour les hommes, il joue un rôle marginal pour les femmes. Cela peut expliquer pourquoi le marché de l’emploi de Nairobi a réagi à la crise des années 1990 en rejetant les femmes. Les différences de genre sont plus frappantes que les différences entre générations et selon l’origine géographique ou sociale. Les discriminations envers les femmes sur le marché de l’emploi de Nairobi sont à considérer sérieusement comme une cause du déclin du taux d’activité des femmes.Since the pioneer analysis of the labour market by the ILO team in the early 1970s, the NUrIP, which collected about 1,600 biographies among a sample of the Nairobi adult population, is the first to provide for a comprehensive view of the social, demographic and employment situation of Nairobi. The analyses draw a picture of surprising stability of the process of entry into adult life in Nairobi. The timing of events remains the same and most of the delay experienced by the younger generation can be attributed to the economic crisis of the 90s. The city of Nairobi is first and foremost the main formal labour market in Kenya. This characteristic that traces back into colonial time vastly influences the model of circular migration between the hinterland and the city and also the household and family formation. Whereas employment is clearly the key to entry into adult life for men, it plays a marginal role for women. That might explain why the Nairobi labour market reacted to the economic crisis of the 90s by rejecting females. Gender differences are more striking than differences by generation or by social or geographical origin. Discrimination against women on the Nairobi labour market should be seriously considered as an explanation for their declining labour participation.ou

Urban Integration in Africa. A Socio-Economic Survey of Nairobi

Nairobi is the main door to the East African market and a safe haven for most international firms and organizations, yet it nurtures so much poverty. Part of the explanation is embedded in the social history of today’s citizens of Nairobi. This book is based on the collection of almost 1600 biographies of men and women aged 25-54. A team composed of researchers from the University of Nairobi and the French Institute for Research in Africa analysed how the Nairobi city-dwellers entered the labour market, had access to independent residence and form their families since the 1960s, and the factors that influence timing of these main paths to adulthood. The results show that men’s entry into adulthood is conditioned on employment, whereas women did not emancipate from their role of mother and spouse. Socio-cultural origins and migration status play a minor role in urban integration while education and gender are crucial. The formal economy declined since the 1980s, not as much to the benefit of informal enterprises as to the expense of the protection of employees. At the same time, youth unemployment increased while women’s labour force participation decreased. The resulting poverty makes it harder for couples to form and sustain a family. This book is an important resource to sociologist, demographers, economists, urban planners and historians who want to know more about urban way of life in Africa.