Aboveground Net Primary Productivity in Grazed and Ungrazed pastures: Grazing Optimisation Hypothesis or Local Extinction of Vegetation Species

The controversy that has surrounded herbivory studies in the last few decades prompted our investigation to establish the extent to which herbivore optimisation hypothesis or compensatory growth evidence is real. We used the traditional movable cage method to collect primary productivity data on herbage, functional groups and key individual grass species in various controlled large herbivore treatments in an east African savanna. The herbivore treatments in triplicate blocks included cattle, wild herbivores with and without mega herbivores and combinations of cattle and wild herbivores also with and without mega herbivores. The findings revealed that at herbage level, most grazed treatments (four out of five) had higher productivity than the ungrazed control and three showed grazing optimisation curve at sixth polynomial degree between monthly productivity and grazing intensity (1-g/ng). At functional group level forbs productivity was higher in the ungrazed control than in any of the grazed treatments while at individual grass species level _Themeda triandra_ productivity was higher in all grazed treatments than in ungrazed control. We conclude against presence of herbivore optimisation hypothesis at herbage, functional group and species level because of lack of attributable grazing effect in grazed treatments that matches complex ecological effects in the ungrazed treatment

The roles of community seed banks in climate change adaption

Although community level seed-saving initiatives have been around for about 30 years, until recently they have received little attention in the scientific literature on climate change adaptation and plant genetic resources. Based on research experiences from various countries, this article argues that community seed banks can enhance the resilience of farmers, in particular of communities and households most affected by climate change. Community seed banks can secure improved access to, and availability of, diverse, locally adapted crops and varieties, and enhance related indigenous knowledge and skills in plant management, including seed selection, treatment, storage, multiplication, and distribution

Whole genome analysis of local Kenyan and global sequences unravels the epidemiological and molecular evolutionary dynamics of RSV genotype ON1 strains

The respiratory syncytial virus (RSV) group A variant with the 72-nucleotide duplication in the G gene, genotype ON1, was first detected in Kilifi in 2012 and has almost completely replaced previously circulating genotype GA2 strains. This replacement suggests some fitness advantage of ON1 over the GA2 viruses, and might be accompanied by important genomic substitutions in ON1 viruses. Close observation of such a new virus introduction over time provides an opportunity to better understand the transmission and evolutionary dynamics of the pathogen. We have generated and analyzed 184 RSV-A whole genome sequences (WGS) from Kilifi (Kenya) collected between 2011 and 2016, the first ON1 genomes from Africa and the largest collection globally from a single location. Phylogenetic analysis indicates that RSV-A transmission into this coastal Kenya location is characterized by multiple introductions of viral lineages from diverse origins but with varied success in local transmission. We identify signature amino acid substitutions between ON1 and GA2 viruses within genes encoding the surface proteins (G, F), polymerase (L) and matrix M2-1 proteins, some of which were identified as positively selected, and thereby provide an enhanced picture of RSV-A diversity. Furthermore, five of the eleven RSV open reading frames (ORF) (i.e. G, F, L, N and P), analyzed separately, formed distinct phylogenetic clusters for the two genotypes. This might suggest that coding regions outside of the most frequently studied G ORF play a role in the adaptation of RSV to host populations with the alternative possibility that some of the substitutions are nothing more than genetic hitchhikers. Our analysis provides insight into the epidemiological processes that define RSV spread, highlights the genetic substitutions that characterize emerging strains, and demonstrates the utility of large-scale WGS in molecular epidemiological studies

Cotrimoxazole prophylaxis impact on Cd4+ cells & infection reduction in HAART naïve HIV infected adults in our urban population, Kenya

Background: The study was undertaken to explore and generate information on the morbidity patterns in HAART Naïve HIV infected adults on oral Cotrimoxazole prophylaxis (CTXp) attending Mbagathi and Kenyatta National Hospitals, comprehensive care centres.Methods: A qualitative , retrospective study design of mixed methods was used which comprised; Clinical data extraction and Secondary data analysis of 450 personal medical records that existed and which met inclusion criteria based on age, baseline CD4+ cells ≥ 350 count, non-pregnant, absence of active TB and on  CTXp for duration of six months at the time of enrollment.Results: The study showed that patients in both Mbagathi district and Kenyatta National hospitals comprehensive care centres (CCC) had at baseline CD4+ cells range; 350-600 and later at 12 months CD4+ cells range; 400-1500. Patients of younger age, when given CTXp, had a consistent high CD4+ cells count (above 1000 CD4+ cells count) while those of older age had CD4+ levels that were fluctuating. The median age was 31 years. In over 50% documentation, common infections were frequent and patients treated with essential antimicrobial drugs. We observed that CTXp prophylaxis may have reduced severity of infections and this could also have supported up to 60% of the resolved infections. The self-reported adherence to CTXp was observed as part of quality monitored care.Conclusion: The findings of this study support work in a number of literature in other studies done outside Kenya on CTXp not associated with a worsened progression of HIV disease. Stockouts should be avoided due to public health implications. Further studies may be done to find out what potential CTXp has on HIV infected Kenyan patients with serious threat of bacterial infections in conjunction with the customized highly active antiretroviral therapy (HAART)

Access and benefit-sharing policies for climate-resilient seed systems.

The synthesis report is part of a series of papers on Integrated Seed Sector Development (ISSD) in Africa’s thematic working group on Matching national realities with global commitments. The thematic working group addressed the main question on how African governments implement their global commitments while fostering a viable pluralistic sector. The main hypothesis was that making these commitments more coherent with the practices and realities of farmers and creating an enabling environment for strengthening multiple seed systems will increase farmers’ access to quality seed. Three main topics were discussed under this theme: access and benefit sharing for climate resilient seed systems; national and regional seed laws that support the development of a robust, integrated seed sector that supports smallholder farmers' needs; and creating room for informal and intermediary seed systems in a UPOV '91 informed Plant Variety Protection system. This study provides an overview of climate related changes in past, present and future and the challenges to access to and exchange of genetic resources for climate change adaptation through different access and benefit sharing regimes in 4 countries – Zambia, Zimbabwe, Rwanda and Uganda. Findings from the studies indicate that most African countries face challenges in accessing required PGR for climate change adaptation because they do not have online accession-level documentation; they have not fully implemented international commitments related to ABS and national and regional seed laws hamper the flow of seeds and genetic resources. As a way forward the paper proposes capacity development for mutually supportive implementation of the ITPGRFA, Nagoya protocol and seed laws in ways which reflect the reality and diversity of different seed systems

Access and benefit sharing policies for climate resilient seed systems: matching global commitments with national realities.

This synthesis paper provides a summary of main findings on climate resilient seed systems and access and benefit sharing of case studies from Uganda, Rwanda, Zambia and Zimbabwe. This study analyses what is actually happening at the national and subnational levels in terms of climate change, its impacts on particular crops, what experiences countries have had to date in terms of accessing, using and sharing benefits derived from genetic resources for climate change adaptation, and what kinds of ABS policy initiatives or reforms could help those countries to make better use of genetic diversity for climate change adaptation in the future. This study is designed to analyze how these different ‘threads’ come together at national and subnational level in the four countries. Findings from these studies indicate that countries are already facing climate change which is affecting farmers and shaping their needs in terms of suitably adapted seed. As a result, the countries are embracing (inter and intra specific) crop diversification as a means to adapt to climate changes. This depends upon accessibility, availability and use of inter and intra specific crop genetic diversity from local, national and international sources. The proportion of PGRFA in the countries’ national genebanks that is potentially adaptable to that country’s changing climate is decreasing over time (as climates change more). National level research and the development of new varieties is also not sufficient to meet these demands. Countries are therefore becoming more interdependent. There are also significant constraints on ability to access, use and share benefits associated with materials in other countries as a result of the lack of on-line accession level documentation (and linked implementation of ITPGRFA and Nagoya Protocol) and lack of proper polices, legislation and guidelines on ABS. The study therefore recommends that international partnerships and programmes are important mechanisms for the exchanges of genetic resources into and out of the four countries for agricultural research and development especially at regional level and that the ITPGRFA and Nagoya Protocol are not self-executing agreements but need to be proactively implemented. In addition, considerable investment in capacity building is necessary for stakeholders – including farmers – to be able to exchange genetic resources in a way that makes seed systems more resilient

An intensive, active surveillance reveals continuous invasion and high diversity of rhinovirus in households

We report on infection patterns in 5 households (78 participants) delineating the natural history of human rhinovirus (HRV). Nasopharyngeal collections were obtained every 3–4 days irrespective of symptoms, over a 6-month period, with molecular screening for HRV and typing by sequencing VP4/VP2 junction. Overall, 311/3468 (8.9%) collections were HRV positive: 256 were classified into 3 species: 104 (40.6%) HRV-A; 14 (5.5%) HRV-B, and 138 (53.9%) HRV-C. Twenty-six known HRV types (13 HRV-A, 3 HRV-B, and 10 HRV-C) were identified (A75, C1, and C35 being most frequent). We observed continuous invasion and temporal clustering of HRV types in households (range 5–13 over 6 months). Intrahousehold transmission was independent of clinical status but influenced by age. Most (89.0%) of HRV infection episodes were limited to <14 days. Individual repeat infections were frequent (range 1–7 over 6 months), decreasing with age, and almost invariably heterotypic, indicative of lasting type-specific immunity and low cross-type protection

Epidemiological and evolutionary dynamics of influenza B virus in coastal Kenya as revealed by genomic analysis of strains sampled over a single season

The genomic epidemiology of influenza B virus (IBV) remains understudied in Africa despite significance to design of effective local and global control strategies. We undertook surveillance throughout 2016 in coastal Kenya, recruiting individuals presenting with acute respiratory illness at nine outpatient health facilities (any age) or admitted to the Kilifi County Hospital (&amp;lt;5-year-old). Whole genomes were sequenced for a select 111 positives; 94 (84.7%) of B/Victoria lineage and 17 (15.3%) of B/Yamagata lineage. Inter-Lineage reassortment was detected in 10 viruses; nine with B/Yamagata backbone but B/Victoria NA and NP segments and one with a B/Victoria backbone but B/Yamagata PB2, PB1, PA and MP segments. Five phylogenomic clusters were identified among the sequenced viruses; (i) pure B/Victoria clade 1A (n = 93, 83.8%), (ii) reassortant B/Victoria clade 1A (n = 1, 0.9%), (iii) pure B/Yamagata clade 2 (n = 2, 1.8%), (iv) pure B/Yamagata clade 3 (n = 6, 5.4%) and (v) reassortant B/Yamagata clade 3 (n = 9, 8.1%). Using divergence dates and clustering patterns in the presence of global background sequences, we counted up to 29 independent IBV strain introductions into the study area (∼900 km2) in 2016. Local viruses, including the reassortant B/Yamagata strains, clustered closely with viruses from neighbouring Tanzania and Uganda. Our study demonstrated that genomic analysis provides a clearer picture of locally circulating IBV diversity. The high number of IBV introductions highlights the challenge in controlling local influenza epidemics by targeted approaches e.g. sub-population vaccination or patient quarantine. The finding of divergent IBV strains co-circulating within a single season emphasizes why broad immunity vaccines are the most ideal for influenza control in Kenya