Local Knowledge on the Changes in Vegetation Composition and Abundance in Rusinga Island, Homa Bay County, Kenya

Local communities have been coping with environmental dynamics since time immemorial, and they often possess considerable knowledge about environmental change, as well as mechanisms of coping with the consequences of such changes. Local knowledge on the changes in vegetation composition and abundance is therefore fundamental for the development of management strategies aimed at sustainable use and conservation of natural vegetation resources. Household interviews (n=150), Key informant interviews (n=30) and Focus group discussions (n=4) were used in this study to extract information on the communities’ perceptions on the status of vegetation in Rusinga Island of Homa Bay County of Kenya, and the suggested management strategies for the environment, particularly the vegetation resources for posterity. Rusinga Island is a biodiversity hotspot and an ancient historic area with numerous archeological sites that have given the World fossils dating back millions of years but the area has been experiencing downward trend in its ecosystems. Majority (86%) of the respondents reported having observed changes in vegetation composition and abundance in the study area. The changes were attributed to deforestation, high human population, overgrazing, inadequate rainfall, and soil erosion. Most (68%) of the respondents perceived the changes had occurred mainly in the forests/hills, in the entire Island (15.3%) and in the homesteads (2.7 %). To reverse the changes, the local community proposed tree planting, protection of existing trees, use of alternative sources of fuel, increased awareness creation on environmental conservation and controlled livestock grazing as the best strategies to reduce vegetation degradation. Besides sensitization and building capacity of the communities to engage in sustainable management of vegetation resources, land restoration interventions in the study area should target the plants species at risk through re-introduction and re-afforestation practices

Woody Plant Species Composition and Diversity in Rusinga Island, Homa Bay County, Kenya

Information on the state of woody vegetation of Rusinga Island is urgently needed in order to develop appropriate and effective conservation guidelines. Rusinga Island is an ancient historic area with numerous archeological sites and a bountiful of birdlife. However, the Island is characterized by highly degraded ecosystems from human disturbances such as cutting down of trees for fuel, construction poles, and overgrazing resulting in a remarkable degradation of flora, alteration of the ecosystems and loss of biodiversity. This study sought to determine the composition and diversity of woody plant species in Rusinga Island to understand the current status in order to develop appropriate and effective conservation measures since no such study has been conducted in the area before. Three hills (Ligongo, Agiro and Wanyama) were selected for sampling and demarcated into three study zones differentiated by the slope gradient and land use. A systematic random sampling approach was adopted to establish 98 sampling plots measuring 20 m x20 m (400m2) for recording tree species and subplots of 10 m by 10 m within the main plots for recording shrubs and lianas across the three study zones at an interval of 200m. A total of 63 woody plant species belonging to 32 families and 51 genera were recorded, out of which 66.7% were trees, 31.7% shrubs and 1.6% lianas. The upper zones had significantly higher species diversity, species richness, evenness and abundance compared to the middle and lower zones. The lower zones depicted a lower abundance of plants and least similarities of species compared to the middle and upper zones. Development of appropriate conservation and management strategies is required in order to protect the woody plant resources from unsustainable human activities and to improve the natural diversity of the Island

Whole Genome In-Silico Analysis of South African G1P[8] Rotavirus Strains before and after Vaccine Introduction over a Period of 14 Years

Rotavirus G1P[8] strains account for more than half of the group A rotavirus (RVA) infections in children under five years of age, globally. A total of 103 stool samples previously characterized as G1P[8] and collected seven years before and seven years after introducing the Rotarix® vaccine in South Africa were processed for whole-genome sequencing. All the strains analyzed had a Wa-like constellation (G1-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1). South African pre- and post-vaccine G1 strains were clustered in G1 lineage-I and II while the majority (84.2%) of the P[8] strains were grouped in P[8] lineage-III. Several amino acid sites across ten gene segments with the exception of VP7 were under positive selective pressure. Except for the N147D substitution in the antigenic site of eight post-vaccine G1 strains when compared to both Rotarix® and pre-vaccine strains, most of the amino acid substitutions in the antigenic regions of post-vaccine G1P[8] strains were already present during the pre-vaccine period. Therefore, Rotarix® did not appear to have an impact on the amino acid differences in the antigenic regions of South African post-vaccine G1P[8] strains. However, continued whole-genome surveillance of RVA strains to decipher genetic changes in the post-vaccine period remains imperative

HEALTH POLICIES IN KENYA AND THE NEW CONSTITUTION FOR VISION 2030

Abstract Promoting global health ensures progress in basic humanitarian values in saving and improving lives. In recent years, improving global health has proven its advanced value in promoting securit

Evolutionary changes between pre- and post- vaccine South African group A G2P[4] rotavirus strains, 2003-2017

The transient upsurge of G2P[4] group A rotavirus (RVA) after Rotarix vaccine introduction in several countries has been a matter of concern. To gain insight into the diversity and evolution of G2P[4] strains in South Africa pre- and post-RVA vaccination introduction, whole-genome sequencing was performed for RVA positive faecal specimens collected between 2003 and 2017 and samples previously sequenced were obtained from GenBank (n=103; 56 pre- and 47 post-vaccine). Pre-vaccine G2 sequences predominantly clustered within sub-lineage IVa-1. In contrast, post-vaccine G2 sequences clustered mainly within sub-lineage IVa-3, whereby a radical amino acid (AA) substitution, S15F, was observed between the two sub-lineages. Pre-vaccine P[4] sequences predominantly segregated within sub-lineage IVa while post-vaccine sequences clustered mostly within sub-lineage IVb, with a radical AA substitution R162G. Both S15F and R162G occurred outside recognised antigenic sites. The AA residue at position 15 is found within the signal sequence domain of Viral Protein 7 (VP7) involved in translocation of VP7 into endoplasmic reticulum during infection process. The 162 AA residue lies within the hemagglutination domain of Viral Protein 4 (VP4) engaged in interaction with sialic acid-containing structure during attachment to the target cell. Free energy change analysis on VP7 indicated accumulation of stable point mutations in both antigenic and non-antigenic regions. The segregation of South African G2P[4] strains into pre- and post-vaccination sub-lineages is likely due to erstwhile hypothesized stepwise lineage/sub-lineage evolution of G2P[4] strains rather than RVA vaccine introduction. Our findings reinforce the need for continuous whole-genome RVA surveillance and investigation of contribution of AA substitutions in understanding the dynamic G2P[4] epidemiology

Comparative whole genome analysis reveals re-emergence of human Wa-like and DS-1-like G3 rotaviruses after Rotarix vaccine introduction in Malawi

G3 rotaviruses rank among the most common rotavirus strains worldwide in humans and animals. However, despite a robust long-term rotavirus surveillance system from 1997 at Queen Elizabeth Central Hospital in Blantyre, Malawi, these strains were only detected from 1997 to 1999 and then disappeared and re-emerged in 2017, five years after the introduction of the Rotarix rotavirus vaccine. Here we analysed representative 27 whole genome sequences (G3P[4], n=20; G3P[6], n=1; and G3P[8], n=6) randomly selected each month between November 2017 and August 2019 to understand how G3 strains re-emerged in Malawi. We found four genotype constellations that were associated with the emergent G3 strains and co-circulated in Malawi post-Rotarix vaccine introduction: G3P[4] and G3P[6] strains with the DS-1-like genetic backbone genes (G3-P[4]-I2-R2-C2-M2-A2-N2-T2-E2-H2) and G3-P[6]-I2-R2-C2-M2-A2-N2-T2-E2-H2), G3P[8] strains with the Wa-like genetic backbone genes (G3-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1), and reassortant G3P[4] strains consisting of the DS-1-like genetic backbone genes and a Wa-like NSP2 (N1) gene (G3-P[4]-I2-R2-C2-M2-A2-N1-T2-E2-H2). Time-resolved phylogenetic trees demonstrated that the most recent common ancestor for each RNA segment of the emergent G3 strains was between 1996 and 2012, possibly through introductions from outside the country due to the limited genetic similarity with G3 strains which circulated before their disappearance in the late 1990s. Further genomic analysis revealed that the reassortant DS-1-like G3P[4] strains acquired a Wa-like NSP2 genome segment (N1 genotype) through intergenogroup reassortment; an artiodactyl-like VP3 through intergenogroup interspecies reassortment; and VP6, NSP1 and NSP4 segments through intragenogroup reassortment likely before importation into Malawi. Additionally, the emergent G3 strains contain amino acid substitutions within the antigenic regions of the VP4 proteins which could potentially impact the binding of rotavirus vaccine-induced antibodies. Altogether, our findings show that multiple strains with either Wa-like or DS-1-like genotype constellations have driven the re-emergence of G3 strains. The findings also highlight the role of human mobility and genome reassortment events in the cross-border dissemination and evolution of rotavirus strains in Malawi necessitating the need for long-term genomic surveillance of rotavirus in high disease burden settings to inform disease prevention and control

A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa

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The evolving SARS-CoV-2 epidemic in Africa: insights from rapidly expanding genomic surveillance

Investment in SARS-CoV-2 sequencing in Africa over the past year has led to a major increase in the number of sequences generated, now exceeding 100,000 genomes, used to track the pandemic on the continent. Our results show an increase in the number of African countries able to sequence domestically, and highlight that local sequencing enables faster turnaround time and more regular routine surveillance. Despite limitations of low testing proportions, findings from this genomic surveillance study underscore the heterogeneous nature of the pandemic and shed light on the distinct dispersal dynamics of Variants of Concern, particularly Alpha, Beta, Delta, and Omicron, on the continent. Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve, while the continent faces many emerging and re-emerging infectious disease threats. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century