Controlled Human Malaria Infection in Semi-Immune Kenyan Adults (CHMI-SIKA): a study protocol to investigate in vivo Plasmodium falciparum malaria parasite growth in the context of pre-existing immunity [version 2; peer review: 2 approved]

Malaria remains a major public health burden despite approval for implementation of a partially effective pre-erythrocytic malaria vaccine. There is an urgent need to accelerate development of a more effective multi-stage vaccine. Adults in malaria endemic areas may have substantial immunity provided by responses to the blood stages of malaria parasites, but field trials conducted on several blood-stage vaccines have not shown high levels of efficacy. We will use the controlled human malaria infection (CHMI) models with malaria-exposed volunteers to identify correlations between immune responses and parasite growth rates in vivo. Immune responses more strongly associated with control of parasite growth should be prioritized to accelerate malaria vaccine development. We aim to recruit up to 200 healthy adult volunteers from areas of differing malaria transmission in Kenya, and after confirming their health status through clinical examination and routine haematology and biochemistry, we will comprehensively characterize immunity to malaria using >100 blood-stage antigens. We will administer 3,200 aseptic, purified, cryopreserved Plasmodium falciparum sporozoites (PfSPZ Challenge) by direct venous inoculation. Serial quantitative polymerase chain reaction to measure parasite growth rate in vivo will be undertaken. Clinical and laboratory monitoring will be undertaken to ensure volunteer safety. In addition, we will also explore the perceptions and experiences of volunteers and other stakeholders in participating in a malaria volunteer infection study. Serum, plasma, peripheral blood mononuclear cells and whole blood will be stored to allow a comprehensive assessment of adaptive and innate host immunity. We will use CHMI in semi-immune adult volunteers to relate parasite growth outcomes with antibody responses and other markers of host immunity. / Registration: ClinicalTrials.gov identifier NCT02739763

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

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Prevalence of Echinococcus granulosus in some selected sites of Ethiopia.

This study assesses the current prevalence status of Cystic echinococcosis in cattle and sheep and echinococcosis in dogs in Assela, Makale and Debre Zeit areas of Ethiopia. Our target areas represent three different agro-ecological zones in Ethiopia. Of the cattle studied the infected were, 17(13.4%) in Assela, 20(23.3%) in Makale, and 3(10%) in Debre Zeit haboured at least one fertile Hydatid cyst. Among the sheep, 23(59%) haboured fertile cysts and no goat was found to have fertile cysts. There was a significant difference in the percentage of infected sheep with fertile cysts from the same group of cattle originating from the three study areas. The percentage fertility of the total cysts examined were 4.2%, 6.8% and 5.5% in Assela, Makale and Debre Zeit respectively. Out of this 56.5% was from Assela, 65.4%, Makale and 66.7% from Debre Zeit were viable. From the sheep examined, 43.6% had fertile cysts with viability of 90.7%. The lung was the most affected organ in both species. A total of 44 dogs, 14 from Assela, 15 from Makale, and 15 from Debre Zeit were  examined for canine echinococcosis. The prevalence of the infection was 7(50%) in Assela, 3(20%) in Makale and 5(33.3%) in Debre Zeit. there was no significant difference between these prevalence rates although noticeable differences in the worm burdens among the three areas were observed.Keywords: Echinococcosis, Prevalence, Ethiopia

Hazard Analysis of Arid and Semi-Arid (ASAL) Regions of Kenya

Introduction: This paper describes a situation analysis on hazards in the Arid and semi-Arid lands of Kenya. The leading hazards affecting the Arid and semi-arid lands are mainly natural and include among others drought, floods, and landslides. Other hazards of importance were found to be war and conflict, HIV/AIDS and fires. Over 80% of these are weather related. Objectives: The overall objective of this study was to prioritize hazards in the ASAL region. Specifically, the study identified the top ten hazards in the ASAL Districts of Kenya, determined Probability of occurrence; Analyzed the potential impact of the hazard and utilizing multiplier effect prioritized the Hazards using a hypothetical model. Methodology: This was a descriptive study conducted in over half of the Kenya’s ASAL Districts in four regions of Lower and Upper Eastern, North Eastern and part of the Coast region. Six Districts were purposively selected per region with six officers from each District all totaling one hundred and forty four. The sectors where respondents were sourced from were Agriculture, Health, local Government, and Provincial Administration, Environment and NGO. The members through a consensus process analyzed hazards in groups of their respective districts using a tool that had been developed and respondents trained on its use. Results: One hundred and forty four (144) officers from Twenty four Districts in the four regions were recruited. One hundred twenty seven(81%) were male and only 27(19% )were female The representation of participants per sector was Governance 25% followed by Civil society organizations 21%, Health 16%, Agriculture and arid lands 15%, Research and scientific institutions 13%. The top Priority Hazards identified using the mean score were Drought and famine (5.4) Epidemics and epizootics (3.8), HIV/AIDS (3.6), War and conflict (2.5), Floods (2.5) Conclusions: The exercise confirmed the priority hazards in the Arid and semi-arid regions of Kenya and described vulnerability factors that included water scarcity, poverty and low educational levels. The region suffers from a variety of hazards in particular Drought and famine, Epidemics including HIV/AIDS and War and conflict. Environmental degradation though given a low score may be more of a perception. There is need to undertake a comprehensive hazard and Vulnerability analysis at regional and country level to inform interventions and other developmental activities. Women should be targeted at the community and leadership level, and efforts to empower them should be stepped up.Keywords: hazard, natural disaster, disaster risk, arid, Keny

Effectiveness of incinerators in the management of medical wastes in hospitals within Eldoret municipality

Introduction and Objectives Medical waste incinerators release into the air a host of pollutants that have serious adverse consequences on public health and the environment. This study aimed at determining the effectiveness of incinerators in Eldoret municipality in the management of medical wastes in relation to its maintenance and operation with an aim of giving recommendations towards reducing environmental pollution caused by emission of toxic pollutants and safeguarding the health of the incinerator operators as well as the surrounding communities.Methodology A cross sectional study was carried out at three health facilities in Eldoret Municipality namely Moi Teaching and Referral Hospital blood Bank Transfusion Centre, Elgon View and Eldoret hospitals. Questionnaires, researcher observation and laboratory investigations of ash samples were used in data collection. The questionnaires were administered to all the personnel operating the incinerators. The ash samples collected were analyzed using Atomic Absorption Spectroscopy.Results The results showed that the incinerators were operated in substandard conditions due to breakdown of the ignition starter, lack of pollution control equipment, and a low combustion temperature. Laboratory investigation of the ash showed that the levels of the heavy metals tested were high compared to the national and international standards. Forty percent (40%) of the interviewees were aware of the health risks they were exposed to and used protective clothing and equipment.Conclusions This study showed that the incinerators investigated are maintained and operated in substandard conditions. The ashes produced contain a wide range of toxic pollutants, including concentrated levels of a number of heavy metals. This poses serious environmental health and occupational safety hazard.Keywords: Incinerator, Medical wastes, Eldore

Taxonomic position and geographical distribution of the common sheep G1 and camel G6 strains of Echinococcus granulosus in three African countries.

International audienceThe taxonomic and phylogenetic status of Echinococcus granulosus strains are still controversial and under discussion. In the present study, we investigated the genetic polymorphism of E. granulosus isolates originating from three countries of Africa, including a region of Algeria, where the common G1 sheep and the camel G6 strains coexist sympatrically. Seventy-one hydatid cysts were collected from sheep, cattle, camels, and humans. Two mitochondrial markers (cox1 and nad1) were used for strain identification. Two nuclear markers (actII and hbx2) were used to study the possible occurrence of cross-fertilization. Despite the heterogeneity observed among the G1 isolates, they were all localized within one robust cluster. A second strong cluster was also observed containing all of the G6 isolates. Both strains appeared as two distinct groups, and no cases of interbreeding were found. Thus, the attribution of a species rank can be suggested. We also found the Tasmanian sheep G2 strain for the first time in Africa. Because of the slight variations observed between the common sheep and the Tasmanian sheep strains, further studies should be carried out to elucidate the epidemiological relevance of this genetic discrimination