First COVID-19 Case in Zambia - Comparative phylogenomic analyses of SARS-CoV-2 detected in African countries

Since its first discovery in December 2019 in Wuhan, China, COVID-19, caused by the novel coronavirus SARS-CoV-2, has spread rapidly worldwide. Whilst African countries were relatively spared initially, the initial low incidence of COVID-19 cases was not sustained for long due to continuing travel links between China, Europe and Africa.. In preparation, Zambia had applied a multisectoral national epidemic disease surveillance and response system resulting in the identification of the first case within 48 hours of the individual entering the country by air travel from a trip to France. Contact tracing showed that SARS-CoV-2 infection was contained within the patient's household, with no further spread to attending health care workers or community members. Phylogenomic analysis of the patient's SARS-CoV-2 strain showed it belonged to lineage B.1.1., sharing the last common ancestor with SARS-CoV-2 strains recovered from South Africa. At the African continental level, our analysis showed that lineage B.1 and B.1.1 lineages appear to be predominant in Africa. Whole genome sequence analysis should be part of all surveillance and case detection activities in order to monitor the origin and evolution of SARS-CoV-2 lineages across Africa

Building an African Leptospirosis Network

Although leptospirosis is a disease of global importance, local context is crucial to formulating effective intervention strategies. Factors including reservoir host species, pathogen type, environmental, and social settings generate context-specific epidemiologies. Diverse climatic zones, agricultural systems, urbanization patterns, and cultural practices in Africa are likely to drive considerable variation in leptospirosis epidemiology. There is growing evidence of a substantial burden of human leptospirosis in Africa that is difficult to quantify in part due to lack of surveillance and clinical awareness of leptospirosis. Leptospirosis is therefore rarely considered as a differential diagnosis for acute febrile illness, and there is little access to diagnostic services for leptospirosis on the continent. In 2016, a virtual network was founded focussing on improving awareness and understanding leptospirosis in Africa. We currently have 40 members from academia, clinical practice, government and non-governmental agencies and others. Current members are based predominantly in institutions outside the continent but increasingly colleagues based in public health, laboratories, veterinary, and academic institutions within Africa are joining. We will share our experiences of developing this network, and our plans for capacity building through identifying and addressing knowledge gaps in our understanding of leptospirosis in Africa

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

Evaluation of formalin-fixed paraffin-embedded tissue samples as a source of sequence data for phylogenetic analysis of Rift Valley fever virus

Rift Valley fever (RVF), caused by an arthropod borne Phlebovirus in the family Bunyaviridae, is a haem-orrhagic disease that affects ruminants and humans. Due to the zoonotic nature of the virus, a biosafetylevel 3 laboratory is required for isolation of the virus. Fresh and frozen samples are the preferred sam-ple type for isolation and acquisition of sequence data. However, these samples are scarce in additionto posing a health risk to laboratory personnel. Archived formalin-fixed, paraffin-embedded (FFPE) tis-sue samples are safe and readily available, however FFPE derived RNA is in most cases degraded andcross-linked in peptide bonds and it is unknown whether the sample type would be suitable as referencematerial for retrospective phylogenetic studies. A RT-PCR assay targeting a 490 nt portion of the struc-tural GNglycoprotein encoding gene of the RVFV M-segment was applied to total RNA extracted fromarchived RVFV positive FFPE samples. Several attempts to obtain target amplicons were unsuccessful.FFPE samples were then analysed using next generation sequencing (NGS), i.e. Truseq®(Illumina) andsequenced on the Miseq®genome analyser (Illumina). Using reference mapping, gapped virus sequencedata of varying degrees of shallow depth was aligned to a reference sequence. However, the NGS did notyield long enough contigs that consistently covered the same genome regions in all samples to allowphylogenetic analysis

Influence de la fertilisation à base des déchets humains recyclés, des engrais minéraux et de leur combinaison sur le comportement de 3 variétés de maïs (Zea mays L.)

 Objectives: The use of municipal solid waste in urban agriculture is a common practice. Recycled human waste made with little or no mineral fertilizers and their effects on crops and soil has however been poorly understood. This work was initiated to evaluate the effects of the combined inputs of recycled human waste and mineral fertilizers on the yield of maize. Methodology and Results: The trial was installed following a factorial design with three replications. The effects of four doses of recycled human waste (0, 1.75, 3.5 and 7 t.ha-1) were evaluated on three varieties of maize (Babungo, Unilu and Katanga). The waste was made alone or with a mineral fertilizer supplements (0 kg, 300 kgNPK+ 200 kg urea ha-1, 150 kg NPK+100 kg urea ha-1). The Babungo variety gave the highest yield (6.6 t.ha-1) compared to the other two varieties who gave similar yields statistically (5.3 t.ha-1 for Katanga variety and 4.4 t.ha-1 for Unilu). Compared to the yield obtained on plots fertilized with human waste or mineral fertilizers alone, yields were increased on plots where the two fertilizers were combined. Conclusion and Application: The profitability of high doses of recycled human waste applied alone or combined with mineral fertilizers is comparable to that obtained with mineral fertilizers applied alone (profitable treatments). In contrast, the low dose of recycled human wastes applied only to give excellent profitability (Ration Value by Cost= 7.73). Katangese has a growing population, this leads to an increase in food needs along with high production of waste and effluents. Recycling of waste involved in environmental sanitation and the fight against poverty through increased yields.Keywords: maize; recycled human waste; yield; mineral fertilizer

Phytostabilisation of copper-contaminated soil in Katanga: an experiment with three native grasses and two amendments.

This study evaluates the feasibility of using the grass species Rendlia altera, Monocymbium ceresiiforme, Cynodon dactylon, and amendments (compost and lime) for the phytostabilisation of soils contaminated by Cu in the province of Katanga (Democratic Republic of Congo). Species were grown on control and Cu-contaminated plots (artificially contaminated with 2,500 mg kg-1 Cu) unamended (NA), amended with 4.5 kg compost m-2 or 0.2 kg lime m-2. R. altera was also grown on contaminated plots amended with 22.5 kg compost m-2 or 1 kg lime m-2. Plant survival, growth, and reproduction were monitored for two years. Cu-concentration in leaves of R. altera and M. ceresiiforme were analysed. pH and extractable Cu (0.01 M CaCl2) in soil were analysed in April 2007 and 2008. Results showed that R. altera seems to be the best candidate because of its highest survival on NA, followed by M. ceresiiforme, while liming was necessary to ensure survival of C. dactylon. Lime increased plant reproduction and reduced Cu accumulation in leaves compared to compost. However, higher survival and number of spikes of R. altera obtained in experiment 2 with 22.5 kg compost m-2 suggest that lime x compost interactions should be investigated in further studies. © Taylor & Francis Group, LLC.SCOPUS: ar.jinfo:eu-repo/semantics/publishe

What is the prevalence of COVID-19 detection by PCR among deceased individuals in Lusaka, Zambia? A postmortem surveillance study

Objectives To determine the prevalence of COVID-19 postmortem setting in Lusaka, Zambia.Design A systematic, postmortem prevalence study.Setting A busy, inner-city morgue in Lusaka.Participants We sampled a random subset of all decedents who transited the University Teaching Hospital morgue. We sampled the posterior nasopharynx of decedents using quantitative PCR. Prevalence was weighted to account for age-specific enrolment strategies.Interventions Not applicable—this was an observational study.Primary outcomes Prevalence of COVID-19 detections by PCR. Results were stratified by setting (facility vs community deaths), age, demographics and geography and time.Secondary outcomes Shifts in viral variants; causal inferences based on cycle threshold values and other features; antemortem testing rates.Results From 1118 decedents enrolled between January and June 2021, COVID-19 was detected among 32.0% (358/1116). Roughly four COVID-19+ community deaths occurred for every facility death. Antemortem testing occurred for 52.6% (302/574) of facility deaths but only 1.8% (10/544) of community deaths and overall, only ~10% of COVID-19+ deaths were identified in life. During peak transmission periods, COVID-19 was detected in ~90% of all deaths. We observed three waves of transmission that peaked in July 2020, January 2021 and ~June 2021: the AE.1 lineage and the Beta and Delta variants, respectively. PCR signals were strongest among those whose deaths were deemed ‘probably due to COVID-19’, and weakest among children, with an age-dependent increase in PCR signal intensity.Conclusions COVID-19 was common among deceased individuals in Lusaka. Antemortem testing was rarely done, and almost never for community deaths. Suspicion that COVID-19 was the cause of deaths was highest for those with a respiratory syndrome and lowest for individuals <19 years