The role of environmental, structural and anthropogenic variables on underpass use by African savanna elephants (Loxodonta africana) in the Tsavo Conservation Area

Wildlife crossing structures are effective interventions for mitigating fragmentation of habitats by linear infrastructure. The 2017 construction of a new railway cutting through the Tsavo Con- servation Area (TCA), home to the largest elephant population in Kenya, affected wildlife movement and habitat connectivity. Although numerous studies have investigated the use of wildlife crossing structures by a wide range of species, few have focused on their use by mega- herbivores. In this study, we examined use of 41 wildlife crossing structures by African savanna elephants (Loxodonta africana) along a 133 km section of new railway in Tsavo, Kenya. We used a generalized linear mixed modeling approach to assess the relationship between elephant crossing rate over 28 months between July 2017 to April 2021 and explanatory factors including crossing structure attributes, livestock presence and proximity to highways, water points and human settlement. We found that structural attributes of crossing structures were most strongly associ- ated with the elephant crossing rate, particularly height and its interaction with type of crossing structure (bridges, wildlife underpasses and culverts). Higher crossing structures were associated with higher crossing rate, with the largest influence of height at culverts and wildlife underpasses. Although bridges comprised only 19.5 % of the 41 available crossing structures, they accounted for a disproportionately high number of elephants crossing events (56 %). The results demon- strated the importance of bridges over designated crossing structures for elephants, with pre- dicted seasonal counts of elephant crossings being 0.31 for average sized culverts, 2.88 for wildlife underpasses and 5.86 for bridges. The environmental and anthropogenic variables were not strongly associated with elephant crossing rate. Our findings have direct application for future siting and design of crossing structures across elephant rang

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