Regulation of a small, discrete African elephant population through immunocontraception in the Makalali Conservancy, Limpopo, South Africa

Populations of the African elephant, Loxodonta africana, are growing rapidly in southern Africa, to the extent that population control has become essential. The management option of translocation is no longer realistically available, whilst culling has become ethically unacceptable, especially to the general public. Previous immunocontraception trials on elephants with Porcine Zona Pellucida (PZP) vaccine demonstrated that it is safe, effective, reversible, remotely deliverable, and has had no evident adverse side effects. We demonstrate effective contraceptive management of a discrete, small population of free-roaming elephants in the Makalali Conservancy, Limpopo province, South Africa. Complete reproductive control has been demonstrated in all 18 original targeted females, who have by now passed the population's average intercalving interval of 56 months without giving birth. A zero population growth rate has been maintained within this target group since August 2002. On the basis of this small sample over a short period, immunocontraception should be considered a viable means of population management as an alternative to long-term culling strategies in small populations.The Humane Society of the United States (HSUS), the National Research Foundation and Amarula.http://www.sajs.co.zahj2024Centre for Veterinary Wildlife StudiesSDG-03:Good heatlh and well-beingSDG-15:Life on lan

Risk factors for Coronavirus Disease 2019 (COVID-19) death in a population cohort study from the Western Cape Province, South Africa

BACKGROUND. Risk factors for coronavirus disease 2019 (COVID-19) death in sub-Saharan Africa and the effects of human immunodeficiency virus (HIV) and tuberculosis on COVID-19 outcomes are unknown. METHODS. We conducted a population cohort study using linked data from adults attending public-sector health facilities in the Western Cape, South Africa. We used Cox proportional hazards models, adjusted for age, sex, location, and comorbidities, to examine the associations between HIV, tuberculosis, and COVID-19 death from 1 March to 9 June 2020 among (1) public-sector “active patients” (≥1 visit in the 3 years before March 2020); (2) laboratory-diagnosed COVID-19 cases; and (3) hospitalized COVID-19 cases. We calculated the standardized mortality ratio (SMR) for COVID-19, comparing adults living with and without HIV using modeled population estimates. RESULTS. Among 3 460 932 patients (16% living with HIV), 22 308 were diagnosed with COVID-19, of whom 625 died. COVID- 19 death was associated with male sex, increasing age, diabetes, hypertension, and chronic kidney disease. HIV was associated with COVID-19 mortality (adjusted hazard ratio [aHR], 2.14; 95% confidence interval [CI], 1.70–2.70), with similar risks across strata of viral loads and immunosuppression. Current and previous diagnoses of tuberculosis were associated with COVID-19 death (aHR, 2.70 [95% CI, 1.81–4.04] and 1.51 [95% CI, 1.18–1.93], respectively). The SMR for COVID-19 death associated with HIV was 2.39 (95% CI, 1.96–2.86); population attributable fraction 8.5% (95% CI, 6.1–11.1). CONCLUSIONS. While our findings may overestimate HIV- and tuberculosis-associated COVID-19 mortality risks due to residual confounding, both living with HIV and having current tuberculosis were independently associated with increased COVID-19 mortality. The associations between age, sex, and other comorbidities and COVID-19 mortality were similar to those in other settings.The Western Cape Provincial Health Data Centre from the Western Cape Department of Health, the US National Institutes for Health (grant numbers R01 HD0804, the Bill and Melinda Gates Foundation, the United States Agency for International Development and the Wellcome Trust.https://academic.oup.com/cid/am2023Veterinary Tropical Disease

MinION 16S datasets of a commercially available microbial community enables the evaluation of DNA extractions and data analyses

New advances in sequencing technology and bioinformatics analysis tools have significantly supported the culture-independent analysis of complex microbial communities associated with environmental, plant, animal and human samples. However, previous work has shown that DNA extraction can have a major influence in the community profile. As such there is a constant need for new methods to efficiently and rapidly prepare and analyze DNA for microbiome research, especially in the case new and emerging technology like the Oxford Nanopore Technologies (ONT) MinION. A commercial standard was used, in triplicate, to evaluate three DNA extraction protocols, including two commercially available and one ”in-house” DNA extraction method. All DNA extractions were done as per manufacturer's instructions and prepared with the same commercial ONT 16S sample preparation kit, prior to being analysed using MinION sequencing. Eight MinION 16S datasets of this microbial reference community were obtained. Reads were initially base called and demultiplexed using ONT's Guppy™ sequencing software (version 3.2.4), filtered using NanoFilt and then classified using Usearch. A set of R scripts are presented to process sintax files generated from Usearch and produce an OTU table that can be used for further analyses. All datasets were deposited into the SRA (NCBI) database. These datasets will allow future extraction kit comparisons using MinION sequencing since a standardize laboratory process using commercially available components, such as the MinION 16S sample preparation kit, microbial reference community and extraction kits, were used. The current ONT 16S workflow making use of the Epi2me agent only provides QC metrics and the ID's of the main genera identified and does not provide any tools currently for further downstream community comparison. The analyses scripts provided in the supplementary material will thus further enable the testing of new datasets against these reference sets and provide users the ability to compare their workflows with ours, thus standardizing comparisons and workflows