Turnaround times – the Achilles’ heel of community screening and testing in Cape Town, South Africa: A short report

Porter JD, Mash R, Preiser W. Turnaround times – the Achilles’ heel of community screening and testing in Cape Town, South Africa: A short report. Afr J Prm Health Care Fam Med. 2020;12(1), a2624. https://doi.org/10.4102/phcfm.v12i1.2624The original publication is available at http://www.phcfm.orgAfrican Journal of Primary Health Care & Family MedicineEarly in the course of the coronavirus infection disease 2019 (COVID-19) pandemic in South Africa, the Department of Health implemented a policy of community screening and testing (CST). This was based on a community-orientated primary care approach and was a key strategy in limiting the spread of the pandemic, but it struggled with long turnaround times (TATs) for the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) reverse transcriptase polymerase chain reaction test. The local experience at Symphony Way Community Day Centre (Delft, Cape Town), highlighted these challenges. The first positive tests had a median TAT of 4.5 days, peaking at 29 days in mid-May 2020. Issues that contributed to long TATs were unavailability of viral transport medium, sample delivery and storage difficulties, staffing problems, scarcity of testing supplies and other samples prioritised over CST samples. At Symphony Way, many patients who tested COVID-19 positive had abandoned their self-isolation because of the delay in results. Employers were unhappy with prolonged sick leave whilst waiting for results and patients were concerned about not getting paid or job loss. The CST policy relies on a rapid TAT to be successful. Once the TAT is delayed, the process of contacting patients, and tracing and quarantining contacts becomes ineffective. With hindsight, other countries’ difficulties in upscaling testing should have served as warning. Community screening and testing was scaled back from 18 May 2020, and testing policy was changed to only include high-risk patients from 29 May 2020. The delayed TATs meant that the CST policy had no beneficial impact at local level

Recognizing Intimate Partner Violence in Primary Care: Western Cape, South Africa

Introduction: Interpersonal violence in South Africa is the second highest contributor to the burden of disease after HIV/ AIDS and 62 % is estimated to be from intimate partner violence (IPV). This study aimed to evaluate how women experiencing IPV present in primary care, how often IPV is recognized by health care practitioners and what other diagnoses are made. Methods: At two urban and three rural community health centres, health practitioners were trained to screen all women fo

Reducing the risks of nuclear war—The role of health professionals

In January, 2023, the Science and Security Board of the Bulletin of the Atomic Scientists moved the hands of the Doomsday Clock forward to 90s before midnight, reflecting the growing risk of nuclear war. In August, 2022, the UN Secretary-General António Guterres warned that the world is now in “a time of nuclear danger not seen since the height of the Cold War.” The danger has been underlined by growing tensions between many nuclear armed states. Read more in the PDF..

Reducing the risks of nuclear war – The role of health professionals

No abstract available

COP27 Climate Change Conference: Urgent action needed for Africa and the world

The 2022 report of the Intergovernmental Panel on Climate Change (IPCC) paints a dark picture of the future of life on earth, characterised by ecosystem collapse, species extinction, and climate hazards such as heatwaves and floods (1). These are all linked to physical and mental health problems, with direct and indirect consequences of increased morbidity and mortality. To avoid these catastrophic health effects across all regions of the globe, there is broad agreement—as 231 health journals argued together in 2021—that the rise in global temperature must be limited to less than 1.5oC compared with pre-industrial levels.  While the Paris Agreement of 2015 outlines a global action framework that incorporates providing climate finance to developing countries, this support has yet to materialise (2). COP27 is the fifth Conference of the Parties (COP) to be organised in Africa since its inception in 1995. Ahead of this meeting, we—as health journal editors from across the continent—call for urgent action to ensure it is the COP that finally delivers climate justice for Africa and vulnerable countries. This is essential not just for the health of those countries, but for the health of the whole world. Read more in the PDF..

Suicide attempts in U.S. Army combat arms, special forces and combat medics

Abstract Background The U.S. Army suicide attempt rate increased sharply during the wars in Iraq and Afghanistan. Risk may vary according to occupation, which significantly influences the stressors that soldiers experience. Methods Using administrative data from the Army Study to Assess Risk and Resilience in Servicemembers (Army STARRS), we identified person-month records for all active duty Regular Army enlisted soldiers who had a medically documented suicide attempt from 2004 through 2009 (n = 9650) and an equal-probability sample of control person-months (n = 153,528). Logistic regression analyses examined the association of combat occupation (combat arms [CA], special forces [SF], combat medic [CM]) with suicide attempt, adjusting for socio-demographics, service-related characteristics, and prior mental health diagnosis. Results In adjusted models, the odds of attempting suicide were higher in CA (OR = 1.2 [95% CI: 1.1–1.2]) and CM (OR = 1.4 [95% CI: 1.3–1.5]), but lower in SF (OR = 0.3 [95% CI: 0.2–0.5]) compared to all other occupations. CA and CM had higher odds of suicide attempt than other occupations if never deployed (ORs = 1.1–1.5) or previously deployed (ORs = 1.2–1.3), but not when currently deployed. Occupation was associated with suicide attempt in the first ten years of service, but not beyond. In the first year of service, primarily a time of training, CM had higher odds of suicide attempt than both CA (OR = 1.4 [95% CI: 1.2–1.6]) and other occupations (OR = 1.5 [95% CI: 1.3–1.7]). Discrete-time hazard functions revealed that these occupations had distinct patterns of monthly risk during the first year of service. Conclusions Military occupation can inform the understanding suicide attempt risk among soldiers.https://deepblue.lib.umich.edu/bitstream/2027.42/136790/1/12888_2017_Article_1350.pd

Common genetic variants in the CLDN2 and PRSS1-PRSS2 loci alter risk for alcohol-related and sporadic pancreatitis

Pancreatitis is a complex, progressively destructive inflammatory disorder. Alcohol was long thought to be the primary causative agent, but genetic contributions have been of interest since the discovery that rare PRSS1, CFTR, and SPINK1 variants were associated with pancreatitis risk. We now report two significant genome-wide associations identified and replicated at PRSS1-PRSS2 (1×10-12) and x-linked CLDN2 (p < 1×10-21) through a two-stage genome-wide study (Stage 1, 676 cases and 4507 controls; Stage 2, 910 cases and 4170 controls). The PRSS1 variant affects susceptibility by altering expression of the primary trypsinogen gene. The CLDN2 risk allele is associated with atypical localization of claudin-2 in pancreatic acinar cells. The homozygous (or hemizygous male) CLDN2 genotype confers the greatest risk, and its alleles interact with alcohol consumption to amplify risk. These results could partially explain the high frequency of alcohol-related pancreatitis in men – male hemizygous frequency is 0.26, female homozygote is 0.07

Rare coding variants in PLCG2, ABI3, and TREM2 implicate microglial-mediated innate immunity in Alzheimer's disease

We identified rare coding variants associated with Alzheimer’s disease (AD) in a 3-stage case-control study of 85,133 subjects. In stage 1, 34,174 samples were genotyped using a whole-exome microarray. In stage 2, we tested associated variants (P<1×10-4) in 35,962 independent samples using de novo genotyping and imputed genotypes. In stage 3, an additional 14,997 samples were used to test the most significant stage 2 associations (P<5×10-8) using imputed genotypes. We observed 3 novel genome-wide significant (GWS) AD associated non-synonymous variants; a protective variant in PLCG2 (rs72824905/p.P522R, P=5.38×10-10, OR=0.68, MAFcases=0.0059, MAFcontrols=0.0093), a risk variant in ABI3 (rs616338/p.S209F, P=4.56×10-10, OR=1.43, MAFcases=0.011, MAFcontrols=0.008), and a novel GWS variant in TREM2 (rs143332484/p.R62H, P=1.55×10-14, OR=1.67, MAFcases=0.0143, MAFcontrols=0.0089), a known AD susceptibility gene. These protein-coding changes are in genes highly expressed in microglia and highlight an immune-related protein-protein interaction network enriched for previously identified AD risk genes. These genetic findings provide additional evidence that the microglia-mediated innate immune response contributes directly to AD development

Genetic effects on gene expression across human tissues

Characterization of the molecular function of the human genome and its variation across individuals is essential for identifying the cellular mechanisms that underlie human genetic traits and diseases. The Genotype-Tissue Expression (GTEx) project aims to characterize variation in gene expression levels across individuals and diverse tissues of the human body, many of which are not easily accessible. Here we describe genetic effects on gene expression levels across 44 human tissues. We find that local genetic variation affects gene expression levels for the majority of genes, and we further identify inter-chromosomal genetic effects for 93 genes and 112 loci. On the basis of the identified genetic effects, we characterize patterns of tissue specificity, compare local and distal effects, and evaluate the functional properties of the genetic effects. We also demonstrate that multi-tissue, multi-individual data can be used to identify genes and pathways affected by human disease-associated variation, enabling a mechanistic interpretation of gene regulation and the genetic basis of diseas