Detection of a SARS-CoV-2 variant of concern in South Africa.

Continued uncontrolled transmission of SARS-CoV-2 in many parts of the world is creating conditions for substantial evolutionary changes to the virus1,2. Here we describe a newly arisen lineage of SARS-CoV-2 (designated 501Y.V2; also known as B.1.351 or 20H) that is defined by eight mutations in the spike protein, including three substitutions (K417N, E484K and N501Y) at residues in its receptor-binding domain that may have functional importance3-5. This lineage was identified in South Africa after the first wave of the epidemic in a severely affected metropolitan area (Nelson Mandela Bay) that is located on the coast of the Eastern Cape province. This lineage spread rapidly, and became dominant in Eastern Cape, Western Cape and KwaZulu-Natal provinces within weeks. Although the full import of the mutations is yet to be determined, the genomic data-which show rapid expansion and displacement of other lineages in several regions-suggest that this lineage is associated with a selection advantage that most plausibly results from increased transmissibility or immune escape6-8.

Readmission and inhospital death 1 year after COVID-19 hospitalization in South Africa.

BACKGROUND: Acute SARS-COVID-19 infection may increase readmission risk compared to other respiratory infections. We assessed the 1-year readmission and inhospital death rates of hospitalized SARS-COVID-19 patients compared to patients hospitalized with other types of pneumonia. METHODS: We determined the 1-year readmission and inhospital death rate of adult patients initially hospitalized with a positive SARS-COVID-19 result, and subsequently discharged, between March 2020 and August 2021, at a Netcare private hospital in South Africa, and compared this to all hospitalized adult pneumonia patients in the 3 years prior to the COVID-19 pandemic (2017-2019). RESULTS: The 1-year readmission rate in COVID-19 patients was 6.6% (328/50,067) versus 8.5% in pneumonia patients (4699/55,439; p < 0.001), with an inhospital mortality rate of 7.7% (n = 251) and 9.7% (n = 454; p = 0.002) for COVID-19 and pneumonia patients, respectively.

Direct and Indirect Effects of the Coronavirus Disease 2019 Pandemic on Private Healthcare Utilization in South Africa, March 2020-September 2021.

BACKGROUND: The coronavirus disease 2019 (COVID-19) pandemic caused severe disruptions to healthcare in many areas of the world, but data remain scarce for sub-Saharan Africa. METHODS: We evaluated trends in hospital admissions and outpatient emergency department (ED) and general practitioner (GP) visits to South Africa's largest private healthcare system during 2016-2021. We fit time series models to historical data and, for March 2020-September 2021, quantified changes in encounters relative to baseline. RESULTS: The nationwide lockdown on 27 March 2020 led to sharp reductions in care-seeking behavior that persisted for 18 months after initial declines. For example, total admissions dropped 59.6% (95% confidence interval [CI], 52.4-66.8) during home confinement and were 33.2% (95% CI, 29-37.4) below baseline in September 2021. We identified 3 waves of all-cause respiratory encounters consistent with COVID-19 activity. Intestinal infections and non-COVID-19 respiratory illnesses experienced the most pronounced declines, with some diagnoses reduced 80%, even as nonpharmaceutical interventions (NPIs) relaxed. Non-respiratory hospitalizations, including injuries and acute illnesses, were 20%-60% below baseline throughout the pandemic and exhibited strong temporal associations with NPIs and mobility. ED attendances exhibited trends similar to those for hospitalizations, while GP visits were less impacted and have returned to pre-pandemic levels. CONCLUSIONS: We found substantially reduced use of health services during the pandemic for a range of conditions unrelated to COVID-19. Persistent declines in hospitalizations and ED visits indicate that high-risk patients are still delaying seeking care, which could lead to morbidity or mortality increases in the future.

The efficacy of pulsed-xenon ultraviolet light technology on Candida auris.

BACKGROUND: Candida auris is an emerging, often multi-resistant, yeast that causes invasive infections in healthcare settings. Patients may be colonized for months and C. auris has been shown to remain viable on surfaces for at least 14 days. It is widely considered that the environment may be a reservoir for transmission of C. auris. The efficacy of pulsed-xenon ultraviolet (PX-UV) mobile devices on C. auris has not been tested previously. In a laboratory setting, we tested efficacy of a PX-UV system on C. auris and C. parapsilosis, another candida known to be responsible for outbreaks in healthcare settings and survive for at least 28 days in the environment. METHODS: Cultures and growth of clinical strains of C. parapsilosis and C. auris was carried out in a broth liquid culture medium at 37 °C until concentration ranges 10 5-10 6 colony-forming units (CFUs) per millilitre were obtained. Glass slides were inoculated with 10 µl of C. auris stock culture and allowed to dry. Slides were positioned perpendicular to the floor at a distance of 1.25 m from the floor. Exposure time were run uninterrupted for 5-, 10- and 15-min cycles at 1- and 2-m distance. RESULTS: There was a 99.4% reduction in C. auris CFU after a 5-min cycle at 1-m distance, and 99.6% reduction after a 10-min cycle at 2-m distance. There was a 98.5% reduction in C. parapsilosis CFU after a 5-min cycle at 1-m distance, and 95.2% reduction after a 10-min cycle at 2-m distance. CONCLUSIONS: The PX-UV mobile device is easy to use and has short cycle times that makes it easier to disinfect all areas outside the room where the patient received care. Further studies are needed in hospital environment, to assess the cumulative impact of repeated sessions.

Federation of Infectious Diseases Societies of Southern Africa guideline: Recommendations for the detection, management and prevention of healthcare-associated Candida auris colonisation and disease in South Africa.

Candida auris has been detected at almost 100 South African hospitals, causing large outbreaks in some facilities, and this pathogen now accounts for approximately 1 in 10 cases of candidaemia. The objective of this guideline is to provide updated, evidence-informed recommendations outlining a best-practice approach to prevent, diagnose and manage C. auris disease in public- and private-sector healthcare settings in South Africa. The 18 practical recommendations cover five focus areas: laboratory identification and antifungal susceptibility testing, surveillance and outbreak response, infection prevention and control, clinical management and antifungal stewardship.

Prospective evaluation of risk factors of cutaneous drug reactions to sulfonamides in patients with AIDS.

BACKGROUND: Persons with HIV infection have increased rates of drug eruptions. OBJECTIVE: Our aim was to evaluate the risk factors of drug eruptions in response to sulfonamides in patients with AIDS, using a case-control analysis. METHODS: One hundred thirty-six patients who were hospitalized for pneumocystosis or toxoplasmosis were evaluated at the onset of treatment for various risk factors, which were then compared among patients with (48, 36%) and without (88, 64%) a drug eruption. RESULTS: In multivariate analysis, high CD8(+) cell count and age less than 36 years indicated a risk of drug eruption (respective odds ratios: 3.5 [95% CI 1.6-7.8], P =.002, and 2.1 [95% CI 1-4.6], P =.06). Markers of viral replication for HIV, Epstein-Barr virus, cytomegalovirus, human herpesvirus 6, and parvovirus B19, slow acetylation phenotype or genotype, and glutathione level were not associated with a risk. Administration of corticosteroids had no preventive effect. CONCLUSIONS: Our results challenge several current concepts regarding drug eruptions by discarding a strong association with glutathione deficiency, slow acetylation, or active viral infections and by showing no preventive effect of corticosteroids.