Large-scale phenotyping of patients with long COVID post-hospitalization reveals mechanistic subtypes of disease

One in ten severe acute respiratory syndrome coronavirus 2 infections result in prolonged symptoms termed long coronavirus disease (COVID), yet disease phenotypes and mechanisms are poorly understood1. Here we profiled 368 plasma proteins in 657 participants ≥3 months following hospitalization. Of these, 426 had at least one long COVID symptom and 233 had fully recovered. Elevated markers of myeloid inflammation and complement activation were associated with long COVID. IL-1R2, MATN2 and COLEC12 were associated with cardiorespiratory symptoms, fatigue and anxiety/depression; MATN2, CSF3 and C1QA were elevated in gastrointestinal symptoms and C1QA was elevated in cognitive impairment. Additional markers of alterations in nerve tissue repair (SPON-1 and NFASC) were elevated in those with cognitive impairment and SCG3, suggestive of brain–gut axis disturbance, was elevated in gastrointestinal symptoms. Severe acute respiratory syndrome coronavirus 2-specific immunoglobulin G (IgG) was persistently elevated in some individuals with long COVID, but virus was not detected in sputum. Analysis of inflammatory markers in nasal fluids showed no association with symptoms. Our study aimed to understand inflammatory processes that underlie long COVID and was not designed for biomarker discovery. Our findings suggest that specific inflammatory pathways related to tissue damage are implicated in subtypes of long COVID, which might be targeted in future therapeutic trials

SARS-CoV-2-specific nasal IgA wanes 9 months after hospitalisation with COVID-19 and is not induced by subsequent vaccination

BACKGROUND: Most studies of immunity to SARS-CoV-2 focus on circulating antibody, giving limited insights into mucosal defences that prevent viral replication and onward transmission. We studied nasal and plasma antibody responses one year after hospitalisation for COVID-19, including a period when SARS-CoV-2 vaccination was introduced. METHODS: In this follow up study, plasma and nasosorption samples were prospectively collected from 446 adults hospitalised for COVID-19 between February 2020 and March 2021 via the ISARIC4C and PHOSP-COVID consortia. IgA and IgG responses to NP and S of ancestral SARS-CoV-2, Delta and Omicron (BA.1) variants were measured by electrochemiluminescence and compared with plasma neutralisation data. FINDINGS: Strong and consistent nasal anti-NP and anti-S IgA responses were demonstrated, which remained elevated for nine months (p < 0.0001). Nasal and plasma anti-S IgG remained elevated for at least 12 months (p < 0.0001) with plasma neutralising titres that were raised against all variants compared to controls (p < 0.0001). Of 323 with complete data, 307 were vaccinated between 6 and 12 months; coinciding with rises in nasal and plasma IgA and IgG anti-S titres for all SARS-CoV-2 variants, although the change in nasal IgA was minimal (1.46-fold change after 10 months, p = 0.011) and the median remained below the positive threshold determined by pre-pandemic controls. Samples 12 months after admission showed no association between nasal IgA and plasma IgG anti-S responses (R = 0.05, p = 0.18), indicating that nasal IgA responses are distinct from those in plasma and minimally boosted by vaccination. INTERPRETATION: The decline in nasal IgA responses 9 months after infection and minimal impact of subsequent vaccination may explain the lack of long-lasting nasal defence against reinfection and the limited effects of vaccination on transmission. These findings highlight the need to develop vaccines that enhance nasal immunity. FUNDING: This study has been supported by ISARIC4C and PHOSP-COVID consortia. ISARIC4C is supported by grants from the National Institute for Health and Care Research and the Medical Research Council. Liverpool Experimental Cancer Medicine Centre provided infrastructure support for this research. The PHOSP-COVD study is jointly funded by UK Research and Innovation and National Institute of Health and Care Research. The funders were not involved in the study design, interpretation of data or the writing of this manuscript

'Self-collected upper respiratory tract swabs for COVID-19 test' : a feasible way to increase overall testing rate and conserve resources in South Africa

CITATION: Adeniji, A. A. 2020. 'Self-collected upper respiratory tract swabs for COVID-19 test' : a feasible way to increase overall testing rate and conserve resources in South Africa. African Journal of Primary Health Care & Family Medicine, 12(1):a2445, doi:10.4102/phcfm.v12i1.2445.The original publication is available at https://phcfm.orgDisparity in the testing rate of SARS-CoV-2 amongst different countries and regions is a very big challenge in understanding the COVID-19 pandemic. Although some developed countries have a very high testing rate and subsequently a high number of confirmed cases, less developed countries have a low testing rate and an illusive positivity rate. Collection of the upper respiratory specimen is not often comfortable. The discomfort could be accompanied with epistaxis and headache in some patients. The trained personnel taking the swab is forced to protect self with personal protective equipment (PPE) to avoid infections that may result from the patient due to provoked cough, sneezing and spitting. This study looks into an efficient means of increasing the testing rate for COVID 19 without compromising the quality. A literature review was conducted on the different modalities of collecting upper respiratory specimens and assessing the efficacy of samples collected using different methods in terms of the laboratory yield of different pathogens. Self-collection of upper respiratory tract specimen for diagnostic purposes is not new. Studies have demonstrated that trained staff-collected nasal swabs are not in any way superior to self-collected or parent-assisted swabs. The laboratory yield of different specimens is not determined by who took the sample but by the anatomical site from where the specimen was collected. Self collection of the upper respiratory swabs will not only increase the testing rate but also preserve the scarce PPE and reduces health care worker’s COVID 19 infection rate in South Africa.https://phcfm.org/index.php/phcfm/article/view/2445Publisher's versio

Patients’ perceptions of the triage system in a primary healthcare facility, Cape Town, South Africa

CITATION: Adeniji, A.A. & Mash, B. 2016. Patients’ perceptions of the triage system in a primary healthcare facility, Cape Town, South Africa. African Journal of Primary Health Care & Family Medicine, 8(1):1-9, doi:10.4102/phcfm.v8i1.1148.The original publication is available at http://www.phcfm.orgPublication of this article was funded by the Stellenbosch University Open Access Fund.Background: In public healthcare facilities, where the patient numbers and the available resources are often disproportionate, triage is used to prioritise when patients are seen. Patients may not understand the triage process and have strong views on how to improve their experience. Aim: This study explored the views of patients who had undergone triage in the emergency centre of a primary care facility. Setting: Gugulethu Community Health Centre, Cape Town. Methods: A purposive sample consisted of five women (one coded green, three orange, one yellow) and four men (one coded green and three yellow). A semi-structured qualitative interview was conducted in either Xhosa or English and the transcripts analysed using the framework method. Results: All of the respondents complained of a lack of information and poor understanding of the triage process. Those coded green experienced the process as biased and unfair and reported that the triage nurse was rude and unprofessional. By contrast, those coded yellow or orange found the triage nurse to be helpful and professional. Most patients turned to support staff (e.g. security staff or cleaners) for assistance in dealing with the triage system. Most patients waited longer than the guidelines recommend and the green-coded patients complained about this issue. Conclusion: Patients did not have a good experience of the triage system. Managers of the triage system need to design better strategies to improve patient acceptance and share information. The important role of support staff needs to be recognised and strengthened.Publisher's versio

Magnitude, trends and prevention of road traffic accidents in the Republic of South Africa

Road traffic injuries (RTIs) constitute one of the five major disease burdens in South Africa with high mortality and morbidity. Thus far, the scientific enquiry into this burden has not been accompanied by successful government efforts to meet the challenge. Currently, more than 1.2 million people die and 20–50 million are with disabilities annually country-wide from RTIs. While there is a progressive reduction in mortality related to human immunodeficiency virus (HIV) conditions as a result of interventions, the mortality from RTI is seen to be progressively worsening as a result of increasing motorisation. There are disparities in the burden of RTI across different countries, with low- and middle-income countries bearing the highest burden. In Africa, 24.1 per 100 000 people die annually from RTI compared to 10.3 per 100 000 people in European countries. This opinion article investigates the magnitude, trends and prevention of RTI in South Africa

Retention of medical officers in the district health services of the Western Cape, South Africa: An exploratory descriptive qualitative study

Background: An adequate health workforce is an essential building block of effective health systems. In South Africa, medical officers (MOs) are a key component of service delivery in district health services. The Stellenbosch University Family Physician Research Network in the Western Cape identified that retention of MOs was a key issue. The aim of this study was to explore the factors that influence the retention of MOs in public sector district health services in the Western Cape, South Africa.Methods: This is a descriptive exploratory qualitative study. Medical officers were purposefully selected in terms of districts, facility types, gender, seniority and perceived likelihood of leaving in the next four years. Semi-structured interviews were performed by family physicians, and the qualitative data were analysed using the framework method.Results: Fourteen MOs were interviewed, and four major themes were identified: career intentions; experience of clinical work; experience of the organisation; and personal, family and community issues. Key issues that influenced retention were: ensure that the foundational elements are in place (e.g. adequate salary and good infrastructure), nurture cohesive team dynamics and relationships, have a family physician, continue the shift towards more collaborative and appreciative management styles, create stronger career pathways and opportunities for professional development in the district health services, be open to flexible working hours and overtime, and ensure workload is manageable.Conclusion: A number of important factors influencing retention were identified. Leaders and managers of the healthcare services could intervene across these multiple factors to enhance the conditions needed to retain MOs

Evaluation of patient characteristics, management and outcomes for COVID-19 at district hospitals in the Western Cape, South Africa : descriptive observational study

CITATION: Mash, R. J. et al. 2021. Evaluation of patient characteristics, management and outcomes for COVID-19 at district hospitals in the Western Cape, South Africa : descriptive observational study. BMJ Open, 11:e047016, doi:10.1136/bmjopen-2020-047016.The original publication is available at https://bmjopen.bmj.comENGLISH ABSTRACT: Objectives To describe the characteristics, clinical management and outcomes of patients with COVID-19 at district hospitals. Design A descriptive observational cross-sectional study. Setting District hospitals (4 in metro and 4 in rural health services) in the Western Cape, South Africa. District hospitals were small (<150 beds) and led by family physicians. Participants All patients who presented to the hospitals’ emergency centre and who tested positive for COVID-19 between March and June 2020. Primary and secondary outcome measures Source of referral, presenting symptoms, demographics, comorbidities, clinical assessment and management, laboratory turnaround time, clinical outcomes, factors related to mortality, length of stay and location. Results 1376 patients (73.9% metro, 26.1% rural). Mean age 46.3 years (SD 16.3), 58.5% females. The majority were self-referred (71%) and had comorbidities (67%): hypertension (41%), type 2 diabetes (25%), HIV (14%) and overweight/obesity (19%). Assessment of COVID-19 was mild (49%), moderate (18%) and severe (24%). Test turnaround time (median 3.0 days (IQR 2.0–5.0 days)) was longer than length of stay (median 2.0 day (IQR 2.0–3.0)). The most common treatment was oxygen (41%) and only 0.8% were intubated and ventilated. Overall mortality was 11%. Most were discharged home (60%) and only 9% transferred to higher levels of care. Increasing age (OR 1.06 (95% CI 1.04 to 1.07)), male (OR 2.02 (95% CI 1.37 to 2.98)), overweight/obesity (OR 1.58 (95% CI 1.02 to 2.46)), type 2 diabetes (OR 1.84 (95% CI 1.24 to 2.73)), HIV (OR 3.41 (95% CI 2.06 to 5.65)), chronic kidney disease (OR 5.16 (95% CI 2.82 to 9.43)) were significantly linked with mortality (p<0.05). Pulmonary diseases (tuberculosis (TB), asthma, chronic obstructive pulmonary disease, post-TB structural lung disease) were not associated with increased mortality. Conclusion District hospitals supported primary care and shielded tertiary hospitals. Patients had high levels of comorbidities and similar clinical pictures to that reported elsewhere. Most patients were treated as people under investigation. Mortality was comparable to similar settings and risk factors identified.https://bmjopen.bmj.com/content/bmjopen/11/1/e047016.full.pdfPublisher's versio