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1.
International Journal of Infectious Diseases ; 116:S22-S23, 2022.
Article in English | Academic Search Complete | ID: covidwho-1719980

ABSTRACT

South Africa moved to lockdown alert Level-1 on 20 September 2020 midnight, lockdown regulations were relaxed, gatherings were permitted with the number of people not exceeding 50% of normal venue capacity. The National Institute for Communicable Diseases was alerted by a clinician of a number of COVID-19 cases amongst young people who reportedly have attended the 2020 Matric Rage Festival, KwaZulu-Natal Province. This prompted an investigation to ascertain the existence of a COVID-19 cluster related to attendance of Rage Festival (Rage) and provide epidemiological characteristics of the cluster. We conducted a retrospective cohort investigation amongst 2 253 attendees. A cluster was defined as the identification/presence of ≥two laboratory confirmed COVID-19 cases amongst individuals who attended the Rage between 27 November to 4 December 2020. COVID-19 confirmed cases were identified using the organizers ticket purchaser and crew record list and the national COVID-19 laboratory confirmed cases line-list. A standardized questionnaire was circulated to 1814 attendees using Google Forms. A case was defined as any person within the cohort with SARS-CoV-2 RT-PCR positive results. Of the 2 253 attendees, 848 (37.6%) cases were identified, of which 846 (99.8%) were revelers and two were crew members (0.2%). Age ranged from 16 to 58 years (Median: 18, IQR: 18-18). The 15-19-year-old age group accounted for 802 (94.6%) of the cases, while 53.0% (425/802) were males. Most cases were from Gauteng (66.2%,561/848), followed by KwaZulu-Natal (30.0%, 254/848). Two of the attendees had positive SARS-CoV-2 results approximately 7-10 days before the festival. The questionnaire response rate was 1.0% (19/1814). Revelers attended other large events and private parties and mask wearing and social distancing was not always practiced. Although organizers observed COVID-19 precautions and protocols;social distancing and mask wearing were compromised. Factors such as mass gathering without using appropriate personal protective equipment, crowded spaces, poor hygiene and ventilation may have produced a conducive environment for SARS-CoV-2 transmission. The study limitations included delayed questionnaire circulation, lack of contact tracing data to determine secondary attack rate, and lack of clinical information amongst cases. Non-pharmaceutical interventions are effective recommended prevention and control measures. [ FROM AUTHOR] Copyright of International Journal of Infectious Diseases is the property of Elsevier B.V. and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full . (Copyright applies to all s.)

2.
Embase;
Preprint in English | EMBASE | ID: ppcovidwho-326897

ABSTRACT

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epidemic in southern Africa has been characterised by three distinct waves. The first was associated with a mix of SARS-CoV-2 lineages, whilst the second and third waves were driven by the Beta and Delta variants respectively1–3. In November 2021, genomic surveillance teams in South Africa and Botswana detected a new SARS-CoV-2 variant associated with a rapid resurgence of infections in Gauteng Province, South Africa. Within three days of the first genome being uploaded, it was designated a variant of concern (Omicron) by the World Health Organization and, within three weeks, had been identified in 87 countries. The Omicron variant is exceptional for carrying over 30 mutations in the spike glycoprotein, predicted to influence antibody neutralization and spike function4. Here, we describe the genomic profile and early transmission dynamics of Omicron, highlighting the rapid spread in regions with high levels of population immunity.

3.
Journal of Endocrinology, Metabolism and Diabetes of South Africa ; : 1-10, 2021.
Article in English | Taylor & Francis | ID: covidwho-1522050
4.
O'Toole, A.; Hill, V.; Pybus, O. G.; Watts, A.; Bogoch, II, Khan, K.; Messina, J. P.; consortium, Covid- Genomics UK, Network for Genomic Surveillance in South, Africa, Brazil, U. K. Cadde Genomic Network, Tegally, H.; Lessells, R. R.; Giandhari, J.; Pillay, S.; Tumedi, K. A.; Nyepetsi, G.; Kebabonye, M.; Matsheka, M.; Mine, M.; Tokajian, S.; Hassan, H.; Salloum, T.; Merhi, G.; Koweyes, J.; Geoghegan, J. L.; de Ligt, J.; Ren, X.; Storey, M.; Freed, N. E.; Pattabiraman, C.; Prasad, P.; Desai, A. S.; Vasanthapuram, R.; Schulz, T. F.; Steinbruck, L.; Stadler, T.; Swiss Viollier Sequencing, Consortium, Parisi, A.; Bianco, A.; Garcia de Viedma, D.; Buenestado-Serrano, S.; Borges, V.; Isidro, J.; Duarte, S.; Gomes, J. P.; Zuckerman, N. S.; Mandelboim, M.; Mor, O.; Seemann, T.; Arnott, A.; Draper, J.; Gall, M.; Rawlinson, W.; Deveson, I.; Schlebusch, S.; McMahon, J.; Leong, L.; Lim, C. K.; Chironna, M.; Loconsole, D.; Bal, A.; Josset, L.; Holmes, E.; St George, K.; Lasek-Nesselquist, E.; Sikkema, R. S.; Oude Munnink, B.; Koopmans, M.; Brytting, M.; Sudha Rani, V.; Pavani, S.; Smura, T.; Heim, A.; Kurkela, S.; Umair, M.; Salman, M.; Bartolini, B.; Rueca, M.; Drosten, C.; Wolff, T.; Silander, O.; Eggink, D.; Reusken, C.; Vennema, H.; Park, A.; Carrington, C.; Sahadeo, N.; Carr, M.; Gonzalez, G.; Diego, Search Alliance San, National Virus Reference, Laboratory, Seq, Covid Spain, Danish Covid-19 Genome, Consortium, Communicable Diseases Genomic, Network, Dutch National, Sars-CoV-surveillance program, Division of Emerging Infectious, Diseases, de Oliveira, T.; Faria, N.; Rambaut, A.; Kraemer, M. U. G..
Wellcome Open Research ; 6:121, 2021.
Article in English | MEDLINE | ID: covidwho-1450989

ABSTRACT

Late in 2020, two genetically-distinct clusters of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with mutations of biological concern were reported, one in the United Kingdom and one in South Africa. Using a combination of data from routine surveillance, genomic sequencing and international travel we track the international dispersal of lineages B.1.1.7 and B.1.351 (variant 501Y-V2). We account for potential biases in genomic surveillance efforts by including passenger volumes from location of where the lineage was first reported, London and South Africa respectively. Using the software tool grinch (global report investigating novel coronavirus haplotypes), we track the international spread of lineages of concern with automated daily reports, Further, we have built a custom tracking website (cov-lineages.org/global_report.html) which hosts this daily report and will continue to include novel SARS-CoV-2 lineages of concern as they are detected.

5.
Afr J Emerg Med ; 11(4): 429-435, 2021 Dec.
Article in English | MEDLINE | ID: covidwho-1450041

ABSTRACT

BACKGROUND: The COVID-19 pandemic is placing abnormally high and ongoing demands on healthcare systems. Little is known about the full effect of the COVID-19 pandemic on diseases other than COVID-19 in the South African setting. OBJECTIVE: To describe a cohort of hospitalised patients under investigation for SARS-CoV-2 that initially tested negative. METHODS: Consecutive patients hospitalised at Khayelitsha Hospital from April to June 2020, whose initial polymerase chain reaction test for SARS-CoV-2 was negative were included. Patient demographics, clinical characteristics, ICD-10 (International Statistical Classification of Diseases and Related Health Problems 10th Revision) diagnosis, referral to tertiary level facilities and ICU, and all-cause in-hospital mortality were collected. The 90-day re-test rate was determined and comparisons were made using the χ2-test and the independent samples median test. RESULTS: Overall, 261 patients were included: median age 39.8 years, 55.6% female (n = 145). Frequent comorbidities included HIV (41.4%), hypertension (26.4%), and previous or current tuberculosis (24.1%). Nine (3.7%) patients were admitted to ICU and 38 (15.6%) patients died. Ninety-three patients (35.6%) were re-tested and 21 (22.6%) were positive for SARS-CoV-2. The top primary diagnoses related to respiratory diseases (n = 82, 33.6%), and infectious and parasitic diseases (n = 62, 25.4%). Thirty-five (14.3%) had a COVID-19 diagnostic code assigned (26 without microbiological confirmation) and 43 (16.5%) had tuberculosis. Older age (p = 0.001), chronic renal impairment (p = 0.03) and referral to higher level of care (all p < 0.001; ICU p = 0.03) were more frequent in those that died. CONCLUSION: Patients with tuberculosis and other diseases are still presenting to emergency centres with symptoms that may be attributable to SARS-CoV-2 and requiring admission. Extreme vigilance will be necessary to diagnosis and treat tuberculosis and other diseases as we emerge from the COVID-19 pandemic.

6.
10th International Conference on Model and Data Engineering, MEDI 2021 ; 12732 LNCS:227-240, 2021.
Article in English | Scopus | ID: covidwho-1342948

ABSTRACT

The collection and sharing of accurate data is paramount to the fight against COVID-19. However, the health system in many countries is fragmented. Furthermore, because no one was prepared for COVID-19, manual information systems have been put in place in many health facilities to collect and record COVID-19 data. This reality brings many challenges such as delay, inaccuracy and inconsistency in the COVID-19 data collected for the control and monitoring of the pandemic. Recent studies have developed ontologies for COVID-19 data modeling and acquisition. However, the scopes of these ontologies have been the modeling of patients, available medical infrastructures, and biology and biomedical aspects of COVID-19. This study extends these existing ontologies to develop the COVID-19 ontology (COVIDonto) to model the origin, symptoms, spread and treatment of COVID-19. The NeOn methodology was followed to gather data from secondary sources to formalize the COVIDonto ontology in Description Logics (DLs). The COVIDonto ontology was implemented in a machine-executable form with the Web Ontology Language (OWL) in Protégé ontology editor. The COVIDonto ontology is a formal executable model of COVID-19 that can be leveraged in web-based applications to integrate health facilities in a country for the automatic acquisition and sharing of COVID-19 data. Moreover, the COVIDonto could serve as a medium for cross-border interoperability of government systems of various countries and facilitate data sharing in the fight against the COVID-19 pandemic. © 2021, Springer Nature Switzerland AG.

7.
Water Quality Research Journal ; 56(2):68-82, 2021.
Article in English | Web of Science | ID: covidwho-1285234

ABSTRACT

The International Water Association (IWA) initiated a Task Force in April 2020 to serve as a leadership team within IWA whose role is to keep abreast and communicate the emerging science, technology, and applications for understanding the impact and the ability to respond to the COVID-19 pandemic and specifically designed for water professionals and industries. Expertise was nominated across the world with the purpose of collectively providing the water sector with knowledge products for the guidance on the control of COVID-19 and other viruses. This review paper developed by a working group of the IWA Task Force focuses on the control of COVID-19. The purpose of this review paper is to provide an understanding of existing knowledge with regards to COVID-19 and provide the necessary guidance of risk mitigation based on currently available knowledge of viruses in wastewater. This review paper considered various scenarios for both the developed world and the developing world and provided recommendations for managing risk. The review paper serves to pool the knowledge with regards to the pandemic and in relation to other viruses. The IWA Task Team envisage that this review paper provides the necessary guidance to the global response to the ongoing pandemic.

8.
S Afr Med J ; 111(2): 100-105, 2021 01 20.
Article in English | MEDLINE | ID: covidwho-1168064

ABSTRACT

The COVID-19 pandemic has resulted in many hospitals severely limiting or denying parents access to their hospitalised children. This article provides guidance for hospital managers, healthcare staff, district-level managers and provincial managers on parental access to hospitalised children during a pandemic such as COVID-19. It: (i) summarises legal and ethical issues around parental visitation rights; (ii) highlights four guiding principles; (iii) provides 10 practical recommendations to facilitate safe parental access to hospitalised children; (iv) highlights additional considerations if the mother is COVID-19-positive; and (v) provides considerations for fathers. In summary, it is a child's right to have access to his or her parents during hospitalisation, and parents should have access to their hospitalised children; during an infectious disease pandemic such as COVID-19, there is a responsibility to ensure that parental visitation is implemented in a reasonable and safe manner. Separation should only occur in exceptional circumstances, e.g. if adequate in-hospital facilities do not exist to jointly accommodate the parent/caregiver and the newborn/infant/child. Both parents should be allowed access to hospitalised children, under strict infection prevention and control (IPC) measures and with implementation of non-pharmaceutical interventions (NPIs), including handwashing/sanitisation, face masks and physical distancing. Newborns/infants and their parents/caregivers have a reasonably high likelihood of having similar COVID-19 status, and should be managed as a dyad rather than as individuals. Every hospital should provide lodger/boarder facilities for mothers who are COVID-19-positive, COVID-19-negative or persons under investigation (PUI), separately, with stringent IPC measures and NPIs. If facilities are limited, breastfeeding mothers should be prioritised, in the following order: (i) COVID-19-negative; (ii) COVID-19 PUI; and (iii) COVID-19-positive. Breastfeeding, or breastmilk feeding, should be promoted, supported and protected, and skin-to-skin care of newborns with the mother/caregiver (with IPC measures) should be discussed and practised as far as possible. Surgical masks should be provided to all parents/caregivers and replaced daily throughout the hospital stay. Parents should be referred to social services and local community resources to ensure that multidisciplinary support is provided. Hospitals should develop individual-level policies and share these with staff and parents. Additionally, hospitals should ideally track the effect of parental visitation rights on hospital-based COVID-19 outbreaks, the mental health of hospitalised children, and their rate of recovery.


Subject(s)
Child Health/standards , Child, Hospitalized/statistics & numerical data , Hospitals/standards , Infection Control/standards , Patient Isolation/standards , Visitors to Patients/statistics & numerical data , COVID-19 , Child , Female , Humans , Infant, Newborn , South Africa
9.
S Afr Med J ; 111(2): 159-165, 2021 02 01.
Article in English | MEDLINE | ID: covidwho-1168063

ABSTRACT

BACKGROUND: Hypertension (HPT) and its complications continue to pose a global threat and contribute to premature mortality worldwide. The adverse interactions between HPT, obesity and COVID-19 are currently being witnessed globally and represent a collision of pandemics. Understanding the burden that this non-communicable disease (NCD) poses in KwaZulu-Natal (KZN) Province, South Africa (SA), would help in developing improved public healthcare strategies. OBJECTIVES: To describe the burden of HPT in all the districts of KZN over a 6-year period. METHODS: HPT data are routinely collected from all KZN public health facilities (both clinics and hospitals) as part of the District Health Information System (DHIS). In this retrospective study, we accessed HPT records from the DHIS over a period of 6 years (2014 - 2019, inclusive). Data collected included the number of patients screened, diagnosed and initiated on therapy for HPT, together with the number of obese patients. RESULTS: The slopes for HPT screening were positive at both clinics and hospitals in KZN (considerably more at clinics than hospitals, with a difference in elevations of slopes of p<0.001), with a significantly greater percentage of the population having been screened at rural clinics than at hospitals (difference in elevation of slopes p<0.001). A significantly greater number of patients aged <40 years (p<0.001) were being screened for HPT at clinics than at hospitals (2017/18, 2018/19, 2019/20), while hospitals screened considerably more patients aged ≥40 years in 2017 - 2018 (p<0.001). The numbers of new hypertensives diagnosed and having treatment initiated were on an upward slope at both clinics and hospitals, with clinics having a greater elevation of slope than hospitals (p<0.001), irrespective of patient age. A significantly greater number of patients aged ≥40 years (p<0.05) were diagnosed with HPT at both clinics and hospitals in KZN (2017/18, 2018/19, 2019/20). KZN clinics remained the first port of call for known hypertensives throughout the study period. Obesity was prevalent at both clinic and hospital level, although figures were significantly higher at clinics. Over 80% of the obesity burden was carried by the rural clinics and hospitals. CONCLUSIONS: Screening, diagnosis, treatment initiation and chronic management of HPT occur mainly at rural clinic level. The SA government needs to heed these findings and redirect resources (staffing and equipment) to this level. The prevalence of obesity was highest at rural healthcare facilities (clinics more than hospitals). More needs to be done to combat the obesity pandemic if we are to win the battle against NCDs (HPT and diabetes mellitus). A significant number of patients aged <40 years are being screened for HPT, which bodes well for the province, as early diagnosis and treatment of HPT are vital to prevent complications.


Subject(s)
COVID-19/epidemiology , Cost of Illness , Hypertension/diagnosis , Hypertension/epidemiology , Adult , Age Distribution , Age Factors , Aged , Ambulatory Care Facilities/organization & administration , Comorbidity , Diabetes Mellitus, Type 2/diagnosis , Diabetes Mellitus, Type 2/epidemiology , Humans , Male , Middle Aged , Obesity/diagnosis , Obesity/epidemiology , Quality of Life , Retrospective Studies , Risk Factors , South Africa
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