Decreased severity of disease during the first global omicron variant covid-19 outbreak in a large hospital in tshwane, south africa

The COVID-19 pandemic has spread very fast around the world. A few days after the first detected case in South Africa, an infection started in a large hospital outbreak in Durban, KwaZulu-Natal (KZN). Phylogenetic analysis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes can be used to trace the path of transmission within a hospital. It can also identify the source of the outbreak and provide lessons to improve infection prevention and control strategies. This manuscript outlines the obstacles encountered in order to genotype SARS-CoV-2 in near-real time during an urgent outbreak investigation. This included problems with the length of the original genotyping protocol, unavailability of reagents, and sample degradation and storage. Despite this, three different library preparation methods for Illumina sequencing were set up, and the hands-on library preparation time was decreased from twelve to three hours, which enabled the outbreak investigation to be completed in just a few weeks. Furthermore, the new protocols increased the success rate of sequencing whole viral genomes. A simple bioinformatics workflow for the assembly of high-quality genomes in near-real time was also fine-tuned. In order to allow other laboratories to learn from our experience, all of the library preparation and bioinformatics protocols are publicly available at protocols.io and distributed to other laboratories of the Network for Genomics Surveillance in South Africa (NGS-SA) consortium.

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The role of copper resistance in Mycobacterium tuberculosis pathogenesis

10.1101/2021.03.11.434961 ◽

2021 ◽

Author(s):

Jon Mitchell Ambler ◽

Matthys Gerhardus Potgieter ◽

Marisa Klopper ◽

Melanie Grobbelaar ◽

Margaretha De Vos ◽

...

Keyword(s):

South Africa ◽

Mycobacterium Tuberculosis ◽

Molybdenum Cofactor ◽

Copper Resistance ◽

New Drugs ◽

Differentially Expressed ◽

Copper Stress ◽

Western Cape ◽

Severity Of Disease ◽

Transcriptomic Level

AbstractDespite the development of new drugs and social interventions, tuberculosis remains a leading cause of mortality. This burden falls disproportionately on developing countries, particularly those where the incidence of HIV is high. In the Western Cape, South Africa, we have identified and isolated two Beijing family strains of Mycobacterium tuberculosis that, despite few differences at a genomic level, differ greatly in their severity of disease caused, providing an opportunity to study virulence in this organism. The aim of this study was to identify differences at a genomic and transcriptomic level that may identify the cause of the different virulence levels observed in the two isolates.The isolates were compared at the transcriptome level under four different growth conditions including oxidative stress. In comparing the transcriptome of the two isolates, an operon containing genes involved in the production of molybdenum cofactor that showed consistently lower levels of expression in the hypervirulent isolate was identified. A copper sensing transcriptional regulator was identified as the most probable regulator, and we found that the Cso operon which it is known to regulate was similarly differentially expressed in the strains.The production of molybdenum cofactor is effected in two ways by copper levels. Through the independent insertion of copper into molybdopterin (MPT), and destabilisation of Fe-S clusters. As MoaA3 contains a Fe-S cluster that is known to be destabilised by copper, and a number of copper sensitive genes are likewise found differentially expressed, it is likely that the strains differ in terms of their levels of resistance to copper.It is therefore hypothesised that the differences in virulence are as a result of different levels of resistance to phagosome copper overload, and the mechanism by which copper levels are linked to the production of molybdenum cofactor is described.Author summaryIn this article, we describe the differences in gene expression of two closely related strains of Mycobacterium tuberculosis isolated in the Western Cape of South Africa that differ in the severity of disease that they cause. We compared the strains at a genomic and transcriptomic level, and in doing so, we discovered a set of molybdenum cofactor genes regulated by a copper sensing transcription factor that came up in all datasets. Further genes linked to copper response were identified, providing greater evidence that the difference between the two strains was the manner in which they responded to copper stress. Phagocytes are known to exploit high levels of copper to kill intracellular bacteria, suggesting an important link between copper and disease. We conclude that resistance to copper toxicity is the most probable reason for the relative increase in virulence, and describe the regulatory relationship between copper levels and molybdenum cofactor synthesis.

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‘This place is making me more depressed’: The organisation of care for suicide attempters in a South African hospital

Journal of Health Psychology ◽

10.1177/1359105316628744 ◽

2016 ◽

Vol 22 (11) ◽

pp. 1434-1446 ◽

Cited By ~ 7

Author(s):

Jason Bantjes ◽

Annemi Nel ◽

Kerry-Ann Louw ◽

Louise Frenkel ◽

Ereshia Benjamin ◽

...

Keyword(s):

South Africa ◽

Suicide Prevention ◽

Ethnographic Study ◽

Optimal Care ◽

Large Hospital ◽

Suicide Attempters ◽

Targeted Interventions ◽

Organisation Of Care ◽

Prevention Interventions ◽

The Impact

People who attend hospital following a suicide attempt represent a well-delineated high-risk group of patients who may be amenable to targeted interventions to reduce the risk of suicidal behaviour. Little is, however, known about how hospitals in South Africa respond to suicide attempters, what quality of care these patients receive or what possibilities exist for hospital-based suicide prevention interventions. We describe an ethnographic study conducted at a large hospital in South Africa to investigate the impact of current procedures and practices on the care received by those who attempt suicide. Findings suggest that the organisation of care within the hospital is a significant barrier to patients receiving optimal care and represents a lost opportunity for suicide prevention. Findings highlight the mismatch between the needs of suicide attempters and current services and call attention to the need for greater psychological input as well as hospital-based suicide prevention interventions that can be offered to patients without necessitating admissions.

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Short-term Projections based on Early Omicron Variant Dynamics in England.

10.1101/2021.12.30.21268307 ◽

2021 ◽

Author(s):

Matt J Keeling ◽

Ellen Brooks-Pollock ◽

Robert J Challen ◽

Leon Danon ◽

Louise Dyson ◽

...

Keyword(s):

South Africa ◽

Sensitivity Analysis ◽

Virus Transmission ◽

Transmission Characteristics ◽

Short Term ◽

Severity Of Disease ◽

Future Risk ◽

Potential Impact ◽

The Uk ◽

The Impact

Throughout the ongoing COVID-19 pandemic, the worldwide transmission and replication of SARS- COV-2, the causative agent of COVID-19 disease, has resulted in the opportunity for multiple mutations to occur that may alter the virus transmission characteristics, the effectiveness of vaccines and the severity of disease upon infection. The Omicron variant (B.1.1.529) was first reported to the WHO by South Africa on 24 November 2021 and was declared a variant of concern by the WHO on 26 November 2021. The variant was first detected in the UK on 27 November 2021 and has since been reported in a number of countries globally where it is frequently associated with rapid increase in cases. Here we present analyses of UK data showing the earliest signatures of the Omicron variant and mathematical modelling that uses the UK data to simulate the potential impact of this variant in the UK. In order to account for the uncertainty in transmission advantage, vaccine escape and severity at the time of writing, we carry out a sensitivity analysis to assess the impact of these variant characteristics on future risk.

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Preliminary demographics for patients with keratoconus attending a university-based clinic in Johannesburg, South Africa

African Vision and Eye Health ◽

10.4102/aveh.v78i1.472 ◽

2019 ◽

Vol 78 (1) ◽

Cited By ~ 1

Author(s):

Elizabeth Chetty ◽

Alan Rubin

Keyword(s):

Quality Of Life ◽

South Africa ◽

Early Intervention ◽

South African ◽

Contact Lens ◽

Demographic Data ◽

Severity Of Disease ◽

Significant Difference ◽

Clinical Records

Background: Keratoconus (KC) is a visually debilitating disease if left undiagnosed and untreated. Early intervention is necessary to ensure a good quality of life for those afflicted by the disease. Although much research has been done in other parts of the world, there is a paucity in the literature that describes the disease from a South African perspective.Aim: The aim of this study was to provide the demographics of KC patients attending a university-based contact lens clinic between January 2007 and December 2017.Setting: Patients diagnosed with KC (N = 206) at a university-based contact lens clinic in Johannesburg, South Africa, were included in this analysis.Methods: A retrospective analysis of clinical records of 206 KC patients was conducted. Demographic data on race, gender, age and severity of disease were analysed and presented.Results: The majority of patients with KC that attended the clinic were female (53%), of mainly African (74%) descent and in their second decade of life. The average age at first visit was 24.0 ± 8.53 and 22.9 ± 7.46 years for males and females, respectively. There was no significant difference in average age between male and female patients (p 0.05). Patients in the first and second decade of life presented at first visit with a greater severity of disease when compared with those in the third decade or older.Conclusion: There is a dire need for larger epidemiological studies to be conducted on South African patients with KC so that early intervention becomes possible. This would greatly influence the quality of life for these patients and positively impact the socio-economic status of the country.

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Time and Latitude in South Africa

International Astronomical Union Colloquium ◽

10.1017/s0252921100026816 ◽

1972 ◽

Vol 1 ◽

pp. 27-38

Author(s):

J. Hers

Keyword(s):

South Africa ◽

Cape Town ◽

Astronomical Observations ◽

Royal Observatory ◽

The Republic ◽

Astronomical Determination ◽

Limited Accuracy ◽

Better Than

In South Africa the modern outlook towards time may be said to have started in 1948. Both the two major observatories, The Royal Observatory in Cape Town and the Union Observatory (now known as the Republic Observatory) in Johannesburg had, of course, been involved in the astronomical determination of time almost from their inception, and the Johannesburg Observatory has been responsible for the official time of South Africa since 1908. However the pendulum clocks then in use could not be relied on to provide an accuracy better than about 1/10 second, which was of the same order as that of the astronomical observations. It is doubtful if much use was made of even this limited accuracy outside the two observatories, and although there may – occasionally have been a demand for more accurate time, it was certainly not voiced.

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Indirect Rule in South Africa

10.1017/upo9781580467421 ◽

2009 ◽

Author(s):

J. C. Myers

Keyword(s):

South Africa ◽

Indirect Rule

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Combining Professional Interests and Travel: People to People Citizen Ambassador Program

Perspectives on Global Issues in Communication Sciences and Related Disorders ◽

10.1044/gics1.2.47 ◽

2011 ◽

Vol 1 (2) ◽

pp. 47-54

Author(s):

Alex Johnson ◽

Amanda Hitchins

Keyword(s):

South Africa ◽

Health Education ◽

Communication Disorders ◽

Social Conditions ◽

Speech Language Pathologists ◽

Exchange Program

Abstract This article summarizes a series of trips sponsored by People to People, a professional exchange program. The trips described in this report were led by the first author of this article and include trips to South Africa, Russia, Vietnam and Cambodia, and Israel. Each of these trips included delegations of 25 to 50 speech-language pathologists and audiologists who participated in professional visits to learn of the health, education, and social conditions in each country. Additionally, opportunities to meet with communication disorders professionals, students, and persons with speech, language, or hearing disabilities were included. People to People, partnered with the American Speech-Language-Hearing Association (ASHA), provides a meaningful and interesting way to learn and travel with colleagues.

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