We're committed to providing affordable genomics sequencing in Africa, with no profit motive. We aim to unleash genomics' potential, support scientific research, and foster biotech, vaccine, therapy, and diagnostics development in Africa.

The Centre for Epidemic Response and Innovation (CERI), based at Stellenbosch University, and the KwaZulu Research and Innovation Sequencing Platform, based at the University of KwaZulu-Natal in South Africa, are offering 15 short-term fellowships for training in genomics and bioinformatics. The 2-week fellowship will cover travel, accommodation, meals, and ground transfers in South Africa.

Welcome to the 2st CERI/KRISP newsletter of 2024. This month, we are thrilled to celebrate Professor Tulio de Oliveira, The Director, for his second recognition by TIME as one of the TIME100 Health 2024's most influential individuals globally.

In a concerted effort to bolster the global fight against HIV/AIDS, leading experts from a host of prestigious institutions convened at the recent HIV Prevention Workshop that took place from 24-26 April 2024 near the Drakensberg, South Africa. The collaboration between the Ragon Institutes of Massachusetts General Hospital, Harvard, and MIT with Durban-based organizations such as the Centre for the AIDS Programme of Research in South Africa (CAPRISA), African Health Research Institute (AHRI), HIV Pathogenesis Programme (HPP), and the University of KwaZulu-Natal (UKZN), underscored the importance of international cooperation in tackling this pressing public health challenge.

The Virology Africa 2024 conference, held from April 15-18 at the Protea Hotel in Techno Park, Stellenbosch, brought together a vibrant community of virologists from across Africa and beyond. Key themes of the conference included One Health, the management of emerging viruses, pandemic preparedness, and advances in vaccinology among others.

In line with the Centre for Epidemic Response and Innovation (CERI)’s commitment to provide high quality genomics services, the laboratory is gearing up to achieve ISO/IEC17025 accreditation – an internationally recognized Standard for testing laboratories. This prestigious accreditation is internationally recognized and is key to laboratories aiming to demonstrate their operational competence and ability to produce valid and high-quality results.

TIME Magazine has recognized Prof Tulio de Oliveira in its inaugural 2024 TIME100 Health list, a new annual compilation that celebrates 100 individuals who have had the most impact on global health this year.

Issued by Stellenbosch University, May 2, 2024. Liaise with Maambele Khosa at maambele@sun.ac.za or +27 79 592 9174 for more information or to schedule interviews.

From April 15th to 17th, 2024, an insightful workshop took place at the KEMRI-Wellcome Trust Research Programme in Kilifi, Kenya, bringing together global health and genomic data experts. This event, in collaboration with Oxford University, aimed at advancing the federated analysis of genomic data for public health, particularly focusing on enhancing rapid data sharing and analysis capabilities during the initial stages of outbreaks and epidemics.

We are thrilled to extend our heartfelt congratulations to the remarkable individuals from the CERI team who recently graduated from Stellenbosch University. Their achievements mark not only personal milestones but also significant contributions to the academic and scientific community. Among these bright stars, we celebrate the accomplishments of Lucious Chabuka, Maambele Khosa, Nikita Sitharam, Somila Ntsiyane, and Yandisa Ntatiso.

The continent – in dire need of its own production capabilities – could once again be at the back of the vaccine queue in the next pandemic

On Friday, April 19th, our newly formed soccer team, CERI FC, played its very first friendly match. The game was held in Stellenbosch, and it was much more than just a soccer match; it was about building a sense of team and community among our research group.

The United World Antiviral Research Network (UWARN) recently held its annual meeting from April 22-24, in Kaohsiung City, southern Taiwan, bringing together key partners from the University of Washington, Senegal, South Africa, Switzerland, Pakistan, and Taiwan. The primary focus was on fostering collaboration and exchanging updates on ongoing research. Participants shared their latest findings, discussed the challenges faced, and highlighted their successes, reinforcing the network’s commitment to advancing the global response to infectious diseases.

The H5N1 strain of bird flu has spread rapidly among mammals in the United States. The first death of a common dolphin due to the virus has been documented and the number of infected cows could be higher than estimated. by Fernanda Gonzalez

Genomic analysis suggests that the outbreak probably began in December or January, but a shortage of data is hampering efforts to pin down the source. By Smriti Mallapaty

Seminar presentation by Prof Lenine Liebenberg 6 March 2024, 1-2 pm, University of Cape Town (UCT), IDM, Wolfson Pavilion Lecture Theatre, Health Sciences, Anzio Road, Observatory.

We invite applications from ambitious post doctoral scientists, to undertake research in a Flagship research programme on epidemics in South Africa. Interested candidates holding a PhD, and with clear evidence of advance computer programming and internationally competitive research.

We invite applications from ambitious post doctoral scientists, to undertake research in a Flagship research programme on epidemics and modeling in South Africa. Interested candidates with background in quantitative methods, which may include Biostatistics, Epidemiology, Econometrics, Data Science, Geography, or Mathematical Modelling

Data collection, ethics and use of AI (artificial intelligence) in healthcare are among the key topics leading global experts addressed at the inaugural Digital Health Africa? (DHA 2024) conference held recently at Stellenbosch University's (SU's) Biomedical Research Institute (BMRI).

As head of the largest genomics institute in Africa and new deputy director at the Genomic Surveillance Unit, Wellcome Sanger Institute, Professor Tulio de Oliveira hopes close collaboration can be 'world changing.'

As pressure intensifies on World Health Organization (WHO) member states to finalise a pandemic agreement by May, insiders are concerned by the snails’ pace of negotiations – primarily because they believe the negotiators have spent an inordinate amount of time on contentious issues while neglecting more procedural issues.

Prof Lenine Liebenberg's determination to find solutions to complex issues drove her to study science. Prof Liebenberg leads the Immunology Research Programme at the Centre for Epidemic Response and Innovation (CERI). South Africa joined the world in celebrating the International Day of Women and Girls in Science on 11 February.

Climate change is our planet’s most immediate existential threat, and will likely only worsen for the foreseeable future. Among its numerous adverse effects on human health, there is strong evidence linking climate change to infectious disease outbreaks.

Une réaction rapide s'impose face à la nouvelle variante à l'origine d'une épidémie de grande ampleur. Des scientifiques africains demandent que le nouveau vaccin très attendu contre le chikungunya soit testé sur l'homme au Sénégal, à la suite de la détection d'une nouvelle souche du virus qui est à l'origine de l'une des plus importantes épidémies de la maladie en Afrique de l'Ouest.

Scientists in Africa are calling for in-human testing in Senegal of the highly anticipated new Chikungunya vaccine, following the detection of a novel strain of the virus that is driving one of the largest outbreaks of the disease in West Africa.

Stellenbosch University's Centre for Epidemic Response and Innovation (CERI) is proud to welcome a new luminary to its ranks, Prof. Thulani Makhalanyane, as Head of Microbiom research.

The Wellcome Sanger Institute’s Genomic Surveillance Unit (GSU) and Stellenbosch University’s Centre for Epidemic Response and Innovation (CERI) announce a new partnership to coordinate the genomic surveillance of infectious diseases globally.

As the world observes World Cancer Day on 4 February, our focus zeroes in on a persistent and deadly adversary — cervical cancer. In South Africa, this disease claims the title of the second most common cancer among women and the leading cause of cancer-related deaths. Women in this country face a one in 42 lifetime risk of developing cervical cancer and with the lack of up-to-date figures, these numbers might be the tip of the iceberg.

Recently, members of the KRISP team in Durban, underwent training on their newly acquired Illumina NextSeq 2000 instrument. This allow KRISP to sequence larger genomes and support the South African and African scientific community.

Prof. Tulio de Oliveira and Dr. Cheryl Baxter discuss the need to invest in Africa scientific development and highlights capacity building activities that succeeded in the continent. Covers the Genomics Africa Fellowship, which trained over 500 fellows in advanced genomics and data analysis for pandemic response.

Academic cooperation between Africa and Europe is forging ahead, as exemplified by two new research collaborations tackling severe infections in children, as well as a genomic surveillance project to control pathogen infections in Africa.

The Cluster of Research Excellence in Genomics for Health in Africa (CoRE-GHA) consortium recently gathered at Stellenbosch University's Tygerberg campus for its first in-person meeting on January 16 and 17, 2024. This marked a significant step forward in fostering collaborative genomic research across continents, setting the stage for dynamic collaboration and promising advancements in health research.

VEME2024 will be organized at FioCruz in Brasilia, Brazil, during August 4 – 9, 2024. The workshop comprises 6 full days of theoretical lectures, practical sessions and keynote presentations. VEME2024 will accept 150 participants in 4 modules.

Here find some TV interviews of Prof. Tulio De Oliveira on the COP28 in Dubai for the launch of the Climate Change and Epidemics 2023 Synthesis Report by CLIMADE

World leaders at the Cop28 summit are told that urgent action is needed to prevent the epidemiological fallout of global warming by the CLIMADE consortium

The increase in epidemics fuelled by climate change across the world, and the severe implications they have on the health of the most vulnerable communities, particularly in the Global South, are captured in a groundbreaking research report on climate change and infectious diseases.

On the first ever Health Day at a COP, a new report on climate change and epidemics was released. This report, which was compiled by over one hundred scientists and policy makers, highlights how climate change is fuelling new epidemics across the world, particularly in countries from the Global South.

A short video that summarises the Climate Change & Epidemics 2023 Report produced Climate Amplified Diseases and Epidemics (CLIMADE) consortium. The video and reportwas released at the COP28 Health Day.

In this special edition of the CERI/KRISP newsletter, we highlight the activities of the Climate Amplified Diseases and Epidemics (CLIMADE) consortium over the past year. On page 2, we feature our participation in the upcoming COP28 meeting in Dubai for the release of the Climate Change and Epidemics 2023 report.

CERI has been funded by the World Bank to develop genomics-based surveillance to pathogens in Africa. Here you find information on the project as well as the support documents such as the POM, ESMP, GRM and SEP documentations for the programme.

This Project Operations Manual (POM) was developed by the core project implementation team at CERI in consultation with other departments, and the World Bank, and describes the management structures and processes related to the implementation of the Project.

Stakeholder Engagement includes the process of engaging stakeholders for a clear purpose to achieve agreed outcomes. It is now also recognized as a fundamental accountability mechanism since it obliges an organization to involve stakeholders in identifying and understanding of the specific program/project and responding to issues and concerns raised by the stakeholders for decisions, actions, and hence improving program/project performance.

CERI Environmental & Social Management Plan (ESMP). The evaluation of the Project’s risks and impacts was done in line with the World Bank’s Environmental and Social Framework (ESF) which was subsequently classified as a low risk rating. Five (5) of the 10 World Bank Environmental and Social Standards (ESS) are applicable to the Project and guides this Environmental and Social Management Plan (ESMP)

Welcome to another edition of the CERI/KRISP monthly newsletter. In this issue, we are excited to highlight the remarkable efforts on advancing climate and health research taking place across Africa in the realm of pathogen surveillance and research capacity building. Our dedicated team of scientists has been making outstanding contributions to this critical field, garnering well-deserved recognition for their exceptional research endeavors.

Stellenbosch University's Research & Innovation Excellence Awards held on October 30, 2023, was a night to remember as the institution celebrated the exceptional contributions of its researchers and innovators ...

The South African Portuguese Chamber of Commerce (SAPCC) & ABSA Business Excellence Gala Awards 2023 held at The Wanderers Club in Illovo, Johannesburg, celebrated outstanding businesses and individuals who've contributed to South Africa's business community. 

The 2023 Nobel Symposium in Chemistry Tuberculosis and Antibiotic Resistance – From Basic Drug Discovery to Clinic was hosted at Stellenbosch University. 

The Centre for Epidemic Response and Innovation (CERI) at Stellenbosch University recently concluded an intensive RNA sequencing training program from October 16th to 23rd.

The recent Data Science for Biology Workshop Series in Durban, South Africa, showcased the intersection of data science and biology, emphasizing the importance of capacity building and fostering collaboration among participants. 

In today's fast-paced era of scientific advancement, being able to secure grants remain essential for driving groundbreaking discoveries and innovative projects. This need is particularly critical for African scientists and researchers, and the Centre for Epidemic Response and Innovation (CERI) has recognized and acted on this imperative.

On September 22nd, CERI had the privilege of hosting 40 bright minds from the African Institute for Mathematical Sciences (AIMS) master's program. The day was filled with insightful discussions centered around the theme of #AIforScience and the exciting possibilities of applying artificial intelligence in the biomedical field ...

In effort to address the crucial connection between climate change and public health, the Botswana Harvard Health Partnership(BHP) and the Embassy of the Federal Republic of Germany Gaborone co-hosted the “Climate Change and Pandemic Preparedness” conference...

Grantees of the European and Developing Countries Clinical Trials Partnership (EDCTP3) and the Bill and Melinda Gates Foundation (BMG) Partnership on Genomic Epidemiology participated in the first GenEpi periodic meeting, which coincided with the BMGF Grand Challenges Annual Meeting, an event designed to explore how the global health community can expand the frontiers of science and innovation to save and improve lives ...

In the ever-evolving landscape of HIV research and treatment, the 30th International Workshop on HIV Drug Resistance and Treatment Strategies awarded Nália Ismael an award for Best Oral Abstract. Nalia is a PhD student at Stellenbosch University in the Faculty of Medicine and Health Science ...

Dr Houriiyah Tegally and Dr Moritz Kraemer from Stellenbosch University and the University of Oxford are looking at human migrations as a result of climate change and their impact on arboviral disease transmission in Sub-Saharan Africa.

Researchers in sub-Saharan Africa and the UK are working together to tackle the health impacts of climate change, thanks to £2.7 million in new research funding from the Foundation.

Implementation of a new public health strategy for pathogens identification and characterization in the context of climate change: IRESSEF a case study in the surveillance of dengue fever, arboviruses and infectious diseases in Senegal

Time: 12h00 | Wednesday, 27 September 2023, Venue: Room 3073, BMRI, Tygerberg Campus or Online, Presenters: Prof. Alex Sigal, Africa Health Research Institute (AHRI)

Amidst the serene landscapes of Stellenbosch, The Africa in the World Festival, a prestigious annual event, brought together visionaries, innovators, and thought leaders. The festival, spanning from 12-16 September 2023, served as a hub for influential speakers and attendees, all driven by a shared purpose: to catalyze positive change and sustainable solutions for Africa and its global diaspora.

Stellenbosch University's Centre for Epidemic Response and Innovation (CERI) is proud to welcome a new luminary to its ranks, Prof. Lenine Liebenberg, as Chief Researcher in Mucosal Immunology. This addition marks a significant milestone for CERI and the field of immunology as a whole.

CERI at Stellenbosch University: School for Data Science and Computational Thinking is looking to hire a grants manager to expand its grant management unit.

The Centre for Epidemic Response and Innovation will be hosting a grant writing and administration workshop Stellenbosch University on the 23-24 October 2023.

A Stellenbosch University-led international consortium has been awarded a multimillion-rand grant to help manage future epidemics in Africa. The grant is from the European and Developing Countries Clinical Trials Partnership, which funded five international awards. The project is the only one led by Africa.

Next week in New York, world leaders are expected to make commitments at the United Nations General Assembly on health and climate — two big issues that are closely intertwined.

As climate change creates a world in which extreme weather is the norm — so too are large-scale, deadly health outbreaks. And these crises aren’t contained to regions — extreme weather in one part of the world can be linked to health outbreaks in another.

Stellenbosch University (SU) is leading an international consortium that recently received a grant of five million euros (approx. R101 million) from the European Union's flagship research and innovation programme, Horizon Europe, to better diagnose, monitor and clinically manage current and future epidemics in Africa.

Graeme Dor, a PhD candidate at the Centre for Epidemic Response and Innovation (CERI), is applying geospatial and molecular epidemiological techniques to enhance understanding of endemic and emerging pathogens, particularly in Africa . He aims to create actionable insights into pathogen dynamics in Africa, establishing systems for ongoing monitoring. His future endeavors will continue to be at the forefront of public health.

This month newsletter’s cover shows the devastation resulting from extreme weather events in Malawi. This is the topic of our main feature article, published this month in Science, that highlights the link between climate change and infectious diseases. We also feature some of the highlights from the recent VEME workshop that was hosted by CERI at Stellenbosch University and brought together 158 individuals from 39 different countries.

This inaugural lecture held on September 5 highlighted two decades of genomics excellence under Prof. de Oliveira's leadership, propelling Africa into a new era of healthcare and research innovation.

In the intricate web of scientific exploration, one thread stands out for its profound influence on clinical research and public health: bioinformatics. The week-long 27th International Bioinformatics & Virus Evolution & Molecular Epidemiology (VEME) Workshop, hosted by the Centre for Epidemic Response & Innovation (CERI) at Stellenbosch University from August 20th to 25th, recently concluded, leaving a trail of insights and inspiration. This workshop showcased the symbiosis between experts and enthusiasts, forging a path into the realm of molecular data analysis and its practical implications.

New RNA sequences show the path that the virus travelled from the Amazon to the densely populated south. Nature highlights our recent paper at Science Advances.

Join us for a thought-provoking discussion by world-leading experts on Insights in to viral discovery, One health & big data analysis. Stellenbosch University, 23 August 2023, 5:30pm-7pm. All Wellcome.

This month newsletter’s cover includes a vintage tram on the streets of the Portuguese capital, Lisbon, to celebrate the Portuguese President Honoring Prof. Tulio de Oliveira with Order of Merit Medal for Outstanding Scientific Contributions. In recognition of women’s month, we highlight the contributions one of our women scientists who has a passion for capacity building.

In a momentous ceremony Portuguese President Marcelo Rebelo de Sousa presented Prof Tulio de Oliveira with the distinguished Order of Merit Medal.

Abdualmoniem's life-changing experience in a foreign land became a tale of humanity, generosity, and friendship.

Zimbabwe, like many other countries in Sub-Saharan Africa, faces the harsh reality of the HIV epidemic. With a substantial portion of the population affected by the virus, innovative approaches are urgently needed to combat its devastating impact.

The CERI family is expanding! With the addition of new students and staff, we are excited to showcase our growing team in this month's news and newsletter. Together, we continue to foster an environment of collaboration, innovation, and excellence in research and education. Stay tuned as we eagerly await more talented individuals to join us in the upcoming months!

The threat of bat-borne viruses in Southern Africa continues to be a major concern for public health and wildlife conservation. In a bid to shed light on this critical issue, the Centre for Epidemic Response and Innovation (CERI) hosted its monthly scientific seminar, featuring esteemed guest speaker Prof. Wanda Markotter, Director of the Centre for Viral Zoonoses at University of Pretoria and a leading expert in zoonotic diseases.

In a momentous ceremony held at the Coastlands Hotel in Musgrave, Durban, on the evening of July 22, 2023, Professor Tulio de Oliveira was bestowed with the prestigious 2023 Discovery Health Lifetime Leadership Award. The distinguished accolade, presented jointly by Discovery and the KwaZulu-Natal Doctors Healthcare Coalition, recognizes Professor de Oliveira's unparalleled contributions to global thought leadership in the research and scientific fields.

In celebration of Women's Month, we shine a spotlight on an extraordinary woman whose contributions to scientific research and leadership has led to significant breakthroughs in HIV prevention. Meet Dr. Cheryl Baxter, the Head of Scientific Support at CERI.

Time: 12h00 | Wednesday, 26 July 2023, Venue: Room 3073, BMRI, Tygerberg Campus or Online, Presenters: Prof. Wanda Markotter, Director of the Centre for Viral Zoonoses, Faculty of Health Sciences, University of Pretoria.

Nations with large volumes of outgoing air traffic accounted for a high proportion of variant exports.

[Stellenbosch, June 25, 2023] -The African Research Universities Alliance (ARUA) and The Guild of European Research-Intensive Universities (The Guild) proudly announce the launch of the Cluster of Excellence (CoE) named Genomics for Health in Africa, an innovative collaboration aimed at advancing genomics research and improving healthcare outcomes across the African continent. The lead universities for this cluster are Stellenbosch University (SU) in South Africa, the University of Bern in Switzerland and University of Tübingen in Germany.

In the pursuit of preventing and treating deadly diseases, Derek Tshiabuila, a PhD researcher at the Centre for Epidemic Response and Innovation (CERI), is delving into the enigmatic realm of viral recombination. With a focus on three highly prevalent viruses in South Africa, Derek's groundbreaking work aims to unravel the secrets of viral evolution, providing invaluable insights into the development of effective prevention and treatment strategies.

The Centre for Epidemic Response & Innovation (CERI) at Stellenbosch University (SU) hosted a training focused on exomes preparation, aimed at advancing the diagnosis and treatment of rare diseases among paediatric patients. By producing Exomes in South Africa in real-time provides medical professionals the ability to diagnose and develop tailored treatment plans for affected children.

Nikita Sitharam, a dedicated bioinformatics Master's student at Stellenbosch University, is revolutionizing epidemic response in Africa through her ground-breaking research on arboviruses genomes. Sitharam's primary focus is the development of innovative dashboards that harness the power of bioinformatics to provide vital information for public health officials and policymakers. Her work has the potential to transform the way arbovirus outbreaks are monitored, analyzed, and combated across the continent.

As we enter the winter season in South Africa, our focus shifts to the northern hemisphere. In May, we had the privilege of attending the World Health Assembly, WHO, and the United Nations in Geneva, Switzerland, where we had the opportunity to participate in the launch of the International Public Health Surveillance Network (IPSN). Additionally, Professor Tulio engaged in significant discussions with the Medical Center for International Diseases (MCID) in Bern and the Geneva 2030 Genomics program.

by Prof Frank Tanser, CERI, University of Stellenbosch, Wednesday 31 May 2023 @12h00, BMRI, Tygerberg Campus, Stellenbosch University or virtually

Professor Tulio visited Bern University in Switzerland and met with the team from the MCID (Multidisciplinary Center for Infectious Diseases). During his visit, they discussed potential collaborations on topics related to pandemic preparedness and emerging infectious diseases. In addition, discussions focused on how to expand genomics to rare diseases and cancer.

Prof. Tulio de Oliveira had the opportunity to visit the Health 2030 Genomics Center in Geneva on the 22 May 2023, where he was able to present some of the research being undertaken at CERI and KRISP.

WHO and partners are launching a global network to help protect people from infectious disease threats through the power of pathogen genomics. The International Pathogen Surveillance Network (IPSN) will provide a platform to connect countries and regions, improving systems for collecting and analyzing samples, using these data to drive public health decision-making, and sharing that information more broadly.

by Prof Tulio de Oliveiea, CERI, University of Stellenbosch & KRISP, UKZN, Wednesday 16 May 2023 17h00-19h00, BMRI, Tygerberg Campus, Stellenbosch University or virtually

Professor Tulio de Oliveira was invited by Dr. Tedros Adhanom Ghebreyesus (Director General WHO) and Dr. Chikwe Ihekweazu (Director of WHO pandemic Hub) to take a position on the leadership committee of the International Pathogen Surveillance Network (IPSN). Prof de Oliveira will be a panellist on the official launch of IPSN as part of the World Health Assembly on 20 May 2023 in Geneva.

Sophisticated genomic surveillance lab aims to keep one step ahead of outbreaks with effective tests, treatments and vaccines

Welcome to the April/May 2023 edition of our newsletter. April was an incredibly busy and exciting month for CERI and KRISP, centered around the launch of the CLIMADE (Climate Amplified Diseases and Epidemics) consortium and the inauguration of the R1.2 billion Biomedical Research Institute (BMRI) at Stellenbosch University. This events brought together leading experts and stakeholders from all over the world to celebrate this momentous occasion and the state-of-the-art facilities that will enable us to lead the way in genomic research.

The WHO Hub for Pandemic and Epidemic Intelligence was established in Berlin with the foundational investment of the Government of the Federal Republic of Germany in September 2021 to support countries, regions, and global actors to avert and manage public health threats more efficiently.

The fellowship is a tailored training opportunity intended to train a pathogen genomics and bioinformatics workforce with expertise to improve outbreak detection and disease surveillance in Africa.

A new coalition, CLIMADE, brings together some of the biggest names in public health to address climate-amplified diseases in Africa and Latin America.

Regarded as the pride of Africa, the facility has opened its doors to the continent and the world – offering training and fellowships to those in the field of genomics.

A sustainable global commitment to pandemic preparedness is instrumental to maintaining the upper hand and winning the battle.

Abbott is joining the Climate Amplified Disease and Epidemics (CLIMADE) consortium, which will use data science to predict, track and control diseases that may be amplified by climate change

Many of Africa's higher education institutions were established by colonial governments to meet the labor needs of the time. Now many universities on the continent want to prepare graduates for the modern job market.

Remember when the weather felt more predictable? When seasons felt consistent, even if we complained about it, and things like wildfires, droughts or flooding seemed like rare events?

In April, we will commence a series of festivities and activities in the lead-up to the inauguration of the BMRI and CERI new state-of-the-art laboratories. This building is dedicated to understanding the genetic and bio-molecular basis of disease with a decidedly African focus

Technology is the best weapon against future pandemics, believes renowned scientist Tulio de Oliveira, a professor of bioinformatics at the School for Data Science and Computational Thinking at Stellenbosch University, who foresees 'an armed race between humans and pathogens”.

The new Biomedical Research Institute on the Tygerberg campus of Stellenbosch University ‘was a 10-year dream costing R1.2-billion’ to address the major health challenges of Africa

CAPE TOWN - The most advanced biomedical research centre on the African continent has opened in South Africa, boasting state-of-the-art research and training facilities.

Genomics Symposium - 17 April 2023, TB Symposium - 18 April, Cardiometabolic research symposium - 20 April. Symposiums are free of charge and will be hosted at the new BMRI building at FMHS Tygergerg Campus of Stellenbosch University.

A leading-edge biomedical research facility, the Biomedical Research Institute (BMRI), was officially launched this week. BMRI is the home of CERI new state-of-the-art Genomics Facilities.

The fellows have come from 42 different countries in the global south. We are privileged to provide the opportunity for knowledge transfer to scientists from all walks of life and to allow them to come together and share their experiences with others and to learn how to become world leaders in genomic surveillance.

VEME2023 will be organized in Stellenbosch, South Africa, during August 20–25, 2023. The workshop comprises 6 full days of theoretical lectures, practical sessions and keynote presentations. VEME2023 will accept 150 participants in 4 modules.

Thomas C. Marlovits is a full Professor and Director of the Institute of Structural and Systems Biology at the University Medical Center Hamburg-Eppendorf in Germany. He is resenting at CERI on the 27 March 2023 a talk entitled: Design and Function of Molecular Machines in Microbial Pathogenesis,

Prof Graeme Meintjes is the Second Chair and Deputy Head of Medicine at the University of Cape Town, and alsoholds the SARChIChair of Poverty-related Infections. He is presenting at CERI on the 22 March 2023 a talk entitled: The ARTIST trial and the expanding role of Tenofovir/Lamivudine/Dolutegravir in ART programmes.

Time: 12h00 | Wednesday, 22 March 2023, Venue: Room 3073, BMRI, Tygerberg Campus or Online, Presenters: Prof. Graeme Meintjes, University of Cape Town (UCT)

The multi-institutional research would develop new strategies to combat HIV in vulnerable populations impacted by COVID-19.

New funding has been awarded for the development of HIV-prevention strategies in rural communities of sub-Saharan Africa. The five-year, $2.2 million research grant from the US National Institutes of Health (NIH), will be used to identify vulnerable groups at high risk of contracting the virus, and design appropriate intervention strategies

I am delighted and honoured to be back in South Africa working at Stellenbosch [University] and with CERI and the Department of Global Health. I love this continent and there is no place in the world I would rather be right now – here is where I feel that I can make the biggest impact, Prof. Frank Tanser.

As part of our special edition of Focus on Africa with guest editor, Professor Thuli Madonsela speak to Professor Tulio de Oliveira – one of the South African scientists who helped identify the Omicron variant. He talks about the discrimination African scientists often face.

CNN feature including Prof. Tulio De Oliveira, from CERI at Stellenbosch University and KRISP, UKZN as one of the four most inspiring minds in Africa in 2022. The film also includes Dr. Shiulile Moyo, Prof Tulio de Oliveira’s past PhD student, who co-discovered with Omicron variant.

From the Amazon jungle to village townships of South Africa, to crowded urban centers in India and finally cutting-edge surveillance sites in Chicago, follow a group of Coalition experts as they race the clock to stay one step ahead of the next viral threat.

Every year, the photo team from Science select the best pictures for Science. Here is some of the other Science collection of 2022’s best, from the edges of outer space to microscopic close-ups, from the genetics of ancient times to the discovery of new species.

NPR is running a series on spillover viruses — that's when animal pathogens jump into people. Researchers used to think spillovers were rare events. Now it is clear they happen all the time. That has changed how scientists look for new deadly viruses. To learn more, we traveled to Guatemala and Bangladesh, to Borneo and South Africa.

Presenter: Prof Darren Martin, University of Cape Town, Date: Wednesday, 22 February 2023, BMRI, Tygerberg Campus, Stellenbosch University

We invite applications from ambitious post doctoral scientists, to undertake research in a Flagship research programme on epidemics in Africa. Fellows will receive a very well paid fellowship and access to some of the best datasets and facilities in the world.

Time: 12h00 | Wednesday, 25 January 2023,Venue: STIAS, Stellenbosch Campus or virtually,Presenters: Prof James R. Carey, University of California Davis (UC Davis)

CAPE TOWN - Health experts have cautioned South Africans that it is too early to panic over the new COVID-19 Omicron subvariant, dubbed "Kraken".

Prevalence of a new subvariant of Omicron is increasing, but whether it will cause a big surge in infections or hospitalizations is not clear.

South Africans, especially the elderly and those with underlying health conditions, are being urged to vaccinate against Covid-19 or get booster shots as a precaution.

LONDON, Jan 3 (Reuters) - Leading scientists advising the World Health Organization said they wanted a "more realistic picture" about the COVID-19 situation from China's top experts at a key meeting on Tuesday as worries grow about the rapid spread of the virus.

Time: 12h00 | Wednesday, 30 November 2022, Venue: STIAS, Stellenbosch Campus or Online, Presenters: Dr Christopher Trisos, directs the Climate Risk Lab for the African Climate and Development Initiative at University of Cape Town.

China's daily COVID-19 cases hit a record high since the beginning of the pandemic, according to the data revealed by the National Health Bureau. The country reported as many as 31,444 domestic cases on Wednesday despite its targeted approach. However, the numbers are relatively small when compared with China's t population of 1.4 billion, AFP reported.

One highlight of the forum was meeting Barack Obama and Dr. Sonia Vallabh. Both have worked against major adversity to develop health solutions. Dr Vallabh is a scientist working on rapid dementia, a genetic disease that killed her mother, and she is also at risk of developing dementia.

The BRICS Network for Genome Surveillance (NGS-BRICS) was established in 2021 and generates and investigates sequence data of viral pathogens of public health importance, such as COVID-19. In the interest of increasing bioinformatics and experimental expertise within BRICS countries. Applications close on 1st of August 2022.

This intensive, hands-on workshop will use microbiome data as a backdrop to learn R. The workshop will feature morning & afternoon sessions taught by expert faculty and technical assistants. All participants will acquire fundamental computational skills, bioinformatics best practices, exploratory data analysis, and modeling techniques. Deadline for application - 7 Aug 2022.

Please find CERI’s & KRISP’s newsletter June/July issue of 2022. This month’s edition is a celebration of more awards and recognition of the tireless efforts of our teams towards the global pandemic response; but also a reflection on the future, not only of the evolution of COVID-19 sub-variants and their repercussions, but also the emergence or continuation of other viral threats. Another area of interest is the evolution of Monkey Pox to a global health emergency and what that means for the African continent.

The Stellenbosch University has received a grant from the International Bank for Reconstruction and Development (IBRD) for Accelerating Genomics-based Surveillance for COVID-19 Response in South Africa (P177439) and intends to apply part of the proceeds to eligible payments for goods and consulting services to be procured under this project.

Presenter: Professor Gerhard Walzl, Stellenbosch University Medical School, Date: 13 Jul 2022, Locations: JN De Villiers Auditorium, Tygerberg Campus or virtually

Please find CERI’s & KRISP’s newsletter June/July issue of 2022. What an eventful and action-packed period it has been! In this issue we feature our recent paper on the real-time tracking of the 2022 Monkeypox outbreak, the renaming of Monkeypox to remove the geographic stigma, and our Nature Medicine publication that identified the BA.4 and BA.5 Omicron lineages and how they drove the 5th wave in South Africa.

Please find CERI’s & KRISP’s newsletter May/June issue of 2022. In this issue, we feature the recent research describing how we worked with the WHO develop an early warning system for emerging SARS-CoV-2 variants and the opinion piece in The Lancet on why African science should have a central place on the world stage and needs to be recognised and supported. We congratulate Professor Tulio de Oliveira and Dr. Sikhulile Moyo on being listed in the Time magazine’s 100 most influential people of 2022.

In South Africa, a network of researchers are studying whether new lineages BA.4 and BA.5 escape immunity from COVID-19 vaccines and prior infections.

As the WHO mulls when to call the Covid pandemic over, attention is turning to the future. Last November, having alerted the world to the new and highly transmissible Omicron variant of the Sars-CoV-2 virus, South Africa-based scientist Tulio de Oliveira saw that country hit with travel bans.

Join the next African Union and Africa CDC 2022 Lecture and Discussion Series of Omicron and other COVID-19 variants of concern –where are we now?, "A New Public Health Order in the 21st Century ", Tuesday, 1 March 2022 at 3:00 pm EAT.

In this webinar, we will hear about the setting up of sequencing and bioinformatic pipelines for SARS-CoV-2, timeliness of data generated and the overall system coordination to inform public health action, with experiences and lessons learned from Denmark, South Africa and Argentina.

Presenter: Prof Tulio de Oliveira, Date: 2 February 2022, Locations: JN de Villiers Auditorium, Clinical Building, University of Stellenbosch Tygerberg Campus & K-RITH Tower Building, Nelson R Mandela School of Medicine, UKZN.

An Omicron investigator, a Mars explorer and an AI ethics pioneer are some of the people behind the year’s big research stories. The Nature’s 10 list explores key developments in science this year and some of the people who played important parts in these milestones. Along with their colleagues, these individuals helped to make amazing discoveries and brought attention to crucial issues.

Scientists in a cutting-edge laboratory at CERI and KRISP do part of the work. Local health workers on foot do the rest. Front Page NYTimes Sunday edition paper covering our work.

Little is known about the Omicron variant, which was first detected in Southern Africa, but the nature of its mutations and its seemingly rapid emergence have concerned governments around the world. Interview with Prof. Tulio de Oliveira at the New Yorker.

What do a seaweed farmer from Tanzania, a scientist in South Africa and a Senegalese influencer all have in common? The BBC's Malu Cursino looks back at how Kaije, Tulio de Oliveira and Khaby made their mark in 2021.

Cape Town - In December 2020, South Africa detected the Beta variant and in May 2021 the Delta variant, thanks to robust genomic surveillance. Professor Tulio De Oliveira, a renowned bioinformatician who identified the Beta variant, explains the criticality of genomic sequencing. Professor De Oliveira is the Director of the KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP) and Centre for Epidemic Response and Innovation (CERI) based in South Africa.

The launch of a new genomics facility, CERI, in South Africa bolsters the continent’s epidemic and pandemic public health response

As United States reveals its plan to offer an extra dose of COVID-19 vaccine, equity and scientific questions abound

A senior scientist from the Instituto Nacional de Saude (INS) de Mozambique spent two weeks at KRISP labs at UKZN to receive training generating whole genomes of SARS-CoV-2.

The Africa Union and Africa CDC, in partnership with KRISP, H3AbioNet, ACEGID and SANBI have started a Webinar series to capacitate African researchers on the generation and analysis of SARS-CoV-2 genomic data in Africa.

The Africa Union and Africa CDC, in partnership with KRISP, H3AbioNet, ACEGID and SANBI have started a Webinar series to capacitate African researchers on the generation and analysis of SARS-CoV-2 genomic data in Africa.

As the world less affluent countries scramble for COVID-19 vaccine and contend with deadly surges of the disease, researchers in South Africa have just documented an ominous development: the collision of the pandemic with HIV/AIDS.

From Alpha to Omega, the labelling system aims to avoid confusion and stigmatization. To quell such confusion and avoid geographical stigmas, everyone should now just call it Beta according to a naming scheme announced on 31 May by the World Health Organization (WHO) in Geneva and described in a forthcoming article in Nature Microbiology.

The Africa Union and Africa CDC, in partnership with KRISP, H3AbioNet, ACEGID and SANBI present a webinar series to capacitate African researchers on the generation and analysis of SARS-CoV-2 genomic data. Webinar: How to make publication-ready professional-looking figures Part II.

What is better than music to simplify and spread the facts on a pandemic clouded by so much misinformation? Watch a video series between musicians and scientists aimed at decrease vaccine hesitancy.

The Africa Union and Africa CDC, in partnership with KRISP, H3AbioNet, ACEGID and SANBI present a webinar series to capacitate African researchers on the generation and analysis of SARS-CoV-2 genomic data. Webinar: NGS genome assembly and quality control.

The Africa Union and Africa CDC, in partnership with KRISP, H3AbioNet, ACEGID and SANBI present a webinar series to capacitate African researchers on the generation and analysis of SARS-CoV-2 genomic data. Webinar: Ancestral state reconstruction and import/export analysis of viral lineages.

The Africa Union and Africa CDC, in partnership with KRISP, H3AbioNet, ACEGID and SANBI present a webinar series to capacitate African researchers on the generation and analysis of SARS-CoV-2 genomic data. Webinar: How to make publication-ready professional-looking figures Part I.

While richer places, such as the U.S., hope to vaccinate most of their citizens within months, poorer countries, like Kenya, expect to reach just small fractions of their populations in that time.

Some people mount an immune response able to fend off a menagerie of coronavirus variants. Nature news covering four of our recent papers on the variant, neutralisation of plasma and Vaccines (Novavax and Astrazeneca)

New research from South Africa’s genomic surveillance network shows that people infected with the 501Y.V2 variant are also immune to other forms of the virus. The team found the protection against the 501Y.V2 variant could also extend to the original virus circulating the country and the variant first identified in Brazil.

Tracking the coronavirus’s evolution, letter by letter, is revolutionizing pandemic science.In the beginning, there was one. The first genome for the virus causing a mysterious illness we had not yet named COVID-19 was shared by scientists on January 10, 2020. That single genome alerted the world to the danger of a novel coronavirus.

The 501Y.V2 variant reportedly produces a high number of antibodies, providing protection against infection by other variants. The findings in laboratory studies offer hope that COVID-19 vaccines based on the 501Y.V2 variant first identified late last year could protect against multiple variants circulating in different parts of the world

B.1.351 may sound sweet to a molecular epidemiologist, but what is the alternative, other than stigmatizing geographical names? News piece at NY Times highlighting our work with WHO on a new nomenclature system for COVID-19 variants

A variant of concern first identified in Brazil has now been found in the UK. Public health officials are investigating the six cases and are deploying more testing to see if it has spread to more people. Some variants, like this one, appear to be more contagious and there are concerns vaccines may not work quite so well against them.

A new SARS-CoV-2 variant, which has dominated Covid-19 infections in Uganda and Rwanda, has been detected in South Africa. The announcement was made by Professor Tulio de Oliveira, director of the KRISP lab. However, de Oliveira told Health24 that is not a variant of concern, and that genome surveillance will monitor this and other variants

Scientists worldwide have been closely monitoring the emergence of coronavirus variants. Although there are a large number of variants, some of them have turned out to be more alarming. Professor Tulio de Oliveira provided an update on the spread of three of these, and said that two more have been placed on the WHO's watchlist.

South Africa’s pause of its rollout of the Oxford/AstraZeneca vaccine in response to concern about a local coronavirus variant sparked global debate —and shone a spotlight on how the country’s science has become vital to understanding where the pandemic may go next.

As potentially more dangerous variants of Covid-19 spread, scientists are taking a crack at giving them clearer names that’ll help in the fight. Another very interesting piece of The Wired magazine one SARS-CoV-2 variants' names

Across the globe, SARS-CoV-2 is evolving ways to evade the immune system and become more infectious. Blown pandemic response plans are to blame. Really interesting but funny piece at The Wired magazine.

Evidence that a variant of the coronavirus identified in South Africa might compromise immunity sparks concerns about vaccine effectiveness.

Efforts to track SARS-CoV-2 sequences have helped identify worrying variants - but researchers are blind to emerging mutations in some regions.

Phylogenetic identification of variants 501Y.V1, 501Y.V2, 501Y.V3 (B.1.1.7, B.1.351, P.1 / Nextstrain 20I, 20H, 20J). Tool also determines nucleotide (NT), amino acids (AA) and codon (CDS) mutations. The mutations list are provided in html and excel formats.

Experts worldwide are urgently studying three coronavirus variants to understand what risks they pose. One variant first identified in the UK, one in South Africa, and one in Japan are probably more contagious than the original strain. They have caused cases to surge and the three nations to lock down. Here are nine key questions about the variants, answered.

One year later and the new coronavirus is still posing new questions for researchers. The recent emergence of new COVID-19 variants across the world has left scientists searching for answers once again as they try to understand what these changes mean for the pandemic - and vaccine roll-outs. As South Africa awaits the arrival of its first shipment of COVID vaccines there are growing concerns about a new coronavirus variant - known as 501Y.V2 - circulating in the country, and what the changes in the virus could mean for how well the jabs work.

A South African tip led to the discovery of mutations around the world. With infections skyrocketing, 'it's a race against time.'. Doctors and nurses at a South African hospital group noticed an odd spike in the number of Covid-19 patients in their wards in late October...

As more lineages emerge, researchers are struggling with a patchwork of nomenclature.

Researchers race to determine why lineages identified in Britain and South Africa spread so quickly and whether they'll compromise vaccines.

A variant identified in Japan in arrivals from Brazil shares 'concerning' characteristics with mutations detected in the UK and South Africa

Countries that conduct a lot of genetic sequencing are more likely to find new strains, say experts

Researchers warn that the new variant may spread faster and could reduce the efficacy of vaccines

The coronavirus has evolved as it has made its way across the world, as any virus is expected to do. But experts have been startled by the pace at which significant new variants have emerged.

Mutation reduces ability of antibodies to bind to virus and could make some shots less effective.

JOHANNESBURG (Reuters) - A variant of the coronavirus first detected in South Africa is unlikely to completely negate the immunising effects of vaccines, a researcher studying it told Reuters.

The variant is up to 70 percent more transmissible than earlier versions, officials said. People in southeast England, including London, were told to stay at home.

Scientists are scrambling to better understand effects of a series of worrisome mutations from in the U.K. and South Africa variants.

'Si nous permettons au virus de continuer à circuler librement, nous lui donnons une grande marge de manœuvre pour mieux s'adapter à la transmission chez l'homme', déclare Tulio de Oliveira, le Brésilien à l'origine de la découverte d'une nouvelle mutation "plus transmissible" du coronavirus qui suscite des inquiétudes dans le monde entier.

President Cyril Ramaphosa expected to announce new restrictions in attempt to slow the surge

Tulio de Oliveira, o brasileiro por trás da descoberta de uma nova mutação "mais transmissível" do coronavírus que vem causando preocupação ao redor do mundo, diz à BBC News Brasil que "se o vírus continuar circulando livremente, o risco dele se adaptar melhor aumenta".

In June, Ravindra Gupta, a virologist at the University of Cambridge, heard about a cancer patient who had come into a local hospital the month before with COVID-19 and was still shedding virus. The patient was being treated for a lymphoma that had relapsed and had been given rituximab, a drug that depletes antibody-producing B cells. That made it hard for him to shake the infection with SARS-CoV-2.

Research still to confirm threat posed but variant does not appear to provoke more serious symptoms

The new variant of SARS-CoV-2 detected in SA has left scientists working round the clock to unravel its mysteries, the health department said on December 19 2020. The department of health issued a lengthy list of questions and answers on Saturday after announcing that the virus that causes Covid-19 has evolved into a new variant.

Durban, 3 December 2020. The KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), University of KwaZulu-Natal has produced over 1000 HIV-1 genomes in record time in South Africa, a significant scientific endeavor to understand how drug resistance has developed to a new and potent antiretroviral (ARV) treatment.

Prof Carl Heneghan & Tom Jefferson write at the Spectator about nosocomial infection in the U.K. In this article they mention our genomics and outbreak response (Lessells, Moosa & de Oliveira 2020) work on a large hospital outbreak in South Africa.

Published in a recent medRxiv* paper, researchers from South Africa, the United Kingdom, and Brazil found that these mutations in SARS-CoV-2 lineages are localized to South Africa. These unique strains, not found elsewhere in the world, are thought to have contributed around 42% to the country's total infection rate.

WHAT: Weekly interaction with members of the media to share critical updates on steps taken to implement key aspects of the joint continental strategy for COVID-19 response; and to also highlight the coordinated efforts by African Union Member States to combat the pandemic in their respective countries.

The Africa Union and Africa CDC, in partnership with KRISP, H3AbioNet, ACEGID and SANBI present a webinar series to capacitate African researchers on the generation and analysis of SARS-CoV-2 genomic data. Webinar: Main Routes of Entry and Genomic Diversity of SARS-CoV-2 in Uganda .

Ahead of the emergence of the SARS-CoV -2 outbreak in South Africa KRISP started preparing for it. KRISP really rose to the occasion in the fight against COVID-19 pandemic in Africa. In the process, KRISP trained 1000s of health care workers, produced genomic protocols & capacitated dozens of laboratories in Africa to respond to the COVID-19 pandemic

The use of genomics to support the response to COVID-19 and containment of the virus in Africa is currently low. To address this suboptimal use of genomics, the Africa Centres for Disease Control and Prevention (CDC) Institute of Pathogen Genomics, in consultation with the Africa CDC led African Task Force for Coronavirus Preparedness and Response (AFTCOR) laboratory technical working group.

The Africa Union and Africa CDC, in partnership with KRISP, H3AbioNet, ACEGID and SANBI present a webinar series to capacitate African researchers on the generation and analysis of SARS-CoV-2 genomic data. Webinar: SARS-CoV-2 whole genome sequencing and quality control .

The Africa Union and Africa CDC, in partnership with KRISP, H3AbioNet, ACEGID and SANBI present a webinar series to capacitate African researchers on the generation and analysis of SARS-CoV-2 genomic data. Webinar: Public Health Alliance for Genomic Epidemiology (PHA4GE): Strengthening Bioinformatics in Public Health .

There have been 17090 more deaths in the country than there were in previous years during the same period. But the official number of Covid-19 deaths is about 6000. There is a significant departure from the historical trends, even under these abnormal circumstances.

South Africa witnessed some 17000 extra deaths from natural causes or 59% more than would normally be expected between early May and mid-July, scientists said, suggesting many more people are dying of Covid-19 than shown in official figures.

The Africa Union and AfricaCDC, in partnership with SANBI, KRISP, H3AbioNet and the Africa Centre of Excellence for Genomics of Infectious Diseases have started a weekly Webinar series to capacitate African researchers on the generation and analysis of SARS-CoV-2 genomic data in Africa.

South Africa has joined the United States, Brazil, India, and Russia as the countries with the most recorded COVID-19 cases. On Saturday, Health Minister Dr Zweli Mkhize announced the country has 350,879 confirmed COVID-19 cases.

The official number of deaths linked to Covid-19 in South Africa doesn't reflect the true scale of the crisis, with provinces that have been hit hardest by the outbreak showing a surge in fatalities, health experts say.

The official number of deaths linked to Covid-19 in South Africa doesn't reflect the true scale of the crisis, with provinces that have been hit hardest by the outbreak showing a surge in fatalities, health experts say.

CAPE TOWN - Genome sequencing, by colleagues at Stellenbosch University and the Network for Genomic Surveillance, was used to trace most of the very first COVID-19 cases reported in the Western Cape back to Europe.

There were multiple — possibly hundreds — of introductions of the novel coronavirus virus to Cape Town from foreign travellers and return citizens, scientists found.

Durban - The newly launched Africa Centres for Disease Control and Prevention Consortium for Covid-19 vaccine clinical trial by the AU Commission is a glimmer of hope as the first vaccine trial gets under way in South Africa.

The Network for Genomic Surveillance in South Africa (NGS-SA) presents a molecular epidemiological study of the first twenty-one SARS-CoV-2 whole genomes sampled in the first port of entry, KwaZulu-Natal (KZN), during the first month of the epidemic.

This report focuses on the first SARS-CoV-2 388 genomes from Africa. These genomes were accessed from GISAID and analysed against a backdrop of reference sequences. By comparing our viral genomes against others, we can infer how and when SARS-CoV-2 was introduced into Africa and how it has spread within the continent.

KRISP is a founding member of the Network for Genomic Surveillance in South Africa. A network of laboratories, scientists and academic institutions that have joined forces to ensure the public health responses to COVID-19 in South Africa have access to the best possible scientific data.

Experts weigh in on how to avoid inaccurate results during Covid-19 testing. Distance, hair and sweat can all affect the reading of the temperature scans you've been experiencing at work, shopping malls and schools.

Nick Hammer chats to Prof Tulio De Oliveira, Dr. Richard Lessells and Prof Yunus Moosa about the trial on the UK of Dexamethasone for COVID-19.

With Covid-19 now growing by leaps and bounds in South Africa, a Mail & Guardian survey has spotlighted the nationwide shortage of staff, equipment and facilities needed to cope with the infected people who are set to flood the healthcare system when the outbreak hits its peak.

L'Afrique apporte sa pierre à la science (9). Cinq cents personnes du Cap, foyer de l'épidémie de coronavirus en Afrique du Sud, participent à une étude en double aveugle sur le vaccin contre la tuberculose.

On 9 March, a patient who had recently traveled to Europe and had symptoms of COVID-19 visited the emergency department of St. Augustine's, a private hospital in Durban, South Africa. Eight weeks later, 39 patients and 80 staff linked to the hospital had been infected, and 15 patients had died—fully half the death toll in KwaZulu-Natal province at that time.

L'Afrique apporte sa pierre à la science (3). Dans une étude saluée par la revue « Science », le laboratoire Krisp établit avec une rare finesse la chaîne de contamination dans un hôpital de Durban.

An investigation into the first major outbreak of Covid-19, at a Durban hospital, shows that staff members spread the virus, raising concerns about the safety of healthcare workers as infections rise.

South Africa leads this continent in many ways. Right now, it is poised to lead Africa into the next, most dangerous phase of the pandemic, as the country braces itself for a dramatic rise in infections that will almost certainly overwhelm its relatively well-resourced healthcare system.

The South African Obstetric Surveillance System Consortium in partnership with the SA MRC Maternal and Infant Health Strategies Unit and KRISP/UKZN invites clinicians from South African obstetric institutions to participate in this national study.

The report outlines in detail how SARS-CoV-2, which causes COVID-19, spread through Netcare's 149-bed facility in Durban. This piece in Bhekisisa also contains simple take-away messages and recommendations on how to protect health care workers and hospitals from COVID-19. Download the full investigative report here.

Durban, South Africa, March 9. A man goes to the emergency room of the San Agustín hospital. He coughs, his head hurts. They admit him and share a stay with a woman who has had a heart attack. That man has just come from Europe, the lady lives in a nursing home.

A new investigative report details the rapid spread of coronavirus disease in St Augustine's Hospital in Durban, and how it could have been prevented. The study, which Bhekisisa has seen, was conducted by researchers at the University of KwaZulu-Natal's (UKZN) Nelson R. Mandela School of Medicine and the KwaZulu?Natal Research Innovation & Sequencing Platform, KRISP.

South Africa's lockdown seems to have stopped the winter influenza outbreak in its tracks. School closures and travel bans are likely to have prevented seasonal flu from taking hold. A mild flu season will help in the fight against Covid-19, but lifting lockdown could result in flu resurging.

As schools get ready to reopen, models suggest the country will still not have enough ICU beds at the virus peak. In the meantime, court battles rage while unions fight to keep miners safe.

This report presents the findings and recommendations of an investigation into a nosocomial outbreak of coronavirus disease 2019 (COVID-19) at St. Augustine's Hospital in Durban, South Africa. The investigation began on 4 April after the identification of a number of confirmed COVID-19 cases and three deaths at the hospital. Investigation methods included medical record reviews, ward visits, and interviews with health care workers and management. A detailed timeline of patient cases was constructed to generate hypotheses as to the spread of infection through the hospital. In addition, DNA sequencing of severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) nucleic acid extracted from nasopharyngeal and oropharyngeal swab samples was performed and phylogenetic analysis was conducted.

The investigation found that between 9 March and 30 April 2020, there were 119 confirmed cases identified at St. Augustine's Hospital (39 patients and 80 staff). Fifteen of the 39 patients died (case fatality rate 38.5%). The most plausible explanation for the outbreak is that there was a single introduction of the severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2)

The coronavirus spread rapidly through Netcare St. Augustine's Hospital and beyond and made up 14% of KwaZulu-Natal's infections by the end of April. The study, seen by Bhekisisa, was conducted by researchers at the University of KwaZulu-Natal's (UKZN) Nelson R. Mandela School of Medicine and the KwaZulu?Natal Research Innovation & Sequencing Platform, Krisp.

An investigation has found there were 119 confirmed cases of coronavirus at Durban's St Augustine's Hospital by the end of last month. The probe into the Covid-19 outbreak at the hospital was led by a team at University of KwaZuu-Natal.

Durban - The Netcare group has welcomed the findings of a report which investigated the outbreak of Covid-19 at the St Augustine's Hospital. On Wednesday, the investigative report was released and showed that between March 9 and April 30, there were 119 people – among them 39 patients and 80 staff members – who had confirmed cases identified at the hospital. Fifteen of the 39 patients died.

The outbreak of coronavirus disease at the Netcare St. Augustine's Hospital in Durban, that led to the infection of at least 135 patients and staff in the hospital complex and people in a nursing home, was caused by a single patient admitted to the facility's emergency department early in March, a new report has found. The virus spread so fast in the hospital that infections caused by the outbreak in the hospital constituted almost 14% of Covid-19 cases in KwaZulu-Natal by the end of April.

The Covid-19 outbreak at St Augustine's Hospital in Durban which forced health authorities to close it down, resulted in 119 people testing positive and 15 patient deaths.

Durban - An investigation into the Covid-19 outbreak at Durban's St. Augustine's Hospital has found the cluster outbreak was as a result of patient to patient transfer after both were admitted to the hospital around the same time.

An investigation has found there were 119 confirmed cases of coronavirus identified at Durban's St Augustine's Hospital by the end of last month. The probe into the COVID-19 outbreak at the hospital was led by a team at UKZN.

A newly released investigation report revealed there were a total of 15 patient deaths and 119 confirmed Coronavirus cases at the Netcare St Augustine Hospital.

The report by a University of KwaZulu-Natal-led research team was made public on Wednesday following an investigation at the facility. A new report shows that 14% of all COVID-19 cases in KwaZulu-Natal can be traced to the coronavirus outbreak at Netcare's St Augustine's Hospital in Durban

Clusters of infections contribute to surge in the Western Cape. Contrary to projections, Gauteng has seen slow rise in numbers. By Pauline Bax and Prinesha Naidoo, Bloomberg.

As President Cyril Ramaphosa eases restrictions on one of the most stringent lockdowns in the world, the number of Covid-19 daily infections has continued to rise. Up to 700 people a day tested positive this week.

Professor Tulio de Oliveira is the director of the KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP) at UKZN. He joins us for another Covid-19 information session.

Nick Hammer chats to Prof Tulio De Oliveira about how the government's interventions, including the travel ban and lockdown, potentially averted the death of at least 20 000 people.

Since Lockdown began on the evening of 26 March 2020, South Africa is yet to see the flattening of the Curve. Professor Tulio de Oliveira has argued that the value of lockdown cannot be underestimated.

As the nation debates about whether lockdown restrictions must be eased, Professor Tulio de Oliveira argues that its value cannot be underestimated.

The coronavirus outbreak in South Africa has hit hardest in the Western Cape, home to the city of Cape Town.

Comparative trajectory analysis from the day of 100th infection shows SA on 11,000 cases, while UK at that point on 161,000

Government interventions, including the travel ban and lockdown, have potentially averted at least 20 000 deaths, says a top scientist

UKZN's Professor Tulio de Oliveira is a bioinformatician from the KwaZulu-Natal's Research, Innovation and Sequencing Platform (KRISP) faculty - and he spoke to us this morning.

KwaZulu Natal's Research, Innovation and Sequencing Platform (KRISP) and the Big Data Flagship Program of the University of KwaZulu-Natal (UKZN) has a multi-disciplinary team of world-renowned experts which mainly focuses on analysis and control of viral outbreaks and genomic analysis.

In our April/May issue of 2020, We have worked very hard to produce and analyse COVID-19 data in real time. We have also sequenced many SARS-CoV-2 genomes in South Africa that showed how the virus was introduced in the country. We also worked with the media to help to translate scientific results to the general public. KRISP believes that open and independent scientific information is represented by good journalism that determines its value to the society it serves.

Cape Town - Confirmed Covid-19 infections in South Africa have risen to 5 951, with 13 deaths recorded in the past 24 hours, Health Minister Zweli Mkhize announced on Friday. This is an increase of 304 confirmed cases on Thursday's figures.

The Covid-19 infection rate could jump from 5% to 10% per day as South Africa emerges from a five-week hard lockdown from Friday. Scientists are expecting a "rapid rise" in infections ahead of the disease hitting its peak in summer.

As South Africa edges towards the end of the so-called hard lockdown, and with an expected spike in Covid-19 cases around the corner, just 27 Covid-19 patients are on ventilator support in hospital, seemingly in line with government's projections. Sarah Evans from News24 highlights our Big Data COVID-19 analysis of in South Africa.

Many deaths are still likely to hapen because of the coronavirus, but a promising vaccine against Covid-19, developed by the University of Oxford, started human trials this week. UKZN scientists warn many deaths still likely before virus is conquered

Scientific research on Covid-19 has been published at an unprecedented scale and speed, but some fear that this is at the cost of scientific rigour. Adele Baleta explores the pros and cons of high-speed science. By Adele Baleta for Spotlight, Daily Maverick and News24, 24 April 2020

The use of data science has become a critical 'gold rush' as research scientists across the globe partner on scientific breakthroughs, to better understand the novel coronavirus (COVID-19) and recommend strategies to help address its complexities

Durban - A team of world renowned scientists based at the University of KwaZulu-Natal has launched a fundraising campaign to support the analysis of Covid-19 data - which could provide vital research and insight on the spread of the virus across both South Africa and globally as the world battles to contain the devastating pandemic.

Scientists at the University of KwaZulu-Natal (UKZN) have launched a fundraising campaign to finance independent research into the Covid-19 outbreak in South Africa. Donors will qualify for Section 18A tax certificates, issued by the UKZN Foundation.

They have produced five of the six COVID-19 viral genomes in the country, which clearly showed how the virus was introduced into South Africa. KwaZulu Natal's Research, Innovation and Sequencing Platform (KRISP) and the Big Data Flagship Programme of UKZN collaborate in a fund raising campaign.

The countries which have had some of the best responses to the COVID-19 pandemic, Singapore and South Korea, have closely followed scientific advice. Our government has already used our results to show that South Africa is flattening the curve. We need your support to ensure that we can keep producing high-level scientific information to guide our national response.

KRISP has partnered with the Pro-Vice Chancellor of Big Data Analysis at UKZN, Prof. Francesco Petruccione to put together a team with more than 20 researchers, including computer scientists, mathematicians, statisticians, bioinformaticians, infectious diseases clinicians, theoretical physicists and quantum computing scientists to analyze the COVID-19 outbreak in South Africa.

Watch the full videos of the Big Data, Genomics and Clinical Medicine presentations of COVID-19 by experts. Full videos of Prof. Salim Abdool Karim, Prof. Tulio de Oliveira and Dr. Richard Lessells in April 2020. Data@breakfast organised by Prof. Francesco Petruccione of UKZN Big Data Flagship program.

The extended five-week national lockdown has postponed South Africa's worst-case Covid-19 scenario to September, a government projection shows. March was arguably the busiest month for President Cyril Ramaphosa in his tenure as head of state. Every other day, the President is putting out fires.

A UKZN seminar series has been moved online in the face of the COVID-19 epidemic. IT was a logical step for UKZN Pro Vice-Chancellor for Big Data and Informatics, Professor Francesco Petruccione, to turn to the online world to continue with his monthly data@breakfast seminar series in a time of national Covid-19 lockdown.

Lessons learned in Eshowe, South Africa, one of the areas worst hit by the HIV pandemic, are being used against coronavirus. Jason Burke in Eshowe writes to The Guardian about KRISP and UKZN work.

Durban - Conflicting information and misinformation about whether to wear a mask or not during the Covid-19 pandemic has left many people confused.The World Health Organisation (WHO) has recommended people not wear a mask unless they are sick with Covid-19 or caring for someone who has the virus.

Durban - ONLY polymerase chain reaction (PCR) tests are being used to test for the coronavirus in South Africa, which can detect infection before patients become symptomatic, and not rapid serological tests, which are not recommended by experts for public use.

Speaking to the media on Wednesday night, Health Minister Zweli Mkhize said, We will only fight coronavirus with facts and evidence-based strategies, not fake news. Mail and Guardian news, 2 April, 2020.

A young single mother has started her own business making masks, which she distributes in rural areas. Currently there's a huge debate on the subject of a face mask's efficiency, with the World Health Organisation saying there is no evidence to suggest it curbs the spread. However, some experts believe it does indeed work, as studies into other coronaviruses proved masks can reduce the risk.

South Africa stands at a crossroads in the fight against the new coronavirus — and winning the battle will hinge on the decisions we make now about how quickly and how broadly we begin to test for the virus. In a grim news cycle, Health Minister Zweli Mkhize's announcement yesterday that the country is evaluating rapid tests for the new coronavirus is something to celebrate. Bhekisisa opinion piece by Dr. Richard Lessells and Prof. Mosa Moshabela.

South Africa's strategy to defeat Covid-19 is to lock down the country and scale-up testing to quickly identify people who may have been infected with the SARS-CoV-2 virus. Health journalism by Adele Baleta for Spotlight 31 March 2020.

Durban - An infectious disease specialist says that although the world is much more prepared to deal with a pandemic than in previous years, African countries are still unable able to respond adequately to a respiratory virus like Covid-19.

Südafrika hat die meisten Corona-Fälle in Afrika. Auch wenn die Zahlen denen in Europa noch hinterherhängen, warnen Experten vor einer rasanten Ausbreitung des Virus. Von Julia Jaki, Kapstadt, 27. März 2020

There is much we do not understand about the virus and how it will affect our bodies, especially after Minister of Health Zweli Mkhize said that 60% to 70 % of people could be infected by Covid-19. The Mail & Guardian asked different experts — including disease specialist Dr Richard Lessells, the National Institute for Communicable Diseases, and the World Health Organisation (WHO) — for information about this coronavirus.

Together with the Big Data group of UKZN, we started a daily update of the data on COVID-19 in South Africa and a weekly update on cases, deaths and genomic data in Africa. All of the scripts for generation of the data is deposited open in repositories as all any data developed by our team.

Three thousand people have died in Italy as a result of Covid-19, with more than 35000 infected. Three weeks ago, the country passed the 150 mark for infected people. It took three weeks to get to that number. In South Africa, we passed the 150 mark on Thursday, two weeks after the first local positive test. Mail and Guardian, 19 March 2020.

The University of KwaZulu Natal's Research Innovation and Sequencing Platform (KRISP) boasts state-of-the-art laboratory facilities and scientific expertise and capacity not commonly found in Africa. This places our multidisciplinary team in the ideal position of being able to play a critical role in supporting the public health response to the COVID-19 pandemic. The team has placed all current research activities and services on hold to focus full-time on helping with this outbreak. Please help to fund it by donating to our activities here.

The National Institute for Communicable Diseases can run hundreds of tests at the same time but ultimately the number of tests South Africa will be able to carry out for the new coronavirus depends on the machines, people and testing supplies available.

We developed an rapid bioinformatics tool for the identification and characterization of novel coronavirus genomes. The tool was released in January 2020 and published in Bioinformatics in February 2020 as an open access tool to help to characterise genomes of COVID-19 viruses.

In our February/March issue of 2020, we highlight our work on the current coronavirus outbreak. We published a software application for rapid identification and characterization of novel coronavirus genomes. Our quick response was lauded by the national and international media. In this issue, we also cover the award from UKZN vice-chancellor to Dr. Veron Ramsuran, launched a CRISPR-Cas9 laboratory and organized talks, exhibitions and training workshops.

KRISP was in the front and second page of Saturday Independent newspaper, including an article on how a reporter from nature has followed our hard work to produce and release the Genome Detective Coronavirus Tool in January 2020.

As news of the deadly Coronavirus spreads across the globe, a Durban man, teaching English in Hangzhou, describes the eerie streets of a city on lockdown and researchers at the University of KwaZulu-Natal (UKZN) prepare for the potential of a Coronavirus outbreak in Durban.

KRISP Talks by Prof. Tulio de Oliveira (KRISP UKZN & CAPRISA), Novel Coronavirus (2019-nCoV) Outbreak: Genomics & Epidemiology. This page summaries resources for coronavirus COVID-19 in KZN and South Africa and internationally. It also present our work on the creation of a genomics and bioinformatics pipeline for fast and accurate analysis of coronavirus genomes. KRISP is bases at K-RITH building, Nelson R Mandela School of Medicine, UKZN, Durban, South Africa.