the gem - July 2024

number 7 - volume 7 July 2024

genomics, epidemics & microbes

the gem

New AI Pioneers We graduate five AI scientists in Africa

Mpox evolution A new clade of Mpox emerge in the DRC read it online

Gen Z in the lab We expand our training to high-school students

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summary

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editorial

new AI pioneers in Africa

Africa’s cholera crisis

Welcome to the inaugural edition of the “the gem: genomics, epidemics & microbes” magazine. The idea of producing a magazine originated during a visit to a friend’s house in Sweden, where discussions about science and public engagement led to the concept.

We feature the five AIMS students who completed AI-driven projects at CERI, addressing global health challenges like arbovirus transmission, digital disease surveillance, dengue prediction, climate disaster impacts, and SARS-CoV-2 variant detection.

We highlight how extreme weather events in Africa over the past three years have led to severe cholera outbreaks, causing over 6,000 deaths and nearly 350,000 cases, with the situation exacerbated by poor sanitation and climate change.

the gem: Centre for Epidemic Response and Innovation (CERI) & South African Centre for Epidemiology and Modeling Analysis (SACEMA), Stellenbosch University, Stellenbosch & KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), UKZN, Durban; director: Tulio de Oliveira; editors: Cheryl Baxter, Lenine Liebenberg, Maambele Khosa art director: Vitor Hugo Szortyka, graphic designers: Maambele Khosa, Vagner Fonseca, Paul Harris; linkedin: www.linkedin.com/company/ceri-su/; websites: www.ceri. org.za, www.sacema.org & www.krisp.org.za; Twitter: @ceri_news, @krisp_news; Youtube: www.youtube.com/@krisp-ceri

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uphill battle to make vaccines

mpox evolution and new clade

We feature a commentary on why Africa, in dire need of its own production capabilities, could once again be at the back of the vaccine queue in the next pandemic.

An mpox outbreak in eastern Democratic Republic of the Congo, caused by a distinct clade I MPXV lineage, involved 241 suspected cases with genomic data suggesting recent sustained human-to-human transmission.

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Gen Z in the lab The 2024 Gen S Campaign, led

by SAMRC, Stellenbosch University, and CERI, provided high school students with hands-on STEM experiences during Youth Month to address South Africa’s critical skills shortage and inspire future scientists

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editorial

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he idea of starting a magazine that highlight our work started in the most unusual of places. It started when I stayed in the house of one of my best friends in south Sweden. My friend, Vitor Hugo Szortyka, is a creative director, an artist and a designer. We were in primary and high school together and we both moved around the world a lot but always kept in contact and visited each other every couple of years as good friends should do. We also have great respect for each others work and were discussing some ideas about science and public engagement. After some ideas, he suggested that we move away from a newsletter and start a magazine. That is where ‘the gem’ idea originated, in a good friends house, with coffee on the verandah on a summer afternoon in Sweden.

The day after, I start my long journey back to the southern tip of Africa and in dozens of hours waiting in airports and inside airplanes, I developed the first sketches of the gem. When I returned to office, I discussed the idea with the head of scientific support at CERI, Dr. Cheryl Baxter. I was expecting her to tell me that I have been wasting my time, which is something that I do very well, but to my surprise, she liked the idea and said that she is happy to help! I went back to my friend Vitor with a first draft, proud of myself, and he again, gently, told me that my ‘design’ was not good, but as good friends do, he did not only criticize but worked for a couple of weeks to produced the master file for the gem magazine. So here we are, launching the gem, which happened by serendipity and positive vibes, on a summer day...

Text a nd inspir a tio n: Tulio de Oliveira

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Artificial Intelligence (AI)

New AI Pioneers Tackle Global Health Challenges text: Ma a m be l e K ho sa photo : Maambele Khosa

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ive students from the African Institute for Mathematical Science (AIMS) are leveraging AI to tackle global health challenges. As part of their Masters degrees, the students completed projects at CERI that focused on arbovirus transmission, enhancing digital disease surveillance, predicting dengue incidence, assessing climate disaster impacts, and detecting SARS-CoV-2 variants. Their innovative work, supervised by experts, aims to advance public health and resilience.

Artificial intelligence is revolutionizing the way we address global health challenges, offering innovative solutions to some of the most pressing issues of our time.

In this spirit, a new group of five students from diverse corners of Africa, completed their master’s projects with us at CERI. Each student brings a unique perspective and a shared determination to harness the power of AI for the betterment of public health.

Carlin Foka, a spirited young man from Cameroon, had

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always been fascinated by the intricacies of mathematics and machine learning. His undergraduate journey at HESTIM in Morocco had laid a solid foundation, and now, as a master’s student at Stellenbosch University, he was eager to apply his knowledge to real-world problems. Carlin’s project, supervised by Dr. Houriiyah Tegally, aimed to uncover the climatic and environmental correlates of arbovirus transmission in Africa using a phylodynamic framework. “This project is a great opportunity for me to apply my passion for mathematics and machine learning to tackle real-life problems related to healthcare,” he said.

Haingo Andry from Madagascar was equally enthusiastic about his project, which focused on enhancing digital surveillance for infectious diseases through large language models. Registered in the MSc. in Mathematical Sciences program, Haingo was drawn to the challenge of applying cutting-edge Natural Language Processing (NLP) techniques to address global health issues. “I chose to do this project as it presents a valuable opportunity to deepen my practical skills in NLP,”

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he explained. Under the guidance of supervisors Dr. Joicy Xavier and Dr. Houriiyah Tegally, Haingo was set to push the boundaries of AI in healthcare.

Olivier Adjagba, a dedicated AI student at AIMS South Africa from Benin, finds his research interests perfectly aligned with CERI’s goals. His project, which aims to explore the geographical links between environmental factors and population density on dengue incidence prediction, merges his passions for AI, healthcare, and climate science. He developed a Deep Learning model using Convolutional LSTM to make the prediction across both time and space. With Dr. Houriiyah Tegally and Prof. José Lourenço as his mentors, Olivier is ready to make significant strides in understanding the impact of climate on disease transmission.

Aness Chelfat, has a keen interest in the intersection of technology and societal impact. His research focuses on quantifying large populations following climate disasters using satellite remote sensing imagery. “I chose this research topic because it is challenging and new to

me. I love learning and exploring new areas, which I find exciting,” Aness says with a smile. “But more importantly, this research could help others, adding value to my studies and allowing me to contribute to society.”

Lastly, Aurel Agbodoyetin, deeply affected by the global disruption caused by the COVID-19 pandemic, is driven by a strong sense of purpose. His work, titled “AIenhanced Classification and Early Detection of SARSCoV-2 Variants for Timely Public Health Response,” aims to address the urgent need for effective strategies against emerging infectious diseases. His work represents a proactive approach, ensuring society is better prepared for future health crises.

As these students finalise their projects, the importance of their work resonates through their dedication and the innovative ideas they bring to the table. Each student, with their unique background and motivation, contributes to the collective goal of advancing knowledge and creating a healthier, more resilient world.

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CLIMADE

Africa’s cholera crisis worsens amid extreme weather events text: A l J a ze e r a a nd A sso cia te d Pr e ss ( AP) photo s: Tsvangirayi Mukwazhi/AP Patrick Ngugi/AP

In southern and East Africa, more than 6,000 people have died since a series of cholera outbreaks began in late 2021.

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xtreme weather events that have relentlessly hit parts of Africa in the last three years have caused crises of hunger and displacement. The storms, floods and drought also leave another deadly threat behind: some of the continent’s worst outbreaks of cholera.

In Southern and East Africa, more than 6,000 people have died and nearly 350,000 cases have been reported since a series of cholera outbreaks began in late 2021.

Malawi and Zambia have had their worst outbreaks on record. Zimbabwe has had multiple waves. Mozambique, Kenya, Ethiopia and Somalia also have been badly affected.

All have experienced floods or drought – or both.

Health authorities, scientists and aid agencies say the unprecedented surge of the water-borne bacterial infection in Africa is the newest example of how extreme weather is playing a role in driving disease outbreaks.

“The outbreaks are getting much larger because the extreme climate events are getting much more common,” said Tulio de Oliveira, a South Africa-based scientist who

studies diseases in the developing world.

De Oliveira, who led a team that identified new coronavirus variants during the COVID-19 pandemic, said Southern Africa’s latest outbreaks can be traced to the cyclones and floods that hit Malawi in late 2021 and early 2022, carrying the cholera bacteria to areas it does not normally reach.

Zimbabwe and Zambia have seen cases rise as they wrestle with severe drought and desperate people rely on less safe sources of water like boreholes, shallow wells and rivers, which can all be contaminated. Days after the deadly flooding in Kenya and other parts of East Africa this month, cholera cases also appeared.

Historically vulnerable, Africa is even more at risk as it faces the worst effects of climate change as well as the El Nino weather phenomenon, health experts say.

The World Health Organization (WHO) calls cholera a disease of poverty, as it thrives where there is poor sanitation and a lack of clean water. Africa has had eight times as many deaths this year as the Middle East, the second-most affected region.

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Billions of dollars have been invested into other diseases that predominantly affect the world’s most vulnerable, like polio and tuberculosis, largely because those diseases are highly contagious and could cause outbreaks even in rich countries. But that is not the case with cholera, where epidemics remain contained.

In what has become a perfect storm, the WHO also said this month that there is a “critical shortage” of oral cholera vaccines in the global stockpile. Since the start of 2023, 15 countries – the desperate few – have requested 82 million doses to deal with deadly outbreaks while only 46 million doses were available.

There are just 3.2 million doses left, below the target of having at least 5 million in reserve. Vaccines alliance GAVI and the UN children’s fund UNICEF said last month that the approval of a new cholera vaccine would boost stocks. But the result of the shortage has already been measured in deaths.

While there are currently cholera epidemics in the Middle East, the Americas and Southeast Asia, Africa is by far the worst-affected region.

Full article: https://www.aljazeera.com/gallery/2024/5/24/africas-cholera-crisis-worsens-amid-extreme-weather-events

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Genomic epidemiology of the cholera outbreak in Malawi - Summary of our publication by Chabuka and colleagues: Since early 2022, in the aftermath of two extreme weather events, Malawi experienced its largest ever cholera outbreak, with over 58,000 reported cases and 1,761 deaths as of May 2023. We generated 49 high-quality, near-complete Vibrio cholerae genomes in Malawi from isolates collected between December 2022 and March 2023 from all three regions of Malawi. Using phylogenetic methods with 2159 publicly available genomes, we present evidence suggesting that the Malawi outbreak strains originated from the Pakistan outbreak, the estimated most recent ancestor of this lineage, named T15, was during the Pakistan floods, and once introduced into Malawi was exacerbated by major floods between June and October 2022. The extreme weather events and humanitarian crises in Malawi provided the environment for the spread of Vibrio cholerae, and the subsequent movement of large numbers of people may have facilitated its spread to susceptible populations in areas relatively unaffected by cholera for over a decade.

Cholera was first reported in Malawi in 1973 and has been endemic since 1998 with annual increases in incidence occurring during the rainy season (NovemberMay), particularly in the southern part of the country.

Prior to 2022, Malawi had experienced three large cholera outbreaks: in 1998-1999, 2001-2002, and 2008-2009.

Since early 2022, in the aftermath of two extreme weather events, Malawi has been experiencing its largest recorded

“The outbreaks are getting much larger because the extreme climate events are getting much more common,” said Tulio de Oliveira, a South Africa-based scientist who studies diseases in the developing world.

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genomics, epidemics & microbes

cholera outbreak, with over 58,000 confirmed cases and 1761 deaths as of the end of May 2023.

Previous genomic analysis has revealed cholera epidemics in Africa to be associated with transcontinental transmission of V. cholerae O1 El Tor sublineages from Asia, followed by regional cross-border spread within Africa. To understand the origin of the current Malawi cholera outbreak, the Public Health Institute of Malawi (PHIM) partnered with the Centre for Epidemic Response and Innovation (CERI), a specialized genomics facility of the Africa Centres for Disease Control and Prevention (Africa CDC) and World Health Organization AFRO (WHO AFRO), to perform in-country genomic sequencing of V. cholerae.

Here, using phylogenetic and phylogeographic methods combined with epidemiological modelling, we present an initial report of the genomic epidemiology of the ongoing cholera outbreak in Malawi.

In this genomic analysis, we provide strong evidence of a link between the large cholera outbreaks in Pakistan and Malawi, consistent with prior genomic analyses revealing the importance of long-range V. cholerae transmission events between Asia and Africa. Our main findings agree with another recent analysis of the Malawi outbreak, and with a genomic analysis of six cases from South Africa in 2023 (three of which were epidemiologically linked to

Malawi). The extreme weather events and humanitarian crises in Malawi provided the environment for the spread of V. cholerae, and the subsequen movement of large numbers of people may have facilitated its spread to susceptible populations in areas relatively unaffected by cholera for over a decade.

The relatively narrow sampling date range for this genomic analysis means that we cannot confidently differentiate whether the introduction of V. cholerae was responsible for initiating the outbreak, or if it just contributed to the later expansion of the outbreak. Additional sequencing of isolates from earlier in the outbreak may help to clarify this. We are also working with partners in other heavily affected African countries to conduct genomic sequencing of V. cholerae isolates, which will help with understanding the extent of cross- border regional transmission at different phases of the outbreak.

Overall, this highlights the need for coordinated global and regional cholera prevention and control efforts, and the importance of heightened awareness, data sharing and preparedness whenever outbreaks are occurring in any part of the world.

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Va c c i n e s

Why Africa is facing an uphill battle to make its own vaccines text: Ve r ity B owm a n, T he Te l eg r a ph photo : Simon Townsley

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

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It was a shocking symbol of the West’s failure to honour its promises.

As governments vaccinated their people against Covid-19, the world was divided into rich and protected, and the poor and vulnerable. Africa, dependent on vaccines produced abroad, was left behind – despite the West’s pledge of equitable vaccine distribution.

But one positive seemed to come from the chaos: Africa and the West came to the realisation that something had to change, and it had to be fast. The continent was in dire need of its own production capabilities.

As the pandemic raged, in March 2022, Moderna, the biotech spearheading a revolution in mRNA vaccine technology, announced it would build a $500 million manufacturing plant in Kenya. It would produce half a billion doses of its Covid-19 vaccine annually, it said.

‘This is major,’ said Kenyan President William Ruto at the time.

But earlier this month Moderna revealed it had paused its plans, throwing its commitment to Africa into

doubt.

‘Moderna is abandoning a commitment to build highly needed and relevant vaccine manufacturing capabilities in Africa,’ said the Africa Centres for Disease Control and Prevention.

The decision is symbolic of the uphill struggle vaccine producers and international players face in breaking ground in the continent, which currently imports 99 per cent of all vaccines it uses.

‘With epidemics and pandemics, there is a cycle of enthusiasm, and less enthusiasm or neglect,’ said Dr Charlie Weller, Head of Prevention, Infectious Disease at Wellcome. ‘But how do we enable the long term sustainability of these manufacturing organisations?’

Moderna said earlier this month that not one African country had ordered its Covid-19 vaccine since 2022, leaving the company with $1 billion in losses and write-offs.

It simply wasn’t affordable for the plans for a new plant to go ahead – something experts have described as a reality check for others.

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The African Union (AU) has meanwhile set a target for the African vaccine manufacturing industry to supply over 60 per cent of the total vaccine doses required on the continent by 2040.

But with many vaccines already produced cheaply and on a mass scale in countries like India, the ‘pharmacy to the world’, it is difficult for local African manufacturers to establish themselves in the market.

Earlier this month the South African government ordered vaccinations from India, despite hosting its own mRNA hub, highlighting the tensions between price pressures and local production.

South African officials said that the decision to give a three-year contract to Indian generic company Cipla instead of approaching Cape Town’s Biovac would save the health department so much money that it could introduce two new childhood vaccines.

Cipla has its vaccinations made by the Serum Institute of India – a well-oiled vaccine conglomerate famed for producing low cost doses for the global south.

A vaccine queue ‘come the next pandemic’ Professor Petro Terblanche, the Managing Director of Cape Townbased Afrigen Biologics, where the WHO’s mRNA Hub is based, told the Telegraph that the move highlights the need to ‘support and nurture’ local production.

‘South Africa has a point scoring system and does make provision for local procurement. But the latter is not the only criteria – affordability is also important in tight budget situations.’

Professor Robin Shattock, the Head of Mucosal Infection and Immunity within the Department of Medicine at Imperial College London, said that affordability is the ‘main hurdle’.

‘It makes no sense to build capacity if there is no need or return on investment … African made vaccines

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will only grow if African countries are prepared to pay some sort of premium for an African made product.’

Professor Shattock believes that there is a moral duty to ensure that vaccines are affordable, rather than where they are made. However, he adds, the reality is that Africa will remain vulnerable until this issue is solved.

‘We are left with key tensions.

Ensuring the lowest costs for life-saving vaccines doesn’t equate to making them in Africa – [but] if ‘African made’ vaccines are to be ensured, increased costs will need to be supported. However, without African capacity, then countries may again find themselves in a queue come the next pandemic.’

Scientific brain drain The mRNA vaccine technology transfer hub in South Africa has trained scientists from 15 countries, including six in Africa, to produce mRNA vaccines themselves.

Afrigen developed an mRNA Covid-19 vaccination within a year of the hub’s launch, but with the market for Covid vaccinations stalling it has been forced to look elsewhere.

The company is now working to develop mRNA vaccines for tuberculosis and HIV, but researchers say it could take decades for such new vaccines to come to market – making the economics of the hub uncertain.

‘We can’t forget they are businesses, and they need to look at economic viability,’ said Dr Weller.

Some say the odds are stacked against Africa when it comes to mRNA production.

‘Africa and multiple countries from around the world and the global South suffer from a big brain drain,’ said Dr de Oliveira.

‘The more that we train, the more people leave … Those individuals then become commodities, where they can essentially work anywhere. in the world.’ Dr. Tulio de Oliveira.

genomics, epidemics & microbes

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“Africa and multiple countries from around the world and the global South suffer from a big brain drain. The more that we train, the more people leave … Those individuals then become commodities, where they can essentially work anywhere in the world.”

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CLIMADE

Sustained Human Outbreak of a New MPXV Clade I Lineage in the Eastern DRC Autho r s: Va ka nia ki EH e t a l . 2 0 2 4 Jo ur na l : Nat Med (2024); https://doi. org/10.1038/s41591-024-031303/2024.05.07.24306997

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fever, lymphadenopathy and vesiculopapular rash. Two distinct genetic MPXV clades exist: clade I mainly in Central Africa, especially the DRC, and is associated with severe clinical symptoms and substantial mortality (4–11%), whereas clade II, largely confined to West Africa until the 2022 global epidemic, causes less severe illness and lower mortality of <4% (ref. 2).

utbreaks of mpox (formerly known as monkeypox) have historically resulted from zoonotic spillover of clade I monkeypox virus (MPXV) in Central Africa and clade II MPXV in West Africa. In 2022, subclade IIb caused a global epidemic linked to transmission through sexual contact. Here we describe the epidemiological and genomic features of an mpox outbreak in a mining region in eastern Democratic Republic of the Congo, caused by clade I MPXV. Surveillance data collected between September 2023 and January 2024 identified 241 suspected cases. Genomic analysis demonstrates a distinct clade I lineage divergent from previously circulating strains in the Democratic Republic of the Congo (DRC). Of the 108 polymerase chain

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reaction-confirmed mpox cases, the median age of individuals was 22 years, 51.9% were female and 29% were sex workers, suggesting a potential role for sexual transmission.

The predominance of APOBEC3-type mutations and the estimated emergence time around mid-September 2023 imply recent sustained humanto-human transmission.

Mpox attracted global attention in 2022 due to a widespread epidemic across nonendemic regions with transmission linked to sexual contact. For more than 50 years, MPXV caused outbreaks in several endemic African countries, predominantly from zoonotic spillover with secondary transmission1. MPXV is an enveloped, double-stranded DNA virus of the Poxviridae family, which includes variola (the causative agent of smallpox, now eradicated), vaccinia (used in smallpox vaccination) and cowpox viruses. In humans, MPXV causes mpox, characterized by

As clade II outbreaks have waned, clade I MPXV infections in Central Africa have been increasing4, especially in remote forest areas, probably from to zoonotic spillover with secondary human-to-human transmission within households8,9.

Progressive annual increases in mpox cases were reported in the DRC, with a record 14,626 cases in 2023, possibly indicating a shift toward increased human-to-human transmission10. We recently documented a cluster of MPXV infections linked to sexual contact in the DRC11.

Concurrently, new mpox cases have continued to emerge in several previously unaffected areas of the DRC. In September 2023, the first-ever mpox cases were detected in Kamituga Health Zone, a densely populated mining area in South Kivu Province in eastern DRC. Initial sequencing of six cases from January 2024 by Masirika et al.12,13 revealed the presence of a divergent lineage of clade I. In this Brief Communication, we describe the results of an investigation into this outbreak, including detailed genomic analysis of cases dating back to September 2023, to elucidate the origins and nature of this event.

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CAN WE BRIDGE THE GAP? 1 5 FE L LOWSHI PS, 2900+ APPLICATIO N S - CAPACI T Y B UI LDI NG I N GE N O MIC AND B I OI NFORMATI CS TRAI NI NG text: M a a m be l e K ho sa photo : M a a m be l e K ho sa

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ast month, we announced a call for applications for 15 fellowships focusing on genomic and bioinformatics training. The response was overwhelming – In just three weeks, we received an astounding 2000+ applications. We’re deeply grateful to everyone who applied, showcasing the immense interest in advancing expertise in these critical fields.

However, this overwhelming response underscores a pressing need: the demand far exceeds our current capacity. While we regret that we can’t accommodate everyone, we recognize the importance of addressing this gap collaboratively. To all applicants, we extend our heartfelt appreciation for your interest and commitment. While we may not be able to offer most of you a fellowship this time, we encourage you to stay engaged and explore future opportunities. Together, let’s continue to work towards building a brighter future in genomics and bioinformatics.

The field of genomics and bioinformatics is pivotal for advancing our understanding of complex biological systems and diseases. It holds the promise for revolutionary advancements in areas ranging from agriculture to medicine. The high number of applications for such a limited number of positions reflects a glaring disparity between the demand for training in these cutting-edge fields and the available opportunities.

Addressing these challenges is no small feat and it cannot be done in isolation.

Collaboration across academia, industry, and government is essential. By pooling resources and expertise, we can create more comprehensive training programs that not only meet the current demand but also anticipate future needs.

In order to respond to the training needs, CERI, KRISP and SACEMA are organizing and delivering the following training events: 15-19 July - Genomic sequencing advanced workshop at CERI, South Africa 22-26 July - Bioinformatic analysis advanced workshop at CERI, South Africa 23-25 July - Separations Training Academy - WGS Workshop, 4-9 Aug - 29th International Bioinformatics & Virus Evolution & Molecular Epidemiology, Brazil 13-15 August - Separations Training Academy - Metagenomics Workshop 16-17 Aug - ISME workshop Microbiome training at CERI, South Africa For more information on our training courses and programs please visit our websites: https://ceri.org.za, https:// sacema.org and https://krisp.org.za

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Meet some of our past fellows:

GENOMICS AFRICA & CLIMADE FELLOW: GENOMICS AFRICA & CLIMADE FELLOW: Julia C Andeko is a researcher at Centre Interdisciplinaires de Recherches Medicales de Franceville (CIRMF), Franceville, Gabon.

Julia C Andeko came to the CLIMADE fellowship CERI at the University of Stellenbosch to receive training on pathogen sequencing to enhance their work in whole genome sequencing of climate amplified diseases and other epidemics in Gabon.

Trained received: Advanced Bioinformatics analysis nd Hands-on sequencing on Illumina sequencing..

Fellowship sponsors: CLIMADE consortium funded by the Rockefeller Foundation and the World Bank.

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DRoberta Lansana is a researcher at the Ministry of Health and Sanitation, Sierra Leone.

Roberta Lansana came to the CLIMADE fellowship CERI at the University of Stellenbosch to receive training on pathogen sequencing to enhance their work in whole genome sequencing of climate amplified diseases and other epidemics in Sierra Leone.

Training received: Advanced Bioinformatics analysis and Hands-on sequencing on Illumina sequencing..

Fellowship sponsors: CLIMADE program funded by the Rockefeller Foundation and World Bank.

GENOMICS AFRICA & CLIMADE FELLOW: Anboukaria Housseni is a researcher at the INRAPE zoonosis laboratory, Comores Anboukaria Housseni came to the CLIMADE fellowship CERI at the University of Stellenbosch to receive training on pathogen sequencing to enhance their work in whole genome sequencing of climate amplified diseases and other epidemics in Comores.

Training received: Advanced Bioinformatics analysis and Hands-on sequencing on Illumina sequencing..

Fellowship sponsors: CLIMADE program funded by the Rockefeller Foundation and World Bank.

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GENOMICS AFRICA & CLIMADE FELLOW: Kevin Sanders da Rosa Carvalho is a researcher at the Instituto Nacional de Saúde Pública, Cape Verde.

Kevin Sanders da Rosa Carvalho came to the CLIMADE fellowship CERI at the University of Stellenbosch to receive training on pathogen sequencing to enhance their work in whole genome sequencing of climate amplified diseases and other epidemics in Cape Verde.

Training received: Advanced Bioinformatics analysis and Hands-on sequencing on Illumina sequencing..

Fellowship sponsors: CLIMADE program funded by the Rockefeller Foundation and World Bank.

GENOMICS AFRICA & CLIMADE FELLOW: GENOMICS AFRICA & CLIMADE FELLOW:

Aloysious Ssemaganda is a researcher at the Uganda National Health Laboratories and Diagnostic Services-Central Public Health Laboratories.

Plácida Iliany Maholela is a researcher at the INS (National Health Institute of Mozambique)

Aloysious Ssemaganda came to the CLIMADE fellowship CERI at the University of Stellenbosch to receive training on pathogen sequencing to enhance their work in whole genome sequencing of climate amplified diseases and other epidemics in Uganda.

Plácida Iliany Maholela came to the CLIMADE fellowship CERI at the University of Stellenbosch to receive training on pathogen sequencing to enhance their work in whole genome sequencing of climate amplified diseases and other epidemics in Mozambique.

Training received: Advanced Bioinformatics analysis and Hands-on sequencing on Illumina sequencing..

Training received: Advanced Bioinformatics analysis and Hands-on sequencing on Illumina sequencing..

Fellowship sponsors: CLIMADE program funded by the Rockefeller Foundation and World Bank.

Fellowship sponsors: CLIMADE program funded by the Rockefeller Foundation and World Bank.

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CLIMADE

Disentangling seasonal introduction & establishment risk of dengue in Africa Autho r s: P o o n gava na n J e t a l . 2 0 2 4 Jo ur na l : medRxiV, https://doi.org/10.110

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he dengue virus is a significant global public health concern that poses a threat to Africa.

Particularly, African countries are at risk of viral introductions through air travel connectivity with areas of South America and Asia that experience frequent explosive outbreaks. Limited reporting and diagnostic capacity hinder a comprehensive assessment of continent-wide transmission dynamics and deployment of surveillance strategies in Africa.

The risk of dengue introduction into Africa from countries of high incidence was estimated based on origindestination air travel flows and epidemic activity at origin. We produced a novel proxy for local dengue epidemic activity using a composite index of theoretical climate-driven transmission potential and population density, which we used, along with travel information in a risk flow model, to estimate the importation risks.

We find that countries in east Africa face higher risk of importation from Asia, whereas for west African

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countries, larger risk of importation is estimated from South America. Some countries with high risk of importation experience low local transmission potential which likely hampers the chances that importations lead to local establishment and transmission. Conversely, Mauritius, Uganda, Ivory Coast, Senegal, and Kenya are identified as countries susceptible to dengue introductions during periods of persistent transmission suitability.

Our work improves the data driven allocation of surveillance resources, in regions of Africa that are at high risk of dengue introductions and establishment. This will be critical in detecting and managing imported cases and can improve local response to dengue outbreaks.

Research in context Evidence before this study Despite the significant global burden of dengue virus globally, Africa remains relatively understudied due to limited reporting and diagnostic capabilities. We searched PubMed for articles in English published on and before May 6, 2024, that included “Dengue OR dengue”, “Africa”, and “importation

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OR imported”. Few studies have investigated the introduction of dengue into African countries. Limited evidence includes phylogeographic studies describing a potential introduction of dengue from Brazil into Angola in 2013 and evidence of multiple historical introductions of dengue from Asia to Africa over several years. Before our study, none had employed a modelling framework to investigate the continental risks of importing dengue via viremic travellers into African countries from other regions of high dengue incidence.

Added value of this study This study provides a novel approach to assessing the risk of dengue importation into Africa, integrating temperature-dependent transmission potential and air travel data. By identifying high-risk regions and highlighting the complex interplay between travel patterns, population density, and ecological factors, our findings enhance the understanding of dengue dynamics in Africa. This information enables targeted allocation of surveillance resources, improving preparedness and response to potential dengue outbreaks in susceptible regions.

Results Dengue introduction risks from high incidence Asian and South American countries into Africa Several countries in Africa are estimated to have high transmission suitability for dengue and simultaneously high population density, indicating elevated potential for local transmission following viral introductions. At the same time, certain countries on the continent are receiving variable, and sometimes high volumes of international passengers from various Asian and South American countries. In 2019, over 504 million travellers entered the African continent from the 14 high-incidence countries.

Of the total number of travellers, 39% originated from Southeast Asia, 34% from South Asia and 27% from South

America). The months with the highest travel volume entering the African continent from these places were November, December, and January.

The risk flow of dengue from countries with high incidence rates, from Asia and South America show that South Africa and Egypt were the countries at higher risk of dengue importation followed by Kenya, Angola, Morocco, Seychelles and Mauritius (Figure 1). Egypt is exposed to significant risk primarily originating from Asia, specifically its biggest risk coming from Malaysia. Kenya, Mauritius, Tanzania, and Uganda exhibit an elevated risk of introduction from India. Risks from Singapore were also high, especially towards Mauritius, South Africa and Egypt. Risks from Vietnam are relatively low across the entire continent, with the most significant potential impact observed in South Africa and Angola.

Additionally, Morocco and Nigeria are identified as regions with a considerable risk of disease introduction from Nicaragua.

The results reveal a general trend that countries in the southern and eastern African region are faced with higher risks of dengue importation from Asia, whereas central, western and a portion of northern African countries face higher risk of introduction from South America. South Africa is seen to receive large introduction risks from both origin regions. When considering the raw risks of introductions overlayed onto the local transmission suitability index across Africa, it becomes clear that high risk of introduction is not necessarily linked to high transmission suitability. For instance, the high risks of introduction into South Africa do not necessarily translate to transmission locally due to very low dengue transmission suitability.

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Fig 1: Mean risk of dengue introduction into African countries in 2019 from 14 countries in Asia and Latin America

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The risk of dengue introduction into African countries from 14 origin countries in As t h e c i r c l e s r e p r e s e n t t h e s i ze o f t h e r i s k av e r a ge d ov e r t h e 1 2 m o n t h s fo r e a c h a i r p is coming from and the fill colour of those countries are consistently matched. The f multiplied by population density to highlight the hotspots of high transmission at the

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sia and Latin America is represented by circles on the African continent. The size of ort in Africa. The colour of the circles represents the country from which the risk ill colour of the African continent represents the index of transmission potential destination.

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PhD Journey: Dr. Farirai Mutenherwa’s

Dr. Farirai Mutenherwa celebrates completing his PhD at the University of Kwazulu-Natal, emphasizing the importance of well-being alongside academic success. His research on ethical issues in HIV phylogenetic analysis highlights the need for privacy, informed consent, and ethical frameworks. He encourages PhD students to maintain a balanced lifestyle and a strong support system for success.

In the challenging world of doctoral research, where passion meets perseverance, finding balance is essential. Farirai Mutenherwa’s journey highlights this balance as he celebrates completing his PhD at the University of Kwazulu-Natal. He emphasizes the importance of prioritizing well-being alongside academic achievements, recognizing it as crucial to his success.

Mutenherwa’s doctoral research focused on the ethical issues in using HIV phylogenetic analysis to study transmission dynamics.

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More awareness ‘key’ to containing Mpox: experts amid rising cases The health department on Thursday confirmed a second death from the disease, barely 24 hours after the first was announced, and four other cases were confirmed by health minister Joe Phaahla. The first death was reported at Tembisa Hospital in Gauteng, while the second was a hospital in uMgungundlovu, KwaZulu-Natal. The department said the second patient was HIV positive and had listed Brakpan, Ekurhuleni, as his residential address.

All patients are men aged between 30 and 39 without a travel history to countries experiencing an outbreak, which suggests there is local transmission of Mpox in South Africa. Phaahla said the department is considering Mpox vaccines for pre- and post-exposure administration for high-risk groups and looking into which population groups should be targeted.

Reacting to the news was renowned bioinformatician Prof Tulio de Oliveira, who said on X it was ‘sad that a preventable and treatable disease is spreading and killing people here’ and that ‘as normal, vaccines have been hoarded by rich countries’. ‘This third generation of the vaccine ... is the current and new generation of vaccine that has been licensed by many countries and produced on a larger scale since 2022 during the Mpox outbreak in the northern hemisphere and seems to be efficient, but [the stock] has been concentrated in rich countries that keep the vaccine for themselves,’ he told TimesLIVE Premium.

Despite this criticism, De Oliveira praised the department for its fast response to the outbreak. ‘That is positive and I found it good that the minister decided to do a briefing highlighting what we knew about Mpox in South Africa and information about the first death. That was appropriate, the early communication and coming from a high-level [person] like the minister.

genomics, epidemics & microbes

Award: microbiome researcher honoured for his contribution to the field Prof. Thulani Makhalanyane, a microbiome researcher at Stellenbosch University, has been awarded the SASBMB Silver Medal for his national and international research excellence. Recognized for his active participation in the South African Society of Biochemistry and Molecular Biology, Prof. Makhalanyane advocates for equitable research partnerships in African microbiome studies.

Prof. Thulani Makhalanyane has been awarded the prestigious Silver Medal of the South African Society of Biochemistry and Molecular Biology (SASBMB) for his outstanding contribution to the field.

Successful Illumina Training Workshop at KRISP Durban, June 10, 2024 – The KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP) at the University of KwaZulu-Natal (UKZN) proudly hosted another successful Illumina training workshop from 7th to 10th June. The workshop was a collaborative effort made possible by our partners, DIPLOMICS (Distributed Platform in Omics) and SEPARATIONS. The four-day event brought together

researchers, scientists, and students keen to enhance their understanding of Illumina’s sequencing technology. The workshop featured in-depth sessions on the latest sequencing platforms, detailed protocols, and hands-on training that provided participants with invaluable practical experience.

“The participants gained significant insights into the Illumina technology, which will undoubtedly contribute to their research and the broader scientific community.”

The workshop covered various aspects of the Illumina technology,

“We are thrilled with the outcome of this workshop,” said KRISP Manager, Dr. Jennifer Giandhari.

Mauritian Scientists Two Weeks HIV Drug Resistance Training Mauritian virologists Mr. Ubheeram Jaykissen and Mr. Lallmahamood Shad completed a two-week training at KRISP in Durban to advance HIV drug resistance testing. This collaboration aims to enhance the Mauritian government’s ability to monitor and

combat HIV/AIDS with cutting-edge methodologies. “Through this collaboration, we aim to bolster the nation’s capacity to monitor and combat HIV/AIDS by implementing state-ofthe-art testing methodologies back home,” said Mr Jaykissen.

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Epidemics & Modeling

INNAUGURAL LECTURE Prof. Frank Tanser Delivers Inaugural Lecture on “The Rise (and Fall?) of South Africa’s HIV Epidemic: A Personal Perspective” text: S te l l enbo sch Unive r sity CCMD photo : Ignus Dreyer

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n April 23, 2024, Prof.

Frank Tanser, the Director SACEMA and of Population Health Innovation Program at CERI delivered an insightful inaugural lecture titled “The rise (and fall?) of South Africa’s HIV epidemic: a personal perspective.”

His talk provided a deep dive into the past, present, and future of HIV epidemic management in South Africa, underlining both the achievements and ongoing challenges.

During his presentation, Prof.

Tanser, a renowned epidemiologist with a rich background in the spatial and temporal dynamics of infectious diseases, discussed his extensive research on HIV, focusing on rural

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African communities most affected by the epidemic. He highlighted the critical need for effective intervention strategies to mitigate the impact of HIV and outlined his contributions towards evolving prevention and treatment policies across subSaharan Africa.

A highlight of his lecture was the discussion on the significant impact of antiretroviral therapy (ART) rollouts, which his research helped to shape, influencing rapid changes in government policies and showcasing a measurable decrease in HIV transmission rates at the community level.

Prof. Tanser also addressed the challenges ahead, emphasizing the need to maintain the momentum in combating HIV through increased ART

coverage and innovative prevention strategies. He detailed his involvement in two significant NIH-funded projects aimed at refining HIV prevention strategies and increasing the uptake of preventative measures among men in rural communities.

Reflecting on global efforts to end the HIV/AIDS epidemic as a public health threat by 2030, Prof. Tanser expressed cautious optimism. He noted that, while tremendous progress has been made, achieving this goal will require continued political will and financial investment.

“Unfortunately, I don’t think the world is on track to end the HIV/AIDS epidemic as a public health threat by 2030, but nevertheless, amazing progress has been made.

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VISITING COLLEAGUES AND FRIENDS Our teams travel around the world

to collaborative work, present at conferences and training events

Stanford, USA A team of four members from CERI and CLIMADE program lead by Dr. Houriiyah Tegally were in Stanford University to present multiple results at the 2024 Ecology and Evolution of Infectious Diseases (EEID) Conference and to engage and develop collaboration with global colleagues on ecology, modelling and evolution of Infectious Diseases The pre-conference started with Dr. Monika Moir and Graeme Dor (PhD student at CERI, Stellenbosch University) participating in two workshop tracks. The workshop was entitled: Disease Ecology in a Changing World: Quantitative Tools to Applied Solutions, that is split into two tracks.

Madison, USA Tulio de Oliveira, renowned for his pivotal role in identifying COVID-19 variants and variants of other viruses including HIV, dengue, chikungunya, hepatitis, and yellow fever, recently led the Steenbock Lectures hosted by UW–Madison’s Biochemistry Department and the Global Health Institute (GHI).

De Oliveira’s visit incorporated engagements with multiple units on campus which reflect the breadth and depth of scientific and public health expertise at UW–Madison. From the state-of-the-art Cryo-Electron Microscopy Research Center (CEMRC) and National Magnetic Resonance Facility at Madison (NMRFAM), to the pioneering interdisciplinary partnerships at the Data Science Institute

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Copenhagen, DK We were invited to attend the Novo Nordisk Foundation (NNF) Global Science Summit, which celebrates the 100 years of the NNF. This was a very exciting summit that was attended by approximately 100 global experts, including: Mr Bill Gates, Co-Chair, Bill & Melinda Gates Foundation: Dr Catherine Kyobutungi, Executive Director, African Population and Health Research Center Dr John-Arne Røttingen, Chief Executive Officer, Wellcome Trust Prof. Mads Krogsgaard Thomsen, Chief Executive Officer, Novo Nordisk Foundation. The summit discussed the main advances in health and science and opened a call for application between the NNF, Bill and Melinda Gates Foundation and the Wellcome Trust.

Kilifi, Kenya 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.

Dr. Houriiyah Tegally, Head of Data Science at the Centre for Epidemic Response and Innovation (CERI), presented the work done within the CLIMADE network and highlighted the crucial role of data integration in understanding and responding to climate-amplified diseases and epidemics in Africa.

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Gen Z in the lab text : Maa mb el e Kho sa p h oto: Maa mb el e Kho sa

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I “”

Inspiring young minds in science will advance Africa” Prof Lenine Liebenberg

Inspiring S o u t h Africa’s future scientists: The 2024 campaign, led by SAMRC, Stellenbosch University, and CERI, offers high school students handson STEM experiences during Youth Month. This immersive program aims to address the country’s critical skills shortage and ignite a passion for science in the next generation.

of high school learners in Science, Technology, Engineering, and Mathematics (STEM). Addressing this need, the Societal Impact Task Team at the South African Medical Research Council (SAMRC) Centre for Tuberculosis Research, alongside Stellenbosch University’s (SU) Department of Biomedical Sciences and the Centre for Epidemic Response and Innovation (CERI), collaborated for the 2024 Generation Science (Gen S) Campaign.

When should young people be formally introduced to careers? This question arises because while we all encounter careers informally early in life, seeing our parents head to the office, ply their trade, or manage a family business; there is much more impact that organizations can achieve by actively accommodating young people in career exploration opportunities.

The initiative strategically coincided with Youth Month, offering STEM school students an immersive experience in scientific disciplines such as Molecular Biology, Human Genetics, Immunology, Medical Physiology, and Clinical Anatomy. From June 18 to 21, divisions across SU’s Biomedical Research Institute (BMRI) hosted activities aimed at nurturing the next generation of scientists.

South Africa currently grapples with a critical skills shortage across various sectors, necessitating the inspiration and education

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At CERI, on June 20th, the lab atmosphere at CERI buzzed with excitement as twenty enthusiastic learners engaged in Next Generation Sequencing training led by Yusasha Pillay, a dedicated lab technician and Masters student. The session included an introduction to CERI, a comprehensive tour of the Genomics Centre, and a demonstration of Oxford Nanopore Technologies’ Midnight Protocol on the GridION sequencer.

Students witnessed the priming of a GridION flow cell, the loading of a SARS-CoV-2 library, and the setup of a sequencing run, followed by hands-on experience in these critical techniques.

“It was truly inspiring seeing the anticipation and curiosity these young learners brought to the lab.

They showed an eagerness to understand complex concepts, were not afraid to ask questions and were incredibly engaged with the hands-on next generation sequencing experience. It is exciting witnessing firsthand a generation who has such inspired views of the world and confidence in how they can contribute to improving it.” said Yusasha Pillay.

Professor Lenine Liebenberg warmly welcomed the learners, setting an inspiring tone for the day.

Accompanying them throughout the program was Dannie Kenny, Science Communications Manager at SU’s Divisions of Molecular Biology and Human Genetics, and Immunology, and Chairperson of the Societal Impact Task Team, who observed firsthand the students’ passion for science.

“As the SU Gen S programme coordinator, I am privileged to spend the full four days with the learners witnessing their excitement and curiosity with each interaction with our researchers. Seeing their confidence and enthusiasm for science grow from one day to the next highlights why programmes like this are of so much value and impact,” remarked Dannie Kenny.

Reflecting on this successful

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programme underscores the importance of investing in youth education and development. By offering a firsthand look into scientific research, programs like Gen S aim to inspire a new generation of scientists who will tackle global challenges head-on.

Looking ahead, organizations in science-based fields are prompted to consider how they can enhance the impact of Youth Month. How can more institutions create meaningful experiences that cultivate the scientific leaders of tomorrow? This reflection opens the door to innovative approaches that can shape the future landscape of scientific research in South Africa and beyond.

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Dr. Odianosen Ehiakhamen, Nigeria CDC during his fellowship at CERI, 2024

SACEMA South African Centre for Epidemiology and Modeling Analysis