̽��ֱ�� of Cambridge - Ian Goodfellow

Track and trace in Sierra Leone

cjb250 — Thu, 30 Sep 2021 13:17:39 +0000

Professor Ian Goodfellow played a crucial role in helping to bring the Ebola epidemic in Sierra Leone to a close in 2014. His team's work helped inform technology used today in the majority of SARS-CoV-2 sequencing, which is keeping us safe in the current pandemic.

Hunting for COVID-19 variants

cjb250 — Mon, 22 Mar 2021 11:06:50 +0000

Professor Sharon Peacock explains the story behind the UK's world-leading SARS-CoV-2 genomics capability.

“We’re in it for the long haul”

cjb250 — Wed, 21 Oct 2020 07:46:34 +0000

In late 2019, a new institute opened on the Cambridge Biomedical Campus. Its timing could not have been better - as the COVID-19 pandemic sent Britain into lockdown several months later, the institute found itself at the heart of the ̽��ֱ��’s response to this unprecedented challenge.

Rapid genome sequencing and screening help hospital manage COVID-19 outbreaks

cjb250 — Tue, 14 Jul 2020 22:30:00 +0000

Since the start of the UK pandemic, when the virus was spreading between people, a team of scientists and clinicians at the ̽��ֱ�� of Cambridge and Cambridge ̽��ֱ�� Hospitals NHS Foundation Trust (CUH) have been reading the genetic code of the virus to see if cases within the hospital are connected. This has enabled the hospital to fully investigate these outbreaks and to improve infection control measures to reduce the risk of further infections.

In addition, the introduction of a screening programme that involved repeat testing of staff, has helped the hospital to investigate clusters of COVID-19 infections, informing infection control measures and breaking chains of transmission. This has helped reduce the number of hospital-acquired infections, ensuring maximum safety for patients and staff as the NHS aims to re-start other services.

Researchers have published details of these investigations in two peer-reviewed journals, Lancet Infectious Diseases and eLife.

Genomic surveillance

Researchers in Cambridge have previously pioneered the use of genome sequencing as a way of managing hospital infections such as methicillin-resistant Staphylococcus aureus (MRSA), vancomycin resistant enterococci (VRE) and Clostridium difficile. They have also used real-time sequencing to rapidly identify transmission chains in epidemics such as the Ebola epidemic in Sierra Leone.

̽��ֱ��researchers have now turned their attention to COVID-19.

SARS-CoV-2, the coronavirus that causes COVID-19, is an RNA virus and as such its genetic code is prone to errors each time it replicates. It is currently estimated that the virus mutates at a rate of 2.5 nucleotides (the A, C, G and T of genetic code) per month. Reading – or ‘sequencing’ – the genetic code of the virus can provide valuable information on its biology and transmission.

As part of the COVID-19 Genomics UK (COG-UK) Consortium, researchers have been sequencing all available positive samples from patients admitted to the hospital with COVID-19 infection as well as a selection of samples collected from patients in regional hospitals across the East of England.

In a five week period from mid-March to late April, the team sequenced over 1,000 viral genomes. They used phylogenetic trees – akin to a ‘family tree’ – to look at how clusters of virus samples might be related, allowing them to help pinpoint particular wards or locations where the disease was spreading.

Dr Estée Török from the Department of Medicine at the ̽��ֱ�� of Cambridge said: “Genome sequencing gives us a rapid and reliable way of identifying cases of COVID-19 infection that are closely related within the hospital. This approach can provide vital information to help us to investigate the possible routes of transmission and to improve infection control measures to limit the spread of infection.”

̽��ֱ��researchers analysed 299 COVID-19 patients and found 35 clusters of genetically identical viruses involving 159 patients. By examining the patients’ medical records and ward location data researchers identified strong links between 58% of cases and plausible links between 20% of cases. ̽��ֱ��epidemiological and genomic data were fed back to the hospital infection control and management teams resulting in implementation of a range of measures to prevent further transmission, including isolation of infected patients, revised procedures for ward cleaning, enhanced use of personal protective equipment (PPE) and changes in staff social distancing behaviour.

As an example, six dialysis patients were admitted to different locations in the hospital with COVID-19 infection over a three-week period. Sequencing revealed that their viral genomes were identical. Epidemiological investigation showed that the patients dialysed at the same outpatient dialysis unit on the same days of the week and identified shared patient transportation and neighbouring dialysis chairs as risk factors for transmission. This enabled the infection control team to enhance infection control measures and prevented additional cases.

Professor Ian Goodfellow, from the Department of Pathology at the ̽��ֱ�� of Cambridge, said: “We’re able to combine genomic data with patients’ medical records to provide real time information to help the hospital review its infection control on a weekly basis. It’s also highlighted possible transmission networks less well documented, such as care homes, outpatient units and ambulance services.”

̽��ֱ��COVID-19 Genomics UK Consortium is supported by funding from the Medical Research Council, part of UK Research & Innovation (UKRI), the National Institute of Health Research and the Wellcome Sanger Institute.

Screening asymptomatic and symptomatic healthcare workers

In addition to genomic surveillance, CUH has implemented a screening programme in which all staff – both symptomatic and asymptomatic – are screened.

In May, Cambridge researchers reported that of the more than 1,000 staff members reporting fit for duty during April, 3% tested positive for the coronavirus.

Now, in a follow-up study published in eLife, they have found that, alongside a decline in patient admissions with COVID-19, the proportion of both asymptomatic and symptomatic healthcare workers testing positive declined rapidly throughout the following month.

̽��ֱ��team performed 3,388 tests at CUH between 25 April and 24 May. These included 2,611 tests on asymptomatic healthcare workers. ̽��ֱ��samples were analysed using a technique called PCR to detect genetic information from the virus on the swab.

̽��ֱ��researchers found that just 21 (0.8%) of the 2,611 tests carried out on asymptomatic healthcare workers returned positive, a large drop compared to the previous month.

Of the 771 tests carried out on symptomatic healthcare workers or those living with someone with possible infection, just 13 (1.7%) were positive – compared to 13% the previous month.

Dr Mike Weekes, from the Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), said: “Screening all staff at the hospital regardless of whether they are showing symptoms has helped us see a dramatic fall in the number of hospital-acquired infections. It means we’re able to spot new outbreaks faster, limiting their opportunity to spread.

“It’s important not to be complacent, though. There will inevitably be new outbreaks that occur – that is, unfortunately, the nature of a pandemic. But we hope our approach will help reassure both staff and patients that the hospital remains a safe place to give and receive care.”

In their report, the team give an example of where four symptomatic staff from the same general medical ward tested positive. In response, the team was able to carry out targeted screening of staff on the ward, allowing them to identify a cluster of infections and prevent further onward transmission.

“ ̽��ֱ��existence of clusters of infection in specific areas of the hospital shows the potential for staff and patients to become infected within the hospital environment,” said Professor Steve Baker from CITIID. “If left unchecked, these clusters could lead to self-sustaining outbreaks. Frequent testing at CUH allowed us to spot these clusters quickly and stop any further transmission.”

̽��ֱ��research was supported by Wellcome, the Addenbrooke’s Charitable Trust, the Medical Research Council, NHS Blood and Transfusion, National Institute for Health Research Cambridge Biomedical Research Centre and Cancer Research UK.

Reference

Meredith, LW, Hamilton, WL, et al. Rapid implementation of real-time SARS-CoV-2 sequencing to investigate healthcare-associated COVID-19 infections. Lancet ID; 14 July 2020; DOI: 10.1016/S1473-3099(20)30562-4

Jones, NK, Rivett, L, Sparkes, D, and Forrest, S et al. Effective control of healthcare worker SARS-CoV-2 transmission in a period of declining community prevalence of COVID-19. eLife; 19 June 2020; DOI: 0.7554/eLife.59391

Cambridge researchers have shown how rapid genome sequencing of virus samples and enhanced testing of hospital staff can help to identify clusters of healthcare-associated COVID-19 infections.

This approach can provide vital information to help us to investigate the possible routes of transmission and to improve infection control measures to limit the spread of infection

Estee Torok

Spc. Miguel Pena

Taking a swab to test for SARS-CoV-2 (COVID-19)

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Tackling COVID-19: Professor Ian Goodfellow

jg533 — Thu, 30 Apr 2020 09:58:31 +0000

This article is part of a series in which we speak to some of the many Cambridge researchers tackling COVID-19. For other articles about our latest COVID-19-related research, click here.

I work in the Department of Pathology at Addenbrooke’s Hospital. Although it’s now closed I’m still here, along with others from the Division of Virology and volunteers from the Department of Medicine. We’re supported by two great Lab Managers, who take it in turns to come in and keep the labs operational. Without them, and the staff working from home placing urgent orders, we’d be in a very difficult position.

I gained experience in setting up rapid diagnostics and in viral genetic sequencing when working on the Ebola epidemic in West Africa, and the recent Ebola outbreak in the Democratic Republic of the Congo. I’m lucky to have a great team of people here in Cambridge, including Dr Luke Meredith who has recently returned from a very stressful six months in South Sudan where he was a World Health Organisation Coordinator for Ebola and COVID-19 testing.

During the COVID-19 pandemic we are sequencing the coronavirus in real time. We collect samples from the Addenbrooke’s diagnostic team, sequence them, piece together the genomes and upload the data to a national server for analysis. ̽��ֱ��process is similar to many molecular methods we use routinely in the lab. We’ve been able to go from a standing start to producing viral sequences within 24 hours. This work is part a large national consortium headed by Professor Sharon Peacock in the Department of Medicine.

Revealing the genetic sequence of the virus can improve knowledge about COVID-19, and can provide invaluable information about the size of the epidemic and potential sources of infections. As highlighted by Dr Mike Ryan from the WHO, preparedness is important, but moving fast is essential. If you don't make decisions quickly then you get behind the epidemic curve. Responding rapidly is more important than making sure everything is 100% correct.

I’ve also been coordinating local volunteers to enable them to support the national response. Working with Rhys Grant in the ̽��ֱ��’s Department of Biochemistry, we’ve set up a website to capture volunteers with skills relevant to COVID-19 testing. Our database now has over 1200 people from Cambridge signed up. We’ve used it to get Cambridge staff engaged in the establishment of the national testing lab in Milton Keynes, and are feeding into local efforts to establish the fourth national testing centre here in Cambridge.

Rapid wide-spread testing of the community is the biggest challenge we face relating to this pandemic. It will be key to stamping out clusters of the infection in the coming months.

̽��ֱ��Cambridge research community has really come together. Everyone is keen to help in the response efforts, and the heads of institutes have been very supportive of anyone wanting to engage. Our staff have a real ‘can do’ attitude and a drive to overcome practical challenges. We’ve been able to engage people from many departments in various aspects of the work very quickly. Trying to wade through regulatory issues is more of a challenge.

We are also involved in developing a programme of research on COVID-19. A new initiative in the Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), led by Professor Ken Smith, has been set up to enable university-wide research on COVID-19. This draws together people from across the ̽��ֱ��, with various skills and interests in different aspects of COVID-19, to engage in collaborative studies. It makes use of the excellent facilities in the new Jeffrey Cheah Biomedical Centre, including a state of the art containment level 3 laboratory that enables work with live COVID-19.

After the pandemic is over I’m really looking forward to taking a well-deserved holiday with my family. Everyday life as an academic is challenging at the best of times, but when you layer on top the pressure of working in a pandemic, trying to support the efforts in multiple ways and trying to juggle so many things, it can really take its toll.

Goodfellow in the lab at Addenbrooke's Hospital with his team

How you can support Cambridge's COVID-19 research effort

Ian Goodfellow is no stranger to infectious disease outbreaks. In 2014 he left behind the safety of his Cambridge lab to join a taskforce fighting the hazardous Ebola outbreak in Sierra Leone. With COVID-19 now sweeping the globe, Goodfellow is once again applying his scientific expertise to finding solutions in real time.

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Call of duty: fighting Ebola in Sierra Leone

cjb250 — Fri, 13 Jan 2017 16:16:43 +0000

On the windowsill of Professor Ian Goodfellow’s office sit photographs of him with his children, and just down the corridor, his wife is carrying out research in the same department. Even at work, he is surrounded by constant reminders of the special things in his life, providing a sense of security.

His work, too – apart from the treadmill of seeking funding – is a secure, safe environment. Goodfellow is a basic scientist, carrying out lab-based studies into viruses such as norovirus, the winter vomiting virus. He doesn’t even come into contact with norovirus patients, so is at no particular risk of contracting this unpleasant, but relatively harmless, infection.

Yet in December 2014, Goodfellow chose to leave all of this security behind – for several months at a time – to join a taskforce fighting one of the most hazardous and frightening emerging infections of recent times, the Ebola outbreak in Sierra Leone. Since the epidemic began in West Africa in 2013 until it was declared over in March 2016, the virus infected more than 28,000 and killed over 11,000 people.

Goodfellow was one of over 30 people from Cambridge, coordinated by Dr Tim Brooks at Public Health England, who lent their support. Goodfellow helped set up one of the first diagnostic laboratories in an Ebola Treatment Centre near Makeni, in northern Sierra Leone, with support from the UK government. This was physically demanding and at times potentially dangerous work. “We had to move several tons of equipment and reagents by hand, in 35°C heat with over 90% humidity on a rather dangerous and very active building site,” he recalls. During their stay they encountered fires, electric shocks, and one of his own postdocs was bitten by both a spider and a snake.

Since the start of the epidemic, Goodfellow and colleagues have sequenced over 600 Ebola genomes, helping provide information about how the virus is evolving in, and how its evolution has been affected by, unprecedented levels of human– human transmission.

Towards the tail end of the epidemic, sequencing allowed researchers to trace the origin of new cases. “To end the epidemic, you need to make sure that any new cases are in transmission chains that are being monitored and are geographically contained, so you can pinpoint where this virus is coming from.”

̽��ֱ��Tonkolili District, for example, had been Ebola-free for several months when a new case occurred. “We needed to know if this new case had come from a new introduction from an animal host, from a neighbouring country, or if it was part of a chain of transmission that had been hidden from the healthcare providers.

There’s a lot of stigma around Ebola, so it was possible there was a whole cluster in a village and that no-one was reporting the cases. That would be a disaster: all of a sudden, you don’t go from one to two cases, you go from one to tens or even hundreds.”

By sequencing the virus, in a very short time they were able to trace the source back to a survivor in whom the virus had persisted, and to take appropriate measures to prevent further spread. In fact, their work showed that Ebola can persist in survivors for over 15 months after infection and be transmitted through unprotected sex, and possibly even from a mother to her child through breastmilk.

Now that the emergency has passed, the treatment centre has closed down, but its equipment is being used at the ̽��ֱ�� of Makeni Infectious Disease Research Laboratory in a building donated by the country’s president, Ernest Bai Koroma. ̽��ֱ��laboratory was kitted out with support from the Wellcome Trust and the Cambridge- Africa Programme, and now functions as a base for local and visiting scientists to carry out research. Goodfellow and his postdoc Dr Luke Meredith have helped train local technicians and researchers in some of the latest techniques in surveillance and sequencing of pathogens such as HIV and hepatitis B.

“We need to avoid ‘parachute science’, where scientists fly in, take samples and leave,” he insists. “It should be about developing sustainable partnerships, about developing local capacity. With training and support, local researchers have the ability to respond to these outbreaks; they just need the equipment and the infrastructure.”

This has already shown its value. A new case arose in January 2016 while neither Goodfellow nor any of his colleagues were in the country, but local scientists were able to use the techniques to trace the source of the infection.

Going to Sierra Leone was not an easy decision for Goodfellow, but he feels that he had a duty to respond. “ ̽��ֱ��academic virology community had a responsibility to offer support. We couldn’t just sit back and watch this massive epidemic explode in front of our eyes with the knowledge that we have skills that could be useful.”

Many of the scientists who went out have struggled to return to their normal work, he says – some even quit their jobs on returning to take up more front-line jobs or to undertake more translational research. For Goodfellow, it has certainly made him appreciate the contribution that basic science makes.

“Basic science can often feel removed from real world applications,” he says, “but the skills you gain from running a laboratory are actually very useful in these kinds of environments. ̽��ֱ��ability to think on your feet and to figure out solutions is invaluable.”

It has also given him some perspective about what he does. “ ̽��ֱ��satisfaction you get from being involved in a response like this and in capacity building is orders of magnitude better than publishing academic papers.”

Cambridge graduate Charlotte Dixon (Churchill), BA (2014) Modern and Medieval Languages, was also part of the Ebola crisis response in Sierra Leone in 2015 while working with the Department for International Development on their Graduate Scheme.

Working in a lab as a basic scientist can often seem far removed from the real world. A year since the World Health Organization declared the Ebola outbreak over, one researcher tells how the skills he learned working in a lab in Cambridge turned out to be surprisingly useful in fighting one of the most terrifying disease outbreaks of recent times.

̽��ֱ��satisfaction you get from being involved in a response like this ... is orders of magnitude better than publishing academic papers

Ian Goodfellow

Belt buckles

Dr Caroline Trotter works on an infectious disease that has killed even more than Ebola. It occurs periodically right across the ‘midriff’ of Africa from Senegal to Ethiopia, in the so-called ‘Meningitis Belt’.

In the last major meningitis outbreak, in 1996, some 250,000 were infected and 25,000 people died. It was at this point that the global health community came together to fight back.

̽��ֱ��Meningitis Vaccine Project (MVP) was launched, a partnership between international health organisation PATH and the World Health Organization (WHO). Working with the Serum Institute of India, MVP developed and rolled out the meningococcal A conjugate vaccine in just 10 years to combat the particular strain that affected the African belt. Since its introduction in 2010, 265 million people have been vaccinated. In Burkina Faso, where the vaccine was first used, a mass vaccination campaign saw 10 million people vaccinated in 10 days.

But even campaigns as huge as this aren’t enough to eliminate the infection, as Dr Caroline Trotter from the Department of Veterinary Medicine, explains: “You get a honeymoon period, but then you see a resurgence of cases.”

Trotter and her team used mathematical modelling to predict the best strategies for ensuring that this did not happen. ̽��ֱ��WHO, who funded her work, used it to shape their guidelines and ensure that the vaccine was introduced into routine vaccination programmes across sub- Saharan Africa.

She and Goodfellow were part of a Cambridge-Africa delegation to ̽��ֱ��Gambia in 2014 – a trip that inspired Goodfellow to lend support to combatting Ebola – and as a result Trotter is now working with collaborators at the Medical Research Council Unit in the country to look at the effect of the vaccine on pregnant women and their babies.

Meanwhile, she continues working with the African Meningococcal Carriage Consortium, a global research effort to study how meningococcal meningitis is spread in Africa, with the hope of gradually tightening the belt on this devastating disease.

̽��ֱ��text in this work is licensed under a Creative Commons Attribution 4.0 International License. For image use please see separate credits above.

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Sexual transmission involved in tail-end of Ebola epidemic

cjb250 — Tue, 17 May 2016 23:12:14 +0000

An international team of researchers has produced a detailed picture of the latter stages of the outbreak in Sierra Leone, using real-time sequencing of Ebola virus genomes carried out in a temporary laboratory in the country.

While the study did not suggest that unconventional transmission was more common than previously thought, the authors describe several instances including a mother who may have transmitted Ebola to her baby via breastfeeding, and an Ebola survivor who passed on the virus sexually a month after being released from quarantine.

̽��ֱ��research, published today in the journal Virus Evolution, suggests that rapid sequencing of viral genomes in the midst of an epidemic could play a vital role in bringing future outbreaks under control, by allowing public health workers to quickly trace new cases back to their source.

Sierra Leone was the most widely affected of the three West African countries worst hit by the Ebola epidemic, with 14,124 cases and 3,956 deaths to date. Without effective vaccines or treatments for the infection, bringing the epidemic under control relied largely on public health measures such as the rapid identification and isolation of Ebola patients, contact tracing and quarantine, as well as encouraging safe burial practices.

By mid-2015 cases in the three most-affected countries had declined, but isolated cases of the disease continued to appear, even though all known transmission chains were thought to be extinguished.

Researchers led by the ̽��ֱ�� of Cambridge and Wellcome Trust Sanger Institute began investigating these cases in a temporary genome sequencing facility set up by Professor Ian Goodfellow. Based in a tent at the Ebola Treatment Centre in Makeni, Sierra Leone, the facility provided in-country sequencing capability to process samples from patients in Makeni and surrounding areas in real time, without the need for sample shipment out of the country.

̽��ֱ��team generated 554 complete Ebola genome sequences from samples of blood, buccal swabs, semen and breast milk collected between December 2014 and September 2015 from Ebola isolation and treatment centres in the north and west of the country. These were combined with 1019 samples sequenced by other groups to create a picture of the viral variants present in Sierra Leone.

They found that during 2015 at least nine different lineages of the virus were circulating in Sierra Leone, eight of which evolved from a single variant that introduced Ebola to the country in June 2014. ̽��ֱ��remaining viruses came from a separate, geographically distinct lineage that originated in Guinea.

Starting in mid-2015 samples from all new Sierra Leone cases were rapidly sequenced in the facility. ̽��ֱ��data, combined with the growing reference set, helped field workers locate the source of infection for some of the final Ebola cases in Sierra Leone. This work revealed that some cases were acquired through unconventional transmission chains and supports a growing body of evidence that the Ebola virus can be found in fluids such as semen or breast milk and may persist beyond the standard quarantine times.

Senior author Professor Ian Goodfellow, from the ̽��ֱ�� of Cambridge, said: “During the initial part of the Ebola epidemic several teams were sequencing samples, but the delays caused by shipping the samples out of West Africa made it difficult to use the sequence data for investigating new chains of transmission. Often by the time the data was published the samples were six months old. To be able to rapidly identify the source of new cases we need to sequence samples and release data in real-time, share samples and share data as it’s produced.”

Dr Matthew Cotten, joint senior author, from the Wellcome Trust Sanger Institute added: “During the epidemic combining our Ebola virus genome sequences with data from other groups provided insight into how the virus was evolving and contributed to an important reference for tracking the source of new cases. As the outbreak progressed, our data also show that quarantines, border control and checking methods were effective, as movement of the virus within and between countries ceased.”

̽��ֱ��sequencing facility set up by the team has now been moved to the ̽��ֱ�� of Makeni, where it forms the focal point of the new UniMak Infectious Disease Research Laboratory. ̽��ֱ��facility is providing world-class training to local students and scientists, which has proven crucial to sequencing the recent new cases of Ebola when no international staff were present.

Dr Jeremy Farrar, Director of the Wellcome Trust, said: “Close contact with an infected individual is still by far the most common way for Ebola to spread, but this study supports previous research suggesting that the virus can persist in bodily fluids for a long time after recovery. These unusual modes of transmission may have contributed to isolated flare-ups of infections towards the end of the epidemic.

“ ̽��ֱ��success of this innovative project shows how important it is to carry out genome sequencing within the affected countries, and for the data to be shared in a rapid and open way as part of the epidemic response. Strengthening laboratory and surveillance facilities where they are currently lacking will also aid early detection, making the world better prepared for infectious disease outbreaks.”

̽��ֱ��research was funded by the Wellcome Trust and is a collaboration between the ̽��ֱ�� of Cambridge and the Wellcome Trust Sanger Institute with support from the ̽��ֱ�� of Edinburgh and Public Health England. ̽��ֱ��Ion Torrent sequencing machines were supplied by Thermo Fisher Scientific.

Reference
Armando et al. Rapid outbreak sequencing of Ebola virus in Sierra Leone identifies transmission chains linked to sporadic cases. Virus Evolution; 18 May 2016; DOI: 10.1093/ve/vew016

Press release from the Wellcome Trust

Some of the final cases of Ebola in Sierra Leone were transmitted via unconventional routes, such as semen and breastmilk, according to the largest analysis to date of the tail-end of the epidemic.

To be able to rapidly identify the source of new cases we need to sequence samples and release data in real-time, share samples and share data as it’s produced

Ian Goodfellow

Medici con l'Africa Cuamm

Messaggi lungo le strade della Sierra Leone

̽��ֱ��text in this work is licensed under a Creative Commons Attribution 4.0 International License. For image use please see separate credits above.

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Ebola legacy lab will improve Sierra Leone’s resilience to future epidemics

cjb250 — Fri, 22 Jan 2016 09:32:16 +0000

̽��ֱ��research, carried out by two local scientists recently trained in next-generation genome sequencing techniques, will provide vital information about the virus that will help international scientists to identify the potential source of the infection.

̽��ֱ��lab at the ̽��ֱ�� of Makeni (UNIMAK) – a collaboration with the ̽��ֱ�� of Cambridge supported by funding from the Wellcome Trust – will be officially opened today by Sierra Leonean Health Minister Dr Abu Bakarr Fofanah.

In the longer-term, the new facility will provide Sierra Leone with a greater ability to identify emerging infectious diseases in the earliest stages, increasing the country’s resilience to future epidemics. It is also expected to become a centre of excellence for research and teaching in the country, which has suffered more than 14,000 cases of the disease since the outbreak began.

̽��ֱ��laboratory evolved from a temporary facility at the Mateneh Ebola Treatment Centre, set up in April 2015 by Professor Ian Goodfellow from the Department of Pathology at the ̽��ֱ�� of Cambridge, who decided to apply his skills as an infectious disease researcher to the global response effort at the height of the Ebola outbreak.

With just a single sequencing machine, provided by Thermo Fisher Scientific and selected for its ability to function in a harsh environment of high temperatures, humidity and dust, the lab quickly began processing samples collected over the course of the epidemic to provide information about the evolution of the virus in real time. To date it has processed more than 1,200 clinical samples (including blood, semen and breastmilk), generating almost 600 full length Ebola virus genomes – the largest single dataset from any laboratory.

Now relocated to its permanent home in the university, with support from the UK Department for International Development, the UNIMAK Infectious Diseases Research Laboratory will provide a world-class environment for the training of local scientists and will bolster the in-country capacity for ongoing disease surveillance.

UNIMAK Infectious Diseases Research Laboratory (Credit: Ian Goodfellow)

In addition to Ebola, researchers will study other infectious diseases such as leptospirosis and Lassa Fever, as very little is known currently about these infections in the local population. ̽��ֱ��information they obtain will be made available to the Sierra Leone Ministry of Health and local healthcare providers so that it may be used to devise better diagnostic and treatment strategies.

Professor Goodfellow said: “We initially set up our makeshift laboratory to provide temporary support during the emergency response to the Ebola epidemic. However, it soon became clear that there was a need to establish a more permanent facility within Sierra Leone to maintain these capabilities for the future.

“What started as little more than a sequencing machine in a tent has since blossomed into a fully functioning laboratory, where a new generation of scientists will train in the latest genome sequencing techniques to allow them to study infectious diseases in the local community.”

Professor Father Joe Turay, Vice Chancellor of UNIMAK, said: “As a university this laboratory will be part of our contribution to building a resilient health system in the country. Our partnership with Cambridge, along with other foundations and institutions, is about supporting UNIMAK in providing the training, research and community services that will strengthen our health infrastructure for post Ebola recovery in Sierra Leone.”

Dr Jeremy Farrar, Director of the Wellcome Trust, said: “ ̽��ֱ��recently confirmed case of Ebola in Sierra Leone serves as poignant reminder of the need to remain vigilant, and the new facilities in Makeni are already playing an important role in this.

“Beyond Ebola, it’s critical that research capabilities are strengthened and maintained in the long-term to build a better picture of health and disease in the local population. Not only will this help to improve the way infections are diagnosed and treated, it will also increase the region’s ability to identify and respond quickly to new epidemic threats as they emerge.”

Adapted from a press release from the Wellcome Trust

Samples from the recently confirmed case of Ebola in Sierra Leone have been analysed at a new infectious diseases laboratory in the country, set up in partnership with the ̽��ֱ�� of Cambridge in the wake of the epidemic.

What started as little more than a sequencing machine in a tent has since blossomed into a fully functioning laboratory, where a new generation of scientists will train in the latest genome sequencing techniques to allow them to study infectious diseases in the local community

Ian Goodfellow

Researchers at the UNIMAK Infectious Diseases Research Laboratory

̽��ֱ��text in this work is licensed under a Creative Commons Attribution 4.0 International License. For image use please see separate credits above.

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