“A global pandemic requires a world effort to end it – none of us will be safe until everyone is safe.” Dr Tedros Adhanom Ghebreyesus, Director-General, World Health Organization
Scientists at the Quadram Institute on the Norwich Research Park are used to working with researchers around the globe. It takes a collective international effort to find answers to some of the big questions we’re faced with.
That global focus applies whether we’re working on micro-organisms in our food or water that can harm human health, the impact of the food we eat on our gut microbiome, or optimising our food to give us a healthier diet.
So, when the SARS-CoV-2 pandemic arrived in early 2020, those global relationships helped form the basis of fast-moving research and real-world responses to the virus and its disease, COVID-19, as it swept across the planet.
To date, the Quadram Institute has sequenced 33,000 SARS-CoV-2 genomes and has provided expertise directly to eight countries* around the world to help with their COVID-19 genomic sequencing efforts and provided analysis training to 133 scientists from 32 countries.
Scientists at the Quadram Institute are working with colleagues in Lahore, Pakistan to help sequence SARS-CoV-2 outbreaks. The sequencing team led by Dr Andrew Page, who led the COG-UK study on COVID-19 and care homes in Norfolk, and sits on the SAGE Social Care Working Group, has just sequenced 100 COVID-19 samples from Lahore in Pakistan. The 100 samples sequenced showed that the current dominant variant in Lahore is the Alpha variant, first identified in the UK.
Quadram Institute research scientist Dr Muhammad Yasir said: “As a former Research Fellow at UHS Lahore, I was approached by Dr Shah Jahan to see if we at the Quadram could help sequence SARS-CoV-2 outbreaks. We know from our experience in the UK that the key to managing this pandemic is tracking and tracing SARS-CoV-2 lineages and I’m pleased that colleagues and community of Pakistan are being benefitted from our expertise.”
Group leader Dr Mark Webber said: “Identifying which variants of coronavirus are circulating within Pakistan helps our colleagues there understand how the virus is spreading locally and to identify where interventions may be most useful. At the Quadram Institute we have developed expertise in sequencing and analysing SARS-CoV-2 genomes and our work with UHS Lahore represents a significant increase in the available data for genomic epidemiology for the region.”
Senior bioinformatician Dr Nabil-Fareed Alikhan said: “Our initial pilot of 100 samples in May has demonstrated that in the Lahore region the dominant lineage has been the Alpha variant . The virus doesn’t respect borders and we must combat it on all fronts if we aim to end the pandemic. Collaborations like these are another step in that direction.”
Scientists at the Quadram have also spent time training scientists at Zimbabwe’s National Microbiology Reference Laboratory to do their first genome sequencing ever and analyse their own data and were able to identify Zimbabwe has also imported the Delta variant from international travellers.
Professor Rob Kingsley said: “We were already working with scientists at NMRL to study typhoid fever in Zimbabwe and we used this close working relationship to rapidly pivot in response to the Covid-19 emergency. Our Zimbabwe colleagues continue to strive to apply the most recent technologies to address the ongoing epidemic.”
Researchers at Quadram have worked with scientists in Bangladesh to build within-country laboratory and analytical capacity to sequence SARS-CoV-2 from Bangladesh outbreaks early in the pandemic, including the first sequencing on a portable sequencer. SARS-CoV-2 strains were analysed and compared with global circulating strains at the time. This fed into the local public health response and contributed to the epidemiological knowledge of SARS-CoV-2 locally, creating a local knowledge base for sequencing and analysis.
Research group leader Dr Nicol Janecko said: “Through an existing project, we were able to quickly re-purpose and coordinate efforts for the laboratory in Dhaka, Bangladesh and help with their local pandemic efforts, while creating an opportunity for cross institute training in sequencing and analysis of SARS-CoV-2. This way, going forward, the technology and knowledge is well placed for future public health efforts.”
The next international project for the Quadram Institute in the fight against COVID-19 includes work to help the Republic of Lebanon sequence samples through an expansion of a pre-existing collaboration with the Lebanese American University and help inform their public health measures.
Long standing links with the MRC Unit in The Gambia have been extended to provide sequencing and bioinformatics support for their SARS-CoV-2 sequencing efforts. The Quadram Institute has assisted with training scientist from across West Africa in SARS-CoV-2 genomic analysis.
Dr Andrew Page said: ‘Giving local scientists in resource constrained countries the knowledge and supplies they need to undertake genome sequencing locally will greatly aid with managing the pandemic. This will enhance the public health response for this pandemic and for future public health challenges.”
*Ireland, Germany, Lebanon, The Gambia, Zimbabwe, Mexico, Bangladesh, Pakistan.