The COVID-19 pandemic highlighted that infectious disease outbreaks caused by both new and previously known pathogens (i.e. infectious disease agents including viruses, bacteria and parasites) are appearing more regularly and frequently. Genomic surveillance, a method used to detect and systematically monitor genetic changes in pathogens by sequencing their genomes, was crucial in understanding the evolution and spread of the SARS-CoV-2 virus in real time.
Using genomic surveillance, scientists and researchers around the world uncovered how the virus circulated, its replication efficiency, emerging mutations, and, once available, vaccine performance. This data informed global public health interventions during the pandemic.
Until late 2020, most Caribbean countries had limited capacity to conduct pathogen genomic surveillance. To address this, researchers at The University of West Indies (UWI) in Trinidad and Tobago implemented the COVID-19 IMPACT project which established local capacity for rapid virus whole genome sequencing for the first time. Led by Commonwealth Alumnus Dr Christine Carrington, a Professor of Molecular Genetics and Virology and the former Head of the Department of Preclinical Sciences of the Faculty of Medical Sciences at UWI, the project enabled SARS-CoV-2 genomic surveillance in seventeen Caribbean countries.
A passion for virology
Dr Carrington has always been interested in understanding viruses and is now an expert in molecular genetics and virology. After completing her under graduation, doctoral and post-doctoral studies in molecular virology in the UK, she returned to Trinidad and Tobago to teach molecular biology and conduct virology research in the Faculty of Medical Sciences at UWI. However, she reminisces that doing laboratory research in Trinidad was challenging and difficult to sustain due to resource limitations, inadequate infrastructure and inefficient institutional research support systems.
In 2014, sparked by her curiosity to learn more about virus evolution and further develop her skills in this field, she was awarded a Commonwealth Professional Fellowship at the University of Oxford. Through the Professional Fellowship, she was introduced to viral phylogenetics (the study of the evolutionary relationships among viruses) and cutting edge tools for analysing virus genetic data.
This was a pivotal opportunity for Dr Carrington’s professional development and in advancing virology research in Trinidad.
“The Fellowship introduced me to a rapidly emerging field of research that was not only necessary but very ‘doable’ in a more resource-limited setting. We still relied on overseas collaborators to sequence the viruses that we collected during our field work, but since the analysis of the sequence data was all computer-based we were able to design and carry out the actual experiments ourselves…all in the computer.”
Following her Fellowship, she returned to UWI and applied her newly acquired knowledge in viral phylogenetics to understanding evolutionary and ecological factors underlying viral emergence and epidemic behaviour. Her research focused on viruses of public health importance in the Caribbean and Latin America, predominantly RNA viruses (those with RNA instead of DNA as their genetic material) and mosquito-borne viruses such as Zika, chikungunya, yellow fever, and dengue.
Responding to the COVID-19 pandemic
Dr Carrington’s knowledge of viruses and genomic surveillance were critical in supporting the Caribbean region in responding to the COVID-19 pandemic. As of 2022, the National Institutes of Health (NIH) reports that the Caribbean and Latin American regions reported approximately 15% of cases and 28% of deaths worldwide. Several factors fuelled the health crises, including pandemic unpreparedness and fragile health systems.
To support the emergency health response in the Caribbean, in early 2020, with the support of UWI, Dr Carrington partnered with the Ministry of Health in Trinidad and Tobago, the Caribbean Public Health Agency (CARPHA) and her collaborators at the University of Oxford and University of London to implement virus whole genome sequencing in order to characterise and generate baseline data on SARS-CoV-2 variants circulating in the Caribbean.
With limited funding, Dr. Carrington and her UWI team set up a nanopore sequencing device and in late 2020 pioneered rapid virus whole genome sequencing in Trinidad and Tobago with the sequencing a small batch of SARS-CoV-2 samples received from CARPHA. The project was conceived as a research project, with funding to cover only about 800 samples from across the Caribbean. However, within two weeks of the project generating its first sequences, the UK reports the first SARS-CoV-2 “variant of concern” and the WHO advised that all countries should carry out genomic surveillance. Demand for sequencing from CARPHA member countries increased dramatically and the COVID-19 IMPACT project pivoted to a more service-oriented role.
“Having that data from the Caribbean was very important because a lot of the global efforts and advice on control [of the virus], vaccines, and therapeutics, are informed by genetic data, as well as other data. But if we [Caribbean region] are not represented in that database, then this means that any peculiarities in our region are not being considered by the wider scientific community.”
Dr Carrington’s efforts in genomic surveillance ensured the genetic data on SARS-CoV-2 variants circulating in the Caribbean was represented in the global database, which helped inform national, regional and global public health strategies.
In 2021, the laboratory’s sequencing efforts were recognised by the Pan American Health Organisation (PAHO) / World Health Organisation (WHO). They provided invaluable support (additional equipment, reagents, laboratory consumables and human resources) that facilitated much needed expansion and more efficient operations. Soon after the UWI laboratory was designated a PAHO/WHO reference sequencing laboratory, with Dr Carrington named as the coordinator.
“Our laboratory’s recognition as a PAHO/WHO reference sequencing laboratory underscored its importance in regional and global SARS-CoV-2 control efforts, and we have since been expanding our capacity beyond COVID-19 to address other pathogens.”
Advancing One Health education and awareness
Dr Carrington’s work has been instrumental in building the region’s ability to detect and respond to infectious disease threats effectively and has positioned the Caribbean as a key player in global virology research.
Following the success of the SARS-CoV-2 virus genome sequencing in the Caribbean, Dr Carrington is now focused on expanding capacity to conduct genome surveillance of other viruses in the region. She has raised funds to enhance laboratory capacity at UWI and supported by an award from the Pandemic Fund, she is leading the establishment of a “One Health Molecular Epidemiology and Genomics (EDGe)” centre of excellence at UWI as part of a larger collaborative project between the UWI, Ministry of Health and Ministry of Agriculture, Land and Fisheries, aimed at revolutionising Trinidad and Tobago’s laboratory capacity for disease surveillance and epidemic investigations in support of pandemic preparedness, prevention and response.
Dr Carrington has a keen interest in One Health, which recognises the deep interconnections between environmental, animal and human health and promotes collaboration across these sectors. The EDGe centre will enhance in-country capacity for pathogen surveillance, genomics and bioinformatics research and training within a One Health framework, and building on academic-public health partnerships established during the COVID-19 pandemic, will serve as research and training resource for local and regional public health institutions.
“As a scientist involved in basic research – research aimed at advancing knowledge and understanding of underlying principles, without a specific practical application or immediate commercial benefit in mind – my primary audience is the scientific community and my work is largely motivated by curiosity. However, as so vividly illustrated by the COVID-19 pandemic, the capacity building, technical skill and research findings generated through basic research are of immense benefit and can be readily deployed and find applications that target and support governments, public health agencies, and the general public.”
Building future researchers’ capacity
Dr Carrington has supported UWI in partnering with public health institutions to combat infectious disease threats and raise public awareness. As part of her academic portfolio and in her role as a technical advisor to the Ministry of Health, Dr Carrington has engaged in outreach and public education on emerging infectious diseases and vaccines.
“Through media briefings, articles, television and radio shows, and symposia, I strived to simplify complex scientific concepts for the general public in order to demystify SARS-CoV-2, viral emergence and vaccines. My volunteer talks and Q&A sessions for schools, private and public institutions, and community groups helped to inform citizens and helped garner support for necessary public health interventions.”
Dr Carrington and her research team at the 2023 UWI Research Awards. Image credit: Arianne Brown-Jordan
As a professor, she strives to share her knowledge and expertise with young researchers. She enjoys working with her doctoral students and providing guidance on their research projects. She also provides training workshops and graduate student mentorship, further developing a new generation of skilled laboratory workers and scientists.
Dr Carrington shares that her Commonwealth Professional Fellowship has directly and indirectly facilitated major enhancement of local research skills, laboratory capacity and networks related to emerging infectious diseases, molecular epidemiology and genomic surveillance.
The ability to build human resources and technical skills of future researchers is one of the biggest outcomes of her Commonwealth Professional Fellowship. She is proud of her former doctoral students who have become highly skilled professionals, contributing to public health both in the Caribbean and on the global stage.
“My PhD students are my pride and joy. When they leave and they go on to work elsewhere, I just enjoy the fact that they are part of the scientific community and contributing in their own way. Even those that are no longer in the Caribbean, still collaborate with us and work in areas that contribute to regional development.”
She acknowledges UWI’s support in providing a platform for students and researchers to build capacity and forge partnerships with public health institutions bridging gaps between academic research and public health applications.
Future plans towards pandemic preparedness
Dr Carrington wants to continue teaching at UWI, supporting and mentoring university students and researchers to develop skills to tackle infectious diseases She will continue to oversee the establishment of the EDGe centre and to expand the UWI’s capacity to guide and local and regional support pandemic preparedness, prevention and response.
Dr Carrington believes that her Commonwealth Professional Fellowship at the University of Oxford was central to the progress in her career. She gained a valuable mentor Professor Eddie Holmes who introduced her to virus evolution, phylogenetics and bionformatics, which underpinned her ability to perform useful and timely research in areas of importance to Caribbean public health. She also became a part of a network of leading researchers in the field of emerging infectious diseases. These connections have accelerated her research work, increased engagements with international organisations and attracted funding for future research projects.
“Prior to the Commonwealth Professional Fellowship, progress was slow. The Fellowship boosted my research progress and my career, and created a ripple effect that did the same for other infectious disease researchers in Trinidad and Tobago, especially through the capacity building and international collaborations that followed.”
Dr Christine Carrington is a 2004 Commonwealth Professional Fellow from Trinidad and Tobago. She completed her Fellowship at the University of Oxford.
