Mobile Menu

World of Genomics: Sri Lanka

Article written by Bethany Hanson, Science Communications Writer.

From ancient Buddhist scriptures detailing selective breeding of seeds, to the oldest living tree thought to be planted by humans, to fully integrated clinical genomics, Sri Lanka is the exciting next stop on the World of Genomics tour.

Fun fact: the country is world famous for the stunning gemstones found in the mountains, including rubies, sapphires and topaz1. One town in the Ratnapura region produces so many gemstones that it has been nicknamed the “Land of Gems”!

The Population of Sri Lanka

Formally known as Ceylon, Sri Lanka is a beautiful island nation situated just off the southernmost coast of India. At its longest point the island reaches 432km and it is divided into 9 provinces1.

The Central Highlands of Sri Lanka are dominated by mountains, plateaus and deep valleys. The edges of the Highlands are sharply defined by stunning escarpments; one named “World’s End” stuns with near vertical, 4,000-foot-high cliffs. The Central Highlands give way to ridge valleys that steadily smooth out as they approached the sea. The Sri Lankan coastline offers a series of striking cliffs, beautiful beaches and vibrant deepwater bays filled with ocean life1.

The Sri Lankan population is made-up of three ethnic groups; Sinhalese, Tamil and Muslim. The Sinhalese are descended from the islands aboriginal population and the Tamil descend from later Indian immigrants in the early 1200s1. The vast majority of Sri Lankans are religious, with 70% of the population identifying as Buddhist, 12.6% as Hindu, 9.7% as Muslim and 6.2% as Roman Catholic.

From the beginning of the 13th century, the Sinhalese Kingdom ruled the southwestern regions, and the Tamil Kingdom ruled the north until the 14th century. The Portuguese arrived in 1505 and had nearly completely colonised the island by 1619. With the help of the Dutch, the Sinhalese ousted the Portuguese but ultimately fell under the control of the Dutch East India Company, which gave the island to the British in 1796. The island was renamed Ceylon as a British colony. It gained independence in 1948 and formally became Sri Lanka in 19781.

In 2004, the island was struck by the Boxing Day tsunami, believed to be the deadliest tsunami in human history, killing 230,000 people across 14 countries. The tsunami devastated Sri Lanka’s coastline, almost completely destroying the port city of Galle1 and killing 31,000 people2.

Geographic and Demographic Information

Summary statistics1

  • Land area: 65,610 km2
    • Gross domestic product (GDP):
    • Total: $74.4 billion USD
    • Per capita: $3,354.4 USD

Population Statistics4

  • Population size:  22,181,000
    • Birth rate:  14.5 (per 1,000 population)
    • Death rate:  7.1 (per 1,000 population)
    • Infant mortality rate: 6.44 (per 1,000 live births)
    • Average life expectancy: 76 years
    • Ethnicity:  74.9% Sinhalese, 11.1% Sri Lanka Tamils, 9.3% Moors (Arab and Indian decent) and 4.1% Indian Tamil.

Healthcare System

The Sri Lankan health care system was founded in 1858 by the formation of the Civil Medical Department and became an official, structured health system in 1926. The system was extensive and well-functioning for both preventative and treatment services. Preventative healthcare is provided by a regional Medical Officer of Health and treatment services are provided by the state via primary care outpatient facilities, tertiary care institutions and specialised hospitals2. The public sector provides 95% of inpatient care and around 50% of outpatient care5.

All state-provided medical care is free at the point of access and the system has received international recognition for their model of “good health at low cost.” Healthcare is relatively accessible across the country due to a well distributed network of care facilities, and patients can self-refer to any hospital in the country. Additionally, the government provides free community ambulances, required medications and diagnostic tests2. However, some vulnerable communities, such as low-income plantation workers, still struggle to access healthcare6.

The health system is funded mostly by tax revenue and private investment. In 2016, health spending constituted 9% of the total governmental budget. However, between 2000 and 2016 health expenditure constituted only 0.4% of the national GDP. Private care is available, but due to the high cost it is only used by a small percentage of the population2.

In the last two years the health system’s lack of funding came to a head as an economic crisis hit the nation following the COVID-19 pandemic. Poverty soared from 13.1% in 2019 to 25.6% in 2022. The system faced shortages of medicine and supplies, with antibiotics, insulin and sterile gauze particularly hard to come by. In 2022, 1.1 million people left Sri Lanka and in the first 6 months of 2023, 1,000 medical specialists left for opportunities abroad. The previously exceptional health care system has buckled under financial pressure and lack of staff, and out-of-pocket expenditure is on the rise5,6.

Health Priorities

The leading causes of death in Sri Lanka are ischaemic heart disease (123.5 per 100,000 people), diabetes mellitus (58.5) and COPD (44.4)9.

The country is facing a rapidly increased non-communicable disease (NCD) burden7. In 2023, NCDs accounted for 81% of all deaths. Recent policies have aimed to encourage the use of community level care centres for treating NCDs, but patients are still turning first to higher level care institutions, such as hospitals and private facilities7. This is adding additional pressure to services already over capacity and is driving up out-of-pocket spending. New policies created by the Ministry of Health using WHO funding have increased screening for NCD risk factors in primary care facilities, but recent progress has been limited by the financial crisis and a lack of digital patient records for referral linkage7. Furthermore, the financial crisis means that vital equipment for NCD risk screening, such as cholesterol strips, are unavailable6,7.

The health system takes a preventative approach and has prioritised social interventions. They have delivered projects to address nutritional interventions from disease and female health education. As a result, Sri Lanka performs better in infant mortality, maternal mortality and life expectancy than neighbouring countries with higher incomes2.

However, the healthcare system in Sri Lanka is facing increased pressure from an ageing population and a rise in non-communicable diseases6. While the pre-COVID system delivered good patient outcomes, it will need significant reform to streamline the convoluted referral processes and prevent escalating wait times6. However due to current governmental funding, a lack of finances will likely hinder these vital changes.

Genomic Medicine Capabilities

Sri Lanka has an ancient knowledge of genetics. Buddhist scriptures from the 4th century document “the law of seeds”, a very early version of selective breeding. Genetic research in Sri Lanka began in the 1880s, as scientists focused on congenital abnormalities. In the inaugural publication of the Ceylon Medical Journal in 1888, Hallock published an article about a child born with an imperforate anus. Then in 1938, two scientists from the Ceylon Medical College published about anatomical abnormalities found in postmortem studies.  Finally in 1982, Corea published his doctoral thesis on the epidemiology of congenital malformations, which was Sri Lanka’s first detailed publication on human genetic research3.

Sri Lanka’s first medical geneticist was Professor Eugene Wickramanayake of the University of Ceylon. In the late 1960s, she created an undergraduate genetics course and started genetic research in her university laboratory. She also ran population genetic studies investigating the Uva Bintenna Veddas indigenous population3.

The country’s Human Genetics Unit (HGU) was opened in 1983 in collaboration with the WHO, to begin offering genetic evaluation and counselling to Sri Lankan patients. Over the rest of the decade, the HGU introduced cytogenetic testing, clinical molecular diagnostics and PCR3.

Since then, the HGU has gone from strength to strength, becoming the country’s national genetics centre. Automated karyotyping became available in 2005, Sanger sequencing and PCR molecular genetic tests in 2006, fluorescence in-situ hybridization in 2012 and next generation sequencing in 2014. They fully sequenced a Sri Lankan genome for the first time in 2010. Furthermore, the Molecular Medicine Unit was established at the University of Kelaniya, to complement the work of the HGU while specialising in infectious disease, forensic genetics and novel solutions for patients with thalassemia3. Multiple private companies also offer genetic testing and counselling often by collaborating with larger private hospitals.

The HGU has successfully implemented medical genetic services into routine clinical practice. Genetic counselling for a range of reasons is available, including infertility, oncogenetics and for neurogenetic disorders. In 2007, they even established a telemedicine service so that genetic counselling could be available to those living in rural areas. The addition of an NGS platform to the HGU allowed for the use of clinical exome sequencing, multigene cancer panels and newborn screening10. However, genomic services are currently not free at point of access to patients of the Sri Lankan National Health Service. Policy to address this is being discussed3.

Genomic medicine has improved the qualify and efficacy of Sri Lankan healthcare and is allowing the country to build a database of Sri Lankan genetic variants for future study3. The HGU research groups cover a range of disciplines and published 90 peer reviewed research papers and over 250 conference abstracts between 2008 and 201910. The unit has received international recognition for its work and has been declared a genetic Centre of Excellence3.

Notable Projects

  • National Birth Defects Surveillance Program – Current data suggests that around 5800 children each year are born with birth defects in Sri Lanka, of which 30% result in severe complications that prevent independent living. This programme, run by the Ministry of Health, seeks to address the lack of data on birth defects in Sri Lankan babies. The family Health Bureau organises and collects the data provided by geneticists and care facilities from across the country3.
  • The Sri Lankan Genome Project – Following the success of the Human Genome Project, Sri Lanka launched the Sri Lankan Personal Genome Project. The study seeks to investigate the genetic history of Sri Lanka’s diverse population and create the Sri Lankan Genome Variation Database. This database currently contains 34 unique genomic variations including 14 medically important ones. To allow easy and equitable access, genomic variations found in the Sri Lankan Personal Genome Project are available online and standardised with other national genome projects.
  • Surveillance of SARS-CoV-2 Variants – In May 2023, scientists successfully used whole genome sequencing on SARS-CoV-2 to identify key variants in Sri Lanka. Based at The Department of Immunology and Molecular Medicine at the University of Sri Jayewardenepura, the study used 20 samples from laboratories across the country to create a comprehensive overview and timeline of the COVID variance in the country. This project will allow scientists and policy makers to stay informed of the ever-evolving landscape of SAR-CoV-2 variants in Sri Lanka.

Notable Organisations and Companies

  • Human Genomics Unit of the University of Colombo – Established in 1983 the HGU is one of the oldest genetic centres in Asia. Founded by Professor Rohan Jayaekara, who still acts as the Unit Director, the unit acts as the National Referral Centre for Human Genetic Medicine and sets standards for genomic medicine in the country. The HGU provides clinical genetic services and genetic counselling to patients and offers undergraduate and postgraduate courses. Additional genetics training is also available to medical health professionals. They also have outreach programmes to raise awareness of genetic conditions in the general public and advocate for the inclusion of genomic medicine in Sri Lankan health policy.
  • Medical Research Institute of Sri Lanka – A scientific hub of biomedical and applied health research covering a wide range of disciplines. The institute is based in the capital city Colombo and opened in January 1900. The MRI provides the only diagnostic ability for virology, chemical pathology and immunology in the country. It is a major provider for Sri Lankan hospitals and functions as a National Laboratory for infectious disease research. The current aim is to expand surveillance for communicable diseases, investigate nutritional challenges faced by the population and provide cutting edge specialist services to patients.

Notable Individuals

  • Prof Eugene Wickramanayake – The first Sri Lankan doctor to formally specialise in human genetics. She received her PhD in Genetics from the University of Glasgow. Following her return to Sri Lanka in 1968, she founded an undergraduate Introduction to Genetic Medicine course. She also ran the first population genetic studies investigating the Uva Bintenna Veddas indigenous population. She later was elected President of the Kandy Society of Medicine and was awarded the Honorary Fellowship of the College of Surgeons of Sri Lanka.
  • Prof Rohan W. Jayasekara – Founder and current Director of the Human Genetics Unit. He received his PhD in Cytogenetics in 1980 from the University of Newcastle. In 1989, he was awarded the Commonwealth Senior Medical Fellowship for his postdoctoral position at Guy’s Hospital in London, UK. In addition to founding the Human Genetics unit in 1983, Dr Jayasekara has created postgraduate and doctorate-level courses in Medical Genetics across four Faculties of Medicine in Sri Lanka and has published 226 peer-reviewed articles. In 2015, following his retirement, he was awarded the Sri Lankan Titular National Honour for outstanding scientific and technological achievement.
  • Senka Bibile – A renowned pharmacologist who founded Sri Lanka’s drug policy, which was used by the World Health Organisation as a model for rational pharmaceutical use. He studied at the Medical College in Colombo, receiving awards for his achievements in Medicine and Surgical Technique. He received his PhD from the University of Edinburgh, Scotland, in 1952. Upon his return, he was appointed the first Professor of Pharmacology and the first head of the of the newly established Pharmacology Department at the University of Ceylon. He was later appointed the first Dean of the Faculty of Medicine at the University of Peradeniya in 1967, where he founded the first Medical Education Unit in Sri Lanka. He played an instrumental role in developing forward-thinking and rational pharmaceutical policy, which ensured that impoverished communities could access drugs at an affordable price. Due to the wide-reaching impact of his work and policies, he is often called the “greatest medical benefactor of humanity that Sri Lanka has produced.”

The Future Genomics Landscape

The HGU has stated that it intends to delve deeper into the genetic history of the Sri Lankan population, expand and improve clinical genetic services and turn their genetic knowledge towards tackling the growing biodiversity crisis on the island.

However, despite the country’s incredible capacity for genomic medicine, services are not freely available on the National Health Service, preventing those who cannot afford out of pocket payments or insurance from accessing care.

Prior to the financial crisis, Sri Lanka was one of the foremost nations in the region for clinical genomic medicine. With continued international support, they could return to providing excellent genomic care and precision medicine to their nation and could even support neighbouring countries in integrating genomic medicine into clinical practise.

References

  1. Arasaratnam, Sinnappah and Peiris, Gerald Hubert. “Sri Lanka”. Encyclopedia Britannica, 9 Nov. 2023, https://www.britannica.com/place/Sri-Lanka. Accessed 10 November 2023.
  2. Rajapaksa L, De Silva P, Abeykoon A, Somatunga L, Sathasivam S, Perera S et al. Sri Lanka health system review. New Delhi: World Health Organization Regional Office for South-East Asia; 2021.
  3. Sirisena, N.D. and Dissanayake, V.H.W. (2019). Genetics and genomic medicine in Sri Lanka. Molecular Genetics & Genomic Medicine, p.e744. doi:https://doi.org/10.1002/mgg3.744.
  4. Worldbank.org. (2017). Sri Lanka | Data. [online] Available at: https://data.worldbank.org/country/sri-lanka.
  5. Sri Lanka: Making Strides Towards a Healthier Future (2022). World Bank. [online] Available at: https://www.worldbank.org/en/news/feature/2022/03/28/sri-lanka-making-strides-towards-a-healthier-future#:~:text=Non%2Dcommunicable%20diseases%2C%20including%20diabetes.
  6. The New Humanitarian. (2023). Patients feel the pain as Sri Lankan healthcare falls victim to economic crisis. [online] Available at: https://www.thenewhumanitarian.org/news-feature/2023/07/11/patients-feel-pain-sri-lankan-healthcare-falls-victim-economic-crisis.
  7. Nair, D., Thekkur, P., Fernando, M., Kumar, A.M.V., Satyanarayana, S., Chandraratne, N., Chandrasiri, A., Attygalle, D.E., Higashi, H., Bandara, J., Berger, S.D. and Harries, A.D. (2023). Outcomes and Challenges in Noncommunicable Disease Care Provision in Health Facilities Supported by Primary Health Care System Strengthening Project in Sri Lanka: A Mixed-Methods Study. Healthcare, 11(2), p.202. doi:https://doi.org/10.3390/healthcare11020202.
  8. Dr Susie Perera (2015). Primary Health Care Reforms in Sri Lanka: Aiming at Preserving Universal Access to Health. [online] Nih.gov. Available at: https://www.ncbi.nlm.nih.gov/books/NBK316262/.
  9. World Health Organization (2020). Global health estimates: Leading causes of death. [online] World Health Organization. Available at: https://www.who.int/data/gho/data/themes/mortality-and-global-health-estimates/ghe-leading-causes-of-death.
  10. HGU -Sri Lanka (2023). Human Genetics Unit – Services. [online] Available at: https://med.cmb.ac.lk/hgu/services/#1527672126911-87039159-8882 [Accessed 16 Nov. 2023].