Original World of Genomics: Egypt article written by Shannon Gunn, October 2021. Updated by Lyndsey Fletcher, June 2023.
For the latest in our World of Genomics series, we visit the Arab Republic of Egypt. Egypt is an emerging power in the genomics space, and it is also home to a very rich history, making it an exciting and intriguing place to investigate genomic ancestry and evolution.
The population of Egypt
Egypt is a transcontinental country spanning the northeast corner of Africa and southwest corner of Asia. It has land borders with Libya, Sudan and Israel, as well as coastlines along the Mediterranean and Red Seas, and the Nile.
Egypt has one of the longest histories of any country – its heritage can be traced back to the 6th-4th millennia BCE (before the common era). Ancient Egypt can not only provide us with insights into the rich culture of ancient civilisation, but it also represents an ideal region to study historical population dynamics. The country has intense, historically documented interactions with important areas in Africa, Asia and Europe. This movement has given rise to an intricate cultural and genetic exchange. Modern Egypt dates back to 1922, when it gained independence from the British Empire. Since then, it has endured social, religious and political unrest. Egypt is continually modernising its economy to better serve a growing population.
Geographic and demographic information
Summary statistics:
- Land area: 1.01 million km2
- Gross domestic product (GDP):
- Total: $1.8 trillion (2022)
- Per capita: $16,980 (2022)
Population statistics
- Population size: 104.6 million (2023 estimate)
- Birth rate: 23 per 1000 (2021)
- Death rate: 6 per 1000 (2021)
- Infant mortality rate: 16 per 1000 (2021)
- Average life expectancy: 70 (2021)
- Male: 68 (2021)
- Female: 73 (2021)
- Ethnicity: Ethnic Egyptians account for 91% of the total population. The largest ethnic minorities in Egypt include the Turks, Greeks, Abazas and Bedouin Arab tribes in the Sinai Peninsula and the deserts to the east, as well as the Siwis in the Siwa Oasis and the Nubian people along the Nile.
Healthcare system
As a result of modernisation efforts over the years, Egypt’s healthcare has made great progress. The healthcare system in Egypt consists of two sectors: public and private. In general, the public healthcare system is of poor quality due to lack of funding and poor staffing levels. Government investment in the public healthcare system sits at just 5% of the budget, and there is a high level of out-of-pocket expenditure.
There are also significant differences between the availability of health services in rural areas compared to those found in big cities like Cairo. Nonetheless, the government ensures basic universal health coverage, and 95% of the population live within 5km of at least one health facility. Meanwhile, private healthcare facilities in Egypt are of high standard, providing more advanced and specialised medical care to more than a third of Egypt’s population.
With a high population density and increasing fertility rates, the Egyptian healthcare system is met with many challenges. Over the past two decades, despite facing challenges, the Egyptian healthcare system has improved in several aspects. For example, by 2006 98% of citizens were offered vaccinations. The country also has a robust health data information system.
Health priorities
Noncommunicable diseases (NCDs), including cardiovascular disease, diabetes, cancer and chronic respiratory illnesses, are the leading causes of death in Egypt. They account for 82% of all deaths in Egypt and 67% of premature deaths. There are a number of risk factors for NCDs among the adult population, including the fact Egypt has one of the most overweight populations in the world and a high prevalence of smoking.
Egypt also has the highest world prevalence of hepatitis C virus (HCV) infection, which is linked with substantial disease and economic burden. As a result, HCV elimination has become a national health priority. In 2014, the Egyptian government introduced a robust screening and treatment program to prevent the spread of HCV, aiming to eliminate the threat of the virus by 2021. Over 50 million individuals were screened, and over 4 million treated. The initiative was deemed a success, significantly lowering the infection levels within the country. As of 2023, around 6% of Egyptian individuals have HCV antibodies and a further 4% are thought to have active infection.
Due to the high frequency of consanguinity in Egyptians, there are also a range of frequent genetic disorders, including autosomal recessive Robinow syndrome and Roberts syndrome.
One of the key challenges for the health sector in Egypt is equity in access to health services. Low investment in health has led to serious compromises in quality, safety and prevention. As a result, the burden of financing healthcare falls mostly on the poor.
Genomic medicine capabilities
With better control of infant mortality due to diarrhoea and infectious disease, genetic diseases have become an increasing health priority in Egypt. The introduction of medical genetics in Egypt began in the 1960s, in the paediatric department of Egyptian universities. Nowadays, human genetic courses are included in the curriculum for medical students in most Egyptian universities. Various specialised postgraduate degrees and training programmes are also available in specific institutions. Genetic diseases are thought to affect around 2-5% of all live births, due to factors such as consanguineous marriages and advanced maternal age.
Mass neonatal screening for inborn errors of metabolism and hypothyroidism is widely available. In 2011, PerkinElmer built the world’s largest neonatal screening laboratory in Cairo. In July 2021, a mass newborn screening initiative was launched, covering 19 diseases. As of May 2022, over 107,000 newborns underwent genetic testing in public hospitals as part of this scheme.
There are also several genetic services offered through the Center of Excellence for Human Genetics. These include multiple specialised human genetic clinics (e.g., prenatal diagnosis), molecular diagnosis of prevalent and rare genetic diseases in four main categories (neurogenetic disorder, limb malformation and skeletal dysplasia, hereditary blood disorders and multiple congenital anomalies), human cytogenetics and biochemical genetics.
Genetic counselling is available at a number of institutes, and over 21,000 families have received counselling at just one of these centres since the 1980s.
Notable projects
Due to the burial rituals of ancient Egyptians, Egypt is a hub of ancient DNA. However, contamination from handling and microbes has created obstacles to the recovery of ancient DNA. As a result, most DNA studies carried out have been on modern Egyptian populations. Genetic analyses of modern Egyptians have provided several insights, including the distribution of specific haplogroups and relationships to other populations.
In recent years, several research groups have undertaken DNA analysis of ancient mummies, largely performing mitochondrial and Y-chromosomal haplogroup analysis. Some notable studies include:
- Khairat et al (2013) were the first group to apply next-generation sequencing technology on Egyptian mummies to ascertain the ancestral lineage of an Ancient Egyptian individual.
- Schuenemann et al (2017) described the extraction and analysis of DNA from 151 mummified ancient Egyptian individuals. These samples spanned 1,300 years of ancient Egyptian history and provided insight into ancient human history.
- Gad et al (2020) used several mummies, including Tutankhamun, to provide information about the phylogenetic groups of their family members and their presence among contemporary Egyptian population data.
In 2020, Wohlers et al, harnessed short- and long-read whole-genome sequencing data to assemble an Egyptian genome de novo. The team have constructed EgyptRef as a community resource.
Notable organisations and companies
- Human Genetics and Genome Research Division at the National Research Centre: Originally a department in 1976, the Human Genetics and Genome Research Division became a division in 2003. It encompasses over 200 specialist staff across eight departments including: Clinical Genetics, Human Cytogenetics, Medical Molecular Genetics, Molecular Genetics and Enzymology, Biochemical Genetics, Prenatal Diagnosis, Immunogenetics, and Orodental Genetics.
- Center of Excellence for Human Genetics (CEHG): The Center was established in 2014 having obtained a grant from the Science and Technology Development Fund. The Center is composed of the departments of the NRC Human Genetics and Genome Research Division, and its main aim is to advance the diagnosis and management of genetic diseases.
- National Society of Human Genetics in Egypt: Established by Dr Samia Temtamy in 2005, the society has several important targets including increasing awareness about human genetics, holding events to increase public and professional knowledge, encouraging students to join societal activities and enhancing national, regional and international networking.
Notable individuals
- Dr Samia Temtamy: Temtamy was the first specialised geneticist in Egypt, having finished her PhD at John Hopkins University in the US. She later established the speciality of Human Genetics at the National Research Centre.
- Nagwa Abdel Meguid: Meguid is an Egyptian geneticist. Her work has helped identify several genetic mutations that cause common syndromes such as Fragile X syndrome and autism.
Future genomics landscape
The CEHG has several future plans, including improving the diagnosis of different genetic diseases that contribute to major chronic diseases. They also hope to identify genetic mutations that are prevalent among the Egyptian population which will help with early diagnosis, prevention and management. In addition, they aim to acquire modern equipment to help train researchers on the new diagnostic technologies. Finally, they hope to increase national and international collaboration to allow mutual exchange of expertise and aid in the future of genomic medicine.
In early 2022, it was announced that the EgyptRef project would wrap-up by the end of 2025, with an aim to represent the entire Egyptian population within the reference genome. After this, it is likely that the reference genome will be used to further Egypt’s genomic research capacity. The findings will also be used to further the use of precision medicine in the country.
In 2021, Egyptian President Abdel Fattah El Sisi was also briefed on a national plan to establish a genome centre that will aim to prepare a map of the Egyptian human genome to discover and accurately determine the genetic characteristics of various diseases. This project will help Egypt enter into the era of precision medicine.
Although the recognition and integration of genomics in Egypt has been slow, it is likely that in the next decade there will be increased uptake across the country. As a result, this will yield important insights relating to Egyptian health and evolution and will aid in our ability to provide precision medicine for all.
References
- Temtamy SA. The Development of Human Genetics at the National Research Centre, Cairo, Egypt: A Story of 50 Years. Annual review of genomics and human genetics. 2019 Aug 31;20:1-9.
- Temtamy SA, Hussen DF. Genetics and Genomic Medicine in Egypt: Steady Pace. Molecular genetics & genomic medicine. 2017 Jan;5(1):8.
- El-Attar EA, Helmy Elkaffas RM, Aglan SA, Naga IS, Nabil A, Abdallah HY. Genomics in Egypt: Current Status and Future Aspects. Frontiers in Genetics. 2022 May 13;13:797465. doi: 10.3389/fgene.2022.797465. PMID: 35664315; PMCID: PMC9157251.
