The Silent Genomes project is a partnership between Indigenous organizations, Indigenous patients, and committed Indigenous and non-Indigenous staff with a variety of expertise, including medical doctors and geneticists. As part of our educational outreach, we would like to explain how genomic research is currently helping to manage the outbreak, and what it could mean to our project.
How COVID-19 impacts Indigenous Peoples and Communities
COVID-19 is a serious threat to our health. Like the flu, it is very contagious: the virus (a coronavirus called SARS-CoV-2) can spread easily and rapidly. As you are probably already aware, most people who are exposed to the virus will experience mild or even no symptoms. Although the virus can cause a severe case in anyone, those with chronic health conditions, or our elders, can be at higher risk and may have a higher chance of not surviving. In keeping with the Silent Genomes Project, this article will mainly refer to genomics in the fight against COVID-19. For clinical information, please refer to the links below.
Indigenous peoples have increased burdens of chronic heart and lung disease, which may make them more vulnerable to the effects of COVID-19. Moreover, many Indigenous people live far from centers that provide acute care, which makes it even more challenging to get necessary treatment.
The way we are managing this pandemic is ‘like trying to build a plane while flying it’. It is gratifying to see the whole world’s efforts to tackle this new virus from a genetic level up to human populations of millions. Scientists and health care practitioners are learning from one another on a daily basis. This includes those who work to ensure that Indigenous people have access to the best of healthcare, so that their voices are no longer silent.
The Silent Genomes team hopes this information provides you with a useful perspective on the coronavirus, how it may impact the lives of Indigenous Peoples, and how genomics can be used in the fight against COVID-19. Please contact us at firstname.lastname@example.org if you have questions, or wish to share information.
- What is a coronavirus?
Human coronaviruses are common and are typically associated with mild illnesses such as the common cold. COVID-19 is shorthand for Coronavirus Disease - 2019. It is a new disease that has not been previously identified in humans. There have been two other specific coronaviruses transmitted to North America, that have spread from animals to humans and which have caused severe illness: Severe Acute Respiratory Syndrome in 2002 (caused by the SARS CoV virus) and the Middle East Respiratory Syndrome in 2012 (related to MERS CoV virus).
- How is genomic technology used to identify viruses?
Just like any living thing, a virus has genetic material (DNA or RNA), where it keeps all information about itself. Coronaviruses are RNA viruses, meaning their genetic information is RNA. Early studies have read and analyzed the RNA from the virus. Knowing the viral RNA code has given us the ability to directly test for COVID-19 and distinguish it from other coronaviruses.
Figure 1. The ACE2 receptors are like the doors of our cells, which the RNA from the Coronavirus uses to enter and change the normal cell functions in lungs, kidneys, heart and gastrointestinal tract.
Direct Diagnosis. You may have seen images of people having a nasal swab to test for COVID-19. The genetic technology called Polymerase Chain Reaction (PCR) is used for the detection of SARS-CoV-2 RNA. Genetic testing is considered a direct and accurate method, since it can search specifically for SARS-CoV-2 RNA in a patient's test sample - no other virus will give a positive test result. After recovery, viral RNA will not be detectable in a patient's sample.
Indirect Diagnosis. There are non-genetic (serology) tests that can also help with the diagnosis of COVID-19, especially for those who are several days into the illness, or may have had the virus without knowing it. These tests are indirect because they look for signs called antibodies which our immune system develops upon the first contact with the virus. Antibody testing may be less specific than genetic testing as it assesses the body’s immune response in the presence of the virus rather than detecting the virus itself. In addition, this test will stay positive after the patient’s recovery, which could point to longer immune defense against this virus. However, much remains to be learned before we can tell how long natural immunity to SARS-CoV-2 lasts.
However, one must keep in mind that some margin of error exists in the testing for COVID-19. Read more on the BC CDC website.
- How can the genetic changes in the virus help with understanding where the virus came from?
Scientists are also using genomic technology to track the paths of travel of the virus around the world. It has been found that SARS-CoV-2, similar to other viruses, has very minor changes in its RNA that can help in tracing how the virus is spreading. Small single changes in the viral RNA can be tracked to see where the virus came from in people who have had the virus (such as changes common to those who visited the US, Europe, or the middle East) and where it is spreading to. These changes in the RNA code assist in the public health efforts to trace the path of the virus.
- How else can genomic technology help in the fight against COVID-19?
Genomic technology can also answer many other types of questions about the virus and the human response to it. Of particular interest, genomic studies have highlighted the value and importance of transparent data sharing across countries, which enables live tracking of the spread of COVID-19. In addition, a number of projects around the world (e.g."COVID-19 Host Genetics Initiative", or “Genomics of COVID-19: molecular mechanisms going from susceptibility to severity of the disease”) are aiming to combine efforts in the fight against the virus. In Canada, an emerging project called CanCOVID, our country’s expert-led response to the Coronavirus, including two Indigenous advisors, Dr. Jeff Reading and Sharon Edmunds, who are also both advisors to the Silent Genomes Project.
Although some treatments are slowly becoming available for SARS-CoV-2 in Canada (for example the antiviral medication called Remdesivir), to date there are no approved vaccines to prevent the virus from causing illness (please refer to Health Canada for current information). However, tremendous efforts are being made to create a vaccine using models from other vaccine development, and there is also a focus on gene-based vaccines which have not been used before.
- Can individual genetic variation decrease or increase our susceptibility to COVID-19?
Early studies have focused on the clinical and epidemiological characteristics,and genomic characterization of the viral RNA. However, differences in human genes (DNA variants) may also be involved in an interaction with the virus, altering a patient's sensitivity to the infection.
Genomic studies that were performed after the first outbreak of SARS in 2002 showed that some DNA variants in humans may alter the disease course. Some of these variants are related to a person’s vulnerability to acquire the disease, while others may relate to the immune response, meaning how certain cells are acting to fight the virus.
Research into the role of human DNA variants in susceptibility to and severity of COVID-19 is underway. Although it may be early in the COVID-19 fight, scientists already seek to understand why some people might naturally be more resistant to the infection. Certain DNA variants may increase or decrease a person’s risk of developing COVID-19, or having a severe case. Efforts are now underway to detect such variants, to be able to predict the course of the disease in each patient or in a group of patients with that same genetic variant. For example:
- It has been hypothesized that some people may not contract COVID-19 because of specific DNA variants encoding the ACE2 [angiotensin converting enzyme 2] receptor, a structure that the virus interacts with to get inside of the cell.
- It has been suggested that a gene cluster related to the ABO blood-group system is related to a genetic susceptibility site in patients with severe COVID-19 infection experiencing respiratory failure.
- Another study suggests that variants of the Human Leukocyte Antigen (HLA) system which it responsible for the regulation of the immune system, may impact the susceptibility to and severity of the infection.
To date, there is still not enough scientific evidence to confirm these preliminary findings. More certain results will be obtained from organized and logical approaches (e.g. repeating the studies with more individuals) and from application of advanced genomic methods (Whole Genome Sequencing). This might help us to identify who is at risk in our society and where more safety precautions are needed.
For more information, please refer to COVID Human Genetic Effort.
- Can the IBVL be helpful in the fight against COVID-19?
The proposed Silent Genomes Indigenous Background Variant Library (IBVL) will be a database showing the frequency of DNA variants found in Indigenous people (without known genetic conditions). It is important that a diversity of populations are represented in background variant libraries, since variants not seen at all in one group of people may be very common in another. Please read more about the IBVL on our IBVL webpage. Whole Genome Sequencing allows identification of many thousands of DNA variants which can help identify variants which decrease or increase our susceptibility to COVID-19.
There are already a few projects around the world, and some planned in Canada, which are focused on analysis of genomic data from people who had different responses to COVID-19. Understanding the genetic factors for why some people experience more severe COVID-19 symptoms than others, can improve treatment and vaccine development. The IBVL will help in these types of studies, because the background variants that are present in Indigenous peoples may be absent in other population databases.
The IBVL that is being developed as part of the Silent Genomes Project could provide the ‘reference’ data important in the understanding and sequencing of Indigenous patients with COVID-19 who have consented to having their genomes explored. The use of the IBVL for this purpose, will be decided upon by the Indigenous-led IBVL Steering/Governance Committee.
Achievements and challenges
If you would like to learn more about COVID-19 symptoms, the current state of the pandemic globally and in Canada, and current research on these topics, please refer to these links:
- COVID-19 Host Genetics Initiative
- World Health Organization: Coronavirus disease (COVID-19) advice for the public: Myth busters
- Health Canada Info and Daily Updates
- Health Canada COVID-19 Outbreak Update
- COVID-19 Immunity Task Force
- COVID-19 Resources Canada
- CBC News: COVID-19 page
- BC Centre for Disease Control (CDC) COVID-19 Dashboard
- BC COVID-19 Self-Assessment Tool
Resources from Indigenous and public health organizations in Canada
The intent is to show how Indigenous Peoples are demonstrating sovereignty, self sufficiency, community empowerment and involvement. These sites listed below are good place to start your search, and offer a number of other links to answer your basic questions.
International Indigenous Resources
Navajo Department of Health:
Being in this together is a part of Good Medicine. To learn how other Indigenous peoples are helping each other get through this:
CKLB Radio (article, 20 March 2020): The National Chief Norman Yakeleya of the Dene Nation advises his people that he is gone to live on the land and that they should do the same to protect themselves from the COVID-19 pandemic