The study of SARS-CoV-2 sequencing has resulted to many important findings about this virus. However, we will need more sequence data from samples around the world to determine the most effective ways to control and prevent Covid-19 infections. Scientists all over the world are working together to create and share valuable information for disease diagnosis and control efforts.
Read more if you’re interested in learning more about genome sequencing and why it matters in the global Covid-19 response.
Getting Information from SARS-CoV-2 Sequencing
As Covid-19 continues to spread around the world, it will start experiencing new evolutionary. Other respiratory viruses can give us an insight into how a Covid-19 evolution may take place. For example, the H1N1 influenza virus that spread around the world in 2009 started evolving antigenically a couple of years after it first appeared. Recent studies have determined signs of adaptive evolution in the spike protein of seasonal coronaviruses. This occurrence is consistent with antigenic evolution.
New evidence also suggests that some Covid-19 variants may already be going through antigenic evolution. This will probably go on as population immunity (through vaccination or natural immunity) grows. Public health agencies continue their efforts to curb and monitor emerging Covid-19 variants.
Animal reservoirs may have an effect on the dynamics of Covid-19 evolution and adaptation.
Viral adaptation is possible through the evolution of the immune system or other viral traits and genetic variation must be present. While the main source of genetic variation in Covid-19 are nucleotide substitutions, researchers are also observing nucleotide insertions and deletions. Recombination is a common occurrence in coronaviruses and may lead to the creation of new Covid-19 strains.
The number of new Covid-19 sequences is unprecedented. Getting new information from the available data is not easy. Many of our current methods rely not only on the sequence itself but on viral samples. Many research laboratories around the world struggle with the metadata that they can release due to patient privacy regulations. This is the reason why many state-run health agencies around the world receive only limited metadata from state health departments.
Privacy is an important concern, but regularly releasing more detailed metadata would significantly improve the methods used to identify and describe viral dynamics and evolution. In addition, SARS-CoV-2 sequencing data are often released with only rough sampling location data. Viral dynamics, however, may be different even with geographically close locations.
Including a patient’s travel history can also improve methods of tracking the virus’ growth and spread. However, this information is not always reported. Since methods to track Covid-19 origin and spread often require an assumption of random samples, when you sequence samples from individuals belonging to the same transmission chain, you must label this information in the sequence metadata to avoid biases in analyses.
Despite the many challenges, a huge amount of SARS-CoV-2 sequencing data is publicly available in GISAID’s EpiCov database. The sequence analyses are conducted in real-time and added on platforms such as Microreact and Nextstrain. This allows experts to view the ongoing evolution of Covid-10 genomes in detail.
Global Partnerships to Collect and Analyze Covid-19 Sequence Data
After the first Covid-19 genome was published, scientists around the globe eventually realized the necessity to collect as much genetic data from as many SARS-CoV-2 strains a possible.
When the pandemic first hit, many research groups tried to create their own protocols in collecting SARS-CoV-2 sequencing information from culture or clinical specimens, especially the ones that tested positive for the virus. Many approaches were introduced, but eventually they were able to standardize sequencing procedures, thanks to the Advancing Real-Time Infection Control Network (ARTIC), an international group made up of scientists from the U.S., U.K., and Belgium.
The group devised a whole genome sequencing method (WGS) of the SARS-CoV-2 virus on the Oxford Nanopore Technologies’ sequencing platforms. Their protocol has been adapted for other sequencing platforms around the world, making it easier for many laboratories to study the virus’ genome.
It is important for sequence data of pathogens of interest be shared publicly, especially during a pandemic. The World Health Organization (WHO) encourages public access to sequence data as it helps authorities inform the public and make the right decisions during outbreaks.
How SARS-CoV-2 sequencing Helps in Covid-19 Response
Genome sequencing is an important and fast-growing tool that helps in the diagnosis of Covid-19 and other viruses. It helps the experts understand how viruses spread and develop solutions to control them.
A genome is defined as an organism’s genetic makeup. It basically works as an instruction manual as it contains all the information you need to create and maintain it. Human genomes, for example, are made up of double-stranded DNA. They are written in a special four nucleotide base “letters”. Human genomes are typically 3 billion base letters long. A virus genome, on the other hand, is tiny and can be made up of the DNA or the RNA.
Coronaviruses are RNA viruses and the Covid-19 virus are made up of one short RNA strand that has 30,000 letters long. Scientists can “read” these letters one-by-one with sequencing.
Genomes Can Identify Viruses
When a new coronavirus sequence is obtained in a sample (usually from the mouth or nose), it can tell whether a patient’s symptoms are those of Covid-19.
It’s interesting to note that virus genomes are constantly changing a few letters at a time as they split or divide and spready by infecting people. You can take advantage of these changes and track the spread of the virus by sequencing, recording, and analyzing genomes.
If more and more scientists perform genome sequencing rapidly and on a large-scale, then it can greatly help public health authorities and epidemiologists in understanding how the virus spreads and how effective efforts to curb it are.
Genome sequencing can also help determine whether the new Covid-19 variants are related to certain patterns or symptoms or level of diseases. In the future, it will be easier to track down new variants. Tracking down new variants is necessary to ensure that vaccines, when developed, are constantly updated with the different strains currently appearing and spreading.