In what could be an answer to all our prayers, researchers from the National Institute for Communicable Diseases (NICD) and the University of the Western Cape’s (UWC) South African National Bioinformatics Institute (SANBI) have sequenced the first SARS-COV-2 genome, which could help contain the spread of coronavirus or even help us to find a cure.
“Next-generation sequencing of pathogens allows us to perform genomic fingerprinting on viruses,” said SANBI researcher and co-author of the new report presenting the sequence Peter van Heusden.
What is a genome?
Van Heusden explained that finding the “fingerprint” of a virus could allow one to understand how it spreads.
“Much like you look more similar to your siblings and cousins than you do to a person chosen at random, this fingerprint of viruses can be used to organise the samples into clusters and thus understand the spread of the disease,” he said.
According to www.nature.com, a genome is the complete set of genetic information in an organism. It provides all of the information the organism requires to function.
Medical scientists Dr Arshad Ismail, Dr Zamantungwa Khumalo, Dr Phillip Senzo Mtshali, Florah Mnyameni, Dr Mushal Allam, Dr Stanford Kwenda at the NICD Sequencing Core, worked with Dr Jinal Bhiman’s group at the NICD’s Centre for Respiratory Diseases and Meningitis on doing the initial sample collection sequencing for this.
“The sample is from a patient’s nose and throat, so it is not ‘pure virus’ . The only way to get a pure virus is to grow or culture the virus and no one wants to do that,” Van Heusden said.
“It is thus challenging to get enough virus DNA from a sample to get a complete virus genome — but the NICD managed to do it,” he added.
Here’s how the genome can help fight coronavirus
SANBI researchers compared the virus genome with a collection of virus genomes from around the world, sourced via the Global Initiative on Sharing All Influenza Data (GISAID) website – a global data-sharing initiative for flu, and now for COVID-19 as well.
“I examined each difference between our South African genome and other genomes to see if the evidence was there to support it,” Van Heusden explained. “In the end, we had six differences.”
These differences are important for two reasons:
“Firstly, they give us a ‘fingerprint’ that is useful to understand the spread of the virus,” Van Heusden said.
“In this case, the version of the virus found in South Africa looks like the ones found in Europe and the US, suggesting that the virus is travelling alongside people travelling between SA and those places. We suspected that already, but this helps to confirm it.”
Secondly, one can look at how the differences impact on the proteins the virus makes.
“Genes don’t directly determine what happens in cells. Proteins are the molecular machines that make cells work and the virus genome is like a recipe book for the proteins the virus needs to do its work (invading cells and making copies of itself),” he said.
Tracking the coronavirus could be made easier
The work is a contribution to the global efforts to track and trace the ongoing coronavirus pandemic. As of 1 April, more than 3 000 SARS-COV-2 genomes were globally sequenced and uploaded to GISAID.
The Nextstrain website provides real-time monitoring of the spread and evolution of the SARS-COV-2 virus, drawing on sequence data stored in GISAID.
“Ideally, you want to be able to analyse virus DNA samples to better understand the spread of disease or predict when an outbreak will occur. With a sufficient number of sequenced genomes, it is possible to reconstruct a phylogenetic tree of the mutation history of a family of viruses,” said Van Heusden.
“This work will be an important part in giving our colleagues at the NICD and in the public health sector more tools to trace the spread of the disease and stop that spread. And ultimately, this work can also contribute to producing a vaccine against COVID-19,” he added.
Currently sequencing such a pathogen is a bit difficult and very expensive.
“We are working hard to optimise the sequencing protocol to make it affordable not only for the local samples, but for samples from other African countries who do not have ready access to these technologies or resources,” said SANBI alumni Dr Allum.
Helping to equip public health workers across Africa
SANBI-UWC is working alongside teams such as Africa CDC to develop sustainable training across the public health institutes in Africa, helping equip public health workers across the continent in tracking and fighting the coronavirus.
SANBI aims to ensure that analytical genomic tools are easily deployed and used in Africa to respond to disease threats like coronavirus — tools like Baobab LIMS — a free and open-source Laboratory Information Management System (LIMS) for biobanking — developed by African and European researchers, already being used in 11 African countries.
Designed for the collection, processing and storage of human biospecimens, Baobab LIMS can be customised to the specific needs of any particular laboratory.
Source: The South African Read More
