South African scientists from the National Institute for Communicable Diseases (NICD) and the South African National Bioinformatics Institute (SANBI) at the University of the Western Cape (UWC) have successfully sequenced South Africa’s first SARS-COV-2 genome.
“Next-generation sequencing of pathogens allows us to perform genomic fingerprinting on viruses,” says Peter van Heusden, SANBI researcher and co-author of the new report presenting the sequence, phylogenetic analysis and modelling of non-synonymous mutations for a SARS-CoV-2 genome that was detected in a South African patient with COVID-19.
“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,” said UWC in a statement.
This fingerprint of the virus isn’t just from one swab, as a swab from a patient isn’t just ‘pure virus.’ Short of growing the virus in a lab, scientists had to get enough virus DNA to create a complete virus genome.
“I examined each difference between our South African genome and other genomes to see if the evidence was there to support it,” Van Heusden explains. “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 notes. “In this case the version of the virus found in South Africa looks like the ones found in Europe and the USA, suggesting that the virus is travelling alongside people travelling between SA and those places. We suspected that already, but this helps confirm it.”
Secondly, they can look at how the differences impact on the proteins the virus makes.
“Genes don’t directly determine what happens in cells,” Van Heusden explains. “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).”
Another SANBI researcher, Dr Ruben Cloete, helped confirm that the changes in the virus genome are mostly neutral, making very little difference in the proteins made by those particular genes.
The work is a contribution to the global efforts to track and trace the ongoing coronavirus pandemic. As of 1 April 2020, more than 3000 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,” says Van Heusden. “With a sufficient number of sequenced genomes, it is possible to reconstruct a phylogenetic tree of the mutation history of a family of viruses.”