As South African enters the 12th day of the nationwide lockdown aimed at containing the spread of Covid-19, local researchers have claimed progress in the fight against the coronavirus pandemic.

The scientists — from the National Institute for Communicable Diseases (NICD) and the University of the Western Cape's South African National Bioinformatics Institute (Sanbi) — have sequenced the first severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome.

The genome essentially provides a genetic “fingerprint” that can help understand the pandemic. It was detected in a South African patient with Covid-19, the respiratory illness caused by the virus.

The UWC said in a statement that scientists across the globe had been working around the clock digging more about the pandemic and virus causing it.

“Next-generation sequencing of pathogens allows us to perform genomic fingerprinting on viruses,” said Sanbi researcher Peter van Heusden, co-author of a new report presenting the sequence, phylogenetic analysis and modelling of non-synonymous mutations for a SARS-CoV-2 genome.

“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.”

Several medical scientists at the NICD did initial sample sequencing for the genome but did not use the “pure virus”, he said.

“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 ... 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,” said Van Heusden.  

Sanbi researchers then 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. In the end we had six differences,” said Van Heusden.

These differences have given scientists a useful fingerprint in understanding the pandemic.

“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,” he said.

“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.

“Ultimately, this work can also contribute to producing a vaccine against Covid-19.”

Sanbi said it aimed to ensure that analytical genomic tools could be easily deployed and used in Africa to respond to disease threats.  

“Public health isn’t just about dealing with the crisis in front of us now. We have to be thinking about the future,” said Prof Alan Christoffels, chair in bioinformatics and human health genomes at the South African Research Chairs Initiative.

“If we learn anything from this pandemic, it’s that the Global South and the Global North are more connected than ever — and we can come together to build a better and healthier world.”