African Scientists Successfully Sequence Local COVID-19 Genome

South African researchers announced the successful genome sequencing of a local sample of SARS-CoV-2, otherwise known as the novel coronavirus, in a report via Maverick Citizen.

Scientists at the NICD (National Institute of Communicable Diseases) together with the South African National Bioinformatics Institute (Sanbi) at the University of Western Cape were able to collect, analyze, and sequence the virus sample collected from the nose and throat of a Kwazulu-Natal patient. The patient, in particular, is thought to have contracted the virus in Italy, from whence they had returned to South Africa in early March.

The South African virus sample will be added to the Global Initiative on Sharing All Influenza Data (GISAID) records. Currently, on the records there exist about 4000 SARS-CoV-2 genetically sequenced virus samples. Though this number is still relatively small, each additional sample provides the database with a much-needed boost in information.

Sanbi researcher and co-author of the report with Dr Arshad Ismail, Peter van Heusden, says that the next challenge is for the genome sequencing to be scaled and sped up in the country.

Congolese and Senegalese scientists have already sequenced 20 and 25 samples respectively since the virus was first detected in those countries.

“When we started last month we had both a laboratory and a computer challenge,” Van Heusden says, as the scientists had to first isolate the virus’ genetic material, the RNA, from the patient’s DNA, as the virus was not lab-grown.

“Humans have about three billion ‘letters’ [the nucleotide bases in our DNA, represented in letters of the alphabet] and we know the virus has about 29,000 of these bases or letters. But our second challenge was that our computers are only able to read chunks of this code of about 150 letters at a time. So it was like piecing together shredded bits of information to be able to see the whole picture,” he continues.

“When we put it together we found that in this patient, the virus had six differences in its 29,000 RNA letters compared with virus samples recorded in China, where the virus was detected at the end of 2019. Six differences is a tiny number and don’t seem to affect how the virus is changing or in the way it produces protein. Proteins are the molecular machines that make cells work and the virus genome is like a recipe book of proteins that the virus needs to invade cells and to make copies of itself.”

Van Heusden says that it is in the identifying of these differences that scientists will spot patterns and anomalies in how the virus is possibly mutating, adapting and replicating. It’s why, he says, there’s an urgency to have more samples sequenced.

“Genetic fingerprinting also means we can organize samples into clusters so we can understand how the disease is spreading,” Van Heusden says.

“Sadly, COVID-19 will not be the only disease that we will need to fight, so we need genome sequencing techniques to reconstruct a kind of family tree of viruses so we can better predict how and when an outbreak may happen in the future, so we can also be better prepared to fight what’s out there,” Van Heusden concludes.

Edited by Luis Monzon

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