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HomeWeekly RoundupSuccessful genome sequencing of SA sample of SARS-CoV-2

Successful genome sequencing of SA sample of SARS-CoV-2

Knowing the enemy of COVID-19 from a genetic perspective adds to understanding the puzzle of the virus that’s killed more than 70,600 people around the world. According to a Daily Maverick report, South African researchers announced in a report the successful genome sequencing of a local sample of SARS-CoV-2, the virus that’s given rise to the COVID-19 pandemic.

Scientists at the NICD (National Institute of Communicable Diseases) together with colleagues at the South African National Bioinformatics Institute (Sanbi) at the University of the Western Cape were able to collect, analyse, and sequence the virus sample collected from the nose and throat of a patient in KwaZulu-Natal. The patient had returned to South Africa from a trip to Italy at the beginning of March.

The report says this is South Africa’s first genetic fingerprint of a locally analysed virus sample to be added to the Global Initiative on Sharing All Influenza Data (GISAID) records. Currently, there are about 4,000 SARS-COV-2 genetically sequenced virus samples in the database. Each addition boosts this still relatively small number of samples, given that there are more than 1.3m confirmed infections worldwide, according to data from the Johns Hopkins Coronavirus Resource Centre.

Peter van Heusden, Sanbi researcher and co-author of the published report with Dr Arshad Ismail, says the next challenge is for the genome sequencing to be scaled up and speeded up in the country. Congolese and Senegalese scientists have already sequenced 20 and 25 samples respectively since COVID-19 was detected in those countries.

South Africa’s listeriosis outbreak in the first months of 2018 was one of the first times whole-genome sequencing was used to pinpoint the source of the disease outbreak. Ismail was at the centre of the listeriosis genome sequencing initiative. The scientists’ efforts meant that the food product – polony – and the factories where the contaminated polony was manufactured could be quickly identified. It helped to contain the spread of the disease.

[link url="https://www.dailymaverick.co.za/article/2020-04-07-sas-first-successful-genome-sequencing-of-a-local-sars-cov-2-sample-will-help-global-fight-against-the-disease/"]Full Daily Maverick report[/link]

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