Scientist at the University of Western Cape (UWC) have made strides in understanding the coronavirus (Covid-19) after successfully sequenced the country’s first genome that could help fight the virus that has brought a national lockdown.
Along with the National Institute for Communicable Diseases (NICD), the professors who work for the university’s South African National Bioinformatics Institute (SANBI), were able to sequence a SARS-COV-2 genome that will provide “fingerprint” that can help to contain the spread of the virus.
Peter van Heusden, SANBI researcher and co-author of the report presenting the sequence, said that the finding came from an analysis and modelling of mutations of a SARS-CoV-2 genome that was detected in a South African patient with Covid-19.
Mr Van Heusden said: “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.
The researcher added that it was not an easy task to extract the DNA from the sample, however it was made possible through the efforts of the NICD.
Mr Van Heusden 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.”
Through the research, Mr Van Heusden explained that he examined the differences between the local genome and foreign samples, and in the end a total of six differences were found.
“These differences are important for two reasons, firstly it helps us to understand that 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, we 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).”
Fortunately for Mr Van Heusden, the research was done prior to the lockdown, however the findings were only published recently.
Mr Van Heusden said: “Luckily for my side of the work it is all on a computer so I can do it remotely. It’s still not pleasant trying to craft an office out of a home though.”
One of the people that worked closely with Mr Van Heusden was Dr Mushal Allam, who is a colleague and alumnus of SANBI.
Dr Allam said that the next step would be now to work with the NICD and other organisations to produce a pathogen for the Covid-19 virus, yet that in itself brings other issues.
Dr Allam said: “We are working hard to optimise the sequencing protocol to make a pathogen that is 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.”
Dr Allum though added that during the lockdown the analysis of creating a pathogen has continued as normal.
“We are facing some small issues in term of buying some kits, however the Department of Health and the World Health Organisation is facilitating that.”