Genomic sequencing

Analyses a virus sample taken from a diagnosed patient and compares it with other cases. Genomic sequencing has been used to trace the source of outbreaks of infectious diseases.

Genomic sequencing has been used to trace the source of outbreaks of foodborne bacteria and hospital infections. It was used to understand the evolution of the 2013-16 Ebola outbreak in West Africa.

As any virus passes from human to human, it mutates or changes very slightly. While the genome of one COVID-19 patient compared with the person they caught it from appears almost identical, after the virus has been transmitted onto further people, differences between the strands of the virus they carry become more apparent. The information from genomic sequencing allows scientists to understand patterns of the spread of pathogens in populations.

After a COVID-19 RT-PCR test returns a positive result, genomic sequencers use sequencing machines to extract RNA molecules from mucous proteins in order to convert them into DNA. Genomic sequencers then ‘read’ the order of DNA nucleotides in a genome to establish its phylogenetic tree—which is like a family tree of viruses. This tree can help scientists understand where genomes come from and how they are related. South Africa’s SARS-CoV-2 genome sequence, for example, has six differences from the original genome of the virus discovered in Wuhan, China.

South African scientists, for example, using phylogenetics, found that South Africa’s SARS-CoV-2 infection came from Europe or North America, where there are very similar sequences. The outbreak was traced to individuals who traveled to Italy, where they were infected, and then returned to South Africa. The infection spread from these cases.


Infectious Disease Transmission


COVID-19ProteinsDNA (Deoxyribonucleic Acid)RNA (Ribonucleic Acid)SARS-CoV-2SwabRT-PCR (real time – reverse transcription polymerase chain reaction)