How SA Pathology “detectives” are using genomic sequencing to link COVID cases

Without genomic sequencing, COVID-19 cases including the Parafield cluster wouldn’t have been able to be linked.

The process is vital in providing supporting epidemiological information to authorities so they can identify the source of the infection, with the hope of acting quickly to stop the spread.

In the Parafield cluster, all cases were able to be linked back to an overseas traveller in a Medi-Hotel.

“We managed to connect the link between the local transmission and the traveller within 48 hours,” SA Pathology medical scientist in microbial genomics, Dr Lex Leong, said.

“Especially for this cluster, the timeliness of making that association and helping Department of Health look for missing links was vital.”

What is genomic sequencing?

Genomic sequencing analyses the virus sample taken from a positive patient and compares its genomic sequence with other cases.

When the virus passes from person to person there are slight “genomic” changes over a period of time.   (Genomes are the complete genetic material of an organism, like a bacteria, virus, animal and human).

The sample goes through several steps to extract RNA from the virus to be analysed. (RNA replaces DNA as a carrier of genetic codes in some viruses like SARS-COV-2).

Experts described the result in a form of a family tree, where the “leaves” of linked cases are close together and almost identical. Whereas for unrelated cases, the leaves will be further away on other branches.

“The virus has evolved very slowly, but it does accumulate enough variations for us to be able to tell that outbreaks are different,” Dr Leong said.

“Doing sequencing of all COVID cases allows us to quickly identify where it has come from and associate them to a cluster or not.”

While there is only one “strain” of the SARS-CoV-2 virus, there are different “variants” on the family tree. What it can’t tell is which case came first.

Dr Lex Leong and Dr Chuan Kok Lim.

Establishing capabilities in SA

Prior to COVID-19, genomic sequencing wasn’t available for viruses in SA.

“I was usually doing genomic testing looking at bacteria and testing pathogens for genomic sequencing,” Dr Leong explains.

“For example if there is a foodborne disease outbreak, the genomic sequencing will link the cases and help authorities link it back to the source.”

Dr Leong, along with virologist and infectious diseases physician Dr Chuan Kok Lim, decided it was necessary to set up the capability in SA and were supported by SA Pathology.

Towards the middle of the State’s first wave in April, they began sequencing all of the positive cases.

“Without the background data from the first wave, we wouldn’t be able to compare to distinctively identify the new cluster,” Dr Lim said.

“If we hadn’t done that we couldn’t have helped with contact tracing for this cluster.”

The approach for COVID is very similar to bacteria and the team is continuing to improve their processes. The turnaround time previously up to a week, is now down to two days, and looking to get it down even further to within hours.

“It’s been a really good collaboration between me and Lex because we have skills that really complement each other,” Dr Lim said.