NSW Health Pathology is a national leader in genome sequencing and its expertise came to the fore during the COVID-19 pandemic. Within two weeks our Westmead laboratory had developed an in-house whole genome sequencing process for the COVID-19 virus.

When the coro­n­avirus SARS-CoV­‑2 first land­ed on Aus­tralian shores in Jan­u­ary 2020, it car­ried with it a genet­ic passport.

Each case of the virus had its own pass­port with a genet­ic stamp show­ing how the nucleotides inside it were ordered.

As with many virus­es, as SARS-CoV­‑2 spread it evolved and mutat­ed, chang­ing the type and order­ing of these nucleotides ever so slightly.

This may sound sin­is­ter, but it is in fact a very use­ful development.

Under­stand­ing how the virus was spread­ing was going to be key to its con­tain­ment. Pro­fes­sor Vitali Sintchenko, lead pathol­o­gist for the Micro­bial Genomics Lab­o­ra­to­ry at NSW Health Pathology’s ICPMR-West­mead, describes nucleotides with­in an RNA genome as the build­ing blocks of a virus.

“In order to under­stand trans­mis­sion path­ways of the pathogen, you must first under­stand the order of these build­ing blocks. You can then iden­ti­fy any pres­ence or absence of changes in the build­ing blocks,” Prof Sintchenko said.

“With whole genome sequenc­ing we cap­ture the sequence of these build­ing blocks very accu­rate­ly and we employ com­plex instru­ments to do it quick­ly and in high volumes.

“Rapid sequenc­ing tech­niques allow us to gain a whole genome wide view of the pathogen very quick­ly and pre­dict or under­stand behav­iours of the virus.

“When we look at nucleotides, we can iden­ti­fy with high accu­ra­cy any vari­ance with­in the virus genet­ic sequence.

“We com­pare virus­es from patients at dif­fer­ent stages of the dis­ease or with a dif­fer­ent his­to­ry of dis­ease and look for poten­tial rela­tion­ships between cases.

“From this we can infer, from genom­ic data, poten­tial trans­mis­sion pat­terns or path­ways that can help track how it has spread through a com­mu­ni­ty and beyond,” Prof Sintchenko said.

Through whole genome sequenc­ing, experts can match new cas­es to clus­ters, or iden­ti­fy the ori­gin of, and rela­tion­ships between COVID-19 cas­es, pro­vid­ing a deep­er under­stand­ing of the spread of the disease.

Whole genome sequenc­ing offers anoth­er line of evi­dence to sup­port con­tact trac­ing by fill­ing in gaps where peo­ple have not or can­not pro­vide all nec­es­sary details to help trace the source.

With­in two weeks NSW Heath Pathology’s West­mead lab­o­ra­to­ry had devel­oped an in-house whole genome sequenc­ing process for the COVID-19 virus, in col­lab­o­ra­tion with aca­d­e­mics from the Uni­ver­si­ty of Syd­ney, soon fol­lowed by NSW Health Pathology’s lab­o­ra­to­ries at Randwick.

In eight months, the team at West­mead suc­cess­ful­ly sequenced more than 1,000 cas­es and dis­cov­ered 51 genom­ic clusters.

Sequences are also uploaded to an inter­na­tion­al virus sequence data­base to assist epi­demi­ol­o­gists and researchers around the world.

Prof Sintchenko says the appli­ca­tion of whole genome sequenc­ing to the inves­ti­ga­tion of COVID-19 has been trans­for­ma­tion­al and the num­ber of genomes uploaded to the inter­na­tion­al data­base has been unprecedented.

“NSW Health Pathol­o­gy is a nation­al leader in genome sequenc­ing, and we have made a sig­nif­i­cant con­tri­bu­tion to data shar­ing to inter­na­tion­al research teams,” Prof Sintchenko said.

“We have very well-devel­oped trans­la­tion­al research col­lab­o­ra­tion between clin­i­cians, sci­en­tists and researchers that has enabled us to achieve what we have in a very short timeframe.”

NSW Health Pathol­o­gy con­tin­ues to work close­ly with Health Pro­tec­tion NSW, pro­vid­ing whole genome sequenc­ing data and report­ing to sup­port their cen­tralised con­tact trac­ing and epi­demi­ol­o­gy teams.

This work is crit­i­cal to iden­ti­fy peo­ple at risk of COVID-19 and min­imise fur­ther spread of the virus in the com­mu­ni­ty and among the most vulnerable.

“The evo­lu­tion and spread of the virus around the globe and in Aus­tralia is fas­ci­nat­ing but com­plex,” Prof Sintchenko said.

“It is like detec­tive work, and we are part of the NSW Health COVID-19 response team.”

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