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Genomic sequencing unlocks streamlined HIV care

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1st December, 2022

In an Australian first, NSW Health Pathology is pioneering the use of whole genome sequencing to more efficiently match people living with HIV with the antiviral drugs most likely to slow or halt the progress of the potentially life-threatening disease.

The updat­ed assay devel­oped by Pro­fes­sor Sebas­ti­aan van Hal, a micro­bi­ol­o­gist cre­den­tialled in pathogen genomics at NSWHP’s Roy­al Prince Alfred lab, iden­ti­fies which par­tic­u­lar HIV strain the patient has and the strain’s like­ly response to every HIV antivi­ral drug on the market.

Armed with the results of this one pow­er­ful genom­ic test, doc­tors will know which antivi­ral drug will be most effec­tive in fight­ing the patient’s HIV infec­tion, and which med­ica­tions may do lit­tle to slow the virus’ progression.

The updat­ed assay, devel­oped with the assis­tance of NSW Health Pathol­o­gy sci­en­tists Thomas Le and Frances Jenk­ins, is a game chang­er in HIV treat­ment. It has effec­tive­ly future-proofed HIV antivi­ral resis­tance test­ing and giv­en clin­i­cians the infor­ma­tion they need to pro­vide more time­ly, tar­get­ed antivi­ral ther­a­py for Aus­tralians liv­ing with HIV.

Pro­fes­sor van Hal said he embarked on accred­i­ta­tion of the assay after spend­ing six months in Oxford, Eng­land learn­ing sequenc­ing analy­sis of pathogens.

“When I came home I saw an oppor­tu­ni­ty to put my new knowl­edge into prac­tice and stream­line what has tra­di­tion­al­ly been a cum­ber­some process for iden­ti­fy­ing antivi­ral resis­tance,” Prof van Hal said.

“It’s excit­ing to know this is an Aus­tralian first using whole genome sequenc­ing tech­nol­o­gy to test and report drug resis­tance in a virus.”

Pro­fes­sor van Hal explains the tech­nol­o­gy and method­ol­o­gy has come a long way since it came to Aus­tralia in the 1980s.

“In the ear­ly days, Sanger-based sequenc­ing test­ed just two of the virus’ genes for resis­tance against the very lim­it­ed num­ber of antivi­ral drugs on the mar­ket at that time,” Pro­fes­sor van Hal explained.

“As a whole new class of antivi­rals was devel­oped and intro­duced to the mar­ket, clin­i­cians turned to ad hoc, bespoke sequenc­ing to under­stand the virus’ resis­tance to them.”

The advent of new­er tech­nolo­gies, such as Next-Gen­er­a­tion Sequenc­ing (NGS), has rapid­ly advanced genomics. In the field of pathogen genomics, the val­ue of this tech­nol­o­gy was quick­ly realised with its appli­ca­tion for whole genome sequenc­ing of virus­es and bac­te­ria, includ­ing those resis­tant to first-line antibi­otics such as the life-threat­en­ing Staphy­lo­coc­cus and SARS-CoV­‑2.

Now, with Pro­fes­sor van Hal’s lead­er­ship, two years in val­i­da­tion, ver­i­fi­ca­tion against World Health Organ­i­sa­tion guide­lines and NATA accred­i­ta­tion, HIV has been added to the list.

Pro­fes­sor van Hal ran the first of what he pre­dicts will be a small but steady stream of requests in Octo­ber 2022.

Thank­ful­ly, the low inci­dence of HIV trans­mis­sion in Aus­tralia today, achieved through strong proac­tive pub­lic health efforts, means the assay will be a niche, but cru­cial, prod­uct in the pathol­o­gy landscape.


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