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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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