New HIV subtype has been identified


  • Nation
  • Wednesday, 06 Nov 2019

Graphic: Abbott

PETALING JAYA: For the first time in 20 years, a new subtype of HIV (human immunodeficiency virus) has been confirmed and identified.

Known as subtype L, it is the latest addition to the viral subtypes classified under the HIV-1 Group M strain, which causes over 90% of HIV infections in the world.

Although a sample of this HIV subtype was first collected in the Democratic Republic of Congo in 1983, followed by two others in 1990 and 2001 respectively, they were unable to be conclusively identified as a new subtype until recently.

Abbott principal scientist Dr Mary Rodgers, who manages the Abbott Global Surveillance Program, explained that the 2001 sample, which the programme had obtained through a collaboration, had too little virus to be sequenced properly with the available tools then.

"We only had a very small part of the viral sequence at that time," she said.

"And so that was the challenge, because we need to have the whole virus sequence to be able to call something a new subtype."

She explained that this was as HIV subtypes have a very high tendency to combine and form something that may look new, but is actually a combination of already-known subtypes known as a circulating recombinant form (CRF).

"A new subtype has to be a completely pure genetic sequence that is different from everything else.

"So, by just having a little part of the virus early on that was different, we couldn't say that the virus was new because it could have been a recombinant," said Dr Rodgers, who is part of the team that identified the new subtype.

Then last year (2018), a new technology was developed that enabled the scientists to zoom in specifically on the virus part of the sample and isolate it enough to be genetically sequenced.

Dr Rodgers explained: "Think of a viral sample from a person as kind of like a haystack.

"The haystack represents all the things in the sample (including genes from the person the sample is from and bacterial genes from the air), but we are really only interested in the little needle that correlates to the HIV that we need to sequence.

"What we literally did in this new method that we developed at Abbott, was that we took a 'magnet' and just pulled out that HIV 'needle', and then got rid of most of the 'hay', so that we could actually just focus our efforts and abilities on sequencing the HIV specifically from the sample, and that turned out very fruitful.

"We got the entire genome in one try and we compared it to see if there were any points where it had recombined with other viruses, and it did not.

"So this allowed us to truly say this is a new subtype of HIV and we have met all the criteria by defining this new genome that we found in the Democratic Republic of Congo."

As to whether this would affect the current diagnostic tests and treatments for HIV, she said: "That's what we're trying to figure out.

"I mean, finding this new strain is really just the beginning and by sharing the sequence with the scientific community at large, we're now enabling others to evaluate how this strain might differ from others in terms of treatment and the development of a diagnostic test that can also detect it."

However, she predicts that this new subtype will probably react to current anti-retroviral treatment the same way as other HIV Group M subtypes do.

The process of identifying the new subtype was published online in the Journal of Acquired Immune Deficiency Syndrome on Nov 6,2019.


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