One for all, all for one

23 November 2012

By Astrid Gall

HIV-1 genome sequences generated by our new method for universal HIV-1 genome sequencing. The tree illustrates the application across the breadth of the HIV-1 genetic diversity. New sequences identified by our method are shown in colour.Credit: Doi: 10.1128/JCM.01516-12

34 million people worldwide are infected with Human Immunodeficiency Virus 1 (HIV-1), the causative agent of AIDS. So why is it that we do not have a vaccine against HIV-1, when we have several vaccines against influenza? And why do we only have ~2000 HIV-1 genome sequences available to analyse the pandemic, when we have ~90,000 genome sequences of human influenza viruses?

One key reason for this discrepancy is that HIV-1 is one of the most genetically diverse viruses known. The HIV-1 diversity within just one infected person at any one time is as great as the diversity of influenza viruses worldwide in an entire year. For example, there are as many as four genetic groups of HIV-1, nine subtypes and 55 circulating recombinant forms, or forms that have swapped their genetic material. This extensive genetic diversity has limited our ability to rapidly and cost-effectively sequence HIV-1 genomes from different populations and geographical regions.

Recently, we have developed the first universal method for HIV-1 genome sequencing. We designed and validated one set of primers that bind to the genetic material, RNA, of all HIV-1 subtypes. Then we used the novel primer set to reverse-transcribe, the process of making a double-stranded DNA molecule from a single-stranded RNA template, and amplify HIV-1 RNA. Coupled with advanced sequencing and computational tools, this allowed us to generate HIV-1 genomes sequences across the breadth of the genetic diversity.

We applied our method to analyse HIV-1 genome diversity and to detect changes in the HIV-1 genome that confer drug resistance. The results were published in our paper ‘Universal Amplification, Next-Generation Sequencing, and Assembly of HIV-1 Genomes’ in the Journal of Clinical Microbiology.

The new method for universal HIV-1 genome sequencing can be used to understand:

- which HIV-1 genotype is present in an infected individual

- how HIV-1 changes over time in infected individuals

- how HIV-1 changes in space and time in the infected population

- how many HIV-1 variants with resistance to drugs exist in patients before receiving treatment, to inform treatment decisions

- how drug resistance in patients receiving treatment develops and is transmitted to others

- which changes in the HIV-1 genome are linked to progression to AIDS (virus genome-wide association study).

We address some of these questions in our current research exploring the interaction of HIV-1 and its human host. We hope that the approach will be adopted by other researchers working on further questions. Altogether, these efforts will help to tackle the global health problem AIDS.
Astrid Gall is a Staff Scientist in the Virus Genomics team at the Wellcome Trust Sanger Institute more…

Intellectual property:

Priority US patent application filed. The Wellcome Trust Sanger Institute is offering non-exclusive licenses to this IP. Contact: Emmanuelle Astoul, Business Development Manager, ea4@sanger.ac.uk

Research Paper:

Gall A, Ferns B, Morris C, et al. (2012). ‘Universal Amplification, Next-Generation Sequencing, and Assembly of HIV-1 Genomes’

Journal of Clinical Microbiology, Published ahead of print 19 September 2012 Doi:  10.1128/JCM.01516-12

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