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Near full-length sequence analysis of a Unique CRF01_AE/B recombinant from Kuala Lumpur, Malaysia
Katherine A Lau1, Bin Wang, Adeeba Kamarulzaman
1Retroviral Genetics Division, Center for Virus Research, Westmead Millennium Institute, Westmead Hospital, University of Sydney, Westmead NSW 2145, Sydney, Australia.
Abstract:
A new HIV-1 circulating recombinant form (CRF), CRF33_01B, has been identified in Malaysia. Concurrently we found a unique recombinant form (URF), that is, the HIV-1 isolate 06MYKLD46, in Kuala Lumpur, Malaysia. It is composed of B or a Thai variant of the B subtype (B') and CRF01_AE. Here, we determined the near full-length genome of the isolate 06MYKLD46 and performed detailed phylogenetic and bootscanning analyses to characterize its mosaic composition and to further confirm the subtype assignments. Although the majority of the 06MYKLD46 genome is CRF01_AE, we found three short fragments of B or B' subtype inserted along the genome. These B or B' subtype regions were 716 and 335 bp, respectively, in the protease-reverse transcriptase (PR-RT) region, similar to those found in CRF33_01B, as well as an extra 590 bp in the env gene region. Thus we suggest that 06MYKLD46 is a possible second-generation HIV-1 recombinant derived from CRF33_01B.
Insights
A novel HIV-1 unique recombinant form (URF), 06MYKLD46, was identified in Malaysia. This URF likely represents a second-generation recombinant derived from CRF33_01B, containing fragments of subtypes B/B' and CRF01_AE.
Area of Science:
- Virology
- Molecular Biology
- Genetics
Background:
- A new HIV-1 circulating recombinant form (CRF), CRF33_01B, has been identified in Malaysia.
- Unique recombinant forms (URFs) of HIV-1 present challenges in understanding viral evolution and transmission dynamics.
Purpose of the Study:
- To determine the near full-length genome of the HIV-1 isolate 06MYKLD46 from Kuala Lumpur, Malaysia.
- To characterize the mosaic composition and confirm subtype assignments of the 06MYKLD46 isolate through phylogenetic and bootscanning analyses.
Main Methods:
- Near full-length genome sequencing of the HIV-1 isolate 06MYKLD46.
- Phylogenetic analysis to determine genetic relationships.
- Bootscanning analysis to identify mosaic structure and subtype origins.
Main Results:
- The HIV-1 isolate 06MYKLD46 is a unique recombinant form (URF) composed of CRF01_AE and subtypes B or B'.
- Three distinct fragments of subtypes B or B' were identified within the 06MYKLD46 genome, located in the protease-reverse transcriptase (PR-RT) and env gene regions.
- These B or B' fragments share similarities with those found in CRF33_01B.
Conclusions:
- The 06MYKLD46 isolate exhibits a mosaic structure with significant CRF01_AE components and interspersed B or B' fragments.
- The genetic makeup of 06MYKLD46 suggests it is a potential second-generation HIV-1 recombinant derived from CRF33_01B.
- This finding contributes to the understanding of HIV-1 recombination patterns in Malaysia.
