Virology
Analysis of the nearly full-length genome of a novel HIV-1 CRF01_AE/B/C recombinant strain isolated in Yunnan Province
Jiafa Liu, Mi Zhang, Bihui Yang, Xuemei Deng, Aisi Sun, Suyun Lei, Jianjian Li
Published 2019-08-31
Cite as Chin J Microbiol Immunol, 2019, 39(8): 601-607. DOI: 10.3760/cma.j.issn.0254-5101.2019.08.007
Abstract
ObjectiveTo analyze the genetic structure and recombination characteristics of a newly discovered HIV-1 unique recombinant strain in Yunnan Province.
MethodsDuring a test for drug-resistant HIV genotypes in Yunnan Province in 2016, a recombinant fragment was found in the pol region of a HIV-1 strain isolated from a patient. Two overlapping segments of the HIV-1 genome were amplified by RT-PCR, and then the products were sequenced. Recombination analysis was performed using RIP, jpHMM and SimPlot3.5 software. A phylogenetic tree was constructed for homology analysis by Neighbor-joining method using MEGA6.06 software.
ResultsA nearly full-length HIV-1 gene sequence with 8 590 bp in length was obtained. Breakpoint analysis indicated that the sequence consisted of CRF01_AE and fragments of B and C subtypes. CRF01_AE was used as the backbone with B and C subtype fragments inserted. The positions were 791 to 1 171 for CRF01_AE, 1 172 to 2 652 for C subtype fragment, 2 653 to 2 977 for B subtype fragment, and 2 978 to 9 380 for CRF01_AE using HIV-1 HXB2 as the reference strain.
ConclusionsSome new strains formed by cross-recombination of CRF01_AE and B and C subtypes were discovered in Yunnan Province in recent years. It was found that the recombination pattern of the newly discovered strain was complex, suggesting that close attention should be paid to the changes in epidemic trends, which was of great importance to understand the current prevalence and epidemic trends of HIV-1.
Key words:
Human immunodeficiency virus type 1; Unique recombinant form; Near-full-length gene sequence analysis
Contributor Information
Jiafa Liu
Department of Laboratory, Yunnan Provincial Infectious Diseases Hospital/AIDS Care Center, Kunming 650301, China
Mi Zhang
Bihui Yang
Xuemei Deng
Aisi Sun
Suyun Lei
Jianjian Li