Genetic Characterization of a Unique Recombinant Originating from CRF55_01B, CRF01_AE, and CRF07_BC in Shenzhen, China

AIDS Research and Human Retroviruses
Tao GuiLin Li

Abstract

Multiple subtypes were found to be epidemic in the Shenzhen men who have sex with men (MSM) population, which always predicts the emergence of a unique recombinant. In 2012, CRF55_01B was first reported, which later was proven to have originated in MSM in Shenzhen city. In this study, we reported a unique recombinant form (URF) of HIV-1 identified in a man who has had sex with men in Shenzhen city. The strain showed a genomic schematic map similar to CRF55_01B with subtype C segments inserted in the gag and pol genes. The full-length genome was amplified in two halves with 1-kb overlap regions. The PCR products were cloned and sequenced. A recombination detection program showed that two subtype C fragments and two subtype B fragments were inserted into the CRF01_AE backbone genome in the gag and pol regions. In the phylogenetic tree, the subtype C fragments clustered with CRF07_BC variants and the other segments grouped with CRF55_01B strains except for one segment that clustered with CRF01_AE. Similar breakpoints between our strain and CRF65_cpx were also observed. The data suggested that the URF strain might be the recombinant form of CRF55_01B, CRF01_AE, and CRF07_BC. This is the first report of a third generation of recombi...Continue Reading

References

Oct 8, 2003·Systematic Biology·Stéphane Guindon, Olivier Gascuel
Jul 18, 2006·Nucleic Acids Research·Ming ZhangMario Stanke
Jun 10, 2010·AIDS Research and Human Retroviruses·Lin LiJingyun Li
Feb 8, 2011·AIDS·Joris HemelaarUNKNOWN WHO-UNAIDS Network for HIV Isolation and Characterisation
Feb 6, 2013·Genome Génome / Conseil National De Recherches Canada·Christian McKinnon, Guy Drouin
Mar 26, 2014·Journal of Acquired Immune Deficiency Syndromes : JAIDS·Jin ZhaoChiyu Zhang

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Citations

Jul 28, 2016·AIDS Research and Human Retroviruses·Dijing JiaLin Li
Nov 30, 2019·AIDS Research and Human Retroviruses·Bingyu LiangLi Ye

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Datasets Mentioned

BETA
KP170487

Methods Mentioned

BETA
PCR
genotyping
RIP

Software Mentioned

Gapstreeze
jpHMM
Map
ContigExpress
- Draw Tool
MEGA3
Fasta
PhyML
MEGA5
Clustal W

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