Genetic Characterization of a Unique Recombinant Originating from CRF55_01B, CRF01_AE, and CRF07_BC in Shenzhen, China.
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 recombination of HIV-1 that originated from CRF55_01B in China. The identification of the URF indicated the severity of the HIV epidemic in Shenzhen MSM and the urgent need for epidemiological surveillance of the new recombination.
1 Department of AIDS Research, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology , Beijing, China .
Tao
T
Gui
Jin
J
Zhao
Changrong
C
Sun
Lin
L
Chen
Yongjian
Y
Liu
Chenli
C
Zheng
Hanping
H
Li
Tianyi
T
Li
Zuoyi
Z
Bao
Xiaolin
X
Wang
Jingyun
J
Li
Lin
L
Li
D002681:China / Q000453:epidemiology; D016000:Cluster Analysis; D023061:Gene Order; D005814:Genes, Viral; D016679:Genome, Viral; D015658:HIV Infections / Q000453:epidemiology / Q000821:virology*; D015497:HIV-1 / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D018451:Homosexuality, Male; D006801:Humans; D008297:Male; D008969:Molecular Sequence Data; D016254:Mutagenesis, Insertional; D010802:Phylogeny; D012367:RNA, Viral / Q000235:genetics*; D011995:Recombination, Genetic; D017422:Sequence Analysis, DNA; D012689:Sequence Homology, Nucleic Acid; D055815:Young Adult
D012367:RNA, Viral