title: Cocirculation of several similar but unique HIV-1 recombinant forms in Guinea-Bissau revealed by near full-length genomic sequencing.
abstract: The dynamic HIV-1 epidemic has resulted in the emergence of several different subtypes and recombinant forms that may differ in biological properties. A recombinant form of CRF02_AG and subsubtype A3 (A3/02) was recently described based on env sequencing and was associated with faster disease progression rates compared with its parental strains. Here, we performed near full-length sequencing of the A3/02 variant to characterize the recombination patterns of a potential novel and more pathogenic circulating recombinant form of HIV-1 in Guinea-Bissau. HIV-1 proviral DNA was extracted from blood samples of individuals infected with the A3/02 recombinant form. The recombination patterns were investigated for six samples that were successfully amplified and sequenced. We found that all six full-length genomes were recombinant forms composed of CRF02_AG and A3 with a recombination hot-spot in the C2 region of env. However, the recombination patterns in the remaining genome differed between samples. Two samples displayed similar recombination profiles, indicative of a homogeneous recombinant form circulating in the population in Guinea-Bissau, whereas the remaining four samples represented unique recombinant forms. The characterization of five different recombination profiles indicated a high frequency of recombination. The recombination breakpoint in the C2 region was identified as the principal common feature shared between sequences, suggesting that this region may have an impact on disease progression rate. Since novel recombinant forms may have characteristics associated with a higher potential of spread in the human population, this study highlights the importance of continuous screening and surveillance of the HIV-1 epidemic.
authors.affiliation: 1 Department of Experimental Medical Science Lund, Lund University , Lund, Sweden .|2 Department of Translational Medicine, Lund University , Malmö, Sweden .
authors.forename: Angelica A
authors.initials: AA
authors.lastname: Palm
authors.affiliation: 2 Department of Translational Medicine, Lund University , Malmö, Sweden .|3 Nuffield Department of Medicine, University of Oxford , Oxford, United Kingdom .|4 Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet , Stockholm, Sweden .
authors.forename: Joakim
authors.initials: J
authors.lastname: Esbjörnsson
authors.affiliation: 5 Department of Clinical Sciences Malmö, Lund University , Malmö, Sweden .
authors.forename: Fredrik
authors.initials: F
authors.lastname: Månsson
authors.affiliation: 6 National Public Health Laboratory , Bissau, Guinea-Bissau .
authors.forename: Antonio
authors.initials: A
authors.lastname: Biague
authors.affiliation: 6 National Public Health Laboratory , Bissau, Guinea-Bissau .
authors.forename: Zacarias José
authors.initials: ZJ
authors.lastname: da Silva
authors.affiliation: 7 Department of Clinical Sciences Lund, Lund University , Lund, Sweden .
authors.forename: Hans
authors.initials: H
authors.lastname: Norrgren
authors.affiliation: 4 Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet , Stockholm, Sweden .|8 Department of Laboratory Medicine Lund, Lund University , Lund, Sweden .
authors.forename: Marianne
authors.initials: M
authors.lastname: Jansson
authors.affiliation: 2 Department of Translational Medicine, Lund University , Malmö, Sweden .
authors.forename: Patrik
authors.initials: P
authors.lastname: Medstrand
mesh_terms: D006169:Guinea-Bissau / Q000453:epidemiology; D015658:HIV Infections / Q000453:epidemiology / Q000821:virology*; D015497:HIV-1 / Q000235:genetics* / Q000472:pathogenicity; D006801:Humans; D008969:Molecular Sequence Data; D011995:Recombination, Genetic; D017422:Sequence Analysis, DNA