title: Fast Dissemination of New HIV-1 CRF02/A1 Recombinants in Pakistan.
abstract: A number of HIV-1 subtypes are identified in Pakistan by characterization of partial viral gene sequences. Little is known whether new recombinants are generated and how they disseminate since whole genome sequences for these viruses have not been characterized. Near full-length genome (NFLG) sequences were obtained by amplifying two overlapping half genomes or next generation sequencing from 34 HIV-1-infected individuals in Pakistan. Phylogenetic tree analysis showed that the newly characterized sequences were 16 subtype As, one subtype C, and 17 A/G recombinants. Further analysis showed that all 16 subtype A1 sequences (47%), together with the vast majority of sequences from Pakistan from other studies, formed a tight subcluster (A1a) within the subtype A1 clade, suggesting that they were derived from a single introduction. More in-depth analysis of 17 A/G NFLG sequences showed that five shared similar recombination breakpoints as in CRF02 (15%) but were phylogenetically distinct from the prototype CRF02 by forming a tight subcluster (CRF02a) while 12 (38%) were new recombinants between CRF02a and A1a or a divergent A1b viruses. Unique recombination patterns among the majority of the newly characterized recombinants indicated ongoing recombination. Interestingly, recombination breakpoints in these CRF02/A1 recombinants were similar to those in prototype CRF02 viruses, indicating that recombination at these sites more likely generate variable recombinant viruses. The dominance and fast dissemination of new CRF02a/A1 recombinants over prototype CRF02 suggest that these recombinant have more adapted and may become major epidemic strains in Pakistan.
authors.affiliation: Duke Human Vaccine Institute, Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America.
authors.forename: Yue
authors.initials: Y
authors.lastname: Chen
authors.affiliation: Duke Human Vaccine Institute, Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America.
authors.forename: Bhavna
authors.initials: B
authors.lastname: Hora
authors.affiliation: Duke Human Vaccine Institute, Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America.
authors.forename: Todd
authors.initials: T
authors.lastname: DeMarco
authors.affiliation: Bridge Consultants Foundation, Karachi, Pakistan.
authors.forename: Sharaf Ali
authors.initials: SA
authors.lastname: Shah
authors.affiliation: Bridge Consultants Foundation, Karachi, Pakistan.
authors.forename: Manzoor
authors.initials: M
authors.lastname: Ahmed
authors.affiliation: Duke Human Vaccine Institute, Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America.
authors.forename: Ana M
authors.initials: AM
authors.lastname: Sanchez
authors.affiliation: Duke Human Vaccine Institute, Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America.
authors.forename: Chang
authors.initials: C
authors.lastname: Su
authors.affiliation: Duke Human Vaccine Institute, Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America.
authors.forename: Meredith
authors.initials: M
authors.lastname: Carter
authors.affiliation: Blood Systems Research Institute, San Francisco, California, United States of America.
authors.forename: Mars
authors.initials: M
authors.lastname: Stone
authors.affiliation: Department of Pathology, Aga Khan University, Karachi, Pakistan.|Department of Microbiology, Aga Khan University, Karachi, Pakistan.
authors.forename: Rumina
authors.initials: R
authors.lastname: Hasan
authors.affiliation: Department of Pathology, Aga Khan University, Karachi, Pakistan.|Department of Microbiology, Aga Khan University, Karachi, Pakistan.
authors.forename: Zahra
authors.initials: Z
authors.lastname: Hasan
authors.affiliation: Blood Systems Research Institute, San Francisco, California, United States of America.
authors.forename: Michael P
authors.initials: MP
authors.lastname: Busch
authors.affiliation: Duke Human Vaccine Institute, Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America.
authors.forename: Thomas N
authors.initials: TN
authors.lastname: Denny
authors.affiliation: Duke Human Vaccine Institute, Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America.
authors.forename: Feng
authors.initials: F
authors.lastname: Gao
mesh_terms: D000293:Adolescent; D000328:Adult; D019143:Evolution, Molecular; D005260:Female; D016679:Genome, Viral; D015658:HIV Infections / Q000821:virology*; D015497:HIV-1 / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008297:Male; D008875:Middle Aged; D015233:Models, Statistical; D010154:Pakistan; D010802:Phylogeny; D011995:Recombination, Genetic; D012044:Regression Analysis; D017422:Sequence Analysis, DNA; D055815:Young Adult