Identificationof a novel first-generationHIV-1 circulating recombinant form (CRF152_DG) among people living with HIV in Karachi, Pakistan
Rashid A. Kang L. Yi F. Getaneh Y. Chu Q. Shah S.A. Abidi S.H. Shao Y.
July 2024American Society for Microbiology
Microbiology Spectrum
2024#12Issue 7
The objective of this study was to characterize a novel circulating recombinant form of human immunodeficiencyvirus type 1 (HIV-1) among people living with HIV in Karachi, Pakistan. We conducted near-full-length genome (NFLG) sequencing on eight samples exhibiting D/G recombination signals in the pol gene region. We successfully obtained NFLG sequences (790-9,614; with reference to the HXB2 genome) from four of the eight samples and then conducted phylogenetic and recombination analyses on them. The four NFLG sequences from our study and one DG unique recombinant form previously identifiedin the United Kingdom (GenBank accession: MF109700) formed a distinct monophyletic cluster with an Shimodaira-Hasegawa approximate likelihood ratio test node support value of 100%. Bootscan analyses of the fiveNFLG sequences of DG recombinants showed that all fiveNFLGs shared the same unique mosaic pattern of recombination breakpoints between D and G clades, with two D fragments in the pol and vif regions inserted into a G backbone. Subregion phylogenetic analyses confirmedthese sequences to be a novel circulating recombinant form (CRF) composed of subtypes D and G. The DG recombinant sequences were eventually designated as CRF152_DG by the Los Alamos HIV Sequence Database staff.
genetic recombination , HIV-1 genetics , molecular epidemiology , Pakistan , phylogeny , United Kingdom
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School of Medicine, Nankai University, Tianjin, China
National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Chinese Center for Disease Control and Prevention, Beijing, China
College of Life Sciences, Nankai University, Tianjin, China
State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First AffiliatedHospital, Zhejiang University, School of Medicine, Hangzhou, China
Ethiopian Public Health Institute, Addis Ababa, Ethiopia
Bridge Consultants Foundation, Karachi, Pakistan
Department of Biological and Biomedical Sciences, Aga Khan University, Karachi, Pakistan
Department of Biomedical Sciences, School of Medicine, Nazarbayev University, Astana, Kazakhstan
Changping Laboratory, Beijing, China
School of Medicine
National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases
College of Life Sciences
State Key Laboratory for Diagnosis and Treatment of Infectious Diseases
Ethiopian Public Health Institute
Bridge Consultants Foundation
Department of Biological and Biomedical Sciences
Department of Biomedical Sciences
Changping Laboratory
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