Abstract
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.
| Original language | English |
|---|---|
| Pages (from-to) | e0052924 |
| Journal | Microbiology spectrum |
| Volume | 12 |
| Issue number | 7 |
| Early online date | May 21 2024 |
| Publication status | Published - Jul 2024 |
Funding
We are thankful to the National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Chinese Center for Disease Control and Prevention, Beijing, China, for the financialsupport and facilitating the coordination. We are also thankful to Prof. Sten H. Vermund, Department of Epidemiology of Microbial Diseases, Yale School of Public Health, Yale University, USA, for critically reviewing the manuscript. This work was supported by the Science Priority Grant 2019SKLID602 and 2021SKLID303 from the State Key Laboratory of Infectious Disease Prevention and Control, the Ministry of Science and Technology of China (2012ZX10004910 and 2022YFC2305201), and the National Natural Science Foundation International/Inter-Organization Cooperation and Exchange Study-NSFC-VR Project (China and Switzerland) (grant number 81861138011). This work was supported by the Science Priority Grant 2019SKLID602 and 2021SKLID303 from the State Key Laboratory of Infectious Disease Prevention and Control, the Ministry of Science and Technology of China (2012ZX10004910 and 2022YFC2305201), and the National Natural Science Foundation International/Inter-Organization Cooperation and Exchange Study-NSFC-VR Project (China and Switzerland) (grant number 81861138011).
| Funders | Funder number |
|---|---|
| Department of Epidemiology of Microbial Diseases | |
| Yale School of Public Health, Yale University | |
| National Natural Science Foundation International | |
| State Key Laboratory of Infectious Disease Prevention and Control | |
| Yale University | 2019SKLID602, 2021SKLID303 |
| Inter-Organization Cooperation and Exchange Study-NSFC-VR | 81861138011 |
| Ministry of Science and Technology of the People's Republic of China | 2012ZX10004910, 2022YFC2305201 |
Keywords
- HIV-1 genetics
- Pakistan
- United Kingdom
- genetic recombination
- molecular epidemiology
- phylogeny
ASJC Scopus subject areas
- Physiology
- Ecology
- General Immunology and Microbiology
- Genetics
- Microbiology (medical)
- Cell Biology
- Infectious Diseases
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