A considerable proportion of CRF01_AE strains in China originated from circulating intrasubtype recombinant forms (CIRF)

Jia, Lei; Gui, Tao; Li, Lin; Liu, Siyang; Li, Hanping; Bao, Zhenmin; Wang, Xiaolin; Zhuang, Daomin; Li, Tianyi; Han, Jingwan; Liu, Yongjian; Li, Jingyun

doi:10.1186/s12879-015-1273-5

Cited by 9 publications

(8 citation statements)

References 35 publications

(52 reference statements)

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“…The 4 th is the exclusion of intersubtypic recombination, whether the components were classified or not (22, 25). The reason is that compared to nucleotide substitution, recombination can dramatically change the content of genome and confuse the phylogenetic relationship (37, 38). To investigate whether the recombination events exist among the potential LTR references and the clinical sequences, RDP4 recombination analysis tool was used to perform systematic recombination analysis (39).…”

Section: Methodsmentioning

confidence: 99%

A unified classification system for HIV-1 5’ long terminal repeats

Guo

Liu

et al. 2022

Preprint

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The HIV-1 provirus mainly consists of internal coding region flanked by the 2 same long terminal repeats (LTRs) at each terminus. The LTRs play important roles in HIV-1 reverse transcription, integration, and transcription by the association with host factors. However, despite of the significant study advances of the internal coding regions of HIV-1 by using definite reference classification, there are no systematic classifications for HIV-1 5' LTRs, which hinders our elaboration on 5' LTR and a better understanding of the viral origin, spread and therapy. Here, by analyzing all available resources of 5' LTR sequences in public databases following 4 recognized principles for the reference classification, 83 representatives and 14 consensus sequences were identified as representatives of 2 groups, 6 subtypes, 6 sub-subtypes, and 9 CRFs. To test the reliability of our established classification system, the constructed references were applied to identify the 5' LTR assignment of the 22 clinical isolates in China. The results revealed that 16 out of 22 tested strains showed a consistent subtype classification with the previous LTR-independent classification system. However, 6 strains, for which recombination events within 5' LTR were demonstrated, unexpectedly showed a different subtype classification, leading a significant change of binding sites for important transcription factors including SP1, p53, and NF-κB. The binding change of these transcriptional factors would probably affect the transcriptional activity of 5' LTR. This study established a unified classification system for HIV-1 5' LTRs, which will facilitate HIV-1 characterization and be helpful for both basic and clinical research fields.

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Section: Methodsmentioning

confidence: 99%

A unified classification system for HIV-1 5’ long terminal repeats

Guo

Liu

et al. 2022

Preprint

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“…The detailed recombination analysis is performed as previously described [ 14 – 17 , 43 , 46 ]. Both the jpHMM and recombination detection program (RDP4) used in the current work take the circularity of the HBV genomic sequences into consideration and can facilitate accurate predictions of recombination breakpoints even close to the 5′or 3′end of the linearized sequence [ 21 , 32 ].…”

Section: Methodsmentioning

confidence: 99%

Characterization of small genomic regions of the hepatitis B virus should be performed with more caution

Jia¹,

Hu²,

Li³

et al. 2018

Virol J

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BackgroundHepatitis B virus is a hepatotropic DNA virus that reproduces via an RNA intermediate. It can lead to an increased risk of serious liver diseases such as hepatocellular carcinoma and is a serious threat to public health. Currently, the HBV are designated based on greater than 8% nucleotide variation along the whole genome. The recombination of HBV is very common, a large majority of which are recombinants between 2 genotypes. The current work aims to characterize a suspected recombinant involving 3 genotypes.MethodsFifty-seven HBV full-genome sequences were obtained from 57 patients co-infected with HBV and HIV-1 by amplification coupled with sequencing. JpHMM and RDP4 were used to perform recombination analysis respectively. The recombination results of a suspected 3-genotypic recombinant were further confirmed by both maximum likelihood phylogenetic tree and Mrbayes tree.ResultsJpHMM recombination analysis clearly indicated one 3-genotypic HBV recombinant composing of B/C/D. The genotype assignments are supported by significant posterior probabilities. The subsequent phylogenetic analysis of sub-regions derived from inferred breakpoints led to a disagreement on the assignment of D segment. Investigating the conflict, further exploration by RDP4 and phylogenies revealed that the jpHMM-derived 3-genotypic recombinant is actually a B/C genotypic recombinant with C fragment spanning 1899 to 2295 (jpHMM) or 1821 to 2199 (RDP4).ConclusionsThe whole analysis indicated that (i) determination of small genomic regions should be performed with more caution, (ii) combinations of various recombination detection approaches conduce to obtain impartial results, and (iii) a unified system of nomenclature of HBV genotypes is necessary.Electronic supplementary materialThe online version of this article (10.1186/s12985-018-1100-x) contains supplementary material, which is available to authorized users.

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“…According to the recombination mechanism and rate estimated, recombination of HIV-1 takes place during reverse transcription. [4][5][6]9 Thus, no recombination evidence suggested that recombination between these highly similar quasispecies is under the sensitivity of RDP4 test. The major limitation of the present study is low time resolution and small gene segments.…”

Section: Quasispecies Diversity During Primary Hiv Infectionsmentioning

confidence: 99%

“…Both intertype recombination and intratype recombination can cause serious epidemics. 8,9 High frequency of mutation and recombination during HIV reverse transcription creates fresh genetic diversity within a host. This is subject to selection pressures from the immune response and antiretroviral treatment.…”

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The Genetic Diversity of HIV-1 Quasispecies Within Primary Infected Individuals

Liu

Jia

et al. 2020

AIDS Research and Human Retroviruses

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HIV has remarkable genetic diversity among populations. The diversity has critical impacts on transmission, immune escape, pathogenesis, and clinical management. HIV-1 diversity originates from frequent mutation and recombination during reverse transcription. This work focuses on the quasispecies genetic dynamics within individuals with primary infections. Eleven men who have sex with men from the Beijing PRIMO Clinical Cohort were identified as primary infection and had three or four series of their anticoagulant blood samples collected. Viral RNA was extracted and amplified using single-genome amplification. Products of the gp120 gene that met single-genome amplification requirements were sequenced. Subtype assortment of all collected sequences was performed using both the jumping profile hidden Markov model (jpHMM) and REGA. Quasispecies diversity at each time was estimated using Mega 6. Intrapatient recombination was analyzed using RDP4. According to the Fiebig classification system, YA-81 belongs to stage III and YA-113 belongs to stage IV. The other samples are all associated with the infection stage of V/VI. YA113 had a dual infection with subtype B and a new unique recombinant form involving CRF01_AE and C. The other eight were infected with CRF01_AE, one was infected with B/C recombinant, and the last one with B. Of the 10 single infections, 8 were caused by 1 founder virus. They all displayed a sharp increase of quasispecies diversity during the sampling times. Two were caused by at least two founder viruses. The diversity of these strains starts at a significantly high level and is followed by a relatively steady trend. Critically, the separate subtypes YA113-B and YA113-CRF01_AE/C both showed a similar trend to those infected by a single founder virus. Recombination analysis revealed that 5 of 11 cases underwent detectable intrapatient recombination. These findings indicate that tracing the dynamics of HIV-1 quasispecies during early infection may be relevant and valuable for understanding pathways of viral diversification and immune escape.

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A considerable proportion of CRF01_AE strains in China originated from circulating intrasubtype recombinant forms (CIRF)

Cited by 9 publications

References 35 publications

A unified classification system for HIV-1 5’ long terminal repeats

A unified classification system for HIV-1 5’ long terminal repeats

Characterization of small genomic regions of the hepatitis B virus should be performed with more caution

The Genetic Diversity of HIV-1 Quasispecies Within Primary Infected Individuals

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