Revisiting the recombinant history of HIV-1 group M with dynamic network community detection

Olabode, Abayomi S; Ng, Garway T; Wade, Kaitlyn E; Salnikov, Mikhail; Grant, Heather E; Dick, David W; Poon, Art F. Y.

doi:10.1073/pnas.2108815119

Cited by 3 publications

(3 citation statements)

References 72 publications

(100 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…As Olabode et al [85] suggested, the fact that sequences of different subtypes present very similar hot zones may be due to the existence of more cases of recombination than is currently described. It is possible that some viruses that are considered pure subtypes may exhibit hidden recombination phenomena.…”

Section: Discussionmentioning

confidence: 86%

Discovering Mathematical Patterns Behind HIV-1 Genetic Recombination: A New Methodology to Identify Viral Features

Guerrero-Tamayo,

Urquijo,

Casado

et al. 2023

IEEE Access

View full text Add to dashboard Cite

In this article, we introduce a novel methodology for characterizing viral genetic features: the Unified Methodology of recombinant virus Identification (UMI). Our methodology converts genomic sequences into spectrograms, applies transfer learning using a pre-trained Convolutional Neural Network (CNN), and employs interpretability tools to identify the genomic regions relevant for characterizing a viral sequence as recombinant. The UMI methodology does not necessitate multiple sequence alignment or manual adjustments. As a result, it operates much faster, has low computational demands, and is capable of handling substantial amounts of data.To validate this, we applied UMI to one extensively studied and documented case: HIV-1 genetic recombination. We worked with all identified HIV-1 complete sequences (13554 sequences up to 2020), searching for mathematical patterns, signatures, that characterize an HIV-1 sequence as recombinant. CNN's hit rate (test accuracy) is 94%, with consistent and differentiated decision areas in each category. Using interpretability tools, we verified that the hot zones were similar for sequences of the same subtype and phylogenetic proximity. The leading areas for classifying a sequence as recombinant or non-recombinant are coincident with genomic regions that play a key role in genetic recombination processes. By applying UMI methodology we found that there is indeed a genome mathematical pattern that assesses an HIV-1 sequence as recombinant. In addition, we located its position. Considering expert knowledge, our results showed a substantial, robust and biologically-consistent hit rate. This type of solution can successfully guide the location and subsequent characterization of relevant areas, avoiding the heavy analysis of multiple sequence alignment and manual adjustments.

show abstract

Section: Discussionmentioning

confidence: 86%

Discovering Mathematical Patterns Behind HIV-1 Genetic Recombination: A New Methodology to Identify Viral Features

Guerrero-Tamayo,

Urquijo,

Casado

et al. 2023

IEEE Access

View full text Add to dashboard Cite

show abstract

“…All remaining regions of the HIV-1 genome have been systematically and phylogenetically classified and the classification has been widely used, except for LTR [22,[60][61][62][63]. However, the rigid need to partition the LTR systematically and phylogenetically has always existed.…”

Section: Discussionmentioning

confidence: 99%

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

Guo,

Yu,

Liu

et al. 2024

PLoS ONE

View full text Add to dashboard Cite

The HIV-1 provirus mainly consists of internal coding region flanked by 1 long terminal repeats (LTRs) at each terminus. The LTRs play important roles in HIV-1 reverse transcription, integration, and transcription. However, despite of the significant study advances of the internal coding regions of HIV-1 by using definite reference classification, there are no systematic and phylogenetic 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 the supplemented 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 supplemented 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.

show abstract

“…HIV-1 M-group lineages, which dominate the HIV-1 pandemic and are responsible for 95% of global HIV infections, are further divided into nine subtypes: A-D, F-H, J, and K ( Robertson et al., 2000 ; Rashid et al., 2022 ). High mutation rate and genomic recombination are hallmarks of HIV-1 infection, which leads to extraordinary genetic variability and evolution ( Smyth et al., 2012 ; Olabode et al., 2022 ). Recombination is a major facilitator through which HIV-1 increases its genetic diversity, which is driven by template switching during its replication cycle ( Cromer et al., 2016 ) and by co-infection with multiple strains at the cellular ( Neher and Leitner, 2010 ) and host levels ( Redd et al., 2013 ).…”

Section: Introductionmentioning

confidence: 99%

Characterization of HIV-1 CRF02_AG/A3/G unique recombinant forms identified among children in Larkana, Pakistan

Rashid,

Kang,

et al. 2023

Front. Cell. Infect. Microbiol.

View full text Add to dashboard Cite

Co-circulation of different human immunodeficiency virus type 1 HIV-1 subtypes among infected populations can lead to the generation of new recombinants. In Pakistan, subtype A1 and CRF02_AG are the dominant strains circulating among key populations. The high prevalence of new HIV infections among the key populations highlights the possibility of recombination between the dominant strains, which can lead to the generation of new recombinants. Here, we identified a recombinant cluster composed of CRF02_AG, sub-subtype A3, and subtype G among HIV-infected children in Larkana. For the study, 10 retrospectively collected samples, with recombination signals in the pol gene, were used to perform a near full-length genome NFLG sequencing. Of the 10 samples, NFLG was successfully sequenced from seven samples. Phylogenetic analysis of the seven NFLGs showed that all recombinants formed a distinct monophyletic cluster and were distinct from known HIV-1 circulating recombinant forms CRFs. Recombination analyses showed that all seven NFLGs shared a similar recombinant structure consisting of CRF02_AG, sub-subtype A3, and subtype G, with a sub-subtype A3 fragment inserted into pol and vif regions spanning from (HXB2: 4218-5518), and a subtype G fragment inserted into vpu, rev, tat and env regions spanning from (HXB2: 5957-8250) of the CRF02_AG backbone. The identification of unique recombinant forms may indicate the presence and transmission of several co-circulating lineages in Larkana, giving rise to newer CRFs. This study also highlights the importance of continuous molecular surveillance to fully understand HIV-1 genetic diversity in Pakistan, particularly in Larkana, which is the epicenter of HIV outbreaks.

show abstract

Revisiting the recombinant history of HIV-1 group M with dynamic network community detection

Cited by 3 publications

References 72 publications

Discovering Mathematical Patterns Behind HIV-1 Genetic Recombination: A New Methodology to Identify Viral Features

Discovering Mathematical Patterns Behind HIV-1 Genetic Recombination: A New Methodology to Identify Viral Features

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

Characterization of HIV-1 CRF02_AG/A3/G unique recombinant forms identified among children in Larkana, Pakistan

Contact Info

Product

Resources

About