Many but small HIV-1 non-B transmission chains in the Netherlands

Bezemer, Daniela; Blenkinsop, Alexandra; Hall, Matthew; Sighem, Ard van; Cornelissen, Marion; Wessels, Els; Kampen, Jeroen J. A. van; Laar, Thijs van de; Reiss, Peter; Fraser, Christophe; Ratmann, Oliver

doi:10.1097/qad.0000000000003074

“…S7)]. In a recent analysis of an updated version of the ATHENA dataset (40), 33 additional VB individuals were found, which suggests that VB diagnoses were stable until roughly 2013 and have since been declining, still with appreciable uncertainty. We calculated the local branching index (LBI), which is a measure of fitness (41).…”

Section: Phylodynamics Of the Vb Variantmentioning

confidence: 99%

A highly virulent variant of HIV-1 circulating in the Netherlands

Wymant

¹

,

Bezemer

²

,

Blanquart

³

et al. 2022

Science

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We discovered a highly virulent variant of subtype-B HIV-1 in the Netherlands. One hundred nine individuals with this variant had a 0.54 to 0.74 log 10 increase (i.e., a ~3.5-fold to 5.5-fold increase) in viral load compared with, and exhibited CD4 cell decline twice as fast as, 6604 individuals with other subtype-B strains. Without treatment, advanced HIV—CD4 cell counts below 350 cells per cubic millimeter, with long-term clinical consequences—is expected to be reached, on average, 9 months after diagnosis for individuals in their thirties with this variant. Age, sex, suspected mode of transmission, and place of birth for the aforementioned 109 individuals were typical for HIV-positive people in the Netherlands, which suggests that the increased virulence is attributable to the viral strain. Genetic sequence analysis suggests that this variant arose in the 1990s from de novo mutation, not recombination, with increased transmissibility and an unfamiliar molecular mechanism of virulence.

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“…This approach allows for a more comprehensive understanding of evolutionary relationships and ancestral sequence reconstruction, in contrast to conventional parsimony methods that treat the gap character as an ambiguous or additional state. Although maximum likelihood and Bayesian methods are commonly preferred for phylogenetic inferences, now, with increasingly growing dataset sizes, parsimony analysis is becoming more popular again, especially for the analysis of very large datasets (Thornlow et al, 2021; Hausdorf, 2022; Bezemer et al, 2022; Torres et al, 2022). Besides being used as a principle in standalone methods (Turakhia et al, 2021; Ye et al, 2022), parsimony can also be utilised as a filter to speed up more complex probabilistic methods (Guindon et al, 2010; De Maio et al, 2023).…”

Section: Introductionmentioning

confidence: 99%

Please Mind the Gap: Indel-Aware Parsimony for Fast and Accurate Ancestral Sequence Reconstruction and Multiple Sequence Alignment including Long Indels

Iglhaut,

Pečerska,

Gil

et al. 2024

Preprint

3

0

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Despite having important biological implications, insertion and deletion (indel) events are often disregarded or mishandled during phylogenetic inference. In multiple sequence alignment, indels are represented as gaps and are estimated without considering the distinct evolutionary history of insertions and deletions. Consequently, indels are usually excluded from subsequent inference steps, such as ancestral sequence reconstruction and phylogenetic tree search. Here, we introduce indel-aware parsimony (indelMaP), a novel way to treat gaps under the parsimony criterion by considering insertions and deletions as separate evolutionary events and accounting for long indels. By identifying the precise location of an evolutionary event on the tree, we can separate overlapping indel events and use affine gap penalties for long indel modelling. Our indel-aware approach harnesses the phylogenetic signal from indels, including them into all inference stages. Validation and comparison to state-of-the-art inference tools on simulated data show that indelMaP is most suitable for densely sampled datasets with closely to moderately related sequences, where it can reach alignment quality comparable to probabilistic methods and accurately infer ancestral sequences, including indel patterns. Due to its remarkable speed, our method is well-suited for epidemiological datasets, eliminating the need for downsampling and enabling the exploitation of the additional information provided by dense taxonomic sampling. Moreover, indelMaP offers new insights into the indel patterns of biologically significant sequences and advances our understanding of genetic variability by considering gaps as crucial evolutionary signals rather than mere artefacts.

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“…This approach allows for a more comprehensive understanding of evolutionary relationships and ancestral sequence reconstruction, in contrast to conventional parsimony methods that treat the gap character as an ambiguous or additional state ( Ogden and Rosenberg 2007 ). Although maximum-likelihood and Bayesian methods are commonly preferred for phylogenetic inferences, now, with increasingly growing dataset sizes, parsimony analysis is becoming more popular again, especially for the analysis of very large datasets ( Bezemer et al 2022 ; Hausdorf 2022 ; Torres et al 2022 ; Kramer et al 2023 ). Besides being used as a principle in standalone methods ( Turakhia et al 2021 ; Ye et al 2022 ), parsimony can also be utilized as a filter to speed up more complex probabilistic methods ( Guindon et al 2010 ; De Maio et al 2023 ).…”

Section: Introductionmentioning

confidence: 99%

Please Mind the Gap: Indel-Aware Parsimony for Fast and Accurate Ancestral Sequence Reconstruction and Multiple Sequence Alignment Including Long Indels

Iglhaut,

Pečerska,

Gil

et al. 2024

Molecular Biology and Evolution

3

0

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Despite having important biological implications, insertion and deletion (indel) events are often disregarded or mishandled during phylogenetic inference. In multiple sequence alignment, indels are represented as gaps and are estimated without considering the distinct evolutionary history of insertions and deletions. Consequently, indels are usually excluded from subsequent inference steps, such as ancestral sequence reconstruction and phylogenetic tree search. Here, we introduce indel-aware parsimony (indelMaP), a novel way to treat gaps under the parsimony criterion by considering insertions and deletions as separate evolutionary events and accounting for long indels. By identifying the precise location of an evolutionary event on the tree, we can separate overlapping indel events and use affine gap penalties for long indel modelling. Our indel-aware approach harnesses the phylogenetic signal from indels, including them into all inference stages. Validation and comparison to state-of-the-art inference tools on simulated data show that indelMaP is most suitable for densely sampled datasets with closely to moderately related sequences, where it can reach alignment quality comparable to probabilistic methods and accurately infer ancestral sequences, including indel patterns. Due to its remarkable speed, our method is well-suited for epidemiological datasets, eliminating the need for downsampling and enabling the exploitation of the additional information provided by dense taxonomic sampling. Moreover, indelMaP offers new insights into the indel patterns of biologically significant sequences and advances our understanding of genetic variability by considering gaps as crucial evolutionary signals rather than mere artefacts.

show abstract

Many but small HIV-1 non-B transmission chains in the Netherlands

Cited by 8 publications

References 26 publications

A highly virulent variant of HIV-1 circulating in the Netherlands

A highly virulent variant of HIV-1 circulating in the Netherlands

Please Mind the Gap: Indel-Aware Parsimony for Fast and Accurate Ancestral Sequence Reconstruction and Multiple Sequence Alignment including Long Indels

Please Mind the Gap: Indel-Aware Parsimony for Fast and Accurate Ancestral Sequence Reconstruction and Multiple Sequence Alignment Including Long Indels

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