Thomas Leitner
YOU?
Author Swipe
View article: wavess: An R package for simulation of adaptive within-host virus sequence evolution
wavess: An R package for simulation of adaptive within-host virus sequence evolution Open
Simulating within-host virus sequence evolution allows for the investigation of factors such as the role of recombination in virus diversification and the impact of selective pressures on virus evolution. Here, we provide a new software to…
View article: Identifying Impacts of Contact Tracing on HIV Epidemiological Inference from Phylogenetic Data
Identifying Impacts of Contact Tracing on HIV Epidemiological Inference from Phylogenetic Data Open
Robust sampling methods are foundational to inferences using phylogenies. Yet the impact of using contact tracing, a type of non-uniform sampling used in public health applications such as infectious disease outbreak investigations, has no…
View article: Hypermut 3: identifying specific mutational patterns in a defined nucleotide context that allows multistate characters
Hypermut 3: identifying specific mutational patterns in a defined nucleotide context that allows multistate characters Open
Motivation The detection of APOBEC3F- and APOBEC3G-induced mutations in virus sequences is useful for identifying hypermutated sequences. These sequences are not representative of viral evolution and can therefore alter the results of down…
View article: Hypermut 3: Identifying specific mutational patterns in a defined nucleotide context that allows multistate characters
Hypermut 3: Identifying specific mutational patterns in a defined nucleotide context that allows multistate characters Open
Summary The detection of APOBEC3F- and APOBEC3G-induced mutations in virus sequences is useful for identifying hypermutated sequences. These sequences are not representative of viral evolution and can therefore alter the results of downstr…
View article: Procollagen-lysine 2-oxoglutarate 5-dioxygenases are responsible for 5R-hydroxylysine modification of therapeutic T-cell bispecific monoclonal antibodies produced by Chinese hamster ovary cells
Procollagen-lysine 2-oxoglutarate 5-dioxygenases are responsible for 5R-hydroxylysine modification of therapeutic T-cell bispecific monoclonal antibodies produced by Chinese hamster ovary cells Open
We present a detailed mass spectrometric analysis of three 2 + 1 T-cell bispecific monoclonal antibodies (TCB mAbs), where an unexpected +15.9950 Da mass shift in tryptic peptides was observed. This modification was attributed to the occur…
View article: Sweden surpasses the UNAIDS 95-95-95 target: estimating HIV-1 incidence, 2003 to 2022
Sweden surpasses the UNAIDS 95-95-95 target: estimating HIV-1 incidence, 2003 to 2022 Open
Background Sweden reached the UNAIDS 90–90–90 target in 2015. It is important to reassess the HIV epidemiological situation due to ever-changing migration patterns, the roll-out of PrEP and the impact of the COVID-19 pandemic. Aim We aimed…
View article: Identification of 2 Novel Subtypes of Hepatitis C Virus Genotype 8 and a Potential New Genotype Successfully Treated With Direct Acting Antivirals
Identification of 2 Novel Subtypes of Hepatitis C Virus Genotype 8 and a Potential New Genotype Successfully Treated With Direct Acting Antivirals Open
Background Hepatitis C virus (HCV) has high genetic diversity and is classified into 8 genotypes and >90 subtypes, with some endemic to specific world regions. This could compromise direct-acting antiviral efficacy and global HCV elimin…
View article: The Number and Pattern of Viral Genomic Reassortments are not Necessarily Identifiable from Segment Trees
The Number and Pattern of Viral Genomic Reassortments are not Necessarily Identifiable from Segment Trees Open
Reassortment is an evolutionary process common in viruses with segmented genomes. These viruses can swap whole genomic segments during cellular co-infection, giving rise to novel progeny formed from the mixture of parental segments. Since …
View article: Architecture and Structure of a Fold-and-Thrust Belt During Initial Inversion of a Salt-Bearing Passive Margin (Jurassic of the Eastern Alps, Austria)
Architecture and Structure of a Fold-and-Thrust Belt During Initial Inversion of a Salt-Bearing Passive Margin (Jurassic of the Eastern Alps, Austria) Open
Inversion of the Austroalpine Triassic salt-bearing passive margin, represented by the Northern Calcareous Alps (Eastern Alps), started in the Late Jurassic. Subsequent deformation during the Cretaceous and Cenozoic mostly preserved the La…
View article: A story of viral co-infection, co-transmission and co-feeding in ticks: how to compute an invasion reproduction number
A story of viral co-infection, co-transmission and co-feeding in ticks: how to compute an invasion reproduction number Open
With a single circulating vector-borne virus, the basic reproduction number incorporates contributions from tick-to-tick (co-feeding), tick-to-host and host-to-tick transmission routes. With two different circulating vector-borne viral str…
View article: Halokinetic growth wedges in platform carbonates: thoughts on subsidence and carbonate production rates
Halokinetic growth wedges in platform carbonates: thoughts on subsidence and carbonate production rates Open
The Northern Calcareous Alps (NCA) in the Eastern Alps (Austria) developed during the Triassic as a Tethys-facing salt-rich passive margin. Extensionally-driven salt tectonics, mobilizing evaporites of Late Permian to Early Triassic age on…
View article: Deformation structures in the evaporitic melange. Case study from the Altaussee salt mine
Deformation structures in the evaporitic melange. Case study from the Altaussee salt mine Open
We investigated the salt deposits found within the Altaussee salt mine, which represent the Permian to Triassic evaporitic Haselgebirge Formation situated in the Northern Calcerous Alps (Austria). The extensive deformation of the evaporite…
View article: The dog originated south of Yangtse river less than 16,000 years ago, from numerous wolves
The dog originated south of Yangtse river less than 16,000 years ago, from numerous wolves Open
We here present a detailed picture of the origins of the dog, giving strong and precise evidence for 'where and when', and thereby also a first tentative picture of 'how, why and by whom' the wolf was domesticated. Previous studies of mito…
View article: Salt-rich versus salt-poor structural scenarios in the central Northern Calcareous Alps: implications for the Hallstatt facies and early Alpine tectonic evolution (Eastern Alps, Austria)
Salt-rich versus salt-poor structural scenarios in the central Northern Calcareous Alps: implications for the Hallstatt facies and early Alpine tectonic evolution (Eastern Alps, Austria) Open
One of the most remarkable features of the central Northern Calcareous Alps (Eastern Alps, Austria) is the widespread presence of Upper Triassic deep-water carbonates (the Hallstatt facies) and Permo-Triassic evaporites resting on deep-wat…
View article: Inferring Viral Transmission Time from Phylogenies for Known Transmission Pairs
Inferring Viral Transmission Time from Phylogenies for Known Transmission Pairs Open
When the time of an HIV transmission event is unknown, methods to identify it from virus genetic data can reveal the circumstances that enable transmission. We developed a single-parameter Markov model to infer transmission time from an HI…
View article: Identifying Impacts of Contact Tracing on Epidemiological Inference from Phylogenetic Data
Identifying Impacts of Contact Tracing on Epidemiological Inference from Phylogenetic Data Open
Robust sampling methods are foundational to inferences using phylogenies. Yet the impact of using contact tracing, a type of non-uniform sampling used in public health applications such as infectious disease outbreak investigations, has no…
View article: Last in first out: SIV proviruses seeded later in infection are harbored in short-lived CD4<sup>+</sup>T cells
Last in first out: SIV proviruses seeded later in infection are harbored in short-lived CD4<sup>+</sup>T cells Open
HIV can persist in a latent form as integrated DNA (provirus) in resting CD4 + T cells of infected individuals and as such is unaffected by antiretroviral therapy (ART). Despite being a major obstacle for eradication efforts, the genetic v…
View article: A novel candidate hepatitis C virus genotype 4 subtype identified by next generation sequencing full-genome characterization in a patient from Saudi Arabia
A novel candidate hepatitis C virus genotype 4 subtype identified by next generation sequencing full-genome characterization in a patient from Saudi Arabia Open
Background and aim Hepatitis C virus (HCV) infection is a major global public health concern, being a leading cause of chronic liver diseases such as chronic hepatitis, cirrhosis, and hepatocellular carcinoma. The virus is classified into …
View article: Modeling the evolution of segment trees reveals deficiencies in current inferential methods for genomic reassortment
Modeling the evolution of segment trees reveals deficiencies in current inferential methods for genomic reassortment Open
Reassortment is an evolutionary process common in viruses with segmented genomes. These viruses can swap whole genomic segments during cellular co-infection, giving rise to new viral variants. Large-scale genome rearrangements, such as rea…
View article: Inferring viral transmission time from phylogenies for known transmission pairs
Inferring viral transmission time from phylogenies for known transmission pairs Open
When the time of an HIV transmission event is unknown, methods to identify it from virus genetic data can reveal the circumstances that enable transmission. We developed a single-parameter Markov model to infer transmission time from an HI…
View article: A novel hepatitis C virus genotype 4 subtype identified by next generation sequencing full-genome characterization in a patient from Saudi Arabia
A novel hepatitis C virus genotype 4 subtype identified by next generation sequencing full-genome characterization in a patient from Saudi Arabia Open
HCV infection is a major global public health concern, being the main cause of chronic liver disease: cirrhosis, chronic hepatitis and hepatocellular carcinoma. HCV strains are classified into 8 genotypes and 93 subtypes with different geo…
View article: Salt‑rich versus salt‑poor structural scenarios in the central Northern Calcareous Alps: implications for the Hallstatt facies and early Alpine tectonic evolution (Eastern Alps, Austria)
Salt‑rich versus salt‑poor structural scenarios in the central Northern Calcareous Alps: implications for the Hallstatt facies and early Alpine tectonic evolution (Eastern Alps, Austria) Open
One of the most remarkable features of the central Northern Calcareous Alps (Eastern Alps, Austria) is the widespread presence of Upper Triassic deep-water carbonates (the Hallstatt facies) and Permo-Triassic evaporites resting on deep-wat…
View article: Migration coupled with recombination explains disparate HIV-1 anatomical compartmentalization signals
Migration coupled with recombination explains disparate HIV-1 anatomical compartmentalization signals Open
The evolution of HIV-1 in a host is shaped by many evolutionary forces, including recombination of virus genomes and the potential isolation of viruses into different tissues with compartmentalized evolution. Recombination and compartmenta…
View article: Molecular and Genetic Characterization of Hepatitis B Virus (HBV) among Saudi Chronically HBV-Infected Individuals
Molecular and Genetic Characterization of Hepatitis B Virus (HBV) among Saudi Chronically HBV-Infected Individuals Open
The study aimed to characterize the genotype and subgenotypes of HBV circulating in Saudi Arabia, the presence of clinically relevant mutations possibly associated with resistance to antivirals or immune escape phenomena, and the possible …
View article: Recombination smooths the time signal disrupted by latency in within-host HIV phylogenies
Recombination smooths the time signal disrupted by latency in within-host HIV phylogenies Open
Within-host Human immunodeficiency virus (HIV) evolution involves several features that may disrupt standard phylogenetic reconstruction. One important feature is reactivation of latently integrated provirus, which has the potential to dis…