Thomas Leitner

• PhD
• http://public.lanl.gov/tkl/ at Los Alamos National Laboratory

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 downstream sequence analyses if included. We previously published the software Hypermut, which detects hypermutatio...

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 downstream sequence analyses if included. We previously published the software Hypermut, which detects hypermutation events in...

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 to assess the progress towards the UNAIDS 95–95–95 targets in Sweden by estimating the proportion of undiagno...

Background Hepatitis C virus (HCV) has a high genetic diversity and is classified into 8 genotypes and over 90 subtypes with some endemic to specific world regions. This could compromise direct-acting antiviral (DAA) efficacy and global HCV elimination. Methods We characterised HCV subtypes ‘rare’ to the UK (non-1a/1b/2b/3a/4d) by whole genome seq...

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. Because large-scale genome rearrangements have the potential to generate new phenotypes, reassortment is important to...

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 strains, resident and invasive, and under the assumption that co-feeding is the only transmission route in a tick...

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 HIV phylogeny constructed of multiple virus sequences from people in a transmission pair. Our method finds the st...

Motivation 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, is not well understood. To understand how this non-uniform sampling method influences a recovered phylogen...

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 variation and timing of formation of this latent reservoir remains poorly understood. Previous studies on when vi...

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 8 genotypes and 93 subtypes, each displaying distinct geographic distributions. Genotype 4 is the most predomin...

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 reassortment, have the potential to quickly generate new phenotypes, making the understanding of viral reassortmen...

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 HIV phylogeny constructed of multiple virus sequences from people in a transmission pair. Our method finds the st...

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 geographic distribution. Genotype 4 is the most predominant in the Middle East and Eastern Mediterranean where has...

Within-host HIV evolution involves several features that may disrupt standard phylogenetic reconstruction. One important feature is re-activation of latently integrated provirus, which has the potential to disrupt the temporal signal, leading to variation in the branch lengths and apparent evolutionary rates in a tree. Yet, real within-host HIV phy...

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 compartmentalization have opposite effects on viral diversification, with the former causing global mixing and the latter c...

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 impact of mutations in the structural characteristics of HBV polymerase. Plasma samples from 12 Saudi Arabian H...

Abstract: 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 impact of mutations in the structural characteristics of HBV polymerase. Plasma samples from 12 Saudi...

The decay kinetics of HIV-1-infected cells are critical to understand virus persistence. We evaluated the frequency of simian immunodeficiency virus (SIV)-infected cells for 4 years of antiretroviral therapy (ART). The intact proviral DNA assay (IPDA) and an assay for hypermutated proviruses revealed short- and long-term infected cell dynamics in m...

A minority of HIV-1-infected patients produce broadly neutralizing antibodies (bNAbs). Identification of viral and host correlates of bNAb production may help develop vaccines. We aimed to characterize the neutralizing response and viral and host-associated factors in Angola, which has one of the oldest, most dynamic, and most diverse HIV-1 epidemi...

Pathogen genomic sequence data are increasingly made available for epidemiological monitoring. A main interest is to identify and assess the potential of infectious disease outbreaks. While popular methods to analyze sequence data often involve phylogenetic tree inference, they are vulnerable to errors from recombination and impose a high computati...

To identify and stop active HIV transmission chains new epidemiological techniques are needed. Here, we describe the development of a multi-biomarker augmentation to phylogenetic inference of the underlying transmission history in a local population. HIV biomarkers are measurable biological quantities that have some relationship to the amount of ti...

Within-host HIV evolution involves latency and re-activation of integrated provirus that has the potential to disrupt the temporal signal induced by the evolutionary race between host immune responses and viral evolution. Yet, within-host HIV phylogenies tend to show clear, ladder-like trees structured by the time of sampling. Recombination complic...

HIV consensus sequences are used in various bioinformatic, evolutionary, and vaccine related research. Since the previous HIV-1 subtype and CRF consensus sequences were constructed in 2002, the number of publicly available HIV-1 sequences have grown exponentially, especially from non-EU and US countries. Here, we reconstruct 90 new HIV-1 subtype an...

Elicitation of potent neutralizing antibodies against genetically diverse HIV-1 isolates is important for an effective HIV-1 vaccine. Some HIV-1 infected patients produce such broadly neutralizing antibodies (bNAbs). Identification of host and viral correlates of bNAb production may help develop the next generation of HIV-1 vaccines. We carried out...

Pathogen genomic sequence data are increasingly made available for epidemiological monitoring. A main interest is to identify and assess the potential of infectious disease outbreaks. While popular methods to analyze sequence data often involve phylogenetic tree inference, they are vulnerable to errors from recombination and impose a high computati...

To identify and stop active HIV transmission chains new epidemiological techniques are needed. Here, we describe the development of a multi-biomarker augmentation to phylogenetic inference of the underlying transmission history in a local population. HIV biomarkers are measurable biological quantities that have some relationship to the amount of ti...

This study aimed to characterize the HCV genetic subtypes variability and the presence of natural occurring resistance-associated substitutions (RASs) in Saudi Arabia patients. A total of 17 GT patients were analyzed. Sequence analysis of NS3, NS5A, and NS5B regions was performed by direct sequencing, and phylogenetic analyses were used to determin...

HIV-1 is a fast-evolving, genetically diverse virus presently classified into several groups and subtypes. The virus evolves rapidly because of an error-prone polymerase, high rates of recombination, and selection in response to the host immune system and clinical management of the infection. The rate of evolution is also influenced by the rate of...

Citation: Di Stefano, M.; Ismail, M.H.; Leitner, T.; Faleo, G.; Elmnan Adem, S.A.; Elamin, M.O.M.E.; Eltreifi, O.; Alwazzeh, M.J.; Fiore, J.R.; Santantonio, T.

Many countries and US states have mandatory statues that require reporting of HIV clinical data including genetic sequencing results to the public health departments. Because genetic sequencing is a part of routine care for HIV infected persons; health departments have extensive sequence collections spanning years and even decades of the HIV epidem...

Spread of HIV typically involves uneven transmission patterns where some individuals spread to a large number of individuals while others to only a few or none. Such transmission heterogeneity can impact how fast and how much an epidemic spreads. Further, more efficient interventions may be achieved by taking such transmission heterogeneity into ac...

Identifying the origin of SARS-CoV-2, the etiological agent of the current COVID-19 pandemic, may help us to avoid future epidemics of coronavirus and other zoonoses. Several theories about the zoonotic origin of SARS-CoV-2 have recently been proposed. Although Betacoronavirus found in Rhinolophus bats from China have been broadly implicated, their...

Molecular HIV surveillance is a promising public health strategy for curbing the HIV epidemic. Clustering technologies used by health departments to date are limited in their ability to infer/forecast cluster growth trajectories. Resolution of the spatiotemporal dynamics of clusters, through phylodynamic and phylogeographic modelling, is one potent...

In recent years, phylogenetic analysis of HIV sequence data has been used in research studies to investigate transmission patterns between individuals and groups, including analysis of data from HIV prevention clinical trials; in molecular epidemiology; and in public health surveillance programs. Phylogenetic analysis can provide valuable informati...

Background: Most HIV infections originate from individuals who are undiagnosed and unaware of their infection. Estimation of this quantity from surveillance data is hard because there is incomplete knowledge about (i) the time between infection and diagnosis (TI) for the general population, and (ii) the time between immigration and diagnosis for f...

Purpose of review: Within-host diversity complicates transmission models because it recognizes that between-host virus phylogenies are not identical to the transmission history among the infected hosts. This review presents the biological and theoretical foundations for recent development in this field, and shows that modern phylodynamic methods a...

Background Emergence of resistance against integrase inhibitor raltegravir in human immunodeficiency virus type 1 (HIV-1) patients is generally associated with selection of one of three signature mutations: Y143C/R, Q148K/H/R or N155H, representing three distinct resistance pathways. The mechanisms that drive selection of a specific pathway are sti...

Background: Global genetic diversity of HIV-1 is a major challenge to the development of HIV vaccines. We aimed to estimate the regional and global distribution of HIV-1 subtypes and recombinants during 1990-2015. Methods: We searched PubMed, EMBASE (Ovid), CINAHL (Ebscohost), and Global Health (Ovid) for HIV-1 subtyping studies published betwee...

The growth of human immunodeficiency virus (HIV) sequence databases resulting from drug resistance testing has motivated efforts using phylogenetic methods to assess how HIV spreads1-4. Such inference is potentially both powerful and useful for tracking the epidemiology of HIV and the allocation of resources to prevention campaigns. We recently use...

Objectives: A 4 years old child born to an HIV-1 seronegative mother was diagnosed with HIV-1, the main risk factor being transmission from the child's father who was seroconverting at the time of the child's birth. In the context of a forensic investigation, we aimed to identify the source of infection of the child and date the transmission event...

Background: Most HIV infections originate from individuals who are undiagnosed and unaware of their infection. Estimation of this quantity from surveillance data is hard because there is incomplete knowledge about i) the time between infection and diagnosis (TI) for the general population and ii) the time between immigration and diagnosis for forei...

HIV is one of the fastest evolving organisms known. It evolves about 1 million times faster than its host, humans. Because HIV establishes chronic infections, with continuous evolution, its divergence within a single infected human surpasses the divergence of the entire humanoid history. Yet, it is still the same virus, infecting the same cell type...

Diversity of the founding population of Human Immunodeficiency Virus Type 1 (HIV-1) transmissions raises many important biological, clinical, and epidemiological issues. In up to 40% of sexual infections there is clear evidence for multiple founding variants, which can influence the efficacy of putative prevention methods and the reconstruction of...

Within-host genetic diversity and large transmission bottlenecks confound phylodynamic inference of epidemiological dynamics. Conventional phylodynamic approaches assume that nodes in a time-scaled pathogen phylogeny correspond closely to the time of transmission between hosts that are ancestral to the sample. However, when hosts harbour diverse pa...

Phylogenetic inference is an attractive means to reconstruct transmission histories and epidemics. However, there is not a perfect correspondence between transmission history and virus phylogeny. Both node height and topological differences may occur, depending on the interaction between within-host evolutionary dynamics and between-host transmissi...

Probability to escape infection. (PDF)

Distance based and topological tree statistics on virus genealogies as epidemic progresses on a network of size 5000. Mean branch length (MBL) as function of the number of infected individuals (A) and as function of the number of taxa (sampled infected individuals) (B) for simulated outbreaks on networks of size 5000 as epidemics progress. Note tha...

Effect of increased rewiring probability (ρ) on network identification. (PDF)

Additional distance based tree statistics on virus genealogies as epidemic progresses on a network of size 5000. Mean branch length (MBL) as function of tree height (A) and internal/external branch length ratio (B) as function of the number of taxa for simulated outbreaks on networks of size 5000. The envelopes represent 95% confidence intervals ar...

Mean branch length as epidemic progresses with varying sampling fraction. The mean branch length as function of number of infecteds, with varying sampling fraction (p = 1-0.25). The envelopes represent 95% confidence intervals around the medians. The curves are obtained using local regression (LOESS). WS (red), ER (green), BA (blue). (TIF)

Infectivity profiles. The first two model specifications represented: (i) constant rate (red line) and (ii) stage dependent infectivity (black lines). The length of the acute phase was assumed constant, t1 = 30 days while β was assumed to be 1/8 year−1. We do not assume a length for the AIDS phase a priori, but if an individual reaches the third st...

Within-host evolution model. The effective viral population size is modelled as a two piece linear function: first, it grows at rate β1 until a random peak time tx, allowed to vary among individuals between ta and tb. After tx, the viral population size decreases or stabilizes at a rate β2. The dashed line represents one possible realization. This...

Additional distance based tree statistics on virus genealogies as epidemic progresses on a network of size 1000. Mean branch length (MBL) as function of tree height (A) and internal/external branch length ratio (B) as function of the number of taxa for simulated outbreaks on networks of size 1000. The envelopes represent 95% confidence intervals ar...

Approximate Bayesian Computation for model choice. (PDF)

Mean branch lengths evaluated as a function of tree height for an epidemic spreading on networks of size 1000. Mean branch length is evaluated at each coalescence event (originating internal branches) and each sampling event (external branches) until every individual is sampled. WS (red), ER (green), BA (blue). (TIF)

The International Committee for the Taxonomy and Nomenclature of Viruses does not rule on virus classifications below the species level. The definition of species for viruses cannot be clearly defined for all types of viruses. The complex and interesting epidemiology of Human Immunodeficiency Viruses demands a detailed and informative nomenclature...

Diversity of the founding population of Human Immunodeficiency Virus Type 1 (HIV-1) transmissions raises many important biological, clinical, and epidemiological issues. In up to 40% of sexual infections there is clear evidence for multiple founding variants, which can influence the efficacy of putative prevention methods and the reconstruction of...

Angola borders and has long-term links with Democratic Republic of Congo (DRC) as well as high levels of Human Immunodeficiency virus (HIV) genetic diversity, indicating a potential role in the initial spread of the HIV-1 pandemic. Herein, we analyze 564 C2V3 and 354 pol publicly available sequences from DRC, Republic of Congo (RC) and Angola to be...

Phylogenetic inference is an attractive mean to reconstruct transmission histories and epidemics. As the interest lies in how HIV-1 spread in a human population, many previous studies have ignored details about the evolutionary process of the pathogen. Because phylogenetics investigates the evolutionary history of the pathogen rather than the sprea...

Angola has an extremely diverse HIV-1 epidemic fueled in part by the frequent interchange of people with the Democratic Republic of Congo (RDC) and Republic of Congo (RC). Characterization of HIV-1 strains circulating in Angola should help to better understand the origin of HIV-1 subtypes and recombinant forms and their transmission dynamics. In th...

Significance Phylogenetic inference of who infected whom has great value in epidemiological investigations because it should provide an objective test of an explicit hypothesis about how transmission(s) occurred. Until now, however, there has not been a systematic evaluation of which phylogeny to expect from different transmission histories, and th...

HIV-1 is subject to immune pressure exerted by the host, giving variants that escape the immune response an advantage. Virus released from activated latent cells competes against variants that have continually evolved and adapted to host immune pressure. Nevertheless, there is increasing evidence that virus displaying a signal of latency survives i...

The proportion of surviving lineages between samples is similar in phylogenies derived from simulated sequences and from clinical data. (A) Typical phylogeny from our simulations. The proportion of surviving lineages from earlier samples is representative of the tree shape (star- to ladder-like). The legend shows samples through time and the surviv...

The effect of activation rate on the persistence and composition of latent genomic fragments. A) The distribution of the number of different latent origins in productively infected cells as a function of activation rate. B) The distribution of the proportion of virus with latent genomic fragments in productively infected cells as a function of acti...

The mean sequence divergence and diversity of HIV-1 populations simulated under the alternative model parameters. After approximately 2 years post-PHI, diversity starts to grow linearly in the latent reservoir (blue solid line) while it starts to saturate in plasma (green solid line). Divergence in the latent reservoir (blue dashed line) grows at a...

The model algorithm. The pseudo-code of our computer simulations, implemented in R. (DOCX)

Number of different latent origins as a function of the proportion of latent lineages in productively infected cells. Envelope indicates the span of 95% of observations, with the mean given by the white line, and the median given by the green line. (TIF)

The effect of recombination on survival of latent lineages under the alternative model parameters. A) Simulations without recombination. B) Simulations with recombination. Grey lines show the proportion of latent lineages in the productively infected cell population of individual simulations, where the bold tan line is the mean proportion of latent...

Survival of different latent genomic fragments has no effect on diversity for concave fitness maps. We ran 1000 simulations with the concave fitness landscape shown in the insert, and categorized the results based on the number of latent genomic fragments from different origins at 1% or greater frequency at 10 years post-PHI. Increasing the number...

The number of epitopes associated with high fitness cost influences sequence diversity. We compiled the simulation results of varying the number of epitopes between 1 and 15 (S4 Table), and re-categorized them based on the number of epitopes associated with high fitness costs (defined here as fitness costs within 15% of the maximum fitness cost obs...

Simulation results when the activation rate is varied, with and without recombination. Increasing the activation rate in simulations with recombination increases the proportion of simulations with persistence (≥ 10%) of virus with latent genomic fragments, and the mean proportion of virus sequences with latent genomic fragments. 100 simulations wer...

Simulation results when the recombination rate is varied. Increasing the recombination rate increases the proportion of simulations with persistence (≥ 10%) of virus with latent genomic fragments, and the mean proportion of virus sequences with latent genomic fragments. As the recombination rate increases, the mean number of latent fragments per se...

Simulation results when the sensitivity of the immune response to new viral antigens in varied, with and without recombination. Increasing the antigen frequency required for eliciting a new immune response in simulations with recombination decreases the survival of virus with latent genomic fragments and sequence diversity while sequence divergence...

Simulation results when the number of epitopes recognized by the immune system is varied, with and without recombination. When the number of epitopes is increased in simulations with recombination, sequence diversity initially decreases, reaching lowest values at 3 and 4 epitopes, and increases thereafter. Sequence divergence follows the reverse tr...

Background: Previous studies have demonstrated that single HIV-1 genotypes are commonly transmitted from mother to child, but such analyses primarily used single samples from mother and child. It is possible that in a single sample, obtained early after infection, only the most replication competent virus is detected even when other forms may have...

Background: HIV-1 is a lifelong disease, often without serious symptoms for years after infection, and thus many infected persons go undetected for a long time. This makes it difficult to track incidence, and thus epidemics may go through dramatic changes largely unnoticed, only to be detected years later. Because direct measurement of incidence i...

Human immunodeficiency virus (HIV) transmission models that include variability in sexual behavior over time have shown increased incidence, prevalence, and acute-state transmission rates for a given population risk profile. This raises the question of whether dynamic variation in individual sexual behavior is a real phenomenon that can be observed...

Analyses of entire viral genomes or mtDNA requires comprehensive design of many primers across their genomes. Furthermore, simultaneous optimization of several DNA primer design criteria may improve overall experimental efficiency and downstream bioinformatic processing. To achieve these goals, we developed PrimerDesign-M. It includes several optio...

HIV-1 can persist for the duration of a patient’s life due in part to its ability to hide from the immune system, and from antiretroviral drugs, in long-lived latent reservoirs. Latent forms of HIV-1 may also be disproportionally involved in transmission. Thus, it is important to detect and quantify latency in the HIV-1 life cycle. We developed a n...

The population-level evolutionary rate of HIV contains vital information about the rate of the epidemic spread due to the fact that the time between transmissions affects the population level divergence. A sequence of rapid transmissions between hosts correlates with a slow evolutionary rate, while a sequence of less frequent transmissions between...

Using the early protein HIV Nef, new HLA class I binding epitopes of importance for immune responses to HIV were predicted for common African alleles. In total we identified 45 epitopes previously not described for the HLA alleles A*30:01, A*30:02, B*58:01 and C*07:01 and compared them to reported epitopes, primarily from HLA-A*02:01, from the Los...

Pathogen phylogenies are often used to infer spread among hosts. There is, however, not an exact match between the pathogen phylogeny and the host transmission history. Here, we examine in detail the limitations of this relationship. First, all splits in a pathogen phylogeny of textgreater1 host occur within hosts, not at the moment of transmission...

The discriminatory power of the noncoding control region (CR) of domestic dog mitochondrial DNA alone is relatively low. The extent to which the discriminatory power could be increased by analyzing additional highly variable coding regions of the mitochondrial genome (mtGenome) was therefore investigated. Genetic variability across the mtGenome was...

Among HIV-exposed infants in resource-limited countries, 8-12% are infected postnatally by breastfeeding. However, most of those uninfected at birth remain uninfected over time despite daily exposure to HIV in breast milk. Thus, we assessed the HIV-inhibitory activity of breast milk. We measured cross-clade neutralization in activated PBMC of Ugand...