Thomas Leitner

Summary

Affiliation: Los Alamos National Laboratory
Country: USA

Publications

  1. pmc Towards estimation of HIV-1 date of infection: a time-continuous IgG-model shows that seroconversion does not occur at the midpoint between negative and positive tests
    Helena Skar
    Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
    PLoS ONE 8:e60906. 2013
  2. pmc Daily sampling of an HIV-1 patient with slowly progressing disease displays persistence of multiple env subpopulations consistent with neutrality
    Helena Skar
    Department of Virology, Swedish Institute for Infectious Disease Control, Solna, Sweden
    PLoS ONE 6:e21747. 2011
  3. pmc A multiple-alignment based primer design algorithm for genetically highly variable DNA targets
    Johanna Brodin
    Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    BMC Bioinformatics 14:255. 2013
  4. ncbi request reprint Sequence diversity among chimpanzee simian immunodeficiency viruses (SIVcpz) suggests that SIVcpzPts was derived from SIVcpzPtt through additional recombination events
    Thomas Leitner
    Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
    AIDS Res Hum Retroviruses 23:1114-8. 2007
  5. pmc Tracing the HIV-1 subtype B mobility in Europe: a phylogeographic approach
    Dimitrios Paraskevis
    Katholieke Universiteit Leuven, Rega Institute for Medical Research, Minderbroederstraat 10, B 3000 Leuven, Belgium
    Retrovirology 6:49. 2009
  6. pmc A jumping profile Hidden Markov Model and applications to recombination sites in HIV and HCV genomes
    Anne Kathrin Schultz
    Institute of Microbiology and Genetics, University of Gottingen, Goldschmidtstr, 1, 37077 Gottingen, Germany
    BMC Bioinformatics 7:265. 2006
  7. pmc The role of recombination in the emergence of a complex and dynamic HIV epidemic
    Ming Zhang
    Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    Retrovirology 7:25. 2010
  8. ncbi request reprint Characterization of novel recombinant HIV-1 genomes using the branching index
    Karin Wilbe
    Department of Virology, Swedish Institute for Infectious Disease Control, SE 171 82, Solna, Sweden
    Virology 316:116-25. 2003
  9. pmc Multiple HIV-1 introductions into the Swedish intravenous drug user population
    Helena Skar
    Department of Virology, Swedish Institute for Infectious Disease Control, SE 17182 Solna, Sweden
    Infect Genet Evol 8:545-52. 2008
  10. ncbi request reprint A multiplex real-time PCR for quantification of HIV-1 DNA and the human albumin gene in CD4+ cells
    Lars E Eriksson
    Department of Virology, Swedish Institute for Infectious Disease Control, Solna, Sweden
    APMIS 111:625-33. 2003

Collaborators

Detail Information

Publications24

  1. pmc Towards estimation of HIV-1 date of infection: a time-continuous IgG-model shows that seroconversion does not occur at the midpoint between negative and positive tests
    Helena Skar
    Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
    PLoS ONE 8:e60906. 2013
    ....
  2. pmc Daily sampling of an HIV-1 patient with slowly progressing disease displays persistence of multiple env subpopulations consistent with neutrality
    Helena Skar
    Department of Virology, Swedish Institute for Infectious Disease Control, Solna, Sweden
    PLoS ONE 6:e21747. 2011
    ..5 years, but that this does not imply directional or balancing selection. We show that the short-term evolution we study here is likely representative for many patients of slow and normal disease progression...
  3. pmc A multiple-alignment based primer design algorithm for genetically highly variable DNA targets
    Johanna Brodin
    Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    BMC Bioinformatics 14:255. 2013
    ....
  4. ncbi request reprint Sequence diversity among chimpanzee simian immunodeficiency viruses (SIVcpz) suggests that SIVcpzPts was derived from SIVcpzPtt through additional recombination events
    Thomas Leitner
    Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
    AIDS Res Hum Retroviruses 23:1114-8. 2007
    ..t.t. and P.t.s. split, SIV superinfection led to further recombination resulting in the emergence of SIVcpzPts. This shows that there have been multiple SIV transfers to chimpanzees at different times in their evolution...
  5. pmc Tracing the HIV-1 subtype B mobility in Europe: a phylogeographic approach
    Dimitrios Paraskevis
    Katholieke Universiteit Leuven, Rega Institute for Medical Research, Minderbroederstraat 10, B 3000 Leuven, Belgium
    Retrovirology 6:49. 2009
    ..However the spatial diffusion of the epidemic from the perspective of the virus has not previously been traced...
  6. pmc A jumping profile Hidden Markov Model and applications to recombination sites in HIV and HCV genomes
    Anne Kathrin Schultz
    Institute of Microbiology and Genetics, University of Gottingen, Goldschmidtstr, 1, 37077 Gottingen, Germany
    BMC Bioinformatics 7:265. 2006
    ..This approach is particularly useful for dealing with recombination events...
  7. pmc The role of recombination in the emergence of a complex and dynamic HIV epidemic
    Ming Zhang
    Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    Retrovirology 7:25. 2010
    ....
  8. ncbi request reprint Characterization of novel recombinant HIV-1 genomes using the branching index
    Karin Wilbe
    Department of Virology, Swedish Institute for Infectious Disease Control, SE 171 82, Solna, Sweden
    Virology 316:116-25. 2003
    ....
  9. pmc Multiple HIV-1 introductions into the Swedish intravenous drug user population
    Helena Skar
    Department of Virology, Swedish Institute for Infectious Disease Control, SE 17182 Solna, Sweden
    Infect Genet Evol 8:545-52. 2008
    ..Because HIV-1 outbreaks can easily be exported from one country to another amongst IVDUs, this prompts continued surveillance in the Baltic Sea Region...
  10. ncbi request reprint A multiplex real-time PCR for quantification of HIV-1 DNA and the human albumin gene in CD4+ cells
    Lars E Eriksson
    Department of Virology, Swedish Institute for Infectious Disease Control, Solna, Sweden
    APMIS 111:625-33. 2003
    ..17 and 51x10-3 copies per CD4+ cell and could be monitored longitudinally, including long-term PI-ART and STI. The measured HIV-1 DNA load may be used to select the best time for the institution or re-institution of therapy...
  11. pmc Classification of hepatitis C virus and human immunodeficiency virus-1 sequences with the branching index
    Peter Hraber
    Theoretical Biology and Biophysics, T 10 MS K710, LANL, Los Alamos, NM 87545, USA
    J Gen Virol 89:2098-107. 2008
    ..In synthetic recombinants, regions without breakpoints are recognized accurately; regions with breakpoints do not represent any known subtype uniquely. Web-based services for viral subtype classification with the BI are available online...
  12. pmc Transmission of single HIV-1 genomes and dynamics of early immune escape revealed by ultra-deep sequencing
    Will Fischer
    Theoretical Biology, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
    PLoS ONE 5:e12303. 2010
    ..Dramatic shifts in the frequencies of epitope variants during the first weeks of infection revealed a complex interplay between viral fitness and immune escape...
  13. ncbi request reprint Limited transmission of drug-resistant HIV type 1 in 100 Swedish newly detected and drug-naive patients infected with subtypes A, B, C, D, G, U, and CRF01_AE
    Irina Maljkovic
    Department of Virology, Swedish Institute for Infectious Disease Control, SE 171 82 Solna, Sweden
    AIDS Res Hum Retroviruses 19:989-97. 2003
    ..It may be important to routinely test for resistance in newly infected cases to improve the choice of drugs for treatment because the virus may revert and resistant forms can become latent...
  14. pmc The evolutionary rate dynamically tracks changes in HIV-1 epidemics: application of a simple method for optimizing the evolutionary rate in phylogenetic trees with longitudinal data
    Irina Maljkovic Berry
    Theoretical Biology and Biophysics, MS K710, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
    Epidemics 1:230-9. 2009
    ..Subtype C in Ethiopia showed an increase in the evolutionary rate when the prevalence increase markedly slowed down in 1995. Thus, we show that the evolutionary rate of HIV-1 on the population level dynamically tracks epidemic events...
  15. ncbi request reprint Rapid epidemic spread of HIV type 1 subtype A1 among intravenous drug users in Latvia and slower spread of subtype B among other risk groups
    Dace Balode
    Department of Virology, Swedish Institute for Infectious Disease Control, SE 171 82 Solna, Sweden
    AIDS Res Hum Retroviruses 20:245-9. 2004
    ..Although some spread of subtype A1 has occurred in the heterosexual group, subtype B dominates among homosexually and heterosexually infected individuals...
  16. doi request reprint Norovirus strains belonging to the GII.4 genotype dominate as a cause of nosocomial outbreaks of viral gastroenteritis in Sweden 1997--2005. Arrival of new variants is associated with large nation-wide epidemics
    Kari Johansen
    Department of Virology, Immunology and Vaccinology, Swedish Institute for Infectious Disease Control, 171 82 Solna, Sweden
    J Clin Virol 42:129-34. 2008
    ..In recent years an increase of the incidence of nosocomial outbreaks caused by noroviruses has been observed throughout Sweden, with high peaks noted in the winter seasons 2002/2003 and 2004/2005, respectively...
  17. ncbi request reprint Identification of two CRF11-cpx genomes and two preliminary representatives of a new circulating recombinant form (CRF13-cpx) of HIV type 1 in Cameroon
    Karin Wilbe
    Department of Virology, Swedish Institute for Infectious Disease Control, SE 171 82 Solna, Sweden
    AIDS Res Hum Retroviruses 18:849-56. 2002
    ..The new recombinant structure has been designated CRF13-cpx in the Los Alamos HIV Sequence Database...
  18. pmc Unequal evolutionary rates in the human immunodeficiency virus type 1 (HIV-1) pandemic: the evolutionary rate of HIV-1 slows down when the epidemic rate increases
    Irina Maljkovic Berry
    Department of Virology, Swedish Institute for Infectious Disease Control, Solna, Sweden
    J Virol 81:10625-35. 2007
    ..g., for IDUs in the FSU, will increase as the population becomes saturated with infections and the virus starts to spread to other risk groups...
  19. pmc Agent-based and phylogenetic analyses reveal how HIV-1 moves between risk groups: injecting drug users sustain the heterosexual epidemic in Latvia
    Frederik Graw
    Theoretical Biology and Biophysics, Los Alamos National Laboratory, NM 87545, USA
    Epidemics 4:104-16. 2012
    ..Increases in susceptibles, through social or geographic movement of IDU, could lead to a boost in HIV-1 infections in this risk group. Targeting individuals that bridge social groups would help prevent further spread of the epidemic...
  20. ncbi request reprint Genetic characterization of the Guinea-Bissau family of Mycobacterium tuberculosis complex strains
    Tuija Koivula
    Swedish Institute for Infectious Disease Control, 17182 Solna, Sweden
    Microbes Infect 6:272-8. 2004
    ..tuberculosis complex tree in between classical M. tuberculosis and classical M. bovis. These observations are discussed in their significance in M. tuberculosis complex classification...
  21. ncbi request reprint HIV type 1 DNA development during long-term supervised therapy interruption
    Lars E Eriksson
    Department of Virology, Swedish Institute for Infectious Disease Control, SE 171 82 Solna, Sweden
    AIDS Res Hum Retroviruses 19:259-65. 2003
    ..The most important clinical predictor of long-term STI failure was the rapid CD4(+) cell decline before PI-ART. In patients with a steep pre-PI-ART slope it may be prudent to continue treatment and not initiate therapy interruption...
  22. ncbi request reprint HIV type 1 CRF13_cpx revisited: identification of a new sequence from Cameroon and signal for subsubtype J2
    Ming Zhang
    Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
    AIDS Res Hum Retroviruses 21:955-60. 2005
    ..This suggests that subtype J may need to be reclassified into subsubtypes J1 and J2. The CRF13 genome consists of fragments from subtypes A1, G, and both J1 and J2 as well as CRF01 and one region that was left unclassified...
  23. pmc Comparative analysis of hepatitis C virus phylogenies from coding and non-coding regions: the 5' untranslated region (UTR) fails to classify subtypes
    Peter T Hraber
    Theoretical Biology and Biophysics, T 10 MS K710, Los Alamos National Laboratory, Los Alamos NM 87545, USA
    Virol J 3:103. 2006
    ..This study used the Shimodaira-Hasegawa test and related statistical techniques to compare phylogenetic trees obtained from coding and non-coding regions of a whole-genome alignment for the reliability of subtyping in different regions...
  24. ncbi request reprint Subtypes A, C, G, and recombinant HIV type 1 are circulating in Bangladesh
    Karl Ljungberg
    Swedish Institute for Infectious Disease Control, and Microbiology and Tumor Biology Center, Karolinska Institute, SE 171 82 Solna, Sweden
    AIDS Res Hum Retroviruses 18:667-70. 2002
    ..This study shows that several HIV-1 subtypes are circulating in Bangladesh, and we conclude that there must have been several introductions of HIV-1 into the Bangladeshi population...