Jan Albert Group
The research in our group focuses on HIV genetic variation, evolution and resistance. We take part in several EU projects, such as Eurocoord and HIVEVO, as well as other international projects and collaborations.
HIV genetic variation, evolution and reservoirs
We study HIV genetic variation, evolution and reservoirs to understand how HIV spreads, escapes immunity, develops resistance and persists as a life-long infection. We aim to provide tools to help curb the HIV pandemic. One area of research concerns molecular epidemiology, spread and incidence of HIV, including analysis of resistant HIV variants. To guide prevention it is essential to have correct and detailed information about the local and global HIV epidemic. We use modern maximum likelihood and Bayesian methods to draw conclusions about epidemiological relationships of HIV strains from patients. Thus, we use these phylogenetic methods to gain detailed information of HIV spread in Sweden and Scandinavia. We also investigate the utility of using phylogenetic methods in combination with other biomarkers (such as the BED serological incidence test) to estimate time-of-infection for individual HIV patients. This approach allows modelling of HIV incidence in Sweden as well as an estimation of the number of undiagnosed patients (Swedish ‘mörkertal’). A second area of research is the application of next-generation sequencing (NGS) to dissect HIV evolution with a previously unattainable resolution. We study how HIV evolves over time within single infected patients using NGS. This approach is used to study the significance of minority variants within HIV populations in single HIV infected patients, for instance minority variants that are resistant to antiretroviral drugs. We also use NGS to investigate how HIV reservoirs are established and maintained.
Inference of Transmission Network Structure from HIV Phylogenetic Trees.
PLoS Comput. Biol. 2017 Jan;13(1):e1005316
Error rates, PCR recombination, and sampling depth in HIV-1 whole genome deep sequencing.
Virus Res. 2016 Dec;():
Establishment and stability of the latent HIV-1 DNA reservoir.
Elife 2016 Nov;5():
Outbreak of enterovirus D68 of the new B3 lineage in Stockholm, Sweden, August to September 2016
R Dyrdak, M Grabbe, B Hammas, J Ekwall, KE Hansson, J Luthander, P Naucler, H Reinius, M Rotzén-Östlund, J Albert
Eurosurveillance, Volume 21, Issue 46, 17 November 2016
Molecular epidemiology and the evolution of human coxsackievirus A6.
J. Gen. Virol. 2016 Dec;97(12):3225-3231
Impaired B cells survival upon production of inflammatory cytokines by HIV-1 exposed follicular dendritic cells.
Retrovirology 2016 Sep;13(1):61
Frequent Respiratory Viral Infections in Children with Febrile Neutropenia - A Prospective Follow-Up Study.
PLoS ONE 2016 ;11(6):e0157398
The global spread of HIV-1 subtype B epidemic.
Infect. Genet. Evol. 2016 Dec;46():169-179
Transmission of HIV Drug Resistance and the Predicted Effect on Current First-line Regimens in Europe.
Clin. Infect. Dis. 2016 Mar;62(5):655-63
Population genomics of intrapatient HIV-1 evolution.
Elife 2015 Dec;4():
A Method to Estimate the Size and Characteristics of HIV-positive Populations Using an Individual-based Stochastic Simulation Model.
Epidemiology 2016 Mar;27(2):247-56
Trends of HIV-1 incidence with credible intervals in Sweden 2002-09 reconstructed using a dynamic model of within-patient IgG growth.
Int J Epidemiol 2015 Jun;44(3):998-1006
Geographic and temporal trends in the molecular epidemiology and genetic mechanisms of transmitted HIV-1 drug resistance: an individual-patient- and sequence-level meta-analysis.
PLoS Med. 2015 Apr;12(4):e1001810
Challenges with using primer IDs to improve accuracy of next generation sequencing.
PLoS ONE 2015 ;10(3):e0119123
Longitudinal Genetic Characterization Reveals That Cell Proliferation Maintains a Persistent HIV Type 1 DNA Pool During Effective HIV Therapy.
J. Infect. Dis. 2015 Aug;212(4):596-607
Global Dispersal Pattern of HIV Type 1 Subtype CRF01_AE: A Genetic Trace of Human Mobility Related to Heterosexual Sexual Activities Centralized in Southeast Asia.
J. Infect. Dis. 2015 Jun;211(11):1735-44
Delayed HIV diagnosis common in Sweden, 2003-2010.
Scand. J. Infect. Dis. 2014 Dec;46(12):862-7
Evaluation of bio-rad geenius HIV-1 and -2 assay as a confirmatory assay for detection of HIV-1 and -2 antibodies.
Clin. Vaccine Immunol. 2014 Aug;21(8):1192-4
Risk of HIV transmission from patients on antiretroviral therapy: a position statement from the Public Health Agency of Sweden and the Swedish Reference Group for Antiviral Therapy.
Scand. J. Infect. Dis. 2014 Oct;46(10):673-7
High intrapatient HIV-1 evolutionary rate is associated with CCR5-to-CXCR4 coreceptor switch.
Infect. Genet. Evol. 2013 Oct;19():369-77
PCR-induced transitions are the major source of error in cleaned ultra-deep pyrosequencing data.
PLoS ONE 2013 ;8(7):e70388
Longitudinal ultradeep characterization of HIV type 1 R5 and X4 subpopulations in patients followed from primary infection to coreceptor switch.
AIDS Res. Hum. Retroviruses 2013 Sep;29(9):1237-44
Performance of ultra-deep pyrosequencing in analysis of HIV-1 pol gene variation.
PLoS ONE 2011 ;6(7):e22741
Low prevalence of transmitted drug resistance among newly diagnosed HIV-1 patients in Latvia.
J. Med. Virol. 2010 Dec;82(12):2013-8
Dynamics of HIV-1 quasispecies during antiviral treatment dissected using ultra-deep pyrosequencing.
PLoS ONE 2010 Jul;5(7):e11345
HIV-2 genetic evolution in patients with advanced disease is faster than that in matched HIV-1 patients.
J. Virol. 2010 Jul;84(14):7412-5
Transmitted drug resistance and type of infection in newly diagnosed HIV-1 individuals in Honduras.
J. Clin. Virol. 2010 Dec;49(4):239-44
Comparative analysis of measures of viral reservoirs in HIV-1 eradication studies.
PLoS Pathog. 2013 Feb;9(2):e1003174
Hematopoietic precursor cells isolated from patients on long-term suppressive HIV therapy did not contain HIV-1 DNA.
J. Infect. Dis. 2012 Jul;206(1):28-34
Raltegravir treatment intensification does not alter cerebrospinal fluid HIV-1 infection or immunoactivation in subjects on suppressive therapy.
J. Infect. Dis. 2011 Dec;204(12):1936-45
Majority of CD4+ T cells from peripheral blood of HIV-1-infected individuals contain only one HIV DNA molecule.
Proc. Natl. Acad. Sci. U.S.A. 2011 Jul;108(27):11199-204