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 CHAIN, 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, Scandinavia and Central America (Karlsson et al., 2012; Skar et al., 2012). 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 modeling 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.

Publications

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.
Angelis K, Albert J, Mamais I, Magiorkinis G, Hatzakis A, Hamouda O, et al
J. Infect. Dis. 2015 Jun;211(11):1735-44

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.
Rhee S, Blanco J, Jordan M, Taylor J, Lemey P, Varghese V, et al
PLoS Med. 2015 Apr;12(4):e1001810

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.
Rhee S, Blanco J, Jordan M, Taylor J, Lemey P, Varghese V, et al
PLoS Med. 2015 Apr;12(4):e1001810

Challenges with using primer IDs to improve accuracy of next generation sequencing.
Brodin J, Hedskog C, Heddini A, Benard E, Neher R, Mild M, et al
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.
von Stockenstrom S, Odevall L, Lee E, Sinclair E, Bacchetti P, Killian M, et al
J. Infect. Dis. 2015 Feb;():

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.
Angelis K, Albert J, Mamais I, Magiorkinis G, Hatzakis A, Hamouda O, et al
J. Infect. Dis. 2015 Jun;211(11):1735-44

Delayed HIV diagnosis common in Sweden, 2003-2010.
Widgren K, Skar H, Berglund T, Kling A, Tegnell A, Albert J
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.
Hawthorne Hallen A, Samuelson A, Nordin M, Albert J, Bogdanovic G
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.
Albert J, Berglund T, Gisslén M, Gröön P, Sönnerborg A, Tegnell A, et al
Scand. J. Infect. Dis. 2014 Oct;46(10):673-7

High intrapatient HIV-1 evolutionary rate is associated with CCR5-to-CXCR4 coreceptor switch.
Mild M, Gray R, Kvist A, Lemey P, Goodenow M, Fenyö E, et al
Infect. Genet. Evol. 2013 Oct;19():369-77

PCR-induced transitions are the major source of error in cleaned ultra-deep pyrosequencing data.
Brodin J, Mild M, Hedskog C, Sherwood E, Leitner T, Andersson B, et al
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.
Hedskog C, Brodin J, Heddini A, Bratt G, Albert J, Mild M
AIDS Res. Hum. Retroviruses 2013 Sep;29(9):1237-44

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.
Skar H, Albert J, Leitner T
PLoS ONE 2013 ;8(4):e60906

Low prevalence of transmitted drug resistance in patients newly diagnosed with HIV-1 infection in Sweden 2003-2010.
Karlsson A, Björkman P, Bratt G, Ekvall H, Gisslén M, Sönnerborg A, et al
PLoS ONE 2012 ;7(3):e33484

Performance of ultra-deep pyrosequencing in analysis of HIV-1 pol gene variation.
Mild M, Hedskog C, Jernberg J, Albert J
PLoS ONE 2011 ;6(7):e22741

Low prevalence of transmitted drug resistance among newly diagnosed HIV-1 patients in Latvia.
Balode D, Westman M, Kolupajeva T, Rozentale B, Albert J
J. Med. Virol. 2010 Dec;82(12):2013-8

Dynamics of two separate but linked HIV-1 CRF01_AE outbreaks among injection drug users in Stockholm, Sweden, and Helsinki, Finland.
Skar H, Axelsson M, Berggren I, Thalme A, Gyllensten K, Liitsola K, et al
J. Virol. 2011 Jan;85(1):510-8

Dynamics of HIV-1 quasispecies during antiviral treatment dissected using ultra-deep pyrosequencing.
Hedskog C, Mild M, Jernberg J, Sherwood E, Bratt G, Leitner T, et al
PLoS ONE 2010 ;5(7):e11345

HIV-2 genetic evolution in patients with advanced disease is faster than that in matched HIV-1 patients.
Skar H, Borrego P, Wallstrom T, Mild M, Marcelino J, Barroso H, et al
J. Virol. 2010 Jul;84(14):7412-5

Transmitted drug resistance and type of infection in newly diagnosed HIV-1 individuals in Honduras.
Murillo W, Paz-Bailey G, Morales S, Monterroso E, Paredes M, Dobbs T, et al
J. Clin. Virol. 2010 Dec;49(4):239-44

Prevalence of drug resistance and importance of viral load measurements in Honduran HIV-infected patients failing antiretroviral treatment.
Murillo W, de Rivera I, Parham L, Jovel E, Palou E, Karlsson A, et al
HIV Med. 2010 Feb;11(2):95-103

 

Related citations

Comparative analysis of measures of viral reservoirs in HIV-1 eradication studies.
Eriksson S, Graf E, Dahl V, Strain M, Yukl S, Lysenko E, et al
PLoS Pathog. 2013 Feb;9(2):e1003174

Single-copy assay quantification of HIV-1 RNA in paired cerebrospinal fluid and plasma samples from elite controllers.
Dahl V, Peterson J, Spudich S, Lee E, Shacklett B, Price R, et al
AIDS 2013 Apr;27(7):1145-9

Hematopoietic precursor cells isolated from patients on long-term suppressive HIV therapy did not contain HIV-1 DNA.
Josefsson L, Eriksson S, Sinclair E, Ho T, Killian M, Epling L, et al
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.
Dahl V, Lee E, Peterson J, Spudich S, Leppla I, Sinclair E, et al
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.
Josefsson L, King M, Makitalo B, Brännström J, Shao W, Maldarelli F, et al
Proc. Natl. Acad. Sci. U.S.A. 2011 Jul;108(27):11199-204

 

Group Members

Professor/överläkare

Jan Albert

Enhet: Jan Albert grupp
E-post: Jan.Albert@ki.se

Administratör

Lisbeth Löfstrand

Telefon: 08-517 711 65
Enhet: Forskargrupp R van Vollenhoven
E-post: Lisbeth.Lofstrand@ki.se

Jan AlbertProfessor/överläkare
Johanna BrodinPostdoc
Robert DyrdakAnknuten
Eva ErikssonAnknuten
Joakim EsbjörnssonPostdoc
Marta GranströmAnknuten
Berit HammasAnknuten
Marianne JanssonAnknuten
Mattias KarlssonAnknuten
Malin SvenssonAnknuten
Lina TheboLaboratorieingenjör
Susanne von StockenströmDoktorand
Susanne von StockenströmForskarstuderande

HIVMicrobiologyVirology