Jan Albert Group

The main research focus in our group is on HIV genetic variation, evolution and resistance. We also study enterovirus evolution and spread.

Jan Albert
Jan Albert, Professor at the Department of Microbiology, Tumor and Cell Biology.

HIV and enterovirus evolution and spread

We study HIV and enterovirus genetic variation, evolution and spread. We aim to provide tools to help curb the HIV pandemic by a better providing understanding of how HIV spreads, escapes immunity, develops resistance and persists as a life-long infection.

One area of research concerns molecular epidemiology, spread and incidence of HIV, including analysis of resistant HIV variants. We also  investigate the utility of using different biomarkers, such as the viral diversity and serological incidence tests, to estimate time-of-infection for individual HIV patients. By this approach we have modelled HIV incidence in Sweden as well as estimated the number of undiagnosed patients in Sweden. We have shown that Sweden has almost reached the first of the UNAIDS 90-90-90 targets, i.e. that more than 90% of all persons living with HIV should be diagnosed.

We use next-generation sequencing (NGS) to study how HIV evolves over time within single infected patients. 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. Our results show that the HIV-1 reservoir is not maintained by ongoing replication  during suppressive antiretroviral therapy, which has been an area of controversy.

Finally, we study the genetic evolution, spread and immunity of enterovirus D68 (EV-D68), which is an emerging pathogen that has caused large outbreaks where some cases have shown severe respiratory and neurological disease, including polio-like acute flaccid myelitis. We use NGS to sequence the entire genome of EV-D68 cases in Sweden and link the sequence data to immunological studies.

Group Members


Challenges in modelling the proportion of undiagnosed HIV infections in Sweden.
Andersson E, Nakagawa F, van Sighem A, Axelsson M, Phillips AN, Sönnerborg A, et al
Euro Surveill. 2019 Apr;24(14):

Women have enhanced bone loss associated with phosphaturia and CD4+ cell restoration during initial antiretroviral therapy.
Kalayjian R, Albert J, Cremers S, Gupta S, McComsey G, Klingman K, et al
AIDS 2018 Nov;32(17):2517-2524

Expert consensus statement on the science of HIV in the context of criminal law.
Barré-Sinoussi F, Abdool Karim S, Albert J, Bekker L, Beyrer C, Cahn P, et al
J Int AIDS Soc 2018 Jul;21(7):e25161

Increase in transmitted drug resistance in migrants from sub-Saharan Africa diagnosed with HIV-1 in Sweden.
Andersson E, Nordquist A, Esbjörnsson J, Flamholc L, Gisslén M, Hejdeman B, et al
AIDS 2018 04;32(7):877-884

Estimating time of HIV-1 infection from next-generation sequence diversity.
Puller V, Neher R, Albert J
PLoS Comput. Biol. 2017 Oct;13(10):e1005775

Error rates, PCR recombination, and sampling depth in HIV-1 whole genome deep sequencing.
Zanini F, Brodin J, Albert J, Neher R
Virus Res. 2017 07;239():106-114

A35 Viral evolution and innate immune responses during acute HIV-1 infection and their association with disease pathogenesis.
Hassan A, Hare J, Kamini G, Yindom L, Kamali A, Karita E, et al
Virus Evol 2017 Mar;3(Suppl 1):

Viral genetic variation accounts for a third of variability in HIV-1 set-point viral load in Europe.
Blanquart F, Wymant C, Cornelissen M, Gall A, Bakker M, Bezemer D, et al
PLoS Biol. 2017 Jun;15(6):e2001855

Defining HIV-1 transmission clusters based on sequence data.
Hassan A, Pybus O, Sanders E, Albert J, Esbjörnsson J
AIDS 2017 06;31(9):1211-1222

Inference of Transmission Network Structure from HIV Phylogenetic Trees.
Giardina F, Romero-Severson E, Albert J, Britton T, Leitner T
PLoS Comput. Biol. 2017 01;13(1):e1005316

Error rates, PCR recombination, and sampling depth in HIV-1 whole genome deep sequencing.
Zanini F, Brodin J, Albert J, Neher R
Virus Res. 2017 07;239():106-114

Establishment and stability of the latent HIV-1 DNA reservoir.
Brodin J, Zanini F, Thebo L, Lanz C, Bratt G, Neher R, et al
Elife 2016 11;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.
Puenpa J, Vongpunsawad S, Österback R, Waris M, Eriksson E, Albert J, et al
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.
Sabri F, Prados A, Muñoz-Fernández R, Lantto R, Fernandez-Rubio P, Nasi A, et al
Retrovirology 2016 09;13(1):61

Frequent Respiratory Viral Infections in Children with Febrile Neutropenia - A Prospective Follow-Up Study.
Söderman M, Rhedin S, Tolfvenstam T, Rotzén-Östlund M, Albert J, Broliden K, et al
PLoS ONE 2016 ;11(6):e0157398

The global spread of HIV-1 subtype B epidemic.
Magiorkinis G, Angelis K, Mamais I, Katzourakis A, Hatzakis A, Albert J, et al
Infect. Genet. Evol. 2016 12;46():169-179

Transmission of HIV Drug Resistance and the Predicted Effect on Current First-line Regimens in Europe.
Hofstra L, Sauvageot N, Albert J, Alexiev I, Garcia F, Struck D, et al
Clin. Infect. Dis. 2016 Mar;62(5):655-663

Population genomics of intrapatient HIV-1 evolution.
Zanini F, Brodin J, Thebo L, Lanz C, Bratt G, Albert J, et al
Elife 2015 Dec;4():

A Method to Estimate the Size and Characteristics of HIV-positive Populations Using an Individual-based Stochastic Simulation Model.
Nakagawa F, van Sighem A, Thiebaut R, Smith C, Ratmann O, Cambiano V, et al
Epidemiology 2016 Mar;27(2):247-56

Six-week follow-up after HIV-1 exposure: a position statement from the Public Health Agency of Sweden and the Swedish Reference Group for Antiviral Therapy.
Gaines H, Albert J, Axelsson M, Berglund T, Gisslén M, Sönnerborg A, et al
Infect Dis (Lond) 2016 Feb;48(2):93-8

Trends of HIV-1 incidence with credible intervals in Sweden 2002-09 reconstructed using a dynamic model of within-patient IgG growth.
Romero-Severson E, Lee Petrie C, Ionides E, Albert J, Leitner T
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.
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 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.
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 Jul;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


Jan Albert

Professor/senior physician
C1 Department of Microbiology, Tumor and Cell Biology