Publications- Jan Albert Group

Original papers

2023

Delayed generation of functional virus-specific circulating T follicular helper cells correlates with severe COVID-19.
Yu M, Charles A, Cagigi A, Christ W, Österberg B, Falck-Jones S, Azizmohammadi L, Åhlberg E, Falck-Jones R, Svensson J, Nie M, Warnqvist A, Hellgren F, Lenart K, Arcoverde Cerveira R, Ols S, Lindgren G, Lin A, Maecker H, Bell M, Johansson N, Albert J, Sundling C, Czarnewski P, Klingström J, Färnert A, Loré K, Smed-Sörensen A
Nat Commun 2023 Apr;14(1):2164

Inferring the multiplicity of founder variants initiating HIV-1 infection: a systematic review and individual patient data meta-analysis.
Baxter J, Langhorne S, Shi T, Tully DC, Villabona-Arenas CJ, Hué S, Albert J, Leigh Brown A, Atkins KE
Lancet Microbe 2023 Feb;4(2):e102-e112

Functional SARS-CoV-2 cross-reactive CD4+ T cells established in early childhood decline with age.
Humbert M, Olofsson A, Wullimann D, Niessl J, Hodcroft EB, Cai C, Gao Y, Sohlberg E, Dyrdak R, Mikaeloff F, Neogi U, Albert J, Malmberg KJ, Lund-Johansen F, Aleman S, Björkhem-Bergman L, Jenmalm MC, Ljunggren HG, Buggert M, Karlsson AC
Proc Natl Acad Sci U S A 2023 Mar;120(12):e2220320120

Human influenza virus infection elicits distinct patterns of monocyte and dendritic cell mobilization in blood and the nasopharynx.
Vangeti S, Falck-Jones S, Yu M, Österberg B, Liu S, Asghar M, Sondén K, Paterson C, Whitley P, Albert J, Johansson N, Färnert A, Smed-Sörensen A
Elife 2023 Feb;12():

2022

Omicron sublineage BA.2.75.2 exhibits extensive escape from neutralising antibodies.
Sheward DJ, Kim C, Fischbach J, Sato K, Muschiol S, Ehling RA, Björkström NK, Karlsson Hedestam GB, Reddy ST, Albert J, Peacock TP, Murrell B
Lancet Infect Dis 2022 Nov;22(11):1538-1540

Evasion of neutralising antibodies by omicron sublineage BA.2.75.
Sheward DJ, Kim C, Fischbach J, Muschiol S, Ehling RA, Björkström NK, Karlsson Hedestam GB, Reddy ST, Albert J, Peacock TP, Murrell B
Lancet Infect Dis 2022 Oct;22(10):1421-1422

Phylogenetic estimation of the viral fitness landscape of HIV-1 set-point viral load.
Zhao L, Wymant C, Blanquart F, Golubchik T, Gall A, Bakker M, Bezemer D, Hall M, Ong SH, Albert J, Bannert N, Fellay J, Grabowski MK, Gunsenheimer-Bartmeyer B, Günthard HF, Kivelä P, Kouyos RD, Laeyendecker O, Meyer L, Porter K, van Sighem A, van der Valk M, Berkhout B, Kellam P, Cornelissen M, Reiss P, Fraser C, Ferretti L
Virus Evol 2022 ;8(1):veac022

Combining biomarker and virus phylogenetic models improves HIV-1 epidemiological source identification.
Lundgren E, Romero-Severson E, Albert J, Leitner T
PLoS Comput Biol 2022 Aug;18(8):e1009741

Neutralisation sensitivity of the SARS-CoV-2 omicron (B.1.1.529) variant: a cross-sectional study.
Sheward DJ, Kim C, Ehling RA, Pankow A, Castro Dopico X, Dyrdak R, Martin DP, Reddy ST, Dillner J, Karlsson Hedestam GB, Albert J, Murrell B
Lancet Infect Dis 2022 Jun;22(6):813-820

Evolution, geographic spreading, and demographic distribution of Enterovirus D68.
Hodcroft EB, Dyrdak R, Andrés C, Egli A, Reist J, García Martínez de Artola D, Alcoba-Flórez J, Niesters HGM, Antón A, Poelman R, Reynders M, Wollants E, Neher RA, Albert J
PLoS Pathog 2022 May;18(5):e1010515

Probabilistic classification of anti-SARS-CoV-2 antibody responses improves seroprevalence estimates.
Castro Dopico X, Muschiol S, Grinberg NF, Aleman S, Sheward DJ, Hanke L, Ahl M, Vikström L, Forsell M, Coquet JM, McInerney G, Dillner J, Bogdanovic G, Murrell B, Albert J, Wallace C, Karlsson Hedestam GB
Clin Transl Immunology 2022 ;11(3):e1379

A highly virulent variant of HIV-1 circulating in the Netherlands.
Wymant C, Bezemer D, Blanquart F, Ferretti L, Gall A, Hall M, Golubchik T, Bakker M, Ong SH, Zhao L, Bonsall D, de Cesare M, MacIntyre-Cockett G, Abeler-Dörner L, Albert J, Bannert N, Fellay J, Grabowski MK, Gunsenheimer-Bartmeyer B, Günthard HF, Kivelä P, Kouyos RD, Laeyendecker O, Meyer L, Porter K, Ristola M, van Sighem A, Berkhout B, Kellam P, Cornelissen M, Reiss P, Fraser C, 
Science 2022 Feb;375(6580):540-545

2021

Seropositivity in blood donors and pregnant women during the first year of SARS-CoV-2 transmission in Stockholm, Sweden.
Castro Dopico X, Muschiol S, Christian M, Hanke L, Sheward DJ, Grinberg NF, Rorbach J, Bogdanovic G, Mcinerney GM, Allander T, Wallace C, Murrell B, Albert J, Karlsson Hedestam GB
J Intern Med 2021 09;290(3):666-676

Interactions between seasonal human coronaviruses and implications for the SARS-CoV-2 pandemic: A retrospective study in Stockholm, Sweden, 2009-2020.
Dyrdak R, Hodcroft EB, Wahlund M, Neher RA, Albert J
J Clin Virol 2021 03;136():104754

2020

Inferring transmission heterogeneity using virus genealogies: Estimation and targeted prevention.
Zhang Y, Leitner T, Albert J, Britton T
PLoS Comput Biol 2020 09;16(9):e1008122

Potential impact of seasonal forcing on a SARS-CoV-2 pandemic.
Neher RA, Dyrdak R, Druelle V, Hodcroft EB, Albert J
Swiss Med Wkly 2020 03;150():w20224

2019

Intra- and interpatient evolution of enterovirus D68 analyzed by whole-genome deep sequencing.
Dyrdak R, Mastafa M, Hodcroft EB, Neher RA, Albert J
Virus Evol 2019 Jan;5(1):vez007

Getting more from heterogeneous HIV-1 surveillance data in a high immigration country: estimation of incidence and undiagnosed population size using multiple biomarkers.
Giardina F, Romero-Severson EO, Axelsson M, Svedhem V, Leitner T, Britton T, Albert J
Int J Epidemiol 2019 12;48(6):1795-1803

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

2018

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, Marrone G, Norrgren H, Svedhem V, Wendahl S, Albert J, Sönnerborg A
AIDS 2018 04;32(7):877-884

2017

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

In vivo mutation rates and the landscape of fitness costs of HIV-1.
Zanini F, Puller V, Brodin J, Albert J, Neher RA
Virus Evol 2017 Jan;3(1):vex003

2016

Outbreak of enterovirus D68 of the new B3 lineage in Stockholm, Sweden, August to September 2016.
Dyrdak R, Grabbe M, Hammas B, Ekwall J, Hansson KE, Luthander J, Naucler P, Reinius H, Rotzén-Östlund M, Albert J
Euro Surveill 2016 Nov;21(46):

Establishment and stability of the latent HIV-1 DNA reservoir.
Brodin J, Zanini F, Thebo L, Lanz C, Bratt G, Neher RA, Albert J
Elife 2016 11;5():

HIV-1 transmission between MSM and heterosexuals, and increasing proportions of circulating recombinant forms in the Nordic Countries.
Esbjörnsson J, Mild M, Audelin A, Fonager J, Skar H, Bruun Jørgensen L, Liitsola K, Björkman P, Bratt G, Gisslén M, Sönnerborg A, Nielsen C, , Medstrand P, Albert J
Virus Evol 2016 Jan;2(1):vew010

Review articles and other publications

[Precision diagnostics in clinical microbiology].
G Giske C, Allander T, Fröding I, Ininbergs K, Mölling P, Engstrand L, Albert J
Lakartidningen 2021 10;118():

Contagiousness in treated HIV-1 infection.
Eriksen J, Albert J, Axelsson M, Berglund T, Brännström J, Gaines H, Gisslén M, Gröön P, Hagstam P, Navér L, Pettersson K, Stenkvist J, Sönnerborg A, Tegnell A
Infect Dis (Lond) 2021 Jan;53(1):1-8

Antiretroviral treatment for HIV infection: Swedish recommendations 2019.
Eriksen J, Carlander C, Albert J, Flamholc L, Gisslén M, Navér L, Svedhem V, Yilmaz A, Sönnerborg A
Infect Dis (Lond) 2020 05;52(5):295-329

Utredning av den initiala smittspridningen av SARS-CoV-2 till och inom Sverige. Underlagsrapport till Coronakommissionen.
Dyrdak R, Albert J.