The Human Virus Microbiome Atlas in

Health and Disease

Björn Andersson, Professor

Dept.of Cell and Molecular Biology

Karolinska Institutet

Science for Life Laboratory

Projects – Andersson group

Virus metagenomics

Skin microbiome in disease

Trypanosoma cruzi – comparative

genomics

Giardia – comparative genomics,

expression analysis

Also: Spruce, Malaria, HIV and

assorted collaborations

Initial goal - Virus discovery

The science of virology is limited to the study of already known

viruses.

Most viruses known today have been identified by isolation in cell

culture. There may be large numbers of unkown unculturable viruses.

Identification of unculturable viruses is a key issue in virology, and

has occupied scientists for decades.

Many patients with viral diseases are never diagnosed.

Several common diseases may be caused by unknown viruses.

20 maj 2015Tobias Allander 5

The needle in the haystack

Virus

Human DNA

Bacterial DNA

Current questions – the human virome

Chronic infections vs virus removal

Disease associations, immunity, large cohorts

Virus evolution

Latency

Outbreaks, zoonosis

Now: Full virome studies using NGS Technical challenges

Recent projects

Identified viruses

Influenza A, B, C

RSV

Metapnneumovirus

Rhino/Picorna (several)

TTV (several)

Human Bocavirus

Measels virus

Parainfluenza 1, 3

Adenovirus

Coronavirus OC43

Coronavirus HKU1

KI polyomavirus

NPA results - viruses

NPA results – three virus families

Orthomyxoviridae

PicornaviridaeParamyxoviridae

Schizophrenia samples

Collaboration with Patrick Sullivan, UNC, Chapel Hill

695 schizophrenia samples, sampled when sickest

67 first episode psychosis samples, schizophrenics

42 first episode psychosis samples, no schizophrenia

Serum samples, virus enrichment+454

Sickest

B19, HepC, GBV-C

Adeno, TTV

First episode schizophrenia

Unclassified flavi and parvo, adeno

Only episode psychosis

Unclassified parvo, adeno

New five-year KAW project, 22 MSEK, 2013-

17

Clinical samples

Virus microbiome

Björn Andersson

Virus discovery, Finishing

Björn Andersson, Tobias Allander, Jan Albert

Follow-up studies:

Collaborative

Michael Lindberg, others

Bacterial microbiome:

Siv Andersson, UU

Single cell bacterial sequencing, functional studies

Mic

robio

me Encephalitis

ALS, Cancer

Pneumonias

Skin disorders

Sample collection network

Ronny Wickström

Britt Gustafsson

Birgitta Henriques-Normark

Niklas Edner

Weimin Ye

Anna Nilsson

MAARS

+others

EU FP7 consortium – Atopic dermatitis and psoriasis

88 AD, 129 PSO, 117 Healthy individuals

Microbiome, transcriptomics, networks, animal models

Skin swabs, skin biopsies, serum

16S rRNA PCR+sequencing, swab+biopsy

Shotgun microbiome sequencing, swab

Virus screening, serum

Status: All data collected

Analysis and publication in progress

16S Data set

17

362390

4327286

912997

940083

114999

3841245

282360

565753

13445

20360

4440643

4411187 5

21

86

44 8

22

064

4 987144

74351

851917

610043

851668

205025

4449324

360483

820692

4301457

1107940

4456068

4369229

4480063

837884

4349859

4306540

4303697

378096

4021335

4482598

4350124

4309323

164003

447320143548098

199374467218

4346894

4348347

4353642

761594

654307

4349519

939571

2110555

4349522

370309

4476950

1003210

4327300912906

505749

87

241

4474056

625320

1081372

1096610

755148

4473664

370134

4481323

851925

4446521

2901965

511475

25259

1004369

4299324

4408996

279980

496787

883806

4471315

429455

4

442153

6

4318084

403853

4439089

103810

25478

3208510

4422405

4047452

1036883

4317476

247720

4422718

995817285376

1131523

16S results

20/05/2015 19

●

●

●

●

●

●

●

●

●

●

●

0

10

20

30

40

50

AD.LES PSO.LES AD.NON_LES CTRL.NON_LES PSO.NON_LES

Nu

mb

er

of

rea

ds(M

bp

s)

20/05/2015 20

0

10

20

AD.LES AD.NON_LES CTRL.NON_LES PSO.LES PSO.NON_LES

% o

f sa

mp

les

10

15

20

25

norm.count

Shotgun results: Fungus

Virus results: Skin swabs

Surprisingly rich

A multitude of phages

Several human viruses

Possible new viruses

Analysis in progress

Virus results: serum

Acknowledgements

CMB, KI, Andersson group

Hamid Darban

Stephanie Prast-Nielsen

Johannes Luthman

Mauricio Barrientos

MAARS EU Consortium, Harri Aleniuscoordinator

Tobias Allander

Bengt Persson, LiU, KI

Fredrik Lysholm

Patrick Sullivan, UNC

Erik Sonnhammer

Jan Albert

Funders: Swedish research Council, STINT, NIH, Wallenberg

Foundation, EU FP7.