IL VIROMA

FABRIZIO MAGGI Dipartimento di Ricerca Translazionale, Università di Pisa

UOC Virologia Universitaria, AOUP

All the nucleic acids (ssDNA, dsDNA, ssRNA, dsRNA) belonging to the virus-like particles associated with a particular habitat, defined over a range of scales from the entire body to a specific organ or tissue

D e f i n i t i o n

Wylie et al. Transl Res 2012; Virgin, Cell 2014; Zou et al. Microbiome 2016; Freer et al. Curr Med Chem 2018

~60% ~30% ~10%

Handley, Genome Med 2016; Houldcroft et al. Nat Rev 2017

• inadeguate bioinformatic tools for

virome analysis

• lack of robust virome database

• of the US$ 920 million invested in microbiome research from 2012 to 2014, only 3% of research was dedicated to studies of virome

L i m itat io n s o f hum a n v i ro m e st u d y i n g

C o m p o s i t i o n

18

18

12

16

5

3

n. viral families

109 particles / gram (gut, oropharynx, skin) 105 - 107 particles / ml (blood, urine)

Popgeorgiev et al. Intervirology 2013; Rascovan et al. Annu Rev Microbiol 2016

S t r u c t u r e

Wylie et al. Transl Res 2012; Virgin, Cell 2014; Zou et al. Microbiome 2016; Freer et al. Curr Med Chem 2018

Core

Variable host

genetic

host physiology (immune system)

host pathobiology (disease status)

host lifestyle (diet)

host environment

host drug therapy

De Vlaminck et al. Cell 2013

V i r o m e s t r u c t u r e i s a f f e c t e d b y i m m u n e m o d u l a t i o n a n d a n t i v i r a l t h e r a p y

T h e h e a l t h y v i r o m e

Moustafa et al. PLOS Pathogens 2017; Rampelli et al. Environ Microbiol 2017; Pilar et al. PNAS 2016

Bacteriophages in ~ 50% of individuals:

• Caudovirales • Microviridae

Eukaryotic viruses • Anelloviridae • Herpesviridae • Papillomaviridae • Adenoviridae

BLOOD 8,240 individuals

GUT

Prevalence

Eberl, Mucosal Immunol 2010; Rosario and Breitbart, Curr Op Virol 2011; Mokili et al. Curr Op Virol 2012

T h e c o m p l e t e v i r o m e

The most sequence reads by metagenomic analyses has features of viral genetic material but no taxonomic

classification

" Me ga" v i ro me

" Lo w - leve l" v i ro m e

60%

20%

20%

The "dark" virome

"The "grey " virome"

The "known" virome

T h e " ex pa nding " v i r us e s

Vu et al. J Clin Virol 2016; Lau et al. Transfusion 2017; DeCaprio et al. Nat Rev 2013

The expanding tissue tropism The expanding viral families T h e A s t r o v i r u s s t o r y

Classic HAstV (1975)*

feces

liquor

blood nasopharyngeal

swab

urine MLB1 (2008)

MLB1 (2008) MLB2 (2011) VA1 (2009)

MLB1 (2008) MLB2 (2011) VA1 (2009)

MLB1 (2008) MLB2 (2011) VA1 (2009)

* Year of first identification

T h e P o l i o m av i r i dae s t o r y

V i r o m e a n d i m m u n e s y s t e m

Virgin et al. Cell 2009

“N ORM A L” i m m u ne system

Virome Immune system

“ I m m u n o l o g i c i m p r i n t ”

R e s p o n s e t o n e w i n fe c t i o n s , va c c i n e s ,

o r n o v e l v i ra l va r i a n t s

I n f l a m m a t o r y a n d n o t i n f l a m m a t o r y d i s e a s e s

d y n a m i s m

Virome: equilibrium between health and disease

Rascovan et al. Annu Rev Microbiol 2016

Crohn’s disease

Type I diabetes

Asthma

V i r o m e – m i c r o b i o t a i n t e r a c t i o n

Pfeiffer and Virgin, Science 2016; Karst, Nat Rev Microbiol 2016

Vi r a l d i s e as e o r

n o d i s e ase

Indirect

Mechanisms of interaction

Direct

Bacteria and/or bacterial components or products interacting with virus:

LPS (poliovirus, MMTV, HIV)

Peptidoglycan (poliovirus)

HBGA glycans (norovirus)

Defensins (adenovirus)

Butyric acid (HIV, EBV, KSHV)

Inducing a tolerogeneic microenvironment (MMTV)

Suppressing Ab production (rotavirus, norovirus)

Suppressing IFN signaling (norovirus)

Microbiota skews the antiviral immune response by:

The “do uble fa c e ” o f t he m ic ro b i o ta

Monedero et al.,Trends Biotech 2018; Iturriza-Gomara and Cunliffe, JID 2017

A n t i - v i r a l e f f e c t

P r o - v i r a l e f f e c t

FMT

responders

P ha ge s a nd fe ca l m ic ro b ia l t ra n s p la ntat io n

Zuo et al. Gut 2017

The restoration of virome community is as important as that of bacterial microbiome in FMT Donor selection based on virome characteristics should be considered in FMT practice

Pts. with Clostridium difficile infection (CDI)

(FMT)

CDI recipients with Caudovirales: • higher richness in donor • higher colonisation level of donor-derived taxa

A n e l l o v i r u s T T V a n d p o s t - t ra n s p l a nt c o m p l i c a t i o n s

2

3

4

5

6

7

8

0 10 20 30 40 50 60 70 80 90 120

150

180

360

TTV

DN

A

(Log

10 c

opie

s /

ml)

Days post - transplant

CMV pos (n. 69)

CMV neg (n. 136) p < 0.001

De Vlaminck et al. Cell 2013; Maggi et al. Sci Rep 2018

Me

an

TT

V D

NA

*

(Log

cop

ies/

ml

95%

CI)

A n e l l o v i r u s T T V v i r e m i a p r e d i c t s C M V r e a c t i va t i o n

+ - 3

4

5 n. 69

n. 136

n. 205; p = 0.001

* measured between 0 and 10 days post-transplant

Me

an

TT

V D

NA

*

(Log

cop

ies/

ml

95%

CI)

Total

Maggi et al. Sci Rep 2018

C M V d e t e c t i o n a c r o s s 4 m o n t h s p o s t - t x

n. 39

n. 27

n. 66; p = 0.033

n. 109

n. 30

n. 139; p = 0.038 3

4

5 Kidney Liver

+ - + -

T TV index in l i ve r / k idney t ra ns p la nt re c ip ie nt s

> 3.45 log10 copies/ml higher probability of CMV

reactivations

TAKE-HOME MESSAGE :

TTV viremia above 3.45 log DNA copies/ml within the first 10 days post-transplant correlates with higher propensity to CMV reactivation

following liver/kidney transplantation

≤ 3.45 log10 copies/ml lower probability of CMV

reactivations

Maggi et al. Sci Rep 2018

C o n c l u s i o n s

Our understanding of the human virome is still fragmented and standardized methods are required for providing a more accurate study of the virome

Assessing the human virome as a whole will be of interest in medical diagnosis and give highly valuable information to monitor the patient management

By now, novel associations and routinely unemployed kinetics of viruses within the virome have important clinical implications for the relationships between transplantation, graft rejection and viral reactivation