Gastroenteric viruses:
Current status
Jim Gray
Professor of Clinical Virology,
UEA &
Consultant Virologist, NNUH
Viruses infecting the gut
Viruses associated with gastroenteritis
• rotaviruses
• caliciviruses
• noroviruses
• sapoviruses
• astroviruses
Rotaviruses
• adenoviruses 40, 41
Adenoviruses
Sapoviruses
Astroviruses
Noroviruses
Viruses infecting the gut
Presumptive gastroenteric viruses
• Torovirus
• Coronavirus
• Parvovirus: Bocavirus
• Picobirnavirus
• Aichi virus
Torovirus
Kobuvirus
Parvovirus
Coronavirus
Noroviruses
Noroviruses
• Family : Caliciviridae
• Non-enveloped small round
structured viruses (27-32 nm
diameter)
• Genome: pos sense ssRNA ~ 7.5kb
• Endemic and epidemic in the
community
• The most common cause of
outbreaks of gastroenteritis
Norovirus
Clinical manifestations
Infects enterocytes of the duodenum and jejunum resulting in
malabsorption and increased secretion
Nausea - 79%
Vomiting - 69%
Diarrhoea - 66%
Fever - 37%
Chills - 32%
Abdominal cramps - 30%
Myalgias -26%
Headache - 22%
Sore throat - 18%
• Incubation period: 10-50h
• Duration of symptoms: 24-48h
• Excrete >106 particles/g or ml
• Infectious dose: 10 virus particles
Seasonality
Norovirus detection
60
% detection
50
40
30
20
<1
1 to 4 5 to 9 10 to
19
20 to 30 to 40 to 50 to
29
39
49
59
60 to 70 to 80 to
69
79
93
controls
case
case
controls
controls
case
controls
case
controls
case
controls
case
controls
case
controls
case
controls
case
controls
case
controls
case
case
0
controls
10
All
age
Age and specimens
Age distribution of norovirus infection in cases of gastroenteritis and agematched controls (IID study: Amar et al)
Temperature inactivation of norovirus
Phylogenetic grouping among noroviruses
Alphatron
Fort Lauderdale
Saint Cloud
Fayetteville Snow Mountain
MelkshamHillingdon
Kashiwa47
Erfurt 546
290/White River
Girlington
Idaho Fall
Hawaii
VA97207
GGIII
314/S19/94
Wortley/90
Amsterdam
Jena
M7
273/Gwyned
Leeds
GGIV
Limburg
Sw43
Seacroft
Newbury
CH126
Mexico
Toronto
GGII
Bristol
Lordsdale
Blakemore
MNV-1
GGV
Chiba
Koblenz
Thistle
Winchester
Malta
318/S05/95
Musgrove
DSV
Stavanger
WhiteRose
Southampton
Norwalk KY89
Hesse
Sindlesham
GGI
Mechanisms for generating genomic and antigenic diversity
Noroviruses
• Genetic recombination during dual infection of a single cell
• Accumulation of point mutations
Rotaviruses
• Genetic reassortment during dual infection of a single cell
• Accumulation of point mutations
• Genome rearrangement
Inter- and Intra-seasonal diversity of NoV genotypes during 2003 to 2006.
Early, mid and late season outbreaks characterised.
Genotype
2003/04
2004/05
2005/06
Early
Mid
Late
Early
Mid
Late
Early
Mid
Late
GI-1
0
0
0
0
0
0
0
1 (5%)
0
GI-2
1 (5%)
0
0
0
0
0
0
0
0
GI-3
1 (5%)
0
0
0
0
0
0
1 (5%)
0
GI-4
0
0
0
0
0
0
0
3 (15%) 0
GI-6
2 (10%)
0
0
0
0
0
0
0
0
GII-1
0
0
0
0
0
1 (5%)
0
1 (5%)
0
GII-2
3 (15%)
1 (5%)
0
4 (20%)
2 (10%)
0
0
1 (5%)
0
GII-3
7 (35%)
3 (15%)
2 (10%)
0
0
0
0
2 (10%) 0
GII-4
1 (5%)
14 (70%)
18 (90%) 14 (70%)
18 (90%)
18* (90%)
9 (45%)
7 (35%) 18 (90%)
GII-6
1 (5%)
0
0
2 (10%)
1 (5%)
0
2 (10%)
0
GII-7
3 (15%)
2 (10%)
0
0
0
1(5%)
6 (30%)
3 (15%) 1 (5%)
GII-8
1 (5%)
0
0
0
0
0
0
1 (5%)
0
Total
20
20
20
20
20
20
20
20
20
Total of
3 GI
4 GII
2 GII
3 GII
3 GII
2 GII
4 GII
3 GI
3 GII
genotypes
6 GII
1 (5%)
6 GII
Early = September/October, Middle = December, Late = March, GII = Genogroup II, GI = Genogroup I, * = February and March
Highlights the fitness of GII-4 to infect the human population against a
background of herd immunity
Sep-07
Jul-07
May-07
Mar-07
Jan-07
Nov-06
Sep-06
Jul-06
May-06
Mar-06
Jan-06
Nov-05
Sep-05
Jul-05
May-05
Mar-05
Jan-05
Nov-04
Sep-04
Jul-04
May-04
Mar-04
Jan-04
Nov-03
Sep-03
GII-4 variants: September 2003 to September 2007
Emergence of GII-4 variants
100%
80%
v11
v10
60%
v8
v6
40%
v5
v4
v3
20%
v2
0%
Calicivirus structure
Norovirus [Norwalk]
Sapovirus
Protruding domain
Norovirus [Grimsby]
Vesivirus (SMSV)
2002/03 epidemic
Autumn
Winter
Spring
Normal winter season
Summer
Unusual
summer
activity
Autumn
Winter
Spring
Summer
Normal
summer
activity
Epidemic winter season
Autumn
Winter
Spring
Normal winter season
Narrowing diversity:
GII4 predominates
GII4 variants emerge
GII4 variant is selected, out of season outbreaks occur, becomes
epidemic
Return to normal season, wide diversity at the
beginning, narrowing as season progresses.
Lack of short-term herd immunity to a new variant
Summer
A
Pre-2002
E
2002 epidemic
A
J
A
A
B
B
B
Structural changes on the P2
domain between GII-4 variants
Electrostatic
surface
E
A
A
A
Molecular surface
B
B
Monoclonal antibodies raised against the
pre-2002 GII-4 strains do not react with the
2002 GII-4 strain and vice versa.
Pre-2002
2002
Food/ water-borne
spread
Modes
of
transmission
Person to person
spread
Environmental
spread
Outbreak tracking
Similarity among NoV GII-4 outbreaks reported between December/06 and
September/07 from different regions of England and Wales. NE = North East, NW
= North West, SW = South West.
Pairwise (OG:100%,UG:0%) (FAST:2,10) Gapcost:0%
P2Domain
100
99
98
97
96
95
94
93
92
Gene encoding the P2 domain
.04/01/07
.
GII-4
NE
.03/01/07
.
GII-4
NE
.04/01/07
.
GII-4
Wales
.15/01/07
.
GII-4
London
.15/01/07
.
GII-4
Wales
.01/02/07
.
GII-4
Wales
.01/01/07
.
GII-4
NW
.18/01/07
.
GII-4
London
.01/02/07
.
GII-4
London
.05/01/07
.
GII-4
NW
.03/01/07
.
GII-4
NE
.02/01/07
.
GII-4
NW
.18/01/07
.
GII-4
SW
.05/01/07
.
GII-4
NE
.30/01/07
.
GII-4
SE
.19/09/07
GII-4 NW
.28/09/07
GII-4 London
.13/03/07
GII-4 SW
s
Clu
100
99
98
97
96
95
94
93
92
91
90
89
88
P2
ter
W
ard
te
Da
III
Kilverston
13.01.10
III
Holt
13.01.10
III
Kimberley
08.02.10
III
Kimberley
26.02.10
III
Holt
18.01.10
III
Holt
25.01.10
III
Holt
15.02.10
III
Kimberley
19.02.10
III
Kilverstone
19.01.10
III
Kilverstone
26.01.10
III
Kilverstone
28.01.10
III
Kilverstone
28.01.10
III
Kimberley
06.03.10
III
Knapton
01.02.10
III
Knapton
08.02.10
III
Knapton
18.02.10
III
Kimberley
07.03.10
VI
Holt
27.03.10
VI
Heydon
17.03.10
VI
Heydon
13.04.10
VI
Kimberley
08.04.10
VI
Holt
22.03.10
IV
Guist
25.02.10
IV
Guist
08.03.10
IV
Docking
14.03.10
I
Mulbarton
13.01.10
I
Mulbarton
12.01.10
I
Hethel
18.01.10
I
Mulbarton
05.01.10
I
Mulbarton
08.01.10
I
Holt
04.01.10
I
Holt
08.01.10
I
Hethel
10.02.10
I
Guist
18.01.10
I
Knapton
04.01.10
I
Knapton
18.01.10
VIII
Heydon
26.04.10
VIII
Brundall
28.04.10
VIII
Holt
25.04.10
VIII
Holt
27.04.10
VIII
Knapton
29.04.10
VIII
Knapton
01.05.10
VIII
Brundall
28.04.10
V
Heydon
04.05.10
V
Knapton
17.03.10
V
Knapton
22.03.10
VII
Gateley
21.04.10
VII
Gateley
18.04.10
II
Langley
12.01.10
II
Dunston
12.01.10
II
Hethel
11.01.10
II
Dunston
18.01.10
II
Hethel
18.01.10
II
Gunthorpe
11.01.10
II
Gunthorpe
20.01.10
II
Gunthorpe
26.01.10
Phylogenetic analysis of NNUH strains
revealed 8 genetic clusters of NoV
were introduced into the hospital in the
2009/ 2010 NoV season
Sequencing the hypervariable region encoding the P2 domain
revealed 8 distinct genetic clusters circulating or co-circulating in the
hospital.
NNUH NoV
Outbreaks, 2010
Moving average of suspected and confirmed cases of norovirus gastroenteritis: Dec 2009 to May 2010
10
Number of Cases
GII-4
Variant 5
Variant 6
9
GII-4
Variant 2
GII-4
Variant 4
8
GII-4
Variant 7
GII-4
Variant 3
7
GII-4
Variant 8
GII-4
Variant 1
6
5
4
3
2
1
10/05/2010
03/05/2010
26/04/2010
19/04/2010
12/04/2010
05/04/2010
29/03/2010
22/03/2010
Date of onset
15/03/2010
08/03/2010
01/03/2010
22/02/2010
15/02/2010
08/02/2010
01/02/2010
25/01/2010
18/01/2010
11/01/2010
04/01/2010
28/12/2009
21/12/2009
0
23d
20d
Date
02.01.10
03.01.10
05.01.10
07.01.10
07.01.10
10.01.10
11.01.10
11.01.10
12.01.10
12.01.10
12.01.10
13.01.10
13.01.10
17.01.10
17.01.10
17.01.10
17.01.10
18.01.10
18.01.10
19.01.10
20.01.10
25.01.10
25.01.10
26.01.10
27.01.10
28.01.10
01.02.10
05.02.10
08.02.10
10.02.10
14.02.10
17.02.10
17.02.10
23.02.10
23.02.10
06.03.10
07.03.10
08.03.10
14.03.10
17.03.10
17.03.10
22.03.10
22.03.10
27.03.10
08.04.10
14.04.10
18.04.10
21.04.10
21.04.10
25.04.10
27.04.10
27.04.10
28.04.10
29.04.10
01.05.10
04.05.10
Ward
KNAPTON
HOLT
MULBARTON
HOLT
MULBARTON
GUNTHORPE
DUNSTON
HETHEL
LANGLEY
MULBARTON
MULBARTON
HOLT
KILVERSTONE
DUNSTON
HETHEL
HETHEL
HOLT
GUIST
KNAPTON
KILVERSTONE
GUNTHORPE
GUNTHORPE
HOLT
KILVERSTONE
KILVERSTONE
KILVERSTONE
KNAPTON
KIMBERLEY
KNAPTON
HETHEL
HOLT
KIMBERLEY
KNAPTON
GUIST
KIMBERLEY
KIMBERLEY
KIMBERLEY
GUIST
DOCKING
KNAPTON
HEYDON
HOLT
KNAPTON
HOLT
KIMBERLEY
HEYDON
GATELEY
GATELEY
HOLT
HOLT
HEYDON
HOLT
BRUNDALL
KNAPTON
KNAPTON
HEYDON
Cluster I Cluster II
I
I
I
I
I
II
II
II
II
I
I
GII-4 genetic clusters
Cluster III Cluster IV Cluster V Cluster VI Cluster VII
Cluster VIII
III
III
II
I
II
III
I
I
III
II
II
III
III
III
III
III
III
III
I
III
III
III
IV
III
III
III
IV
IV
V
VI
VI
V
III
VI
VI
VII
VII
34d
VIII
VIII
VIII
VIII
VIII
VIII
VIII
V
Environmental NoV sampling
At the conclusion of the outbreak
and after clinical cleaning
• Cleansers/ disinfectants
• Equipment
• Nurses station
• Bedside environment
• Furniture, fixtures and fittings
Environmental norovirus sampling
6 wards post-cleaning
Site
No. tested
No. positive
percent positive
Cleansers and disinfectants
Soap dispensers
Alcohol dispensers
Sub-total
13
7
20
6
3
9
46.2
42.9
45.0
Equipment
Non-invasive ventilator
IV pump
Pulse oximeter
BP machine (handles, cuffs, buttons)
Tympanic thermometer
Temporal thermometer
Tourniquet
Sub-total
1
1
6
24
3
1
1
37
1
1
4
10
1
0
0
17
100.0
100.0
66.7
41.7
33.3
0.0
0.0
45.9
Nurses station
Notes trolley
Computer keyboards
Computer mouse
Telephone
6
10
8
10
4
4
1
1
66.7
40.0
12.5
10.0
1
1
6
24
3
1
1
37
No. tested
1
1
4
10
1
0
0
17
No. positive
100.0
100.0
66.7
41.7
33.3
0.0
0.0
45.9
Nurses
station
Cleansers
and disinfectants
Notes
trolley
Soap dispensers
Computer
keyboards
Alcohol dispensers
Computer
Sub-total mouse
Telephone
Sub-total
Equipment
Non-invasive ventilator
Bedside
IV pump environment
Pulse oximeter
Patients'
bowls
BP machine
(handles, cuffs, buttons)
Bedspace
basket
Tympaniclockers
thermometer
Patients'
Temporal
thermometer
Bed frame
Tourniquet
Bed
controls
Sub-total equipment
Patientline
Patients' call bells
Nurses station
Sub-total
Notes trolley
Computer keyboards
Furniture,
fixtures and fittings
Computer
mouse
Chairs
Telephone
Carpet
Sub-total
Remote
control
Zimmer frame
Bedside environment
Shelf
Patients'fitments
bowls
Shower
Bedspace
Hand
rails/ basket
grab rails
6
13
10
7
8
20
10
34
1
1
6
2
24
1
3
2
1
1
2
37
5
8
21
6
10
8
1
10
1
34
1
1
1
2
8
1
26
64
34
91
1
10
1
1
42
10
1
12
01
01
17
1
1
9
4
4
1
1
10
1
1
1
24
19
66.7
46.2
40.0
42.9
12.5
45.0
10.0
29.4
100.0
100.0
66.7
100.0
41.7
100.0
33.3
100.0
0.0
100.0
0.0
50.0
45.9
20.0
12.5
42.9
66.7
40.0
12.5
100.0
10.0
100.0
29.4
100.0
100.0
100.0
100.0
50.0
100.0
34.6
percent positive
Equipment
Non-invasive ventilator
IV pump
Pulse oximeter
BP machine (handles, cuffs, buttons)
Tympanic thermometer
Temporal thermometer
Tourniquet
Sub-total
Site
2
1
2
1
2
5
8
21
2
1
2
1
1
1
1
9
100.0
100.0
100.0
100.0
50.0
20.0
12.5
42.9
131
71
201
1
1
18
126
626
12
24
36
124
111
373
2
1
61
101
81
10
127
34
239
61
31
91
1
1
14
19
45
102
11
03
01
170
0
0
40
40
10
130
10
75
100.0
46.2
100.0
42.9
100.0
45.0
100.0
100.0
50.0
100.0
34.6
100.0
19.2
66.7
16.7
41.7
16.7
33.3
12.5
0.0
9.1
0.0
0.0
45.9
0.0
0.0
66.7
0.0
40.0
0.0
12.5
0.0
10.0
23.6
29.4
31.4
2
1
2
2
1
2
100.0
100.0
100.0
percent positive
No. positive
Furniture, and
fixtures
and fittings
Cleansers
disinfectants
Chairsdispensers
Soap
Carpet dispensers
Alcohol
Remote control
Sub-total
Zimmer frame
Shelf
Equipment
Shower fitments
Non-invasive
ventilator
Hand
rails/
grab
rails
IV pump
Taps oximeter
Pulse
Cupboard/
handles
BP
machinedrawer
(handles,
cuffs, buttons)
Toilet flushthermometer
handles
Tympanic
Door handles
Temporal
thermometer
Light switches
Tourniquet
Fridge handles
Sub-total
Tables
Commode
Nurses
station
Notes
Fan trolley
Computer
Toilet seatkeyboards
Computer
TV switch mouse
Telephone
Sub-total
Sub-total
Total (all sites)
Bedside environment
Patients' bowls
Bedspace basket
Patients' lockers
No. tested
Patients' bowls
Bedspace basket
Patients' lockers
Bed frame
Bed controls
Patientline equipment
Patients' call bells
Sub-total
Site
Kimberley Ward
No. positive
percent positive
No. tested
No. positive
percent positive
• Two wards re-cleaned
and re-sampled
After 2nd clinical clean
No. tested
Norovirus:
Environmental contamination
After 1st clinical clean
2
1
3
1
0
1
50.0
0
33.3
2
1
3
0
0
0
0
0
0
Equipment
Pulse oximeter
BP machine (handles, cuffs, buttons)
Tympanic thermometer
Sub-total
1
6
2
9
1
5
1
7
100
83.3
50.0
77.8
1
6
2
9
0
1
1
2
0
16.7
50.0
22.2
Nurses station
Computer keyboards
Computer mouse
Telephone
Sub-total
2
2
3
7
2
1
0
3
100
50.0
0
42.9
2
2
3
7
1
0
0
1
50.0
0
0
14.3
Bedside environment
Patients' call bells
Sub-total
1
1
0
0
0
0
1
1
0
0
0.0
0.0
Furniture, fixtures and fittings
Shower fitments
Hand rails/ grab rails
Taps
Toilet flush handles
Door handles
Light switches
Sub-total
3
5
4
1
4
1
18
3
1
1
0
0
0
5
100
20.0
25.0
0
0
0
27.8
3
5
4
1
4
1
18
1
0
1
0
0
0
2
33.3
0.0
25.0
0.0
0.0
0.0
11.1
Total (all sites)
38
16
42.1
38
5
13.2
Site
Cleansers and disinfectants
Soap dispensers
Alcohol dispensers
Sub-total
Environmental monitoring: 2011
Date
Ward: Holt
Soap dispenser
Bed frame
Patient's locker
Patients line equip
Call bell
Notes trolley
Computer keyboard
Computer mouse
Telephone
Shower fitment
Hand rails/ Grab rails
Tap
Toilet flush handle
Door handle
Light switch
Soap dispenser
Soap dispenser
Blood pressure machine
Blood pressure cuff
Pulse oximeter
Tympanic thermometer
Patient washbowl
Bay door handle
Hand wash basin
Digital thermometer
14/12/2010
20/01/2011
08/02/2011
15/03/2011
NoV detected
Neg
Neg
Neg
Neg
Neg
Neg
Neg
Neg
Neg
Neg
Neg
Neg
Neg
NoV detected
Neg
Neg
Neg
Neg
Neg
Neg
Neg
Neg
No swab
No swab
NoV detected
NoV detected
Neg
Neg
Neg
Neg
Neg
Neg
Neg
NoV detected
Neg
Neg
Neg
Neg
Neg
Neg
Neg
Neg
Neg
Neg
Neg
Neg
Neg
Neg
No swab
NoV detected
Neg
Neg
Neg
Neg
Neg
Neg
Neg
Neg
Neg
NoV detected
Neg
Neg
Neg
Neg
Neg
Neg
NoV detected
Neg
No swab
Neg
Neg
No swab
Neg
Neg
NoV detected
Neg
NoV detected
NoV detected
Neg
NoV detected
NoV detected
NoV detected
NoV detected
NoV detected
Neg
Neg
Neg
NoV detected
NoV detected
Neg
NoV detected
NoV detected
NoV detected
NoV detected
Neg
Neg
NoV detected
Neg
No swab
surveillance
outbreak
Reduced risk of spread
Ward closure
Increased risk of spread
Virus
variant/
mutant
Low infectious dose
Cohort
nursing
Adherence to
hand washing
practices, soap
and water
High attack
rate
Patients
Potential vaccines
Surface finishes
allowing decontamination
Staff affected
Risk of norovirus
spread within the
hospital
environment
Reduced staffing
Elbow/automatic
taps on
handbasins
Single rooms
with en suite
Projectile
vomiting
Soft furnishings
contaminated
Environment
Hand contact
surfaces
contaminated
Unrestricted
visiting/
admissions
Open wards
Also consider:
• Bed occupancy rates
• Built environment
• Infection control procedures
• Admission Units
Keys to the success of gastroenteric viruses
• Low infectious dose ~ 10-100 virus particles
• Noroviruses 107 particles per gram/ml
• Rotaviruses 1011 particles per gram/ml
• Stability in the environment
• Norovirus survives up to 80oC
• Rotavirus survives in the environment for months
• Protected by the matrix – faeces and vomit, which also inactivate
chlorine-based disinfectants
• Non-enveloped viruses – resistant to many disinfectants and alcohol
• Short term immunity ~ 6 months
• 16% of the population excrete NoV in the absence of symptoms
• 14% of the population excrete rotavirus in the absence of symptoms
• Multiple routes of transmission - person to person contact, through
ingestion of contaminated water or food or by contact with contaminated
environmental surfaces
• RNA genome replication results in the accumulation of point mutations
• Segmented rotavirus genome replication results in reassortment
• Dual infections can result in recombination or reassortment
• Rotaviruses are associated with zoonotic infection
• Hospital-acquired infections are predominantly associated with GII-4
• There are multiple introductions into hospitals, of variants of GII-4,
throughout the NoV season and many rotavirus strains co-circulate in the
human population
• Antibody-escape mutants and rotavirus reassortants are selected and
driven by herd immunity resulting in epidemics in an immunologically
naive population