Viral Gastroenteritis

Viral Gastroenteritis:

Outbreaks and Testing

Christopher J. McIver, Senior Hospital Scientist,Microbiology Department (SEALS), Prince of Wales Hospital.

• Enteric caliciviruses

• Detection methods

• Epidemiologic observations

• Aspects of molecular phylogeny

Prof. William Rawlinson, SEALS, University of NSW

Dr. Peter White, SEALS, University of NSW

Dr. Grant Hansman, National Institute of Infectious Diseases, Tokyo

Rowena Bull, University of NSW

Elise Tu, University of NSW

Thanh Nguyen, SEALS

Phoebe Lee, SEALS

0

10

20

30

40

50

60

Bacteria Parasites Rotavirus Adenovirus Astrovirus NV GI NV GII NPI

Emergency ward (n = 120)

Isolation ward (n = 110)

Elise Tu, 2004

CAMPYLOBACTER

020

4060

80100

120

1 14 27 40 1 14 27 40 1 14 27 40 1 14 27 40 1 14 27 40 1 14 27 40 1 14 27 40 1 14 27 40 1

CA

SES

1998 1999 2000 2001 2002 2003 2004 2005

0

10

20

30

40

50

60

Bacteria Parasites Viruses NPI

Emergency ward

Isolation ward

ROTAVIRUS

0

20

40

60

80

100

120

1 14 27 40 1 14 27 40 1 14 27 40 1 14 27 40 1 14 27 40 1 14 27 40 1 14 27 40 1 14 27 40 1

CA

SES

1998 1999 2000 2001 2002 2003 2004 2005

RSV

0

20

40

60

80

100

120

1 14 27 40 1 14 27 40 1 14 27 40 1 14 27 40 1 14 27 40 1 14 27 40 1 14 27 40 1 14 27 40 1

CA

SES

1998 1999 2000 2001 2002 200 2004 2005

SESIAH Public Health Unit

0

10

20

30

40

50

60

Jan Feb Mar Apr May Jun Jul Aug Sept Oct Nov Dec

Rotavirus 2003 (n = 1701)



Norovirus 2004 (n = 1130)

Norovirus 2005 (n = 298)

%

0

50

100

150

200

250

Nov Dec Jan Feb Mar Apr May Jun Jul Aug Sept Oct

Hospitals and residential home outbreaks

All other settings

Month

Seasonality for Norovirus, England and Wales, 1992 - 2000

First virus associated with acute gastroenteritis

Resistant to culturing

Difficult to detect

? Appropriate interventions

Sapporo

27 - 32 nm

Single stranded

Positive-sense RNA

~ 7,800 nucleotides

Family: Caliciviridae

Calicivirus Prevalence Population at risk

Symptoms

Norovirus Common All ages Mild

Sapovirus Infrequent Young children

Less severe

Genogroup Susceptible Viruses

GI Norwalk virusBaltimore virusSouthampton virusDesert Shield

GII Outbreaks world-wideCamberwell virusFrankston virus

GIII

GIV

GV Mice

Symptom Number Percentage

Nausea 29 58

Diarrhoea and vomiting

21 42

Vomiting (without

diarrhoea)

11 21

Diarrhoea (without vomiting)

11 21

Abdominal pain

20 40

Fever 19 38

Marks et al. 2000. Epidemiol. Infect. 124:481-487

• Contact with persons with gastroenteritis

• Contact with contaminated areas (vomit or faeces)

• Consumption of contaminated food / water

• Age group

• Health care institutions

• Closed environments

Kaplan et al. 1982. Ann. Intern. Med. 96:756-61

•Vomiting in more than half of affected persons

•Mean (or median) incubation period: 24 – 48h

•Mean (or median) duration of illness: 12 – 60h

•Bacterial pathogen not detected

•Moderately sensitive (68%)

•Highly specific (99%)

Turcios et al. 2006. CID. 42:964-969

• Implementation of more-specific prevention and control measures

• Surveillance of prevalence (including genotypes)

•True burden

Morphologically intact

> 106 particles / gram

Increased sensitivityLability of viral RNA

PCR inhibitorsGenetic diversity

Antigens more stablePresent in higher concentrations

Simple and rapid

Broadly reactiveNon-specific reactions

IDEIA™Norwalk-like virus (Dako Cytomation, UK)

Genogroup I and II-specific capture monclonal antibodies(capsid protein)4 monclonal antibodies – GI10 monclonal antibodies – GII10% faecal suspension3 h performance time

ParameterIn-house PCR OligoDetect, Light

Diagnostics

Richards et al., 2003. J Clin Virol

26:109-115

Sensitivity 64.3 71.4 55.5

Specificity 100 96.9 98.3

PPV 100 93.8 95.0

NPV 76.2 83.8 76.9

Total 30 53 479

Evaluation IDEIA™Norwalk-like virus (Dako Cytomation, UK)

27 – 35 nmSingle-stranded / positive sense RNA genome

Outbreak Setting Strain Genotype

1 Nursing home US95/96 GII/4

2 Day care US95/96 GII/4

3 Hospital-geriatric US95/96 GII/4

4 Hospital-pediatric US95/96 GII/4

5 Day care Sydney cluster GII/3

6 Day care Sydney cluster GII/3

7 Nursing home US95/96 GII/4

8 Wedding US95/96 GII/4

9 Hospital US95/96 GII/4

10 Prison Hawaii-like GII/1

11 Community US95/96 GII/4

White et al. 2002. J Med Virol. 68:113-118

Norovirus outbreaks July, 1997– September, 2000.

Noel et al. 1999. Identification of a distinct common strain of “Norwalk-like viruses”having a global distribution. J Infect. Dis. 179:1334-144.

“95/96-US” strain predominated in 1995-96 winter season.

How does the virus spread to geographically distant locations in US and abroad.

What mode(s) of transmission or selective factor(s)allowed the sudden emergence and rapid spread of strain.

“95/96-US” predominated in 1995-96 was replaced in the following season by a greater variety of strains.

NSW Public Health Bull 2004. 15:184-188

Late autumn early winter (mainly nursing homes and some hospitals)

May, 100 outbreaks (3,294)

August, 17 outbreaks (184)

July 04 – Aug 04All outbreaks 188Nursing homes 139Hospitals 33Child care 12Schools 1Other 3

Outbreak Setting Strain Genotype

1 Hostel Hunter GII/4

2 Nursing home Germanton GII/4

3 Cruise ship Hunter GII/4

4 Nursing home Hunter GII/4


6 Nursing home HunterSaitama T24b

GII/4GI/1

7 Hospital Germanton GII/4

8 Nursing home HunterGermanton

GII/4GII/4

9 Hostel Hunter GII/4


11 Lodge Hunter GII/4


Rowena Bull, Elise Tu, Peter white, UNSW

Norovirus outbreaks March – July, 2004.

Farmington Hills strain

Marc-Alain et al. 2004. Outbreaks of acute gastroenteritis on cruise shipsand on land: Identification of a predominant circulating strain of norovirus– United states, 2002. J Infect. Dis. 190:27-36.

Sharp increase in outbreaks - 2002 (cruise ships and on land)Clinical manifestations (increased vomiting, environmental persistence)facilitated the spread of this strain in closed settingsCruise ship outbreaks featured higher attack rates and persistedlonger on successive cruises than did outbreaks caused by otherNorovirus strains.Herd immunity that would be expected to develop to some degreeafter exposure of a population to an emergent GII/4 strain (i.e. 95/96-US) does not seem to have prevented the emergenceof a related GII/4 strain.Consistent with very early observations that strain-specific protective immunity may last only 6 months.

Number of norovirus outbreaks reported in the Netherlands in the winter seasons from 2000/2001 to 2004/2005

Sept. Oct. Nov. Dec. Jan. Feb. Mar.

2000/2001

3 1 4 3 13 11 8

2001/2002

2 6 8 14 18 12 8

2002/2003

7 11 33 52 26 12 2

2003/2004

1 1 1 2 9 4 3

2004/2005

9 18 31 13 - - -

Annelies Kroneman et al. 2004. Eurosurveillance

Hunter-like

US95/96 cluster

Hunter ’04 cluster

Sydney 198N/04S

AY081134 MoraAF406793 DOUG4770/00O

Sydney 776/99O

AJ004864 GrimsbyAF414425 Burwash LandingAF080549 95/96-US

Sydney 642/97SSydney 284/97S


Sydney 917J/02OSydney 812J/01O

AY502017 GermantonSydney 198N/04S

AY578985 b4s6oxford

Sydney 4262/01SAY502023 Farmington Hills

Hunter 913K/04OManly 388P/04ORamsgate 336I/04O

Hunter 504D/04OHunter 273C/04O

Jannali 611C/04O

Jannali 670H/04OKogarah 4006/04OKogarah 393H/04O

Manly Vale 098M/04ODulwich Hill 194M/04O

Sydney 4288/02S

Sydney 762I/04SSydney 267J/04S

0.1

Sydney 591/97S7676

100

AB039779 U17100

100

85100

100

10069

69

Picton 081/03OAY919139 Picton 554/03O70

79

9199

98

93

80100

10090

7492

100

100

75

Sydney 348/97O

100

U46500 CamberwellX86557 LordsdaleX76716 Bristol

Turramurra 604J/04OHunter 990O/04OHunter 120A/04O

Sydney 4228/04SHunter 284E/04O

Dulwich Hill 203D/04ODulwich Hill 197P/04O

Dulwich Hill 190I/04OTurramurra 597U/04O

Sydney 625K/04OHunter 956S/04OCruise Ship 532D/04O

FarmingtonHills cluster

Sydney 715D/04S

Sydney 4360/02S

Sydney 4337/02SAF425768 Oberhausen

Sydney 4136/01S

Sydney 4384/02S

L23830 OTH25U22498 Mexico

U02030 Toronto

Sydney1696/98S

Sydney 4480/02SSydney 4209/01SSydney 4134/01SAY845056 C14/02O

Sydney 2113/98S

Sydney 2145/98OAY588132 2212/98O

Sydney 2086/98S

C14-like recombinants

2212-like recombinants

C14-like recombinant

AJ277608 LeedsSydney 4477/02S

Sydney 4237/01SAY237413 Mc17*

AY038599 Virginia 207AY237414 Mc24*

AF195848 AmsterdamAB039780 U25

AY077644 Limburg

Su2445/03O

AJ277620 SeacroftSydney 4012/02SSydney 1347/98S


X81879 MelkshamU70059 Snow Mountain 2

Sydney 4264/01SAY237415 Mc37*AF427117 Erfurt

AF414422 New Orleans 306AJ277607 Hillingdon

AF397905 SchwerinU07611 Hawaii

Picton 037/03O

Longbay/00OAF414421 Pt Canaveral

GII.11

GII.6

GII.4

GII.2

GII.10

GII.5

GII.12

GII.1

GII.3

GII.9

GII.8

GII.7

US95/96 cluster


Sydney 198N/04S

AY081134 MoraAF406793 DOUG4770/00O

Sydney 776/99O






AY578985 b4s6oxford




Jannali 611C/04O



Sydney 4288/02S


0.1

Sydney 591/97S7676

100

AB039779 U17100

100

85100

100

10069

69

Picton 081/03OAY919139 Picton 554/03O70

79

9199

98

93

80100

10090

7492

100

100

75

Sydney 348/97O

100








Sydney 715D/04S

Sydney 4360/02S

Sydney 4337/02SAF425768 Oberhausen

Sydney 4136/01S

Sydney 4384/02S

L23830 OTH25U22498 Mexico

U02030 Toronto

Sydney1696/98S

Sydney 4480/02SSydney 4209/01SSydney 4134/01SAY845056 C14/02O

Sydney 2113/98S

Sydney 2145/98OAY588132 2212/98O

Sydney 2086/98S

C14-like recombinants

2212-like recombinants

C14-like recombinant


Sydney 4237/01SAY237413 Mc17*



AY077644 Limburg

Su2445/03O

AJ277620 SeacroftSydney 4012/02SSydney 1347/98S


X81879 MelkshamU70059 Snow Mountain 2

Sydney 4264/01SAY237415 Mc37*AF427117 Erfurt

AF414422 New Orleans 306AJ277607 Hillingdon

AF397905 SchwerinU07611 Hawaii

Picton 037/03O

Longbay/00OAF414421 Pt Canaveral

GII.11

GII.6

GII.4

GII.2

GII.10

GII.5

GII.12

GII.1

GII.3

GII.9

GII.8

GII.7

US95/96 cluster


Sydney 198N/04S

AY081134 MoraAF406793 DOUG4770/00O

Sydney 776/99O






AY578985 b4s6oxford




Jannali 611C/04O



Sydney 4288/02S


0.1

10090

7492

100

100

75

Sydney 348/97O

100








Sydney1696/98S

y yAY845056 C14/02O

Sydney 2113/98S

Sydney 2145/98OAY588132 2212/98O

Sydney 2086/98S2212-like recombinants


Sydney 4237/01SAY237413 Mc17*



GII.4

GII.9

GII.8

GII.7

US95/96 cluster


Sydney 198N/04S

AY081134 MoraAF406793 DOUG4770/00O

Sydney 776/99O






AY578985 b4s6oxford




Jannali 611C/04O



Sydney 4288/02S


0.1

10090

7492

100

100

75

Sydney 348/97O

100








Sydney1696/98S

y yAY845056 C14/02O

Sydney 2113/98S

Sydney 2145/98OAY588132 2212/98O

Sydney 2086/98S2212-like recombinants


Sydney 4237/01SAY237413 Mc17*



GII.4

GII.9

GII.8

GII.7

Hunter (2004)

Farmington Hills(2001-02)

95/96 (< 2000)

R. Bull et al. 2005.

0 1

AlphatronSaitama U17Su608D

SeacroftET11

ET09ET186

ET13ET194Yamaguchi

ET69ET71

ET67Saitama T37a

ET53ET49OberhausenC14ET47

Sydney 2212ET15

ET17OTH 25

MexicoToronto 24

SchwerinHawaii

LBAY574EQVMH

Snow MountainHillingdon

ET73Erfurt

Mc37Leeds

ET57Mc17

ET59VirginiaSaitama U25

AmsterdamLordsdale

CamberwellET06

ET65ET07

004/95M-14ET02

DOUG4770Mora

Burwash Landing95/96-US subset

ET196ET198ET55

AnchorageET61

ET63Mc99

GermantonFarmington Hills

ET200

Greater diversity

Recombinants

E. T. V Tu. 2004

RNA polymerase

Capsid

Switching between two 2 RNA templates

Phylogenetic grouping

Molecular epidemiologic studies

Immunity does not protect against variant strains

Impact vaccine design

• Isolate/ cohort symptomatic patients• Place on contact and airborne precautions• Emphasis on hand washing/ cleansing after patient

contact or environment• Duck bill masks (patient’s with explosive diarrhoea or

vomiting)• Advice to relatives• Terminal clean room/ ward• ? Stop new admissions via A&E for 24 h

Infection Control Strategies

Infection Control Strategies

• Symptomatic staff (nausea/ vomiting/ diarrhoea) excluded from duty

• Excluded infected staff from duty until symptom

free from diarrhoea or vomiting for 48hrs

• Agency staff to work in wards not affected

• Daily meeting to review outbreak

0

2

4

6

8

10

1215

-Feb

16-F

eb

17-F

eb

18-F

eb

19-F

eb

20-F

eb

21-F

eb

22-F

eb

23-F

eb

24-F

eb

25-F

eb

26-F

eb

27-F

eb

28-F

eb

1-M

ar

2-M

ar

3-M

ar

4-M

ar

5-M

ar

6-M

ar

7-M

ar

8-M

ar

9-M

ar

10-M

ar

11-M

ar

12-M

ar

13-M

ar

14-M

ar

15-M

ar

16-M

ar

17-M

ar

18-M

ar

19-M

ar

Other

Volunteer

Teacher

PSA/Porter

Adm in/exec

SMO

JMO

Allied health

Nurse other

Nurse ward

Relative

Patient

Onset of symptoms

Total cases = 102Patients = 26Detected 4/23 (17%)

Inpatient 1EIA nRT-PCR

Inpatient 1 Yes YesInpatient 2 No YesInpatient 3 No YesStaff 1 No YesOutpatient 1 Yes -Outpatient 2 Yes -

___________________________________________________________

Nausea 24h

Diarrhoea < 48h

Fever ~ 3 days , not more than 38.5o C

Myalgia and aching joints (Increased during illness, lasted ~ 2 weeks)

Coughing and swollen glands towards end of illness

Case Cont Case Cont Case Cont Case Cont Case Cont Case Cont Case Cont

N 857 574 32 17 136 69 96 58 170 72 313 244 102 102

NLV 5.1 1.1 15.2 0 8.7 1.5 3.1 1.7 5.9 1.4 3.9 0.8 1.0 1.0

SLV 2.4 1.5 4.2 8.3 4.9 5.0 6.1 0 2.8 0 0.6 0.7 0 0

Overall < 1 y 1-4 yrs 5-14 yrs 15-29 yrs 30-59 yrs > 60 yrs

Chadwick. D and Goode J. A. Gastroenteris viruses - Novartis Foundation 2001

Physician-based study

The Netherlands from May 1996 – May 1999

0

100

200

300

400

500

600

JAN FEB MAR APR MAY JUN JUL AUG SEPT OCT NOV DEC

20052006

0

100

200

300

400

500

600

JAN FEB MAR

Rota/Adeno/Astro

Norovirus

Month

1 Aged care hospital Jul-97 200 26 82 Day care centre Aug-97 7 6 53 Geriatric ward Mar-98 11 11 24 Paediatric ward Mar-98 15 15 85 Day care centre Aug-98 3 2 16 Day care centre Oct-98 4 4 27 Nursing home Feb-99 20 3 38 Wedding Nov-99 39 2 29 Hospital Jul-00 33 7 710 Prison Jul-00 33 17 811 Community setting Sep-00 6 2 2

Source Date Cases Tested Pos

White et al. (2002). JMV

30.883.318.253.350.050.010010010047.0100

Rat

e

Timing of collection

Preservation of samples (RNAse activity)

Limit of detection

Internal controls

Condition Positive Negative Total

Asthma 12 32 44

Non-asthma 3 17 20

P = 0.3536 (considered not significant)

Relative risk = 1.818CI = 0.5759 – 5.741

Rhinovirus = 9/12 Diarrhoea = 0Vomiting = 3/12

Respiratory illnessBronchiolitisCough

Rhinovirus = 0 Diarrhoea = 0Vomiting = 1

D. Dable. 2001

170 patients (< 18 y), gastroenteritis

Treated at Sydney Children’s Hospital

Timeframe: 2001 – 2002; 2004

Negative (94/170): Salmonella, Shigella, Campylobacter.Rotavirus, Adenovirus, Astrovirus and Norovirus)

7/94 (7.4%) positive for Sapovirus

7/170 (4.1%) “minimal” prevalenceHansman et al. 2006. EID

Research group Setting Prevalence %

Kirkwood & Bishop (2001)

Melbourne 0.56

Wright et al. (1998) SE Australia (1980-96) 0.32

Grohman et al. (1991) Sydney 0.46

Hansman et al. (2006) Sydney 4.1

GI

GIV

GV

GII

GIIIPEC porcine strainSydney53*

C12

Mex340Sydney4106Mc10

cruise shipSydney77*London/29845Mc2

Bristol1000

819

848

708

437

Sydney4402NK24Arg39

Sydney3*SW278Ehime1107

Houston27Parkville

Stockholm318Sydney40*

Sydney31*Manchester

Sapporo

999

994

1000

619

832

893

0.05

Sakaeo15

Common cause - gastroenteritis

Immunogenic detection - under scrutiny

Molecular detection methods favoured

Emergence of GII/4

Recombinant strains

Diversity of Sapovirus in Sydney

Improvements needed

Documents

Viral Gastroenteritis