South African Ebola Mobile Laboratory · President of Sierra Leone, Dr Ernest Bai Koroma to reflect...
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Transcript of South African Ebola Mobile Laboratory · President of Sierra Leone, Dr Ernest Bai Koroma to reflect...
South African Ebola Mobile Laboratory operation in Sierra Leone
Janusz T. PaweskaHead Center for Emerging and Zoonotic Disease
NICD-NHLS
6th FIDSSA Congress South Africa, 05 – 08 October 2015
Year Country Virus Cases Deaths CFR (%)
1976 DRC ZEBOV 318 280 88
1977 DRC ZEBOV 1 1 100
1994 Gabon ZEBOV 52 31 60
1995 DRC ZEBOV 315 250 79
1996 Gabon ZEBOV 37 21 57
1996-1997 Gabon ZEBOV 60 45 75
1996 South Africa ZEBOV 2 1 50
2001-2002 Gabon ZEBOV 65 53 82
2001-2002 RC ZEBOV 57 43 75
2002-2003 RC ZEBOV 143 128 90
2003 RC ZEBOV 35 29 83
2005 RC ZEBOV 12 10 83
2007 DRC ZEBOV 264 187 71
2008-2009 DRC ZEBOV 32 15 47
2014 DRC ZEBOV 66 49 74.2
Total (n=15, over 38
years)
1459 1143 74.2
18
Year Country Virus Cases Deaths CFRc (%)
1976 Sudan SUDV 284 151 53
1979 Sudan SUDV 34 22 65
2000-2001 Uganda SUDV 425 224 53
2004 Sudan SUDV 17 7 41
2011 Uganda SUDV 1 1 100
2012 Uganda SUDV 11 4 36
2012 Uganda SUDV 6 3 50
Total (n=7, over
36 years)
778 412 50
2007 Uganda BDBV 149 37 25
2012 DRC BDBV 36 13 36
Total 185 50 27
21
Guinea 2013-15
SL 2014-15
Liberia 2014-15
Ebola Statements
• We know how to fight this disease
• It is not a mystery
• We know the science
• We know how to prevent it from spreading
• We know how to care for those who contracted it
So why Ebola containment was not working in Guinea, Sierra Leone and Liberia
• Do we know how to fight this disease?
• Is it not a mystery?
• Do we know the science?
• Do we know how to prevent it from spreading?
• Do we know how to care for those who contracted it?
EVD epidemic in West Africa
unprecedented both in size and scale
EVD outbreaks 2013-2015: WHO 01 October 2015
881 cases among health care workers of 513 were fatal
(58.2%)
Year Country Virus Cases Deaths CFRc (%)
2014-15 Guinea ZEBOV 3810 2536 66.6
2014-15 Liberia ZEBOV 10672 4808 45.1
2014-15 Sierra Leone ZEBOV 14089 3955 28.1
Sub-total 28571 11299 39.5
2014-15 Nigeria ZEBOV 20 8 40
2014-15 Mali ZEBOV 8 6 75
Senegal ZEBOV 1 0 0
Spain, USA, UK,
Italy ZEBOV 7 1 14.3
Sub-total 36 15 41.7
TOTAL 28607 11314 39.6
TOTAL all previous outbreaks 2422 1605 66.3
Ebola hits the virgin soil • First EVD outbreak
• Fragile political and infrastructure systems where the EVD epidemic concentrate.
• Guinea, Sierra Leone and Liberia are still rebuilding their economies after suffering through years of civil war.
Strategy for controlling Ebola is well known but it’s full implementation and execution in West Africa was severely hampered by many challenging limitations
Strategy for controlling EVD
Factors in health-care-worker EVD infections
•inconsistent recognition/triage of Ebola patients;•overcrowding of hospitals/clinics;•limitations in physical layout of hospitals;•lack of training in PPE and inadequate supply of PPE; and,•limited supervision of and adherence to infection control.
Chronology of the EVD outbreak
A 2-year-old boy, who died in December 2013
in the village of Meliandou, Gueckedou Prefecture, Guinea was the index case of the current EVD epidemic.
His mother, sister, and grandmother then became ill with similar symptoms and also died.
People infected by those initial cases spread the disease to other villages.
Early cases are misdiagnosed as other diseases more common to the area.
The Ebola is spreading
unrecognized for several
months
25 March 2015
EVD outbreak officially recognized in four south-eastern districts of Guinea.
Rapid spread in neighbouring countries.
Evolution of the Ebola Outbreak
OriginalEpicenter
Late May
Mid June
Late July
Moa WharfFreetown
Sierra Leone
A global threat?8 August 2014 WHO declares the Ebola outbreak in West Africa
as Public Health Emergency of International Concern
19 Sept 2014 UN Security Council declares Ebola outbreaks in
West Africa as Threat to Peace and Security
• UN Mission to Combat Ebola: United Nations Mission for Ebola Emergency Response (UNMEER) have five priorities:
– stopping the outbreak
– treating the infected
– ensuring essential services
– preserving stability
– preventing further outbreaks
Quantum Leap needed to advert EVD disaster
• outbreak is out of control
• cases are rising faster than the ability to contain them
• Ebola outbreaks need to be stopped at source to reduce risks of spreading the virus globally
Ebola in West Africa
• It is more than a health threat or a public health emergence of international concern ....it became a humanitarian and socio-economic crisis!
David Nabarro, who is leading the UN's fight against Ebola, says it scares him more than SARS. Photo: Jean-Marc
Ferre
"I remember working on SARS and being scared, but this is much worse than SARS. It is just spreading faster and faster and faster."He is not the only person so concerned. As Dr Nabarro visited recently the White House , the former US Central Command commander, retired General Charle Zinni, said the the threat from Ebola outweighed that of the Islamic State.
"I would say Ebola is the greater global threat,“ I think ISIS certainly is a regional threat. It can create problems in our country and other countries, but it's not an existential threat. Ebola can become an existential threat on a global level."
Source Photo: Jean-Marc Ferre
Two young orphans whose parents have died of Ebola
sharing a meal in Kenema, Sierra Leone.
EVD in Sierra Leone
May, 2014
Ebola is spreading across Sierra Leone
June, 2014
Ebola is spreading across Sierra Leone
June, 2014
July, 2014
Expanding spread & emerging hot spots
August, 2014
Expanding spread & emerging hot spots
August, 2014
Expanding spread & emerging hot spots
17 Aug 2014 Arrival of 1st
NICD EMLU Team
September, 2014
Expanding spread & emerging hot spots
November
Expanding spread & emerging hot spots
Ebola posters and messages highly visible in Freetown, at the road sides, shops and public buildings as part of the Ebola awareness
health campaign efforts.
Support needed
• Technical experts:– Contact tracers
– Epidemiologists
– Infection control specialists
– Psychologists
– Logisticians
– Clinicians
– Diagnosticians
• Ambulances and vehicles for– Surveillance
– Burials
– Transfer of cases to holding and treatment canters
• Supplies– Hospital, medical
NICD Mobile Laboratory in Sierra Leone
• The NICD EMLU was deployed in Sierra Leone, Freetown as part of WHO-GOARN EVD international outbreak response in West Africa.
23 Aug: completion of setting up the MLU
Major operational areas: • administration, data analysis, reporting of results and
communication• specimens receiving area• serology and PCR extraction room• PCR master mix room• PCR positive control room• PCR room• PCR gel analysis• dressing room• biocontainment negative pressure chamber. Much effort was made for emergency wiring to allow for rapid switch to generator mode in case of power failure.
Laboratory layout
Aug 24: Arrival of UN delegation, including
Drs. Nabaro (UN) and Fukunaga (WHO) to
visit the NICD Mobile Laboratory at Lakka
Hospital, Freetown.
Aug 25: President of the Republic of Sierra
Leone Dr Ernest Bai Koroma and other
governmental officials delegation visiting
the NICD MLU at Lakka Hospital.
Aug 25: NICD MLU declared to be fully
operational
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No
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Daily RT-PCR results over 5 week operation NICD MLU Freetown-Lakka
Tested Positive Max. daily opt. cap.
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Week 1 Week 2 Week 3 Week 4 Week 5
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Trend in no. submissions over a 5 week period: NICD MLU Freetown-Lakka
No. tesed No. positive Average tetsed per day Max. daily capasity Trend no. tested
Rotation of NICD MLU TEAMS
Pre-deployment and on site training of NICD staff for Ebola diagnostic work in Freetown-Lakka, Sierra Leone
RT-PCR results in blood and buccal swabs
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1600
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No. tested No. positives
Total: blood & swabs Aug 2014 - Oct 2015
Period Tested No. pos. % pos
25Aug/Sept 1479 860 58.1
Oct 1174 491 41.8
Nov 1414 522 36.9
Dec 1448 348 24.0
Jan 921 93 10.1
Feb 387 34 8.8
March 438 24 5.5
April 130 2 1.5
May 79 1 1.3
June 143 1 0.7
July 130 1 0.8
August 242 2 0.8
September 296 0 0.0
October 169 0 0.0
Total 8450 2379 28.2
RT-PCR results in blood from suspected EVD cases
Blood: Aug 2014 - Oct 2015
Period Tested No. pos. % pos
25Aug/Sept 1215 757 62.3
Oct 644 292 45.3
Nov 686 308 44.9
Dec 845 266 31.5
Jan 549 79 14.4
Feb 201 26 12.9
March 152 20 13.2
April 50 2 4.0
May 49 0 0.0
June 50 1 2.0
July 61 1 1.6
August 138 2 1.4
September 18 0 0.0
October3 0 0.0
Total 4662 1754 37.6
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Blood Buccal swabs
RT-PCR results in buccal swabs
Swabs: Aug 2014 - Oct 2015
Period Tested No. pos. % pos
25Aug/Sept 264 103 39.0
Oct 530 199 37.5
Nov 728 214 29.4
Dec 603 82 13.6
Jan 372 14 3.8
Feb 186 8 4.3
March 286 4 1.4
April 80 0 0.0
May 30 1 3.3
June 93 0 0.0
July 69 0 0.0
August 104 0 0.0
September 277 0 0.0
October 166 0 0.0
Total 3788 625 16.5
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No. tested No. positives
RT-PCR percentage positivity in blood and buccal swabs
% positivity: Aug 2014-Oct 2015
Period Blood Swabs
25Aug/Sept 62.3 39.0
Oct 45.3 37.5
Nov 44.9 29.4
Dec 31.5 13.6
Jan 14.4 3.8
Feb 12.9 4.3
March 13.2 1.4
April 4.0 0.0
May 0.0 3.3
June 2.0 0.0
July 1.6 0.0
Aug 1.5 0.0
Sept 0.0 0.0
Oct 0.0 0.0
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Blood Buccal swabs
RT-PCR Training of SL staff and handover to SL MHS
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Blood Buccal swabs
Training of SL Staff
Handover and running of NICD-established EML by SL staff
Training of local staff in Ebola RT-PCR, biocontainment and logistic operational procedures.
Handover of the NICD EMDF to the Sierra Leone
Ministry of Health
Visit to Sierra Leone State House
NICD delegation represented by Prof. Janusz Paweska (middle right) and Dr Petrus Jansen van Vuren (right) accompanied by Dr Phumzile Mlambo-Ngcuka, a United Nations Under-Secretary-General and the Executive Director of UN Women, former Deputy President of South Africa from 2005 to 2008 (middle left) visiting the President of Sierra Leone, Dr Ernest Bai Koroma to reflect on the South African contributions in combating the EVD in Sierra Leone and specifically to discuss the handover of the operation of the NICD Ebola Molecular Diagnostic Facility to the Sierra Leone Ministry of Health and Sanitation, 23 March 2015.
Handover of the NICD EMDF to the Sierra Leone Ministry of Health & Sanitation
The official handover of the NICD EMDF to the Sierra Leone MoHS took place on 24 March 2014. The handover meeting was attended by the
representatives of the Sierra Leone Ministry of Health and Sanitation and the National Institute for Communicable Disease:
Deputy Minister of Health 1: Hon. Foday Sawi-Lahai
Deputy Chief Medical Officer 2: Dr Amara Jambai
Director Hospitals and Laboratory Services: Dr Matt-Lebby
National Manager Laboratory Services: Dr Abdul Kamara
Deputy Manager, National Laboratory Services: Ms Doris Harding
NICD: Prof Janusz Paweska, Dr Petrus Jansen van Vuren
EMDF Operational Manager: Mr Osman Conteh
EMDF Diagnostic Manager: Mr Dauda Sowa
EMDF Deputy Operational Manager: Mr Kelfala Konneh
EMDF Deputy Diagnostic Manager: Mr Idrissa L. Kamara
Handover of the NICD EMLU to SL MoHS – 24 March 2015
Documents reviewed, signed and issued
• Safety and Operational Manual (SOM)
• Signed-off training of local staff• Certification of competence in operation of
EMDL as per SOM• Equipment inventory list• Reagents and consumables inventory list• Laboratory specimen register• EVD investigation forms • Agreement on EMDL capacitation by NICD
No. DescriptionTrainee
sign
Trainer
sign Date
1 Technical and structural components
of the Facility (EMDF Operations and
Safety Manual)
2 Facility security and access
(EMDF Operations and Safety Manual)
3 Operational logistics
(EMDF Operations and Safety Manual)
4 Daily check of biocontainment devices
(Appendix 5.2)
5 Disinfectant preparation
6 Donning and doffing of PPE
7 Specimen reception and data logging
8 Preparation of lysis buffer
9 Hot processing of specimens,
aliquoting and storage of specimens
10 RNA extraction
11 RT-PCR master mix
12 Template and positive control addition
(Appendix 5.14)
Trainee
sign Trainer
sign Date
13 SmartCycler run set-up
14 Interpretation of results
15 Results recording
16 Updating of Ebola master database
17 Reporting of results
18 Storage and inventory of reagents and
consumables
19 Maintenance and equipment
verification
20 Decontamination of biocontainment
devices
21 Bio-waste management
22 Confirmation of reading EMDF
Operations and Safety Manual
Training checklist
EMDL capacitation by NICD
• NICD will continue to provide technical support until the termination of the EMDF operation.
• The technical support will include further guidance and ad hoc consultation via telecommunication and if required additional NICD staff deployment for on-site assistance.
• Supply of reagents, consumables, and PCR machines if still required.
• Support in maintenance and repairs of biosafety devices.
• After termination of the EMDF operation the CEZD-NICD staff will conduct a full decontamination of the building and assist in its re-designing for the TB Reference Laboratory function.
NICD EMLU Teams
1st (Chantel le Roux, Petrus Jansen van Vuren, Günther Meier,
Janusz Paweska) & the 2ed (Phumza Lekhuleni Ohaebosim,
Nadia Storm, Alan Kemp) team.
3rd team (Lisa Ming Sun, Desiree du Plessis, Dr Petrus Jansen
van Vuren, Orienka Hellferscee, and Busisiwe Mogodi) in the
office of the SA NICD Ebola Mobile in Freetown-Lakka, Sierra
Leone, November 2014.
The 3rd team (Busisiwe Mogodi, Orienka Hellferscee, Lisa Ming Sun, Desiree du
Plessis, Petrus Jansen van Vuren) & the 4th team (Günther Meier, Janusz
Paweska) team.
4th (Günther Meier, Janusz Paweska) & 5th team (Nishi Prabdial-Sing, Deidre
Greyling, Shayne Loubser, Cardia Fourie) in the office of the SA NICD Ebola
Mobile in Freetown-Lakka, Sierra Leone, December 2014.
The 3rd NICD Ebola Mobile Laboratory team
going home. Hand wash and temperature
check point at the sea coach water taxi station
on the bank of Sierra Leone River. 06
December, 2014. Freetown.
Team 4, 5 and 6. Team building exercise on Lakka beach. Proudly waving
the national South African flag on the scene of a beautiful sunset. Sierra
Leone, December 2014. SL staff: Ousman Conteh, Dauda Sowa and Kelfala
Knonneh and 6th team: Mark Goosen, Prabha Naido, Gunther Meier, Stewart
McColloch and Terence Scott.
7th Serisha Naicker, Alexandra Moerdyk, Wesly Dlamini and 8th (Pertus Hansen van Vuren, Janusz Paweska. SL Staff.
Lessons• Investments being made in South Africa in building diagnostics and
surveillance capacity for formidable pathogens, including establishing of BSL4 laboratory facility and the development of mobile deployment capacity are important contributions to South African efforts in being prepared to respond and control outbreaks of dangerous pathogens, and be able to support other African countries.
• Mobile deployment capacity should be supported by emergency budget which could be rapidly operationalized, available on the scene of outbreak, and be able to effectively address changing needs.
• Field laboratory capacity requires continuous training and adequate staffing.
• Field laboratory testing capacity require further improvements.
CONCLUSIONS• Laboratory confirmation of EVD suspected cases was essential in the successful control
of EVD outbreak and minimizing its further geographic spread.
• Deployment of the NICD EMDF in SL significantly contributed to international efforts in bringing the outbreak under control.
• The Western Urban Area of Sierra Leone, where the SA NICD EMDF operates, remained a hotspot of the EVD epidemic for months.
• During the EVD crisis in the capital of Sierra Leone, for weeks the NICD EMDF was the only Ebola diagnostic capacity to respond to overwhelming demand for EVD diagnosis.
• The Ebola field molecular laboratory became a valuable site for training of South African scientists on the scene of Ebola outbreak - a life experience.
• This initiative became a nucleus of a rolling deployment that has produced much-needed medical specialists trained in the field of highly dangerous pathogens and constitutes the largest Ebola outbreak response in the history of the NICD and South Africa on foreign soil.
CONCLUSIONS
• The national staff became fully integrated into all aspects of functions and operation of the laboratory. Capacity development and training of local staff enabled successful hand over of the laboratory to the Sierra Leone MoHS.
• The NICD/SA role in the provision of Ebola diagnostic services was acknowledged by Sierra Leone MoHS, African Union, UN agencies, including WHO, UNICEF, WFO, IAEA, CDC, many other national and international Ebola outbreak response partners, and the South African parliament itself.
• At the time of Public Health Emergency of International Concern, selflessness, compassion, solidarity, dedication ,professionalism and extraordinary efforts have further elevated the standing of the NICD as an important and unique public health resource in Africa.
Acknowledgements
• My Family
• NICD MLU Team’s Families & Friends
• CEZD staff, particularly SVPRL
• NICD/NHLS Management
• Ministry of Health RSA
• MoHS SL
• SL international medical staff
• WHO
• GOARN
• GDD
• IAEA
• CDC
• Roche
Thank you for your attention
Sierra Leone, Freetown-Lakka, NICD Mobile Lab, September 2014
