HEALTH SECRETARIE’S

COMMITTEE REPORT

STRENGTHENING AND EXPEDITING THE LABORATORY INVESTIGATIONS OF

COVID19 PATIENTS

MINISTRY OF HEALTH AND INDIGENOUS MEDICAL SERVICES

07TH APRIL, 2020

 EXECUTIVE SUMMARY

The Report on strengthening and expediting the laboratory investigations of Covid19 patients sums
up the work of the Health Secretary’s committee, a 5-member working group, which was appointed
by order of the Secretary of Health, on 3rd April 2020. Within the overall context of improving
laboratory facilities for testing of COVID19 patients, the Committee was mandated to perform a
full review of the testing facilities and propose a way forward.

PART ONE of the Report presents the detailed context of the appointment of the Committee, the
composition of the group and its Terms Of Reference. Most members of the Committee were local
experts with extensive knowledge of the local and international health systems.

PART TWO of the Report outlines the method of work of the Committee. It summarizes the depth
and breadth of analyses, debates, reviews, research and consultations that the Committee undertook
during the three days of its work.

PART THREE of the Report summarizes the situation analysis of the laboratory system and testing
facilities, focusing also on the technological context of public and private health system.

PART FOUR outlines the principles of recommendations that the Committee made to Ministry of
Health. The main recommendations hinge on:

1. Increasing the throughput of existing PCR machines under the Ministry of Health,
Universities and Private sector. Obtaining new PCR machines is not a priority at
present.
2. Continuous availability of adequate supplies with a good buffer stocks.
3. Streamline donations on requirements.
4. Multiple testing solutions including point of care PCR, Rapid testing of Ag and Ab,
Mobile screening with pooling of samples and ELISA testing should be established for
better control. Remote patients’ management system to be established.
5. Facilitation committee to be established for community screening, protocol
development and to support newly established PCR testing facilities.
6. Continuous relevant stakeholder consultation should be encouraged.

The annexes to the Report are a set of working documents that guided or informed some of the
recommendations of the Committee.
1
 TABLE OF CONTENTS

EXECUTIVE SUMMARY......................................................................................................... 1
INTRODUCTION ....................................................................................................................3
METHOD OF WORK ...............................................................................................................5
SUMMARY OF THE SITUATION ANALYSIS ......................................................................6
1. Current Process of Testing in Sri Lanka ........................................................................ 6
2. Ability of the RT – PCR testing under the Ministry of Health ...................................... 7
3. Availability of Infrastructure for Conventional PCR Labs ............................................. 7
Total No. of PCR Machines available in Sri Lanka ...............................................................................8
4. Adequacy of present PCR testing to combat the present COVID pandemic ................ 9
PCR capacity of the country at present ...................................................................................................9
5. Available options........................................................................................................... 10
6. Medical Laboratory Staff Requirement ........................................................................ 10
7. Other Equipment for Patient Management ................................................................. 10
Bio safety Cabinets (BSL 2 & BSL 3): .............................................................................................. 11
Other Equipment and Instruments: ...................................................................................................... 11
8. Availability of CT – Scanners for testing ...................................................................... 12
9. Donations of COVID -19 Equipment ........................................................................... 12
10. Process of Community Screening through Mobile Laboratories ............................. 12
MAIN RECOMMENDATIONS ............................................................................................ 15
Annex-1: List of key experts .................................................................................................................. 16
Annex-2: GeneXpert Installation Database in Sri Lanka .................................................................. 17
Annex-3: Capacity of Conventional PCR laboratories in Ministry of Health and Other Ministries
in Sri Lanka ............................................................................................................................................... 18
Annex 4: RT – PCR / PCR Machine availability in other Ministries .............................................. 21
Annex-5: POCT Real Time PCR to confirm COVID-19 ................................................................. 25
Annex-6: Rapid Test Kits ....................................................................................................................... 26
Annex-7: Comparison of available methods for COVID 19 diagnosis .......................................... 28
Annex-8: Available CT – Scanners in Institutions of Ministry of Health ....................................... 30
Annex-9: Flow chart showing the process of Community Screening through Mobile
Laboratories .............................................................................................................................................. 31
ENDORSEMENT OF THE REPORT BY THE COMMITTEE ........................................ 32

2
 Part one

INTRODUCTION

COVID19 is a rapidly spreading infection caused by a relatively infectious and resilient virus. Out of
the infected patients, only 20% show symptoms requiring hospital admissions. 80% of infected
patients remain in the population spreading the virus and being carriers of COVID19. Out of the 20%
of those who are admitted 5% will need Intensive Medical Care (ICU) and special attention would be
required to curb the spread of infection through these patients to others including the staff members.

The rapid transmission and the high rate of mortality and morbidity show the gravity of the condition.
Sri Lanka marked 178 confirmed cases as of today and 5 fatalities by 06.04.2020 which indicate a
significant growth in new cases. The World Health Organization recommends to perform testing in
every suspected case as an important part of the control.

The virus has a long incubation period with most patients presenting in asymptomatic status during
incubation. As a result, the infected people are spreading the virus without knowing it. Therefore, early
detection and treatment are of utmost importance and they are the universally accepted way to control
the disease spread.

Further, to reduce the transmission of the disease in the community, screening tests to identify the
COVID19 carriers is a must. Early detection will enable to reduce the escalating community spread
and create the possibility of early treatment.

Due to the novelties of the virus, and continues evolvement, the situation is leading to high level of
uncertainties with several unpredictable factors. Therefore, early detection is essential to reduce
the risk of spread. Increase testing could prevent a large influx of patients, burdening the health
system.

3
In April 03, 2020 (SH/CORONA/05/2020) by the secretary of Health, appointed 5-member working
committee “to assess and submit recommendations with regards to performing laboratory testing for
COVID19 infection”. The committee was officially called, was made up of the following members;

1. Dr. Amal Harsha De Silva Deputy Director General (Medical Service) II

(Chairman)
2. Mr. Sudath Rathnaweera Senior Assistant Secretary (Investigations)
3. Eng. Janapriya Karunaathilake Deputy Director General (Biomedical Engineering)
4. Dr. M. R. E. Bellana Director (Laboratory Services)
5. Mr. Ravi Kumudesh Medical Laboratory Technologist

The Terms Of Reference (TORS) of the Committee were as follows:

1. To assess the number of PCR machines under the Ministry of Health in various institutions
and report the capacity of the output of those machines.
2. To assess the possibility of mobilization of Polymerase Chain Reaction (PCR) machines
available under the higher education Ministry for testing of COVID 19 suspects.
3. To assess the capacity of the private sector in relation to PCR testing and other testing for
COVID 19 suspected cases and to report their willingness to participate and support the
testing mechanisms.
4. To report the number of PCR machines ordered so far through donations, other foreign
agencies and government funds and the probable date to initiate testing by those machines
and their capacity to help the situation.
5. To assess the role of CT Scanners in the testing of COVID19 from the available machines
and the expected purchases of CT Scan machines, assessing their usage in the near future,
staff requirements etc.
6. To assess the possibility of initiating and the requirement of a project for rapid testing in
the community for COVID 19.
7. To report the options for testing, in the instances when people travelling from high risk
areas to low risk areas without being subjected to quarantine procedures unnecessarily
(considering the incident at Lindula area).

4
 Part two

METHOD OF WORK

During its initial meeting with the Secretary of health, the Committee adopted the following method
of work.

1. To discuss strengths, weaknesses, opportunities and threats in relation to the laboratory testing
of COVID19 by looking at the government, university and private health system under key
areas, namely: availability of PCR machines; willingness for testing; human resources for testing
and capacity of testing etc.
2. To take note of existing strategies, guidelines, protocols and procedures for testing of
COVID19 within the health sector and to form an opinion as to their effectiveness, degree of
implementation and continuing relevance and by so doing propose a way forward.
3. To take note of international best practices, where applicable, and to discuss and agree on how
they might apply to the Sri Lankan context.
4. To contact and discuss on a wide range of issues with relevant Medical Specialists in the field
of combating COVID19, relevant professional colleges and relevant groups of health care
workers to know their opinions and obtain their suggestions on key issues. List of few names
are provided in Annex-1.
5. To reach decisions as to what might be the best way forward, for the Ministry of Health of Sri
Lanka, through evidence-based consensus, after all issues had been taken into consideration.
6. To agree on a list of deliverables, taking into consideration the given terms of reference and
also, what the committee, considered as other equally important deliverables.
7. To agree to attempt to finish the work requested of it within a three-day period as requested.

5
 Part Three

SUMMARY OF THE SITUATION ANALYSIS

After diagnosing the 1st COVID-19 patient, Sri Lanka has performed around 1600 COVID-19
detection tests as of 03rd April 2020. The country is still under curfew. In order to eliminate the virus
and to restore normalcy in the country, it may need to vastly expand the testing capacity. At least the
country must have the capacity to test 10,000 people a day in an emergency, considering the number
of people under quarantine (self and in quarantine centers).

1. Current Process of Testing in Sri Lanka

 The current practice in Sri Lanka to diagnose COVID-19 is to obtain a sample from respiratory
tract of a suspected case and refer to a PCR laboratory for PCR testing.
 Twenty-eight hospitals have been designated up to now by the Ministry of Health to treat
patients with symptoms.
 In the early days of the outbreak of the disease, the Medical Research Institute (MRI) in
Colombo has been quick to carry out Reverse Transcriptase RT-PCR tests and all the
specimens of the country have been sent to MRI.
 Similarly, the National Institute of Infectious Diseases (NIID) sent the specimens to the
research laboratory of the Sri Jayewardenepura University of the Ministry of Higher Education.
 After that, Corona RT-PCR testing was also started by virology laboratories established at
Karapitiya Teaching Hospital, National Hospital Kandy and Anuradhapura Teaching Hospital.
 In addition to the above laboratories, the following hospitals also have the facilities to conduct
COVID-19 tests.
I. National Institute of Infectious Diseases
II. Teaching Hospital, Ragama
III. Teaching Hospital Jaffna
IV. Teaching Hospital, Kegalle
V. Teaching Hospital, Ratnapura
 At the same time, the following hospitals and healthcare institutions attached to the Ministry
of Health are also identified as places with expertise, manpower and equipment to carry out
this test.
I. National Blood Centre
II. The National STD/ AIDS Control Program
6
 III. National Institute of Health Sciences, Kalutara
IV. Apeksha Hospital, Maharagama
V. National Institute of TB and Respiratory Disease centers

2. Ability of the RT – PCR testing under the Ministry of Health

 Currently there are around 54 PCR machines, under the Ministry of Health. Total number of
PCR machines available in the country is provided in Page 8.

 Page 9 provides PCR capacity of the country at present.

 It is also assumed that in the event of an emergency, the laboratory will be able to perform
three times more than currently performed number of tests in a 24/7 operation.
 This number of tests can be further increased if a “sample pool system” is practiced.
 Therefore, it is observed that there is no severe dearth of availability of RT-PCR machines in
Sri Lanka.
 Under the National Institute of TB and Respiratory Diseases program there are 36 PCR
machines around the country as presented in Page 8. They can be utilized for the current
situation as necessary, provided supply of cartridges could be ensured without interruptions.

3. Availability of Infrastructure for Conventional PCR Labs

 In the present context, it is vital to assess the availability of facilities/ resources in Sri Lanka to
conduct such tests to confirm the disease and provide necessary treatments as soon as possible.
 Sample delivering to the PCR centers is risky, due to the high possibility of contamination.
However, it must be further investigated to see whether the current PCR labs can be utilized
for COVID 19 testing.
 Annex-2, Annex-3 and Annex-4 provides details of the assessment carried out to identify the
availability of current infrastructure for testing in the Ministry of Health and other ministries.

7
 Total No. of PCR Machines available in Sri Lanka

Under the Ministry of Under the Ministry of Higher Private Sector

Health Education
Health Number University Number Institution Number
Institution
MRI 07 Colombo 05 Nawaloka 01
Hospitals PLC
NH Kandy 01 Peradeniya 10 Durdans 02
Hospital
TH Karapitiya 01 Sri 03 Asiri Group 04
Jayawardenapura
TH Anuradhapura 01 Open University 05 Lanka 02
(OUSL) Hospitals
CNTH 01 Sabaragamuwa 02 Gene Tech 06
TH Jaffna 01 Rajarata 05
Apeksha Hospital 01 Ruhuna 07
NIHS Kalutara 01 South Eastern 01
STD (AIDS) 01 Eastern 02
Control
Programme
Blood Bank 01 Uva Wellassa 02
IDH 01 Wayamba 02
Chest Disease 36 Kelaniya 01
Control
Programme
(Gene Expert)
Kegalle (POC) 01
Ragama (POC) 01
Sub Total 55 Sub Total 45 Sub Total 15
GRAND TOTAL 115
(Source: Personal communications)

8
4. Adequacy of present PCR testing to combat the present COVID pandemic
 According to the available evidences, 20% of people infected with the virus do not show any
symptoms (asymptomatic), 60% show only mild symptoms, and may not be hospitalized.1
 It is estimated that up to 80% of coronavirus cases can be cured without hospitalization but
the patient can be a carrier of the disease.
 This situation is confirmed by the disease history of some patients found in Sri Lanka. For
example, a pregnant mother in Kalutara and a 42-year-old man in Matara have been diagnosed
with Covid19 after the quarantine period.
 The highest number of cases reported in a single day in Sri Lanka, were reported for the
asymptomatic patients and this is the first time that COVID-19 diagnosis tests has been done
in people with no symptoms.
 Accordingly, a parallel mechanism for the PCR screening process should be implemented.
Because according to the prevailing system, most of the COVID-19 suspects are either in
quarantine centers or free at large in the community.

PCR capacity of the country at present

Current
Available Number Maximum with
Station Average Test
of PCR machines current facilities
No
MRI 7 120-150 150
NIID 1 20 40
NH Kandy 1 60 140
TH Anuradhapura 1 60 60
TH Karapitiya 1 25 60
TH Ragama 1 25 40
University Jaffna 1 20 40
DGH Ratnapura 1 0 30
Apeksha 1 0 25
Kalutara 1 0 0
TH Kegalle 1 0 0
(Source: College of Microbiologists)

1
https://www.weforum.org/agenda/2020/03/people-with-mild-or-no-symptoms-could-be-spreading-covid-19/
9
5. Available options
 Since the gold standard of COVID-19 is RT-PCR, it is necessary to increase the throughput
of tests using the available PCR testing facilities.
 While we preserve the present testing mechanism it is also suggested to find more options to
reach the community.
 The committee paid close attention to the situation. Further it explored the possibility of using
the following options available in Sri Lanka.
I. Point of Care RT PCR Testing (Annex-5)
II. Rapid antigen and antibody Test Kits (Annex-6)
 A comparison of the advantages and disadvantages of existing technologies is included in this
report (Annex-7).
 When all these technologies are considered individually, there is a possibility missing certain
number of patients.
 Accordingly, it is observed that the best way to overcome these limitations is to use all methods
of testing in a timely manner.

6. Medical Laboratory Staff Requirement

 Clinical Virologists, Bacteriologists, Medical Laboratory Technologists and support staffs are
required to perform these tests.
 Since there are trained and qualified Medical Laboratory staffs in each hospital and healthcare
institution to perform the corporate RT-PCR testing, there are no constraints to maintain that
service for 24 hours.
 Also, other laboratory tests for other conditions are very low at the moment so there is no
constraint on conducting field tests or obtaining the required manpower.

7. Other Equipment for Patient Management

 After identification of the COVID 19 patient, the patient has to be admitted to the nearest
hospital which has a dedicated COVID 19 treatment ward.
 To save lives of the patients and to reduce the mortality rate it is vital to facilitate the hospitals
with patient management infrastructure.
 Biochemical Investigations:
i. The capability to test the below tests has a wide chance of protecting the patient without
letting to severe or critical condition.

10
 a. PCT (Procalcitonin)
b. D-Dimer
ii. In the previous confirmed cases some of the patients has died or led to very critical
condition, due to non-recognition of the type of pneumonia. i.e., whether it is caused due
to a viral infection or bacterial infection. There are 2 type of patients.
o Patients with pneumonia for a bacterial infection with Covid19 symptoms
o Covid19 patients who get pneumonia due to a bacterial infection at the recovery
stage

Hence for the differentiation of bacterial and viral infection, PCT test is very important.

 Bio safety Cabinets (BSL 2 & BSL 3):

i. Also, since the contamination of the disease through air is now a major issue, not only
the laboratories but other high risk facilities such as the ICUs, HDUs and other areas
also need to have such units to ensure the health and safety of all the front line
healthcare staff.
ii. Therefore, we highly recommend that swift action be taken to strengthen the infra-
structure of the high risk hospital environment by installing appropriate technologies
such as laminar flow type air disinfection units and providing them the front line
healthcare workers with the much needed personal protection equipment and
accessories adequately as at this moment they are the most vital resource that can fight
this pandemic in the weeks to come when the situation escalates.
iii. Therefore, it is vital to have a medical grade laminar flow type air disinfection unit
installed in the bus/ facility to confirm that the ambient air within the laboratory is
sterile and conducive for long term exposure.
iv. This is vital especially taking in to account the risk of contamination by air as confirmed
by the WHO and through the many cases reported from other countries.
v. Also, it is vital that a mobile BSL2 or BSL3 type of a Bio Safety cabinet be also installed
in the facility.

 Other Equipment and Instruments:

i. Following instruments and equipment are important in safe and efficient laboratory
service.
o Biochemistry analyzer which can be kept inside safety cabinet
o Five-part complete blood count/ Full Blood Count analyzer

11
 o Centrifuge
o Portable Air Sterilizer

8. Availability of CT – Scanners for testing

 The availability of CT scan in Sri Lanka is provided in Annex-8.
 Ordering and supplying more CT scanners may be time consuming and maybe require more
resources.
 However, considering the role of COVID-19 treatment centers – NIID, Homagama BH,
Mulleriyawa BH need to be provided with CT- scanners immediately considering the role
that they are already performing as Covid -19 treatment centers.
 Also, mobile CT is also an appropriate option which should be considered additionally.

9. Donations of COVID -19 Equipment

 At the moment donations are received in a less organized manner. These donations should be
further streamlined.
 A list of equipment required for Covid-19 testing need to be prepared and made available in
the ministry and the donations should be accepted only if local agent is available for
maintenance and repairs and continuous supply of consumables and reagents.

10. Process of Community Screening through Mobile Laboratories

 Identify the population clusters/ groups for screening
i. Quarantine Centers
ii. Traced contacts of the confirmed cases
iii. Community groups as and when recognized
iv. Sample groups from the highly vulnerable districts
v. Drive through Screening centers for people crossing the districts
vi. People who are willing to do the tests
 For cases such as the Lindula incidence, the solution could be proposed as making available
testing methods at community level.
 Categorize the sample for PCR testing and Rapid testing

12
 i. Patients presenting with fever or new onset of cough or difficulty breathing with travel
history or contact with travelled person or confirmed COVID 19 patient (Probable
case)
ii. Persons travelled outside of Sri Lanka in the past 14 days (Probable case)
iii. Patients presenting with fever or new onset of cough or difficulty breathing with travel
history or no contact with travelled person or confirmed COVID 19 patient
iv. Persons who had close contact with a confirmed or probable case of COVID-19
v. Persons have close contact with anyone with acute respiratory illness in the past 14
days
vi. Persons with no symptoms or contact or travelled history (No testing required)
 Screening will be carried out using rapid COVID 19 Ab test kit and rapid PCR test kit.
 This screening is focused on persons with no symptoms with close contact history with
COVID 19 confirmed patients or travelled persons, persons with symptoms without contact
history with COVID 19 confirmed patients or travelled persons and persons with travel
history.
 At present most of these categories are under quarantine process or self-isolation.
 COVID 19 Ab test kit is used for the persons with history more than 7 days of contact,
travelled or symptoms and rapid PCR is used for screeners with less than 7 days of symptoms
or contact or travelled history.
 This process enhances early detection and avoids unnecessary isolation and quarantine process.
Further this process can screen the population faster and reliably. Following graphic
presentation shows the process of screening with rapid test kits. Flow chart summarize the
screening process is provided in Annex-9.

13
 Community Screening Process Graphical Presentation
Repeat the
Test

Yes NO

NO
01 Registration & 02 03 Specimen 04 Testing at Result Positive
Questionnaire Examination Collection the patient site

Yes

POCT PCR and Rapid Tests

Test Done in
PCR

14
 Part four

MAIN RECOMMENDATIONS

1. Increasing the throughput of existing PCR machines under the Ministry of Health and
redistributing them to testing centers with supervision
2. Private sector PCR machines should be utilized for COVID-19 testing under the protocols
of the Ministry of Health.
3. Utilizing the university PCR machines specially during patient escalation
4. Purchasing of new PCR machines is not a priority at present.
5. Continuous availability of cartridges, reagents, VTM, swabs, test kits, consumables and
PPEs should be ensured with adequate buffer stocks.
6. Accepting donations and new purchases should be streamlined as per the requirement.
7. Protocols should be established for screening of patients, community members, high-risk
front-line employees and people in quarantine etc.
8. Remote patients’ management system to be established.
9. Multiple testing solutions including point of care PCR, Rapid testing of Ag and Ab, Mobile
screening and ELISA testing should be established. Pooling of samples for screening.
10. Facilitation committee to be established for community screening and to support newly
established PCR testing facilities.
11. Continuous relevant stakeholder consultation should be encouraged.

15
 Annex-1: List of key experts

1. Prof. Jennifer Perera Dean, Faulty of Medicine, Colombo

2. Prof. Indika Karunathilaka President SLMA
3. Prof. Sujeewa Amarasena Vice Chancellor, University of Ruhuna
4. Prof. Asiri Abeygunawaradana Dean, Faulty of Medicine, University of Peradeniya
5. Prof. Wasantha Devasiri Dean, Faulty of Medicine, Karapitiya
6. Prof. Sanath Lamabadusuriya Emiretus Professor, Paediatrics
7. Prof. Vajira Dissanayaka Professor of Genetics, Faulty of Medicine, Colombo
8. Prof. Neelika Malavige Director Center of Dengue, UoSJ
9. Prof. Kumar Mendis Family Medicine, University of Kelaniya
10. Dr. Shirani Chandrasiri President College of Microbiologist
11. Dr. Sapumal Dhanapala President College of CCP
12. Dr. Jude Jayamaha Virologist, MRI
13. Dr. Kapila Jayaratne Consultant Community Physician
14. Dr. Dulmini Kumarasinghe Virologist, MRI
15. Dr. Sujatha Pathirage Microbiologist, MRI
16. Dr. Nadeeka Janage Virologist, MRI
17. Dr. Geethani Galagoda Virologist, Lanka Hospital
18. Dr. Veranja Liyanapathirana Microbiologist, FoM, University of Peradeniya
19. Dr. Nishali Ekanayaka Histo Pathologist, MRI
20. Dr. Muditha Abeykoon Microbiologist, BH Kegalle
21. Dr. Gaya Katulanda Chemical Pathologist, NHSL
22. Dr. (Mrs) Susie Perera DDG(PHS)I
23. Dr. (Mrs) Paba Palihawadana DDG (PHS)II
24. Dr. Sudath Samaraweera Chief Epidemiologist
25. Dr. Jayaruwan Bandara Director MRI
26. Dr. Kithsiri Edirisinghe CEO, IIHS
27. Dr. Sunil Rathnapreya Secretary of the Private Hospitals Association
28. Dr. Ravi Rannaliya Director, IHP
29. Dr. C.L.K.Atapathtu Assistant Registrar, SLMC
30. Ms. Prabhani Pushpamalie Secretary, Collage of Medical Laboratory Science SL
31. Mr. Danushka Nalinda Medical Laboratory Technologist

16
 Annex-2: GeneXpert Installation Database in Sri Lanka
No. Name of the Hospital Location
Under TB Control Programme
1 NTRL, Welisara Microbiology Lab
2 NTRL, Welisara Microbiology Lab
3 The National Hospital of Sri Lanka Microbiology Lab
4 Teaching Hospital, Kurunegala Microbiology Lab
5 Teaching Hospital, Batticaloa Microbiology Lab
6 Teaching Hospital, Anuradhapura Microbiology Lab
7 Provincial General Hospital, Badulla Microbiology Lab
8 Teaching Hospital, Karapitiya Microbiology Lab
9 Provincial General Hospital, Rathnapura Microbiology Lab
10 District Chest Clinic, Kandy Chest Clinic
11 Chest Clinic, Jaffna Chest Clinic
12 TH Kegalle Microbiology Lab
13 National Institute of Health Science, Kalutara Microbiology Lab
14 LRH Microbiology Lab
15 Prison Hospital, Welikada Microbiology Lab
16 District General Hospital - Hambantota Microbiology Lab
17 District General Hospital - Nuwaraeliya Microbiology Lab
18 Ashfroff Memorial Hospital - Kalmunai Microbiology Lab
19 District General Hospital - Polonnaruwa Microbiology Lab
20 District General Hospital - Ampara Microbiology Lab
21 District General Hospital - Monaragala Microbiology Lab
22 Central Chest Clinic - Colombo Microbiology Lab
23 Sub Chest Clinic – Colombo South Teaching Hospital / Kalubowila Microbiology Lab
24 District General Hospital - Matara Microbiology Lab
25 District General Hospital - Matale Microbiology Lab
26 Base Hospital - Puttalam Microbiology Lab
27 District General Hospital - Trincomalee Microbiology Lab
28 District General Hospital - Mullativu Chest Clinic
29 District General Hospital - Vavuniya Microbiology Lab
30 District General Hospital - Mannar Microbiology Lab
31 Colombo Municipal Council Microbiology Lab
Under National STD/AIDS Control Programme
32 National STD/AIDS Control Programme (NSACP) PCR Laboratory
33 STD Clinic, Anuradhapura STD Clinic
34 STD Clinic, Mahamodara STD Clinic
Other
35 Apeksha Hospital,Maharagama Haematology Lab
36 Sri Jayawardenapura General Hospital Microbiology Lab
(Source: Ministry of Health)

17
 Annex-3: Capacity of Conventional PCR laboratories in Ministry of Health and Other Ministries in Sri Lanka
No District Population High risk No of Availability of Available Is this Current Maximum
District patients PCR institute institute Average number of
Yes/ found as at laboratory already Test No tests that
No 04.04.2020 Yes/ No dedicated can be run
for in a day
COVID19 with
patients current
facilities
1. Jaffna 583,882 Yes TH Jaffna Teaching Yes
RT PCR is hospital Jaffna
available. But no
Biosafety
cabinet,
Refrigerated
Centrifuge, PCR
hood or
Freezers
available.
Director THJ
has made
request for
them.
University of University of No 20 40
Jaffna Jaffna
Has RT PCR
lab. Planning to
carry out PCR
testing for TH
Jaffna. ?Already
initiated Will
continue until
TH Jaffna
facility is
established
2. Kilinochchi 113,510
3. Mannar 99,570
4. Mullaitivu 92,238
5. Vavuniya 172,115
6. Puttalam 762,396 Yes RT PCR at North Colombo Yes 25 40
NCTH. Teaching
Conducts Hospital
testing
7. Kurunegala 1,618,465
8. Gampaha 2,304,833 Yes
9. Colombo 2,324,349 Yes Department of Medical 120-150 150
Virology Research
Conducts Institute
testing
RT PCR National 20 40
available Institute of
Conducts Infectious
testing disease, Angoda
RT PCR University of Sri 80
available J’Pura
Conducts
testing
RT PCR Apeksha hospital No 0 25
available
10. Kaluthara 1,221,948 Yes
11. Anuradhapura 860,575 RT PCR TH Yes 60 60
available Anuradhapura
Conducts
testing
12. Polonnaruwa 406,088
13. Matale 484,531
14. Kandy 1,375,382 RT PCR National 60 140
available Hospital Kandy
Conducts
testing
15. Nuwara Eliya 711,644

19
16. Kegalle 840,648
17. Ratnapura 1,088,007 ?RT PCR TH Rathnapura 0 25
Borrowed from
Sabaragamuwa
University. Also
with the help of
the TB
laboratory of the
hospital. PCR
testing initiated.
18. Trincomalee 379,541
19. Batticolao 526,567
20. Ampara 649,402
21. Badulla 815,402
22. Monaragala 451,058
23. Hambanthota 599,903
24. Matara 814,048
25. Galle 1,063,334 RT PCR TH Karapitiya 25 60
available

(Source: Laboratory services, Ministry of Health)

20
 Annex 4: RT – PCR / PCR Machine availability in other Ministries
RT- PCR PCR Bio safety PCR hood Incinerator Workstation Trained staff
Cabinet /
Autoclave
1. Ministry of Higher
education
a. University of Colombo 5 Yes
b. University of 10 Yes
Peradeniya
c. University of SJP ? Available 7. Fully Yes
Utilized
d. University of Kelaniya 1 Yes
e. University of 1 Yes
Moratuwa
f. University of Jaffna ? Available Yes
.Utilized
g. Open University 5 Yes
h. University of 2 Yes
Sabaragamuwa
i. University of 2 Yes
Wayamba
j. Eastern University 2 Yes
k. South Eastern 1 Yes
University
l. Uva 2 Yes
m. Ruhuna 7 Yes
Sub total 51

2. Ministry of rural 1 RT - PCR Yes Yes Incinerator RNA Have trained

Economy: USDA - extraction staff
Veterinary Research 2008 room
Institute – Gannoruwa PCR room
21
 Dr.Kasagala For avian Mater mix With well-
0713471072 influenza room established
Has – 80 system.
Dr.K.D.Ariyapla DG, refrigerators Already
DAPH 0714419863 as well working with
viruses, so
aware with
BS
3. Ministry of Rural Professor
Economy has already
Faculty of Veterinary informed
Science Army Chief
Prof Jayantha regarding
Rajapakse 0714446715 their
availability.
4. Agriculture sector: 2 RT-PCR yes No Have a fully Yes.
Faculty of Agriculture- machines incinerator equipped
Peradeniya Each 96 but have Biotechnology Most willing
Prof. Pushpakumara samples per autoclaves laboratory to carry out
Dean- Faculty of cycle the testing
Agriculture
0714933591 1 more
smaller RT
PCT
5. Antifilariasis campaign 1 RT PCR yes Yes Yes Yes
DD– Dr. Priyadarshani
Samarasinghe
0714413318
Ms. Lakmali -
0712539878

6. Institute of Have several Yes

Biochemistry and RT PCR.

22
 Molecular Biology and Information
Biotechnology provided to
Director, Prof. Vice
Shiroma Handunetti Chancellor,
,0715352597 Uni.
Colombo –
Prof.
Chandrika
Wijeratne
7. Ministry of Power and New 2 RT Yes
Energy PCR with
Director General other
Sri Lanka Atomic necessary
Energy Board equipment
National RCA purchased
Representative to for MoH.
IAEA Awaiting Air
flight to get
them down
to SL. Will
arrive within
1-2 days.
Hon.
Minister
officially
informed
8. Ministry of Higher A list of Yes
Education PCR
Professor Sampath machines
Amaratunga, available at
Chairman, UGC each
0714191558 University
was given by

23
 sir.
Annexure 1

All together
57 machines
9. Navinna Ayurveda Laboratory
Research Center facility
Dr. Wasantha available.
0718129005 Already a
meeting
planned
with MoH
and UGC
officials in
this regard.

24
 Annex-5: POCT Real Time PCR to confirm COVID-19

This is one of its PCR systems to do RT PCR at any location without confining to the high-end
Laboratory. Since this product is specially designed for Point of Care Testing purpose, the reagents,
consumables required from the point of specimen collection to the test result comes as a total package.
Hence different steps can be performed individually.

Similarly, the virus transport media used for this test will be in the same package, and specially designed
Virus inactivation Media reduce the possibility of contamination. It is a significant advantage in field
inspections and can save money by minimizing the specific safety precautions.

The testing time can be limited to one hour and this machine can test for antigen - Ag.

Comparison of Conventional PCR laborotory and the POCT PCR Machine

Currently in Sri Lanka, this technology is used for Dengue & TB, and now has the capability of
COVID-19 testing. This product is recognized and recommended by the Indian government for
COVID-19 community screening. Refer the attachment 1. Performance Evaluation Report by Indian
Council of Medical Research.
 Annex-6: Rapid Test Kits

The test often involves testing for antibody - Ab, which uses blood as the specimen. A simple
appliance for testing is commercially manufactured and results can be observed in as little as 20
minutes. However, use of rapid test kits parallel to the POCT PCR tests shortens the diagnosis
window period, will be helpful in early detection of COVID 19 patients.

It is recommended to perform the test only after seven days after the virus infected, as this will be
tested by antibodies.

Figure 1- Daily variation of Ab and Ag levels of COVID19 patients

26
 Figure 2 - Laboratory diagnosis of COVID-19

In the same time, it has to be noted that since the rapid tests for the particular corona virus is very
new to the market, and the test sensitivity and accuracy of the tests are low, compared to PCR
technology. Hence if the test result indicates a negative, it is recommended to perform the same test
in another 5 days. If the result is positive, recommended to direct the patient in to a COVID 19
dedicated ward.

27
 Annex-7: Comparison of available methods for COVID 19 diagnosis

RT PCR POCT PCR IgM/IgG Rapid

Turnaround Time 6 Hrs
Operation Organized Laboratory
Expensive utility cost
for equipment’s and
infrastructure
Complicated
operation System,
BSL Level Labs,
Three Departments,
Maximum PPE
Test
1 Hr 20 Mts
Can use at Field Special Facilities
Minimum
Low utility cost Minimum Utility cost
Less complicated Simple operation
operation System system
BSL Level labs not Minimum PPE
required, Measures should be
Can use small space, taken to prevent
even Inside Vehicle abuse
Minimum PPE

Transport/Storage Need to be transferred Can be done at patient Can be done at patient

to central lab & Batch site, test can be done site, test can be done
analysis by singles by singles

Clinical Value Important 100% similar to RT ?

PCR
Infectivity Very High Comparatively very Very High
low
Sensitivity Good Good Being evaluated
Specificity Good Good Being evaluated
Results Very good Very good Being evaluated
(By experts at MRI)

28
Clinical Significance of the Test Results

29
 Annex-8: Available CT – Scanners in Institutions of Ministry of Health

No. Date of installed Hospital Location

1 1/28/2016 Trincomalee DGH CT Room
2 1/28/2016 Welisara NHRD CT Room
3 1/13/2015 Peradeniya TH CT Room
4 1/13/2015 Kegalle DGH CT Room
5 1/13/2015 Monaragala DGH CT Room
6 11/16/2011 Polonnaruwa DGH CT Room
7 7/28/2007 Matara GH CT Room
8 4/25/2014 Ragama NCTH CT Room
9 4/25/2014 Kalubowila CSTH CT Room
10 4/25/14 Peradeniya SBSCH CT Room
11 4/25/14 Rathnapura PGH CT Room
12 4/25/14 Kurunegala PGH CT Room
13 4/25/14 Hambanthota DGH CT Room
14 2/15/08 Anuradhapura TH CT Room
15 8/24/16 Lady Ridgeway Hospital CT Room
16 7/1/10 National Hospital CT Room
17 10/9/07 Batticaloa TH CT Room
18 7/13/05 Ampara DGH CT Room
19 8/10/11 Jaffna TH CT Room
20 5/10/07 Karapitiya TH CT Room
21 1/1/00 Badulla PGH CT Room
22 1/1/00 Maharagama AH CT Room
23 5/10/06 Kandy TH Main X-Ray Unit
24 7/24/17 Chilaw DGH CT Room
25 12/20/17 Horana BH CT Room
26 7/17/17 Karapitiya TH CT Room
27 6/7/18 Anuradhapura TH CT Room
28 8/16/06 Kalutara DGH CT Room
29 8/7/99 National Hospital CT Room
30 1/15/01 Karapitiya TH CT Room
31 8/24/16 Lady Ridgeway Hospital XRay Dept.
32 1/1/00 National Hospital HDU

30
Annex-9: Flow chart showing the process of Community Screening through Mobile
Laboratories

Social groups
1. Patients presenting with fever or new onset of cough or difficulty breathing with travel history or contact
with travelled person or confirmed COVID 19 patient (Probable case)
2. Persons travelled outside of Sri Lanka in the past 14 days (Probable case)
3. Patients presenting with fever or new onset of cough or difficulty breathing with no travel history or no
contact with travelled person or confirmed COVID 19 patient
4. Persons who had close contact with a confirmed or probable case of COVID-19
5. Persons have close contact with anyone with acute respiratory illness in the past 14 days

Persons travelled outside of Sri Lanka in the past Patients presenting with fever
14 days (Probable case) or new onset of cough or
Patients presenting with fever or new onset of difficulty breathing with travel
cough or difficulty breathing with no travel history history or contact with
or no contact with travelled person or confirmed travelled person or confirmed
COVID 19 patient COVID 19 patient (Probable
Persons who had close contact with a confirmed case)
or probable case of COVID-19
Persons have close contact with anyone with Rapid PCR
acute respiratory illness in the past 14 days or/and RT PCR
at testing
Centres

> 7 days < 7 days

COVID 19 Ab Test Rapid PCR Positive Negative

Persons travelled outside of Sri Lanka in the past 14
days (Probable case)
Persons who had close contact with a confirmed or
probable case of COVID-19
Persons have close contact with anyone with acute
respiratory illness in the past 14 days
Patients presenting with fever or new onset
of cough or difficulty breathing with no travel
history or no contact with travelled person or
confirmed COVID 19 patient
Persons who had close contact with a
confirmed or probable case of COVID-19
Persons have close contact with anyone with Isolation under
acute respiratory illness in the past 14 days obdservation and
repeat RT PCR

Positive Negative

Positive Negative Positive Negative

Repeat test after 14

COVID 19 Patient
days
Conrim with RT PCR
Observe Clinical COVID 19 patient
(Optional) Negative for COVID 19
symptoms Confimed COVID 19
Confirm with RT PCR Self Isolation No Risk
(Optional) patient

Negative with no Negative with clinical

Positive
clinical symptoms symptoms

Negative for COVID 19

Isolate for 21 days
No Risk

31
 ENDORSEMENT OF THE REPORT BY THE COMMITTEE

Name Signature

Dr. Amal Harsha De Silva

Mr. Sudath Rathnaweera

Eng. Janapriya Karunaathilake

Dr. M. R. E. Bellana

Mr. Ravi Kumudesh

32