Analytical Chemistry Laboratory - Argonne National Laboratory
National Health Laboratory Services
30
National Health Laboratory Services PORTFOLIO COMMITTEE PRESENTATION DR KAMY CHETTY JUNE 2020
Transcript of National Health Laboratory Services
National Health Laboratory ServicesPORTFOLIO COMMITTEE PRESENTATION
D R K A M Y C H E T T Y
J U N E 2 0 2 0
About NHLS
The National Health Laboratory Service (NHLS) is a schedule 3A Public Entity which
was established in 2001 by an Act of Parliament to provide diagnostic pathology
laboratory services to the National and Provincial Health Departments.
South Africa’s largest public health laboratory service with 233 laboratories in nine
provinces
The NHLS Divisions include:
National Institute for Communicable Diseases (NICD): An institute of the NHLS responsible for surveillance and monitoring of communicable diseases
National Institute for Occupational Health (NIOH): NIOH is an NHLS institute which investigates occupational diseases and provides a range of services to support occupational health
South African Vaccine Producers
Introduction
As of 8 June 2020, the NHLS has conducted 492 704 tests.
The NHLS has increased the number of test done each month with a massive
increase in the number of tests being performed during the month of May
where the figures more than doubled between April and May.
In the first week of June 105 023 tests were done. Month Tests Done
February 276
March 6 341
April 94 203
May 232 862
1-7 June 105 023
Number of Tests per Province by NHLS
Data as at 08 June 2020
Province Name Positive Inconclusive Negative Total Cases Positivity Rate
WESTERN CAPE 21 232 814 92 335 114 381 18,56%
EASTERN CAPE 3 999 150 69 915 74 064 5,40%
GAUTENG 1 846 138 149 980 151 964 1,21%
KWAZULU-NATAL 1 509 36 84 292 85 837 1,76%
FREE STATE 214 10 35 306 35 530 0,60%
NORTH WEST 100 1 4 021 4 122 2,43%
MPUMALANGA 76 4 7 862 7 942 0,96%
NORTHERN CAPE 76 13 8 966 9 055 0,84%
LIMPOPO 24 1 9 534 9 559 0,25%
UNKNOWN 5 4 241 250 2,00%
Total 29 081 1 171 462 452 492 704 5,90%
Data as at 08 June 2020
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 7 0 2 0 5 3 1 7 8 2 9 7 15 8 14211124262721241522322742282033533727466553107507673806992135115234216100141189237231196222307377335247150298495375339445509353369503600647645480444545402605666476411531589836926827610679
1,7271,4181,5521,3971,0151,3981,246
19122524213114 2 5 1210 7 1411 7 33 1 2 33 6 5 20 9 2819549520135366631532477921722302912661931042364303545966297265734695659138291,243
8657931,2431,175
1,5811,4661,7301,6461,8401,6261,8812,660
3,2403,014
4,658
3,6073,278
6,020
5,091
3,8773,988
7,5397,2106,373
5,2805,837
8,985
11,494
6,912
5,0014,268
5,929
8,1048,6649,166
7,8318,161
7,2417,077
9,348
11,370
9,730
7,3457,004
7,7636,695
7,830
10,1559,843
6,296
8,878
9,8699,0088,785
9,208
10,507
8,060
10,132
16,746
12,856
15,78415,209
13,379
11,421
13,008
0 0 3 0 1 0 1 1 0 2 1 1 0 1 0 0 0 0 1 0 0 0 0 0 1 1 0 0 0 1 0 1 0 1 2 0 0 3 1 0 0 0 01 3
2 1 2 0 1 33 1
30 0
0 12 0
0 011
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20,0002
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Daily Count Total COVID-19 Tests in the NHLS Labs
Positive Negative Inconclusive
Number of Tests per Week by NHLS Data as at 08 June 2020
Week No Week Start Date Week End Date Positive Negative Inconclusive Total Tests
5 2020-01-27 2020-02-02 0 19 0 19
6 2020-02-03 2020-02-09 0 82 4 86
7 2020-02-10 2020-02-16 0 64 4 68
8 2020-02-17 2020-02-23 0 42 3 45
9 2020-02-24 2020-03-01 0 82 1 83
10 2020-03-02 2020-03-08 9 230 2 241
11 2020-03-09 2020-03-15 18 365 3 386
12 2020-03-16 2020-03-22 63 1 321 6 1 390
13 2020-03-23 2020-03-29 154 3 075 9 3 238
14 2020-03-30 2020-04-05 186 5 457 11 5 654
15 2020-04-06 2020-04-12 314 9 634 3 9 951
16 2020-04-13 2020-04-19 547 18 919 27 19 493
17 2020-04-20 2020-04-26 1 130 33 400 62 34 592
18 2020-04-27 2020-05-03 1 905 52 091 25 54 021
19 2020-05-04 2020-05-10 2 349 48 963 47 51 359
20 2020-05-11 2020-05-17 3 626 60 272 159 64 057
21 2020-05-18 2020-05-24 3 618 55 586 308 59 512
22 2020-05-25 2020-05-31 4 730 64 315 140 69 185
23 2020-06-01 2020-06-07 9 186 95 527 310 105 023
24 2020-06-08 2020-06-14 1 246 13 008 47 14 301
Total 29 081 462 452 1 171 492 704
PROCESS FOR TESTING
Image Source: American Society for Microbiology
Basic Lab Process
Preparation of sample (placing swab
in media, vortex swab, pipette for
extraction)
Extraction of RNA. Reverse transcription
of DNA
Thermo Cycler (PCR). Amplification of
DNA.
n
Cluster 1Separate Extraction and PCR equipment Nimbus Seegene 7 BioRad CFX 96 DX 14(Open Platforms)
EasyMag 10 Thermocyclers
Cluster 2Integrated Extraction and PCR Roche Cobas 6800/8800 14(Automated Closed Platforms)
GeneXpert 277*
Abbott M2000 4
Cluster 3Awaiting Arrival/Installation of Equipment King Fisher Quan Studio
Hain Hain PCR
Hamilton
Current Testing Capacity
Separate extraction and PCR platforms:
Use Nimbus (automated) and EasyMag (Semi-automated). Once extracted, specimen is transferred to PCR machine.
BioRad with different kits ~5,000 tests in 24hrs
Fully automated integrated systems:
Roche Cobas C6680/8800 ~15,000 in 24hrs
GeneXpert 325 instruments ~ 15,000 in 24hrs
Capacity at the NHLS Virology Laboratories as at end May
The PCR equipment that the NHLS has in the provinces
Province CFX 96 DX Cobas 6800/8800 GeneXpert Abbott M2000
Eastern Cape 3 1 44 0
Free State 1 2 18 1
Gauteng 4 4 40 1
KwaZulu Natal 1 2 75 1
Limpopo 0 2 35 0
Mpumalanga 0 2 19 0
North West 0 0 17 0
Western Cape 5 1 29 1
TOTAL 14 14 277* 4
*Excludes Northern Cape
Capacity at the NHLS Virology Laboratories as at end May
The Extraction equipment that the NHLS has in the provinces
Province Nimbus EasyMAG MagnaPure
Eastern Cape 2
Free State 1 1
Gauteng 3 2 1
KwaZulu Natal 2
Limpopo
Mpumalanga
North West
Western Cape 1 5
TOTAL 7 10 1
Available PCR Test Kits Weekly Supply
Open Platforms (needs separate extraction)
Low Throughput Machine High Throughput Integrated System
Seegene 240 134 Abbott M2000 30 000 GeneXpert 10 000
Roche Lite Mix 3 045 Roche Cobas 10 000
Thermofisher 226 960
IDT 152 713
SanSure 4 200
SUB TOTAL 627 052 30 000 *20 000
TOTAL 677 052
* This is where huge quantities are required.
Available Extraction Test Kits Weekly Supply
Extraction Platforms
MagnaPure 7 294
EasyMAG 2 763
Nimbus 5 390
Total 15 447
* Extraction supply limits the PCR process
Unprocessed Specimens
As of 09/05/20
As of 14/05/20
As of 21/05/20
As of 25/05/20
As of 28/05/20
As of 04/06/20
As of 09/06/20
Total 49 550 58 930 101 000 96 480 83 767 81 069 70 219
* Unprocessed Specimens Definition - Older than 3 days from registration at the laboratory* A reasonable time to clear a sample through the laboratory, if all reagents (test kits) and resources
are available is 48-72 hours.
Backlogs of Unprocessed Specimens per Province
Region 09/05/20 14/05/20 21/05/20 25/05/20 28/05/20 04/06/20 09/06/20
Eastern Cape 8 350 7 000 23 000 22 802 21 000 21 355 21 953
Free State 200 4 300 6 000 8 800 1 767
Gauteng 15 000 13 000 23 000 24 076 24 000 28 395 23 000KwaZulu-Natal 12 000 18 000 28 000 22 802 22 000 20 751 18 000Western Cape 14 000 16 630 21 000 18 000 15 000 10 568 7 266
Total 49 550 58 930 101 000 96 480 83 767 81 069 70 219
Testing Priorities
The Testing Strategy is prioritised according to the following categories and will be
identified on the request form through colour coding:
Category 1: Prioritise testing for those with a medical need and for clinical diagnosis
Category 2: Testing for High Risk individuals
Category 3: Testing of critical frontline workers and essential service personnel
Category 4: Surveillance
Category 5: Screening in targeted hotspots
To prepare for lack of test kits and for Surge: Additional Equipment for NHLS Virology Laboratories
Instruments Type of Instrument Current Additional Total
BioRad CFX96 PCR 14 12 26
QuanStudio PCR 0 7 7
HAIN PCR PCR 0 4 4
GeneXpert Automated high throughput 277 3 280
Cobus Automated high throughput 14 1 15
Hamilton Extraction 0 5 5
Nimbus Extraction 7 6 13
HAIN GenoXtract Extraction 0 6 6
KingFisher Extraction 0 5 5
EasyMag Extraction 10 0 10
TOTAL 322 49 371
Strategy to Upscale Number of Tests
Increase number of extraction equipment and diversify platform to have multiple suppliers.
Explore alternative methods of extraction.
Increase number of PCR platforms to increase throughput.
Advocate for better supply of test kits for higher throughput machines.
More targeted and focused testing to allow better use of limited resources.
Use of rapid diagnostic serology tests.
Use of spare capacity in private sector (limited).
Use of spare capacity in academic sector (limited).
Support from Other Stakeholders African Union Medical Procurement Platform has sourced 2 million testing kits
from China and other suppliers for South Africa.
Dept Agriculture, Land Reform and Rural Development has loaned seven RNA extraction platforms and 38 mobile veterinary units, facilitated by Minister Didiza and Minister Mkhize.
Support from WHO, WHO Afro, CDC Africa, Russia, Alibaba and Jack Ma Foundation with supplies of test kits.
Support from the Solidarity Fund for purchasing of reagents.
Support and donations from Orlando Pirates, Kaiser Chiefs and MultiChoice; VW, BMW, Sasol, ABSA, TOTAL, Medshield, Gift of the Givers.
Provincial Action Plans
Western Cape Targeted Testing based on prioritising samples based on in-hospital and high risk
Large share of high throughput test kits allocated to Western Cape
Equipment Additional extractors for Tygerberg and Greenpoint
Additional PCR machines for each of the laboratories
Laboratories Greenpoint Laboratory added as an additional testing site
Collaboration with Centre for Proteomic and Genomic Research (CPGR) from Monday and Centre for Infectious Diseases Research in Africa (CIDRI), South African Tuberculosis Vaccine Initiative (SATVI) and UCT Lung Institute in the pipeline
Collaboration with private laboratories
Process Heat extraction process started at GSH.
Eastern Cape Recruitment of Staff
38 new staff recruited, including a pathologist, a scientist and 18 technologists, 20 clerks
Equipment
East London – new extractor and PCR equipment
PE – additional extractor and PCR
Process
Streamlined registration process to allow for categorisation of samples
Heat activation used in PE
Partnerships
Collaboration with private laboratories
Gauteng Recruitment of Staff to increase capacity
DGM – 11 people; CMJAH – 13 people and TAD 7 people
Created separate registration and receiving for COVID in Braamfontein with 15 new clerks employed
Equipment
Additional extraction and PCR equipment
Process – pooling, heat extraction and lysis
Decentralise to Chris Hani Baragwanath, Helen Joseph, Tambo Memorial
Kwa-Zulu Natal Recruitment of staff – 73 already employed, still recruiting new technologists
Equipment Addington – 3 new Abbott Alinity currently being verified to free up Abbott M2000 for COVID-19
and a GeneXpert Infiniti 48-48
IALCH – Hamilton extractor from Dept. of Agriculture
Process Pooling and lysis being used
Laboratories Edendale, Ngwelezane and Madadeni are being validated (existing Cobus and GeneXpert)
Academic laboratory collaboration with Molecular Diagnostic Services (MDS). Global Health Innovation (GHI) should be online on Monday. Neuberg Global Laboratory , Africa Health research Institute (AHRI) and Kwa-Zulu Natal Research Innovation and Sequencing Platform (KRISP) by end of next week.
The NHLS has upscaled our capacity on a national level in a short space of
time to provide significant numbers of tests on a weekly basis
Whilst demand for testing has been high, we have been increasing our
outputs to reduce the backlog
The NHLS remain committed to delivering quality testing and all attempts will
be made to ensure support for the targeted testing strategy
Conclusion
33
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91124
131
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1123
64
12791
88
44 56
3566
35
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8
35
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138
12168
3466
2.4% 1.8%
4.3%3.4%
4.1%
22.4%
3.6% 3.3%4.7%
9.3%
12.6%
1.4%
3.4%
6.5%5.5%
4.4%5.2%
3.5%4.5% 4.9%
7.8% 7.2%5.5%
2.1%
4.4% 4.5%6.2%
8.9%
4.4%2.7%
5.8%
0.0%
5.0%
10.0%
15.0%
20.0%
25.0%
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Fri Sat Sun Mon Tue Wed Thu Fri Sat Sun Mon Tue Wed Thu Fri Sat Sun Mon Tue Wed Thu Fri Sat Sun Mon Tue Wed Thu Fri Sat Sun
EASTERN CAPE
INCONCLUSIVE NEGATIVE POSITIVE +Rate
163
281
241
186
89
152
378
210
177
298
332323
318
384
448519
536
411344
468
281
527 523
431
325
440
399
661
781 677
463
9.1% 8.8%
14.1%
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10.8%
15.8%16.0%
10.5%12.0%
15.9%17.2%
18.7%18.7%
14.9%
18.0%
20.7%
23.8%23.0%
26.7%
22.3%
24.7%23.5%
28.2%27.8%
24.2%
26.7%27.9%28.0%
25.2%24.6%
0.0%
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Fri Sat Sun Mon Tue Wed Thu Fri Sat Sun Mon Tue Wed Thu Fri Sat Sun Mon Tue Wed Thu Fri Sat Sun Mon Tue Wed Thu Fri Sat Sun
WESTERN CAPE
INCONCLUSIVE NEGATIVE POSITIVE +Rate
76 27
28 21
12
5631
42 11 13
20
1113
31
17
10 10
10
1718
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23
41
27 1314
42 30
27
55 48
2.8%
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0.4% 0.5%0.6%
0.4%0.6%
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0.7%0.8%
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0.4% 0.5%
1.5%
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1.3%1.2%
0.0%
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GAUTENG
INCONCLUSIVE NEGATIVE POSITIVE +Rate
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18 14
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10
34
32
27
315
78
17
6
24
915
23
1819
1232
8
19 23 7
23
20
46
14
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0.5%0.7%
1.2%
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1.0% 0.9%
1.7%
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KWAZULU-NATAL
INCONCLUSIVE NEGATIVE POSITIVE +Rate
1
21
24
3
6
5
1
141 1
25 6
3
0.0% 0.0%0.3%
0.0% 0.0%0.4%
0.0% 0.0% 0.0% 0.0% 0.0% 0.0% 0.0%0.2%
0.0% 0.0% 0.0% 0.0%
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FREE STATE
INCONCLUSIVE NEGATIVE POSITIVE +Rate
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1 1
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110.0%
14.8%
0.0% 0.0% 0.0%
1.6% 1.5%
0.0% 0.0% 0.0% 0.0%1.2% 1.4%
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Fri Sat Sun Mon Tue Wed Thu Fri Sat Mon Tue Wed Thu Fri Sat Sun Mon Tue Wed Thu Fri Sat Sun Mon Tue Wed Thu Fri Sat Sun
NORTH WEST
NEGATIVE POSITIVE +Rate
0.5%
0.2%
1.4%
0.0% 0.0% 0.0% 0.0% 0.0% 0.0% 0.0% 0.0% 0.0% 0.0%
0.7%
0.3%
0.0% 0.0% 0.0% 0.0%
0.3%
0.0%
0.2%
0.0% 0.0% 0.0% 0.0% 0.0% 0.0% 0.0% 0.0%0.0%
0.2%
0.4%
0.6%
0.8%
1.0%
1.2%
1.4%
1.6%
0
100
200
300
400
500
600
01
-May
02
-May
03
-May
04
-May
05
-May
06
-May
07
-May
08
-May
09
-May
10
-May
11
-May
12
-May
13
-May
14
-May
15
-May
16
-May
17
-May
18
-May
19
-May
20
-May
21
-May
22
-May
23
-May
24
-May
25
-May
26
-May
27
-May
28
-May
29
-May
31
-May
Fri Sat Sun Mon Tue Wed Thu Fri Sat Sun Mon Tue Wed Thu Fri Sat Sun Mon Tue Wed Thu Fri Sat Sun Mon Tue Wed Thu Fri Sun
LIMPOPO
NEGATIVE POSITIVE +Rate
5
6
3
4
1
1
1
1
1 1
1
1
2.1% 1.7%0.7%
7.5%
0.6%0.0% 0.0% 0.0% 0.0% 0.0% 0.0% 0.3% 0.6%
0.0% 0.4%0.9%
0.0% 0.0%1.0% 0.6%
0.0% 0.0% 0.0% 0.0% 0.0% 0.0%
12.5%
0.0%0.0%
2.0%
4.0%
6.0%
8.0%
10.0%
12.0%
14.0%
0
50
100
150
200
250
300
350
400
450
01
-May
02
-May
03
-May
04
-May
05
-May
06
-May
07
-May
08
-May
09
-May
10
-May
11
-May
12
-May
13
-May
14
-May
15
-May
16
-May
17
-May
18
-May
19
-May
20
-May
21
-May
22
-May
23
-May
24
-May
25
-May
26
-May
27
-May
28
-May
Fri Sat Sun Mon Tue Wed Thu Fri Sat Sun Mon Tue Wed Thu Fri Sat Sun Mon Tue Wed Thu Fri Sat Sun Mon Tue Wed Thu
MPUMALANGA
NEGATIVE POSITIVE +Rate
2
1 1
4
1
5
9
15
0.0% 0.0% 0.0% 0.0% 0.0% 0.0% 0.0% 0.0% 0.0% 0.0% 0.0% 0.0% 0.0% 0.0% 0.0%
2.0%
0.0% 0.0%
0.6%
0.0% 0.0% 0.0% 0.0%
0.5% 0.5%
0.0%0.4%
0.0%
2.8%
1.4%
6.3%
0.0%
1.0%
2.0%
3.0%
4.0%
5.0%
6.0%
7.0%
0
100
200
300
400
500
600
700
8000
1-M
ay
02
-May
03
-May
04
-May
05
-May
06
-May
07
-May
08
-May
09
-May
10
-May
11
-May
12
-May
13
-May
14
-May
15
-May
16
-May
17
-May
18
-May
19
-May
20
-May
21
-May
22
-May
23
-May
24
-May
25
-May
26
-May
27
-May
28
-May
29
-May
30
-May
31
-May
Fri Sat Sun Mon Tue Wed Thu Fri Sat Sun Mon Tue Wed Thu Fri Sat Sun Mon Tue Wed Thu Fri Sat Sun Mon Tue Wed Thu Fri Sat Sun
NORTHERN CAPE
INCONCLUSIVE NEGATIVE POSITIVE +Rate
