Strategic planning to augment the testing capacity for COVID-19 in India

Abstract

Background & objectives: Nearly 5,500 tests for coronavirus disease 2019 (COVID-19) had been conducted on March 31, 2020 across the Indian Council of Medical Research (ICMR)-approved public and private laboratories in India. Given the need to rapidly increase testing coverage, we undertook an exercise to explore and quantify interventions to increase the daily real-time reverse transcription-polymerase chain reaction (qRT-PCR)-based testing capacity over the next few months. The objective of this exercise was to prepare a potential plan to scale-up COVID-19 testing in India in the public sector.

Methods: Potential increase in daily testing capacity of the existing public laboratories was calculated across the three base scenarios of shifts (9, 16 and 24 h). Additional testing capacity was added for each shift scenario based on interventions ranging from procurement of additional qRT-PCR machines, leveraging spare capacity on available qRT-PCR machines not drafted into COVID-19 testing, to in-laboratory process optimization efforts.

Results: Moving to a 24 h working model in the existing approved laboratories can enhance the daily testing capacity to 40,464 tests/day. The capacity can be further bolstered by leveraging qRT-PCR and nucleic acid amplification test (NAAT)-based machines available with the Multidisciplinary Research Units (MRUs), National AIDS Control Organisation (NACO) and National Tuberculosis Elimination Programme (NTEP). Using combination/multiplex kits, and provision of automated RNA extraction platforms at all laboratories could also optimize run time and contribute to capacity increase by 1.5-2 times.

Interpretation & conclusions: Adopting these interventions could help increase public sector’s daily testing capacity to nearly 100,000-120,000 tests/day. It is important to note that utilization of the scaled-up testing capacity will require deployment of additional workforce, procurement of corresponding commodities for testing and scale-up of sample collection and transportation efforts.

Full text

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© 2020 Indian Journal of Medical Research, published by Wolters Kluwer - Medknow for Director-General, Indian Council of Medical Research
Strategic planning to augment the testing capacity for COVID-19
in India
Nivedita Gupta1, Tarun Bhatnagar4, Kiran Rade3, Manoj Murhekar4, Raman R. Gangakhedkar1, Anu Nagar2 &
ICMR COVID Team#
1Division of Epidemiology & Communicable Diseases, Indian Council of Medical Research, 2Department of
Health Research, Ministry of Health and Family Welfare, 3WHO Country Oce for India, New Delhi &
4ICMR-National Institute of Epidemiology, Chennai, Tamil Nadu, India
#ICMR COVID Team: Ira Praharaj, Sidhartha Giri, Neeraj Aggarwal, Harmanmeet Kaur, Neetu Vijay, Arvind
Bhushan, Salaj Rana, Swati Gupta, Jitendra Narayan, Indian Council of Medical Research, New Delhi, India
Background & objectives: Nearly 5,500 tests for coronavirus disease 2019 (COVID-19) had been
conducted on March 31, 2020 across the Indian Council of Medical Research (ICMR)-approved
public and private laboratories in India. Given the need to rapidly increase testing coverage, we
undertook an exercise to explore and quantify interventions to increase the daily real-time reverse
transcription-polymerase chain reaction (qRT-PCR)-based testing capacity over the next few months.
The objective of this exercise was to prepare a potential plan to scale-up COVID-19 testing in India in
the public sector.
Methods: Potential increase in daily testing capacity of the existing public laboratories was calculated
across the three base scenarios of shifts (9, 16 and 24 h). Additional testing capacity was added for
each shift scenario based on interventions ranging from procurement of additional qRT-PCR
machines, leveraging spare capacity on available qRT-PCR machines not drafted into COVID-19
testing, to in-laboratory process optimization eorts.
Results: Moving to a 24 h working model in the existing approved laboratories can enhance the daily
testing capacity to 40,464 tests/day. The capacity can be further bolstered by leveraging qRT-PCR and
nucleic acid amplication test (NAAT)-based machines available with the Multidisciplinary Research
Units (MRUs), National AIDS Control Organisation (NACO) and National Tuberculosis Elimination
Programme (NTEP). Using combination/multiplex kits, and provision of automated RNA extraction
platforms at all laboratories could also optimize run time and contribute to capacity increase by 1.5-2
times.
Interpretation & conclusions: Adopting these interventions could help increase public sector’s
daily testing capacity to nearly 100,000-120,000 tests/day. It is important to note that utilization of
the scaled-up testing capacity will require deployment of additional workforce, procurement of
corresponding commodities for testing and scale-up of sample collection and transportation eorts.
Key words Capacity - laboratory - real-time reverse transcription-polymerase chain reaction test
Indian J Med Res 151, February & March 2020, pp 210-215
DOI: 10.4103/ijmr.IJMR_1166_20
Quick Response Code:
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GUPTA et al: AUGMENTING COVID-19 TESTING IN INDIA 211
Coronavirus disease 2019 (COVID-19), rst
detected in China, has spread to more than 200
countries across the world1. The WHO declared
the disease a pandemic on March 11, 20202.
Since January 2020, India has undertaken several
measures to contain and manage the spread of the
disease including international and domestic travel
restrictions, rational screening and mandatory
quarantines3. One of the key strategies for containing
the disease across the world, is to undertake
widespread testing for COVID-19 followed by
isolation and treatment of conrmed cases and
containment measures for clusters of conrmed
cases4. The WHO recommends the real-time reverse
transcription-polymerase chain reaction (qRT-
PCR) diagnostic panel for the detection of 2019
novel coronavirus, a strategy that India has also
adopted5. As on March 31, 2020, the daily testing
was close to approximately 5,500 tests across public
and private laboratories6. Delays in testing can
lead to large disease cluster forming, unchecked
progression of severe cases and overburdening of
the health system with critically ill patients. The
present study explores and quanties interventions
to scale-up qRT-PCR-based testing capacity per day
across public laboratories in India. The interventions
range from optimizing the existing capacity of
manual qRT-PCR instruments through multiple
shifts and reduction in laboratory-level manual RNA
extraction eort; deploying additional manual and
automated machines from other public institutes
and research organizations and procuring automated
high-throughput instruments. The objective of this
exercise was to prepare a potential plan to scale-up
COVID-19 testing in India in the public sector.
Material & Methods
The various options for scaling up testing facilities
were discussed. The potential daily testing capacity
calculated for various scenarios, as follows:
(i) Batch size = 36 of 45 possible samples (20% of slots
blocked for conrmatory tests); run time/batch with
manual extraction = 5 h/batch; run time/batch with
automated extraction = 3 h/batch (1/4th of the public
laboratories already use automated RNA extraction);
no down time on machines.
(ii) Batch size = 36 of 45 possible samples (20% of
slots blocked for conrmatory tests); run time/batch
with automated extraction = 3 h/batch (all public
laboratories use automated RNA extraction); no down
time on machines.
(iii) Batch size = 45 of 45 possible samples (no slots
blocked for conrmatory tests); run time/batch with
manual extraction = 5 h/batch; run time/batch with
automated extraction = 3 h/batch (1/4th of the public
laboratories already use automated RNA extraction);
no down time on machines.
(iv) A total of 42 additional manual qRT-PCR machines
deployed from medical and research units; batch
size = 36 of 45 possible samples (20% of slots blocked
for conrmatory tests); run time/batch with manual
extraction = 5 h/batch (all additional machines to
run on manual RNA extraction); no down time on
machines.
(v) About 10-20 per cent of available nucleic acid
amplication test (NAAT)-based point-of-care (POC)
testing platforms under the National Tuberculosis
Elimination Programme (NTEP)7 can be considered
for COVID-19 testing; batch size = 4/run; run time/
batch = 2 h/batch; 25 per cent of load reduction in the
existing tuberculosis (TB) case load due to reduced
footfall; no down time on machines.
(vi) Seventy to hundred per cent of the available
automated qRT-PCR-based platforms under the
National AIDS Control Organisation (NACO)8 can
be considered for COVID-19 testing; batch size = 90/
run; run time/batch = 8 h/batch; 90 per cent of spare
capacity available due to reduced patient footfall
and potential deferral of non-diagnostic HIV viral
monitoring; no down time on machines.
(vii) Twelve high-throughput automated qRT-PCR-based
platforms to be deployed by the Indian Council of
Medical Research (ICMR) (two already in country);
daily capacity = 1400 samples in 24 h; 80 per cent of
utilization/day; no down time on machines.
An item-wise projection was also made for
commodities required to activate the scaled-up testing
capacity under various assumptions on the start dates
of dierent interventions (Table I).
Results
Several options have been proposed to be enacted
upon in the short and medium term. Short-term
measures can be implemented with the existing
diagnostic equipment already present in the public
sector. These include:
(i) Optimization of starting capacity: The existing 216
manual qRT-PCR machines in approved laboratories
can be enhanced from one shift (9 h scenario) to two
shifts (16 h scenario) and further to three shifts (24 h
scenario), thereby increasing the capacity to 40,464
tests per day (Figs 1-3).
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212 INDIAN J MED RES, FEBRUARY & MARCH 2020
Table I. Assumptions on start dates of dierent interventions
Intervention Intervention subtype Number of
machines (approx.)
Start date
Increase in working
hours
Move to 16 h shifts All April 10
Move to 24 h shifts All April 20
Redeploy qRT-PCR
machines in MRUs
qRT-PCR machines in co-located MRUs 60 per cent April 10
qRT-PCR machines in the remaining MRUs 40 per cent May 3
Leverage qRT-PCR
machines under NACO
Co-located machines 65 per cent May 15
Remaining functional machines 35 per cent June 1
Leverage NAAT POC
machines under NTEP
30 per cent of ~100 machines 30 May 15
30 per cent of ~100 machines 30 May 21
40 per cent of ~100 machines 40 May 31
Additional machines installed with BSL-2 150 June-December
Automated high-
throughput platform
to be deployed or
procured by the ICMR
Delhi 1 machine 1 April 5
Bhubaneswar 1 machine 1 April 20
Accenture 1 machine 1 May 15
4-10 newly procured machines installed in tranches 4-10 June 1
Automated RNA
extraction machines
30 laboratories per week till all laboratories 33 per cent May 8
67 per cent May 15
100 per cent May 23
Combination kits Some laboratories 50 per cent May 1
All laboratories 100 per cent June 1
qRT-PCR, real-time reverse transcription-polymerase chain reaction; ICMR, Indian Council of Medical Research; TB, tuberculosis;
NTEP, National Tuberculosis Elimination Programme; POC, point-of-care; NAAT, nucleic acid amplication testing; NACO, National
AIDS Control Organisation; MRUs, Multidisciplinary Research Units; BSL-2, biosafety level 2
Fig. 1. Impact on overall daily testing capacity by intervention type in nine working hours (conservative). qRT-PCR, real-time reverse
transcription-polymerase chain reaction; NAAT, nucleic acid amplication test; MRU, Multidisciplinary Research Unit; POC, point-of-care;
NACO, National AIDS Control Organisation; NTEP, National Tuberculosis Elimination Programme.
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GUPTA et al: AUGMENTING COVID-19 TESTING IN INDIA 213
(ii) Redeployment of manual qRT-PCR machines: There
are 42 manual qRT-PCR machines in Multidisciplinary
Research Units (MRUs). These can be redeployed and
allocated for COVID-19 testing.
(iii) Procurement of combination testing kits that can do
both screening and conrmatory tests in one machine
run.
(iv) High-throughput automated platform: Operationalizing
high-throughput platforms capable of conducting up to
1400 tests/day/machine. Two machines have already
been installed in the country at National Institute of
Biologicals (NIB), Noida, Uttar Pradesh and Regional
Medical Research Center (RMRC), Bhubaneshwar,
Odisha.
(v) High-throughput automated platform with NACO:
Leveraging spare capacity available due to reduced
footfall in lockdown situation on functional
automated high-throughput qRT-PCR latforms under
NACO; these platforms have U.S. Food and Drug
Administration (FDA) Emergency Use Authorization
Fig. 2. Impact on overall daily testing capacity by intervention type in 16 working hours (moderate).
Fig. 3. Impact on overall daily testing capacity by intervention type in 24 working hours (aggressive). Grey area is the expected additional
tests (20,000) that can be conducted if all the laboratory resources operate at full eciency.
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214 INDIAN J MED RES, FEBRUARY & MARCH 2020
(EUA) for COVID-19 testing. Currently, these are
used for early infant diagnosis and HIV viral load
monitoring. Two third of the functional machines
have been co-located in the existing ICMR-approved
laboratories.
(vi) Point-of-care NAAT-based automated platform
with NTEP: The existing public sector laboratories
approved by the ICMR cover only 114 of the 736
districts in the country; the laboratory network needs
to be decentralized to increase coverage and ease
sample transportation concerns. About 100 of the
operational POC NAAT-based machines across the
725 districts in the country, used for TB diagnosis,
are biosafety level 2 (BSL-2) approved and can be
considered for capacity sharing.
For platforms under the NACO and NTEP, supply of
corresponding reagents and cartridges from international
suppliers will have to be secured. The ICMR has already
approved some of the closed platforms with these
programmes for COVID-19 diagnosis. Medium-term
measures involve a lag time depending on supply-side
contingencies. These include:
(i) Procurement and installation of automated RNA
extraction platforms along with the procurement
of requisite extraction kits: Currently, only about
25 per cent of the laboratories (29 laboratories)
have automated RNA extraction capability, while
the remaining conduct time-consuming and
cumbersome manual extraction. Installation and/
or operationalization of automated RNA extraction
platforms supported by requisite extraction kits at
the remaining 75 per cent of the laboratories could
increase testing capacity by 1.5-2 times within the
same operating hours.
(ii) High-throughput automated platform: Ten additional
high-throughput automated machines may be
procured and deployed in the country.
(iii) Point-of-care automated NAAT platform with NTEP:
An additional 150 machines under the NTEP can
be considered for capacity sharing after getting the
required BSL-2 approvals.
Table II outlines the total commodities that would
be required to utilize the scaled-up testing capacity.
Discussion
A potential plan to scale-up COVID-19 testing
in the public sector was prepared in India. By
implementing all the above mentioned interventions,
public sector’s daily testing capacity could be scaled-
up to nearly 100,000-120,000 tests/day (depending
on conservative, moderate or aggressive operating
scenarios), which can help enhance readiness for
worst-case scenario. In order to utilize the scaled-
up testing capacity, increased workforce, adequate
testing commodities and collection of enough
samples/day would be critical. Commodities required
to operationalize the plan include viral transport
medium (with two swabs) commercially available,
RNA extraction kits, testing kits for manual qRT-
PCR (combination kits), automated qRT-PCR kits and
platforms and testing kits (probe, primer and Master
Table II. Total commodities required in order to activate scaled-up testing capacity as per timelines in Table I
Items
Commodities
Projected requirement Total
April
1-15
April
16-30
May
1-15
May
16-30
June
1-15
June
16-30
April 1 -
June 30
VTM (with two swabs) (commercially available) 5,50,000 6,50,000 11,15,000 14,60,000 19,75,000 19,75,000 77,25,000
RNA extraction kitsa,b 5,00,000 5,00,000 8,80,000 12,25,000 14,00,000 14,00,000 59,05,000
Testing kits (complete)
For manual qRT-PCR (combination kits)c0 0 2,80,000 4,20,000 14,00,000 14,00,000 35,00,000
For automated qRT-PCR (ICMR) 50,000 1,50,000 1,00,000 1,00,000 2,00,000 2,00,000 8,00,000
For automated qRT-PCR (NACO) 0 0 75,000 75,000 1,75,000 1,75,000 5,00,000
For POC automated NAAT (NTEP) 0 0 60,000 60,000 2,00,000 2,00,000 5,20,000
Testing kit (probe, primer and MasterMix separately)
For manual qRT-PCR 5,00,000 5,00,000 6,00,000 8,05,000 0 0 24,05,000
aOnly 1/4th of the laboratories out of the existing approved laboratories have automated RNA extraction capability. Additional
procurement of automated RNA extraction equipment is planned. Prospectively, only automated RNA extraction kits should be procured,
which are compatible with the RNA extraction machines procured, bThe RNA extraction kits required are one per manual qRT-PCR test,
cProjection for requirement of combination kits (screening + conrmatory). VTM, viral transport medium
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GUPTA et al: AUGMENTING COVID-19 TESTING IN INDIA 215
Mix separately) for manual qRT-PCR. Additionally,
all private and government medical colleges may be
urged to eventually create the state-of-the-art virology
laboratories and support the country’s ght against
COVID-19. Furthermore, sample collection and
transportation eorts will have to keep pace with the
increased available testing capacity at the laboratories.
Financial support & sponsorship: None.
Conicts of Interest: None.
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For correspondence: Dr Nivedita Gupta, Division of Epidemiology & Communicable Diseases, Indian Council of Medical Research,
Ansari Nagar, New Delhi 110 029, India
e-mail: guptanivedita.hq@icmr.gov.in
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