Republic Of Zachistan

Diagnostics capacity assessment for Dunyamwera disease

Disease Overview:

Dunyamwera is an infectious disease that has been classified as a pandemic by all major global health agencies.
Since the outbreak was first reported three months earlier, almost 3 million cases have been confirmed globally,
with many more unconfirmed cases expected to manifest in the near future. In Zachistan, a large African country
with a population of 50 million, 380 cases have been confirmed over the past month, and the government has
assembled a team of key officials, research institutions, development partners, and pharmaceutical company
leaders to tackle the challenge of the pandemic. Testing, tracking and tracing is essential to the government’s
strategy for action, and the government hopes to undertake a rapid assessment of the diagnostics capacity of
the country. CHAI has been tasked with supporting the government in conducting this analysis, which is expected
to inform key policy decisions.

Current diagnostics scenario:

Presently, the diagnostic procedure for identifying Dunyamwera virus involves the collection of Buccal Swabs
from suspected patients. Phlebotomists (experts in patient sample collection) visit the suspected patients and
collect the samples using buccal brushes from inside the mouths of the patients, from the cheek tissue. The
procedure does not require collection of blood specimens. The buccal swab is then transported to the diagnostic
labs in a secure, temperature-controlled carrier. Presently, there are 200 labs spread across the country, and
each lab has 1 RT-PCR machine.

At the lab, the lab technicians use RT-PCR machines to confirm the presence of the Dunyamwera virus in the
samples. The DNA from the swab is extracted using a manual extraction method by the lab technicians, and the
process is time consuming. For running the diagnostic tests in the RT-PCR machines, screening test kits are used,
which contain a mix of chemicals and control samples. The extracted DNA is mixed with the reagents in the
testing kits, and this mixture is loaded in one of the slots in the RT-PCR machine. One test kit is required per
sample. The test kits are supplied by a number of local and international manufacturers. Due to the global
demand, orders for test kits have to be placed much in advance, as the lead times for procurement are
substantial.

The national guidelines presently recommend that for each tested sample which shows a positive presence of
the virus in the screening test, a confirmatory test be conducted. Due to this reason, some capacity of the RT-
PCR machines is allocated to confirmatory tests in each batch, thus reducing the available capacity for screening
tests.

Planned interventions to improve diagnostics capacity:

Ever since the beginning of the Dunyamwera-23 outbreak, the government of Zachistan has been continuously
working with the manufacturers (pharma companies), research institutions, and development partners to
identify specific solutions for increasing the diagnostic capacity of the country.

Last week, one pharmaceutical company made a breakthrough in the technology for test kits. They have
produced a new combination test kit, which can conduct both the screening and confirmatory tests
simultaneously from the same sample. This is expected to remove the requirement of conducting confirmatory
tests, freeing up capacity for additional tests in each cycle of the RT-PCR machine. The government of Zachistan
understands that this is a significant opportunity to increase the overall testing capacity, and hopes to place
procurement orders for these. The procurement lead times for the combination testing kits are unclear, and the
government presently estimates that sufficient testing kits will be made available for 50 labs each in four
tranches of procurement.
Further, research by global players has led to the development of an automated DNA extraction equipment,
which became available last week. Since the manual DNA extraction process is time consuming, the new
machines are expected to decrease the cycle time of testing, and hence enable more number of cycles per
machine per day.

The government of Zachistan placed an order for automated extraction machines immediately, and 20 such
machines have arrived in the country over the past week, and have been dispatched to 20 different labs.
Zachistan hopes to make the automated DNA extraction machines available at all 200 labs over the coming
months, and has placed orders for the same. Zachistan has agreed with the manufacturers to cover the
remaining 180 labs in tranches of 30, 60, and 90 labs over this period. As before, because the global demand for
these machines is high, procurement lead times may vary substantially from those presently agreed with the
manufacturers.

The daily test capacities for all types of RT-PCR machines are present in the Appendix.

The Challenge:

The challenge being faced in all African countries is that presently the visibility into diagnostic capability of the
countries is limited, and hence policy decisions are being made on inaccurate estimates of testing capacity. The
government of Zachistan has declared a lockdown of routine businesses, and has mandated enforcement of
social distancing measures to prevent the transmission of the infection. CHAI is working with the Ministry of
Health of Zachistan to estimate the testing capacity of the country over the next 6 months (180 days), supported
by strong quantitative analysis, to enable the ministry in making sound data based decisions.

Further, orders for test kits need to placed with different manufacturers, who are asking for advance payments
to confirm orders. This will ensure supply security of test kits over the next few months.

Since procurement lead times may vary, the government has asked CHAI to create a flexible capacity assessment
model, which the decision makers can use to compare various alternate scenarios, by varying the inputs related
to procurement lead times of combination testing kits and automated extraction machines.

Requirements:

1. Create a flexible diagnostics capacity assessment excel model which lets the decision makers vary the
inputs (coverage of interventions, and days of switch for automated extraction machines and
combination testing) to compare various scenarios of daily and cumulative testing capacity for the next
six months (180 days) in Zachistan. Use this model to calculate the cumulative testing capacity for
Zachistan with intervention details as listed in Appendix B and Appendix C.

2. Estimate the quantity of combination test kits and non-combination test kits required over the next
6 months (180 days), assuming all machines are utilized to their full capacity.

3. Present this analysis in 3-4 slide PowerPoint which is to be used by CHAI to present to the Ministry
of Health officials from Zachistan.

Please make reasonable assumptions wherever required, and mention them within the excel file.

Appendix:

A. Daily Testing Capacity by machine type

S. Type of RT-PCR Number of machines of type on Daily Test Capacity per machine (In
No. Machine Day 0 number of tests)
1 Basic (Manual
extraction with
180 36
non-combination
kits)
2 Automated
extraction with
20 108
non-combination
kits
3 Manual extraction
with combination 0 45
kits
4 Automated
extraction with 0 135
combination kits

B. Intervention 1 - Switch to Combination Testing

S. Tranche Coverage of Intervention (Number Day of Switch

No. of labs switching to combination (Assuming today to be Day 0)
testing)
1 Tranche 1 50 33
2 Tranche 2 50 76
3 Tranche 3 50 108
4 Tranche 4 50 144

C. Intervention 2 - Switch to Automated DNA Extraction

S. Tranche Coverage of Intervention (Number Day of Switch

No. of labs switching to Automated (Assuming today to be Day 0)
Extraction)
1 Tranche 1 30 26
2 Tranche 2 60 48
3 Tranche 3 90 84