[Ip-health] The Economist: How to build and deploy coronavirus testing at unprecedented scale - Countries will have to do it to end their lockdowns safely

Thiru Balasubramaniam thiru at keionline.org
Thu Apr 23 04:00:12 PDT 2020


https://www.economist.com/science-and-technology/2020/04/22/how-to-build-and-deploy-coronavirus-testing-at-unprecedented-scale


Covid-19
How to build and deploy coronavirus testing at unprecedented scale
Countries will have to do it to end their lockdowns safely

Science and technology
Apr 22nd 2020


SARS-CoV-2, the virus that causes covid-19, is an unobtrusive piece of
biological machinery. It spreads parasitically through the respiratory
tracts of human beings, often without provoking symptoms in those who carry
it. Yet for some, particularly the old, it is deadly. This combination of
properties make the pandemic both dangerous and difficult to stop. As of
April 22nd it had killed 182,000 people.

So far, every country that has reduced covid-19 infection to low levels has
relied to some degree on “social distancing”—that is, either encouraging or
forcing people to stay at home, and to keep well apart if they find that
they have to go out—to prevent the virus from spreading. On top of this
many are in any case fearful to go out, lest they catch the illness.
Without a vaccine or therapeutic drugs, neither of which is guaranteed,
countries therefore face a future of bouncing in and out of lockdown every
few months, with infection rates ebbing and flowing in response. The result
will be mounting death tolls, depressed economies and confidence-sapping
uncertainty. This can, however, be partly ameliorated by extensive testing
for the virus. Testing enables the government to keep tabs on the disease,
reveals which social-distancing measures work, and, if those testing
positive remain at home, instils confidence in the public that it is safe
to go out.

Economies of scale
America is in a particularly tight spot. Parts of its government responded
slowly to the pandemic to start with, and it now faces high levels of
infection that are spread across the country. In response, a consensus is
emerging among its scientists, economists and public-health officials that
a massive increase in testing capacity—creating a system that can test
millions of people a day for the virus—will be needed to get the place out
of lockdown safely. A testing system of this kind has never been built
before. It will be expensive, costing tens, possibly hundreds of billions
of dollars in America alone. But it offers a way to return to something
approaching normal life with a degree of confidence that the pandemic is
under control.

The goal of this new testing regime would be to track down every carrier of
the virus so that those at risk of spreading it could be isolated. The
contacts of anyone who tested positive would be traced and tested as soon
as possible, to cut off further chains of transmission. Trevor Bedford, who
studies viruses and immunity at the Fred Hutchinson Cancer Research Centre
in Seattle, has said that what is currently known about the virus suggests
that the system must track down and isolate all of an infected person’s
contacts within 48 hours of their positive test if the transmission chain
is to be broken. If testing and tracing can do this, then people can go
safely about their lives.

Currently, the test employed to find out if someone is infected looks for
the virus itself using a technique called reverse transcription-polymerase
chain reaction (RT-PCR). This starts by sticking a Q-tip-like swab deep
into the nose or throat of the individual to be tested, to retrieve a
sample of mucus that may or may not contain the virus. This sample is then
run through a process (reverse transcription) that copies any fragments of
viral RNA (the molecule in which SARS-Cov-2’s genes are written) into DNA,
a chemical more easily handled by established testing methods. These first
amplify the quantity of DNA present (the polymerase chain reaction), and
then run it through a detector to find out what it is. Other tests, which
look for antibodies produced when someone comes into contact with the
virus, are being devised as well. These will also be able to find out who
has been infected in the past.

The number of tests of all kinds that America needs in order to lift its
lockdown safely is a matter of debate. Plans floated in recent weeks by
various think-tanks have come up with vastly different figures. All are
large. That by a working group at the Edmond J. Safra Centre for Ethics at
Harvard University, published on April 20th, suggests America will need to
test between 5m and 20m people per day, which is 2-6% of the population.
Another, put forward on April 21st by experts convened by the Rockefeller
Foundation, outlines ideas that could get America to 30m tests per week in
eight months’ time.

Ignition sequence start
That would not be easy. By the time this edition of The Economist is
published, America will have carried out more than 4.5m SARS-CoV-2 tests
since it began the process in February. Over the first two weeks of April,
the average number of tests per day was around 1m a week. The country has
struggled to get to even this level of testing, so expanding it ten or 100
times will be a big challenge.

The Rockefeller plan suggests current testing numbers in America can be
tripled by bringing into the programme laboratory capacity that exists
already, but which is not being used. That would involve identifying all
American high-throughput laboratories that can be adapted for the task,
sorting out the regulatory approvals they will need and stumping up the
money.

Some states are already doing this. Those with big research universities,
such as Massachusetts (home to Harvard and the Massachusetts Institute of
Technology, MIT, among others), have an advantage here. The Broad
Institute, a joint MIT-Harvard enterprise run by Eric Lander, one of the
leaders of the Human Genome Project, has begun doing SARS-CoV-2 tests and
might, when up to speed, be able to manage to do 1m of them a day. In other
places commercial laboratories could be put to the task. In Wisconsin Exact
Sciences, a firm that specialises in cancer tests, has rejigged a large
part of its laboratory to process 20,000 covid-19 tests a week.

Making more use of so-called point-of-care machines would be another way to
increase testing capacity. These small boxes are already used to test for
viruses in thousands of hospitals and clinics around the world, and adapted
versions have recently been introduced to detect SARS-CoV-2. Point-of-care
machines can process throat swabs in around 15-30 minutes. Ramping up
production of them would be useful in bringing testing capacity to, say,
rural areas where collecting and returning throat swabs to a big central
laboratory might take too long. The supply chains for electronics and
reagents for these machines, however, rely heavily on China, and so
building more of them now might not be easy.

The jump from 3m tests per week to 30m will need big, new labs on the scale
of the Broad to be dotted around the country. Each of these would process
hundreds of thousands of tests a day, using robotics and automation.
Testing needs to become simpler, too. Collecting samples for RT-PCR tests
is invasive, and the tests themselves are complicated. Scaling the process
up to millions a day is an “impossible” mission according Severin Schwan,
the boss of Roche, a Swiss pharmaceutical giant that makes point-of-care
testing machines.

Other testing methods are possible, but as yet unproven. Scientists at
Rutgers University in New Jersey recently demonstrated a way to look for
signs of the virus in spit samples (which are easy to obtain) instead of
throat swabs (which are notoriously difficult and uncomfortable to
collect). On April 13th America’s Food and Drug Administration (FDA)
granted spit tests an emergency-use authorisation. Generic spit kits that
can be tweaked to do this are already widely available and can be
transported to processing laboratories at ambient temperatures.

All this new testing infrastructure will require trained people to run it,
says Scott Becker of America’s Association of Public Health Laboratories.
Much of the handling of samples in laboratories is routine stuff, so people
can be trained quickly to do it. But analysing the results needs highly
trained experts—and in some states such people must be licensed, too. Those
analysts who currently exist are already putting in extended shifts, says
Mr Becker, and this cannot be sustained over a pandemic that will be “a
long, long haul”.

Swabbing the noses or throats—or even collecting the spittle—of millions of
people a day would also require a huge number of new hires. For now, teams
from America’s National Guard have been helping with that in outbreak
hotspots, such as some prisons, and at drive-through testing sites. And
then there are the 300,000 contact-tracers that America would need,
according to another group of experts who assessed that matter recently, to
get in touch with those who have been in recent proximity to people who
test positive. New contact-tracers can, however, be trained in a day, so
lots of those who have suddenly found themselves without a job might be
redeployed as such. San Francisco, for example, has put librarians to the
task. The thousands of members of America’s Peace Corps who have had to
return from duty abroad because of the pandemic might also usefully be
deployed for this purpose.

The supply of reagents and components needed to run millions of tests a day
must be secured, too. Until now, one of the main obstacles to their mass
production has been the lack of a strong signal from the federal government
that more are needed—though that changed on April 21st when Congress
approved the spending of $25bn on testing. The two main suppliers of nasal
swabs in America, Copan and Puritan, make just 6m a week between them.
Roche says that it is currently capable of supplying “millions” of tests
per month. That a firm like Roche is still thinking in terms of tests per
month, rather than tests per day or per week, does, though, suggest there
is a long road ahead.

Paul Romer, a professor at New York University and winner of the 2018 Nobel
prize in economics, who also advised on the Rockefeller Foundation’s work,
says that university laboratories have already shown they could get around
supply issues in the ramping-up of testing. “If you look at reagent
bottlenecks, people have found other reagents that they can swap out
instead of the FDA-approved ones. They’ve shown you don’t even need to
include the RNA extraction [from throat-swab samples] that requires these
reagents.” Freeing universities and research institutions from red tape
would be crucial, he believes, in ensuring any efficiencies and new
discoveries that simplify or speed up testing are able to spread rapidly.

Don’t stop me now
Scaling up testing infrastructure will also face regulatory hurdles. For
example, swabs on their way to be tested are classified as a biohazard in
the United States, and require special containers and shipping protocols.
Building and managing such an unprecedented amount of testing capacity in
such a short space of time will also need co-ordination. The Harvard group
proposes the formation by the federal government of a Pandemic Testing
Board to oversee these decisions. It would be composed of leaders from
business, government and academia, among others, and would be given powers
to oversee the construction of laboratory capacity and to ensure the supply
and distribution of the materials needed to carry out the tests themselves.

The cost for all this? The Harvard group estimates around $15bn per month
and that it would need to be in operation for a year or more, depending on
when (and if) treatments and vaccines became available. That price tag may
seem eye-watering, but lockdown costs far more. Estimates place the cost to
America of the pandemic at up to $400bn a month. Given the alternative,
building the largest medical-testing system the world has ever seen is a
steal.


-- 
Thiru Balasubramaniam
Geneva Representative
Knowledge Ecology International
41 22 791 6727
thiru at keionline.org


More information about the Ip-health mailing list