How France's Covid test and trace strategy became overwhelmed

OnOn Thursday September 17th the French health minister Olivier Véran held the first of what will become weekly regular briefings to inform the French public of the latest news about the SARS-CoV-2 or Covid-19 epidemic. The move marks a change from the first part of the epidemic in the spring when the country's top public health official, Jérôme Salomon, gave daily briefings.

Véran said he was worried about the way the epidemic was spreading. Some 48 of France's 101 départements or counties were above the alert threshold for cases, 12 of them were at red alert, and the number of people having to go to hospital with the virus had increased. At the current rate of growth, the intensive care capacity of hospitals in the southern region of Provence-Alpes-Côte d’Azur would reach saturation point in four weeks, the minister warned.

Meanwhile new restrictions are being imposed in the eastern city of Lyon and the Mediterranean city of Nice, following on from similar clampdowns in Bordeaux and Marseille. The health minister also threatened the closure of bars in Marseille and the overseas region of Guadalupe if the situation gets worse.

Yet Olivier Véran insisted that “we must live with the virus” and “maintain our social and economic life”. This is the official government line set by prime minister Jean Castex since the end of the long summer break. Instead, the health minister simply urged the French public to “limit gatherings of friends and family” in the most affected areas and for older people to “reduce the number of people” that they see each day.

At the same time the country's public health body Santé Publique France was publishing its weekly bulletin on the virus. And it made the minister's presentation seem upbeat by comparison. All the indicators are now at red. The number of deaths doubled in a week, going from 129 to 265. Indeed, on Friday the daily figure for deaths in hospital and care homes jumped to 154, including 123 in hospitals, though it seems this number was largely inflated by a late reporting of deaths by one hospital. The number of patients in intensive care across the country had meanwhile risen by 48% and the number of all hospitalisations by 45%.

The only source of apparent comfort was the fact that the number of positive Covid-19 tests had risen by just 8% in a week, from 51,983 to 56,227. Yet Santé Publique France said that this was probably an “under-estimate” of the number of confirmed cases because of the “saturation in testing capacity in certain regions”. On Friday September 18th the daily figures showed an increase of 13,215 more positive cases in 24 hours, and the 24-hour figure on Saturday was just under 13,500.

What has become clear is that not only has France lost control of the epidemic, but that its main measuring instrument – its ability to test positive cases – is in the process of getting broken.

In both the public and the private sector, biologists in charge of laboratories across France are all sounding the alarm. In the public sector very few responded to Mediapart's requests for interviews. In just a few terse words, Professor Astrid Vabret, who heads a teaching hospital virology laboratory at Caen in west France, summed up their predicament in an email: “Virologists are completely overwhelmed by the screening tests. Thousands of tests to be done are accumulating in our fridges. Sorry, but I don't have a minute to myself at the moment...”

“We lack machines and [chemical] reagents, many laboratories are in short supply,” said Lionel Barrand, president of the body representing younger scientists in the profession, the Syndicat des Jeunes Biologistes Médicaux. “The staff can't take any more, teams are working round the clock. We're regularly assaulted [editor's note, in France many tests are done at local laboratory clinics]. In the [Paris region], Marseille, Lyon and Toulouse the testing system has already broken down.” He said that the delays in tests carried out there are at odds with the need to isolate those with the virus, and also with the tracing of people that infected people have been in contact with. Yet both of these practices are seen as vital to check the spread of the virus. “We're under water, it's terrible,” he said.

Anne Souyris, assistant mayor in charge of health at city hall in Paris, finds the aquatic metaphor almost amusing. “In reality we've never got out of the water,” she said. “Since the start of this crisis, the main feature of this government has been a lack of anticipation. Each time it's the same: they hadn't foreseen....”

The city authorities wanted to erect a testing tent, open to all, in each arrondissement or district in Paris, to help tackle the high-risk period after the summer break. In the end the Paris regional health authority, the Agence Régionale de Santé d’Île-de-France, limited the number to three rather than twenty testing tents. The number of tests the city is carrying out has now actually fallen, from 2,500 tests a day up to September 8th, down to fewer than 1,500 in the past week. The city said this was at the request of laboratories who had been clogged up by a backlog of “late analyses”.

On Tuesday September 15th a Tweet from a journalist at Canal Plus satellite channel showed the queue for the testing tent in the XIXth arrondissement stretching around the local town hall:

Anne Souyris said that the delay in a person getting a test and then receiving the results varied between “two days and a week”. Yet the government has now reduced the period that a person with a positive test should stay in self-isolation to seven days. So at this level of delay the test becomes pointless.

The Paris regional health authority acknowledged that it was an “unacceptable situation” which they blame in particular on a “resurgence of the epidemic”.

“We went about it completely the wrong way,” said François Blanchecotte, president of another body representing laboratory biologists, the Syndicat des Biologistes. “We let the virus circulate actively. And now it's got into the care homes. I've just tested one in the Indre-et-Loire [editor's note, a département in western central France]: there are 20 residents who are positive, the staff are affected, there's already been one death.”

There is a cost involved in the testing, too. “It's between 272 million euros and 318 million euros a month for the tests paid for by [the state-run] Social Security,” said François Blanchecotte. That does not include the costs of the testing provisions put in place by local authorities, hospitals and regional health authorities.

Blanchecotte blames the situation on the decision of President Emmanuel Macron on July 14th to allow free Covid-19 tests for all, rather than the previous system under which members of the public needed a prescription to ensure their state health insurance covered it. “When you decide to open the test free to everyone, without prescriptions, you clog up the system!” said François Blanchecotte. “And now I am being asked to test entire classes, gyms, the medical faculty at Tours [editor's note, city in west-central France]. How do I do that?”

'How do you test 50,000 students quickly?'

At the end of lockdown in May, France's Scientific Committee – which advises the government on the epidemic - set a target of 700,000 Covid-19 tests a week. But at first there was not enough demand for this. Then on Bastille Day President Macron made his announcement that the public would no longer need a prescription to get tested. Demand grew, and then rose massively after the end of the summer holidays. In the last three weeks this has led to the large increase in the number of positive tests. It has also as a result increased the number of 'contacts' – those the people infected had been in contact with – who themselves needed tests. In the past week France has seen 1.2 million tests carried out, though this could be the upper limit of how many tests can be performed.

Yet not all the available testing resources are being used. Philippe Froguel, the head of a laboratory at Lille in northern France which carries out the polymerase chain reaction (PCR) tests commonly used to detect Covid-19, said that there are machines and reagents which are not being used. “Biology laboratories in public hospitals have received Chinese machines from the state which are capable of doing 2,000 tests a day and which are not being used at full capacity,” he said. Jean-Paul Feugeas, president of the association for biologists at teaching hospitals the Syndicat National des Biologistes de CHU, acknowledged: “Our problem at the hospital is finding the personnel.”

Speaking last Thursday September 17th, health minister Olivier Véran accepted that there was a “bottleneck”. He also acknowledged that a decision had been made to allow “each French person to get a free test. We take responsibility for that.” He again repeated that laboratories should test quickly - and as a priority - “those people who have a medical prescription, symptoms, personal contacts who are at risk, and health professionals”. That included domestic care workers, he said.

Yet biologist Boris Loquet, who heads a group of laboratories in Marseille, painted a picture of “queues, the anxiety of a section of the population, a telephone switchboard that's exploding”. He said that the people calling insisted they were 'contacts' of people who had tested positive - and thus required testing. “When you dig into it they are in reality contacts of contacts,” he said. “Today everyone is the contact of a contact! How can you explain to them that they're not priorities?” Boris Loquet agreed that such is the scramble for tests that “polite people” or those who have difficulties with the language or mobility have quite a low chance of getting a test, even if they have symptoms.

Health minister Olivier Véran last week made just one announcement to help with the issue of delays in getting tests, and that is is limited to the Paris region: twenty testing centres will be opened six days a week until the end of the winter. There will also be allocated time slots which are dedicated just to priority cases.

Professor Renaud Piarroux, epidemiologist at the Pitié-Salpêtrière, hospital in Paris, meanwhile warns that there is now a “high level of circulation” of the virus in France. “Now we have to come to terms with the epidemic,” he said. In his view the aim of carrying out a million PCR tests in France is “basically for show”. Professor Piarroux said: “Massing testing isn't an end in itself. The objective is to test people at risk quickly to allow them to self-isolate. By testing all over the place in the summer we scattered our efforts.”

The Pitié-Salpêtrière epidemiologist has been involved in the development of a project called Covisan in the Paris region. Mobile units get in contact with people who have tested positive, meet them, and if they agree enter their homes. But Covisan only exists in and around Paris. At a national level the 'tracing' of positive cases and their contacts is carried out on the phone by officials from the state health insurance agency. Professor Piarroux regrets the lack of direct contact. “You have to focus on the positive cases and their contacts, to help them to self-isolate,” he said. “In many cases a simple phone call isn't enough.” He also points out that the average number of contacts declared to the insurance authority by those who test positive has gone down, from five in July to three today.

There is currently a confusion between two very different strategies. On the one hand there is the testing of people with symptoms and who are at high risk. On the other there is mass testing, which aims to snuff out a return of the epidemic by tracking the prevalence of positive cases in the general population. Having attempted to deploy mass testing without the resources, the government is now focussing back on the former approach of testing for people with symptoms and at high risk.

Bruno Lina, a professor of virology and member of the Scientific Committee, has been trying to get people to understand this distinction. He heads one of the biggest virology laboratories in France, at the teaching hospital in Lyon, and acknowledges that they have found it hard to meet the demand. “For each sample you also need administrative work that enables you to follow the cases,” he said. “The demand hasn't stopped growing. But in the hospital human resources are hard to find.”

Just like biologists at laboratories in the private sector, Professor Lina is also overwhelmed by particular demands for “mass testing”, for example to test an “entire university” where there has apparently been a cluster of cases. This type of situation has already occurred in Toulouse, Lille and Lyon. “How do you test 50,000 students quickly?” he asks.

One possible source of help in the near future could be new tests for SARS-CoV-2. On Wednesday September 16th a decree in the official government publication, the Journal Officiel, authorised the use of antigen tests. These still use a nasopharyngeal swab at the back of the throat and nose. But while PCR tests require the use of a machine, the antigen tests give their results on a strip of paper, a bit like a pregnancy test.

Then on Friday September 18th France's independent health advisory body the Haute Autorité de Santé gave the go-ahead for saliva PCR tests, though only in cases of people who have Covid-19 symptoms.

Professor Lina said that more time and further trials were still needed to work out just where these new tests fit into the overall “testing strategy”. In particular there is still work to do on testing how sensitive they are. The current nasopharyngeal PCR swab test will remain the most sensitive. It collects the sample at the back of a person's nose and throat and then uses a technique of amplification in the lab to detect the virus's DNA.

“We look to multiply the presence of the virus,” explained Bruno Lina. “We speak of a cycle threshold. To find the virus you do up to 50 cycles. The number of cycles at which you find the virus is important: if you find some after 20 cycles then there's a lot of virus; if it's after 50 cycles then there's not much of it. But these are not false positives; when there's little virus it can mean that the person is at the end of their infection but it can also be they are right at the start, and become contagious in the following days.”

The antigen and saliva tests will be less sensitive than the nasopharyngeal PCR swab tests. “But if they enable more tests to be carried out, more quickly, to detect the people who are carrying a lot of virus and are thus more contagious, then there is a real risk-benefit gain,” he said.

Professor Lina imagines a situation where a care home could be tested using antigen tests within 30 minutes “to evaluate the situation very quickly” or to carry out “mass testing with saliva tests at a university” without the need to put on personal protective equipment. But he warns: “These tools are not going to change things fundamentally. There is still a considerable amount of work to be done, which poses enormous organisational problems.”

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The French version of this article can be found here.

English version by Michael Streeter