Misc 04/11/2020

Labs confident rapid tests will prevent a second collapse

Demand has tripled compared to the first wave and the machines are working at full capacity

Gemma Garrido Granger
5 min
Un científic treballant en proves de cribratge del Covid-19 en un laboratori.

Santa Coloma de GramenetOliver has been in close contact with a covid-19 positive and has been homebound for five days without getting the PCR test health protocols prescribe. Once the sample was taken, he was told it would be a little more than 48 hours before he got the result, because the laboratories were overwhelmed. He was told it would take a further five days, and so it was: by the time he got the result, Oliver had completed the ten-day quarantine. The acceleration of the pandemic has required more tests than ever, but over-demand has congested laboratories, which have sometimes seen the volume of daily samples to be analysed triple. Almost all services have now caught up, but there are still people who are waiting for their results.

The laboratories consulted by ARA warn that they are at the limit of their clinical capacity and that they are worried that they do not have enough hands or material resources to take on the growing amount of work. Thermocyclers, the machines for analysing the samples of potentially infected people, work 24 hours a day, seven days a week, and this intensive use sometimes ruins the robots.

"We now have response times of a maximum of 24 hours but we cannot guarantee that this will continue to be met next week or even this week," explains Mireia Canal, the technical director of the Laboratori de Referència de Catalunya. This centre analyses tests made by regional hospitals and a large part of the primary care centres in the coastal areas of the country, from Blanes to Tortosa, via Mataró and Barcelona.

The Department of Health admits some occasional delays in the notification of test results and attributes this to laboratories' overload. Between 18 and 31 October alone, a total of 529,277 tests were performed in Catalonia, 11.7% of which were positive. PCRs represent 90% of the diagnoses.

The laboratory at Vall d'Hebron Hospital, which serves a large number of clinics, was one of the most affected by the outbreak of the second wave a fortnight ago. Results for tests carried out between 19 and 23 October were given between Friday 30 October and this Tuesday 3 November. According to sources in the Vall d'Hebron hospital, the processes are now normalised, but the microbiology service has taken 15 days to process results. "The delayed samples have already been processed and we are once again providing results in 24 hours, maximum 48 hours", they assure.

Positivity of PCRs

Percentage of positive results in relation to the total number of tests done (daily data)

[See the evolution of covid-19 through other key indicators]

Antigens work

The Laboratori de Referència de Catalunya has tripled the number of tests it carried out weekly in the first wave: it has gone from 5,000 to 15,000. And both the Vall d'Hebron hospital in Barcelona and the Germans Trias hospital in Badalona are doing between 5,000 and 6,000 a day. "Last week, when the system collapsed, we reached a peak of up to 7,000 samples per day," explains the clinical director of the Badalona hospital, Ignacio Blanco. The microbiologist attributes this drop of 2,000 tests to the fact that the Health Department has paused mass screenings and has implemented the rapid test as a diagnostic test, also among symptomatic patients. "But we're still working at maximum capacity," he says.

The temporary prioritisation of antigen tests to PCR should give laboratories some breathing space, agrees Salut. Catalonia is in a phase of mitigation, which means that community transmission is so powerful that it is almost impossible to follow the chains of contagion. Now anyone can be infected. "The more the virus is spread and the more cases there are in the community, the less likely it is that the antigen tests will be wrong and are therefore more reliable", says the coordinator of the covid-19 monitoring unit, Dr Jacobo Mendioroz.

The microbiologists consulted are confident that this technique will prevent further saturation in their laboratories. "The antigen tests are sure to help us, even though we cannot forget that PCR is the reference test. We will do as we have up to now, week by week, seeing if we can meet the current demand," explains Canal.

Since its progressive implementation, which now started three weeks ago, 52,764 rapid tests have been performed. However, these resources have not been evenly distributed throughout the country: 71% of the rapid diagnoses have been carried out in the city of Barcelona (with 15,844 tests done) and in the municipalities of the northern (14,271) and southern (7,413) metropolitan areas. In the regions of Girona, 4,214 tests have been performed; in Central Catalonia, some 3,624; in Tarragona, 2,886, and in Lleida, 2,816. In contrast, in Terres de l'Ebre only 1,108 tests have been performed, and in Alt Pirineu and Aran, 395.

Blanco also welcomes the implementation of rapid testing in primary schools because it "prevents samples from people with symptoms that are clearly positive" from clogging up the system. Although he recalls that antigens do not have the same sensitivity as molecular tests, the clinical director of the Germans Trias hospital assures that with patients with symptoms it has very good results. A study in which a team from a centre in Badajoz has collaborated confirms that it also works well in the case of asymptomatic patients, despite reservations and never as a main detection strategy.

"With asymptomatic patients or, for example, if we want to carry out tests in care homes, we will have to evaluate what loss of sensitivity we accept. The best option would be to guarantee repetition strategies, that is to say that the tests can be repeated once a week or every two weeks to recover the loss of sensitivity", Blanco details. So far, geriatric hospitals have performed 3% of the country's rapid tests, some 1,500 in total.

Intensive use robots, depletion of stocks

However, the large number of tests to be analysed is not the only reason for delayed response times. Microbiologists warn that access to reagents is becoming increasingly complex and that suppliers are also at risk of running out of stock. "We could not supply ourselves properly this summer because the manufacturers did not have reagents either, and now we also have problems accessing consumables and basic materials such as spikes, pipettes or labels. All these things, which all centres use and which are essential, are beginning to be in short supply," says Canal.

Both the Laboratori de Referència de Catalunya and the Microbiology Service of the Germans Trias y Pujol Hospital in Badalona, as well as many others, have opted for diversification of suppliers to have more room for manoeuvre, as they did in the first wave. This means that if a manufacturer runs out of stock, laboratories can order compatible products from another manufacturer or use thermocyclers from other brands.

"This strategy, which practically all laboratories use, gives us oxygen. But this is like a domino: if one piece falls, we all fall," warns Blanco. The microbiologist explains that his laboratory - which analyses a large part of the evidence collected from the northern metropolitan area - tries to keep at least three weeks' worth of stock. But there can also be technological errors: some machines, which are subject to incessant activity 24 hours a day, begin to fail, as happened in the Vall d'Hebron. "This can happen to all of us", other labs attest. They fear that it could also happen to them.