How Can Clinical Laboratories Prepare for the Next Pandemic?

Different microbiologists reflect on challenges encountered during the COVID-19 pandemic and suggest potential solutions in preparation for future outbreaks.

While tidying up in the residents' ward the other day, we found a copy of the first PCR order placed in our laboratory for the diagnosis of a new coronavirus that has been causing severe respiratory illness in the Wuhan region of China since late 2019. The order date was 21 February 2020. We had to be prepared. Just in case.

On 25 February at noon we went down to the canteen of the hospital Clínic Barcelona. It was 13:00, as it was almost every day. Dr Josep Costa, a doctor from the virology section of the microbiology service - now retired - was on duty. He was called in at 1.15pm. He was still on the first course. We had a suspected coronavirus that had arrived, I think, the same day. The conversation stopped. We all looked at him intently, trying to guess what they were saying to him. No need, the expression said it all: it's already here.

Photo: Aleix Cabrera / ISGlobal

From epic to wearing down

The arrival of SARS-CoV-2 was expected, yes, but nothing could have prepared us for three years and multiple pandemic waves. Initially, with the uncertainty, the epic outweighed the capacity to respond, but this epic-response pairing was diluted as the waves came and went and the wear and tear took its toll. Neither we nor the rest of the world were prepared for what was to come. In just a year, global GDP fell by 3% (the equivalent of the economies of Japan and Germany combined in a year): a virus shook the global economy. Vaccines arrived in record time, a medical milestone. At the same time, social networks were filled with people with metal spoons attached to their arms. They must have been bored.

Labs learn lessons from pandemic

To mark the third anniversary of the pandemic, the journal Clinical Microbiology and Infection (CMI) commissioned us to conduct a peer review of pandemic preparedness and lessons learned from the perspective of clinical microbiology laboratories. Researchers from ISGlobal, Denmark, UK, Norway and Germany participated in this review. In theory, it was a straightforward exercise. However, when I circulated a first draft, some co-authors pointed out that there were paragraphs that were more emotional than descriptive. I saw this immediately and changed them. Post-traumatic stress? I wouldn't rule it out.

Areas of the laboratory most affected by COVID

With the first two authors, we went through the areas where we had suffered the most and what we had learned.

1. Pre-analytical phase. This is the phase that always causes the most problems in any laboratory: masses of samples arriving, unlabelled samples, badly sealed samples, badly taken samples and lots of phone calls (some with clear signs of desperation, others of helplessness). We were unprepared, but we tightened up the circuits as best we could. Then the COVID sick leaves began. Less staff, more work. An explosive combination. In retrospect, we came out of the situation quite well. The technical staff, who were trained in record time, played a key role in this victory. A partial victory.
2. The analytical phase. This is the one we know best. Once the sample has been accepted as good, we put it in the thermocycler and check whether the PCR is positive or not. Simple, isn't it? Not really. One of the biggest challenges at the time was the availability of reagents. There was rationing, a lack of rapid platforms and sometimes unpredictable global stock-outs.
3. Post-analytical phase or delivery of results. Lots and lots of calls. Response times we could not predict. Without IT services, the battle was lost.

That was our perception. But also that of clinical laboratories across Europe.

How can we prepare for the next pandemic and what have we learned?

First of all, you have to manage your teams very well internally. The key word is communication. You need a knowledge transfer strategy that is fast and effective: the maximum number of people trained in the maximum number of techniques. Remember that we are talking about long-distance careers. This will allow us to ensure the necessary redundancy in the event of illness, attrition, etc. We must place great emphasis on the pre-analytical phase, i.e. the sample collection, transport and reception cycle. It is necessary to have staff exclusively dedicated to these tasks and with a spare wheel. This part is very tiring for the staff and we must not forget that in crisis or overload situations, telephone interactions are not always pleasant.

First of all, you have to manage your teams very well internally. The key word is communication. You need a knowledge transfer strategy that is fast and effective: the maximum number of people trained in the maximum number of techniques

Wherever possible, shared services must be used. In particular, one of the turning points in the management of the pandemic was access to responsive IT services, which accelerated response times and helped to automate processes that would otherwise have seemed impossible due to the sheer number of samples.

Foto: Aleix Cabrera / ISGlobal

The final conclusion is that you cannot work in isolation: you need very good coordination with other hospitals, especially district hospitals, where the burden of care often overwhelms the response capacity of the staff. Dealing with the current pandemic and preparing for new ones is not the responsibility of individual hospitals. Governments must be prepared to allocate budget lines beyond the health budget to protect the most vulnerable populations and to manage access to reagents to carry out the thousands of tests needed for epidemiological control and to monitor the evolution of the pandemic.

You cannot work in isolation: you need very good coordination with other hospitals, especially district hospitals, where the burden of care often overwhelms the response capacity of the staff

All of these points are discussed in this brief review. If the conclusions were put into practice, the result would be laboratories with good response capacity and preparedness, well-coordinated teams, and a before and after in the calendar. If we can develop an effective global vaccine in record time, it is not impossible that, with good laboratory preparedness, a new global outbreak can be avoided.

Read the CMI paper "Viral Epidemic Preparedness: A Perspective from Five Clinical Microbiology Laboratories in Europe"