“The impact of COVID on the molecular department of microbiology laboratories”

COVID has had a profound, and ongoing impact on microbiology laboratories and everyone who works in them. But today I want to write about molecular departments in particular. This department and the staff that work in them have had some momentous experiences and unexpected changes over the last couple of years.

Prior to COVID, we just had a few staff working in the molecular department at the microbiology laboratory where I work. We had a limited after-hours and weekend service. Pre-COVID, we were working hard to expand our molecular menu and staffing but as with all such changes, it was a slow process.

COVID changed all that…

When COVID first arrived in NZ in early 2020, it took a few weeks for the first diagnostic tests to be set up in the reference centres, and another couple of months for such assays to arrive at our (regional) lab. When we were finally able to offer diagnostic testing in-house, we could not initially keep up with demand so testing had to be prioritised to hospital inpatients.

Pooling of samples and the arrival of new testing platforms allowed our test capacity to quickly increase, but that brought other issues. New staff had to be recruited & after-hours and weekend molecular rosters had to be dramatically extended. As these SARS-CoV-2 assays were all new, they had to undergo test validations, which then needed to be written up for accreditation purposes. This validation work put extra pressure on staff that were already processing far more samples than they would normally. In addition, worldwide demand for test consumables, along with border restrictions created supply issues, which meant maintaining an effective service could be extremely difficult at times.

Several of our non-molecular microbiology staff were periodically drafted into the molecular department to help with sample pooling and to process all the COVID PCRs. This allowed us to offer 24/7 COVID PCR testing. It was all hands on deck!

Other molecular (& culture based) tests were “rationed” in order to allow for the avalanche of COVID testing. Clinical microbiologists like myself tightened up the clinical acceptance criteria for molecular assays such as enteric PCRs & STI multiplex PCRs in order to free up both testing platforms and staff for COVID testing. We also clamped down on relatively low value culture-based testing such as sputum culture and skin and nail mycology from the community setting.  The other main role for clinical microbiologists was to approve out of hours “rapid SARS-Co-V testing” on rapid testing platforms such as GeneXpert. This led to several disrupted nights’ sleep, but we know we got off lightly from the pandemic compared with the staff who were actually doing the tests!

During the peak of the SARS-CoV-2 PCR testing surge, we were processing in excess of 3000 SARS-CoV-2 PCR tests per day. Normally we would do 1000-1500 microbiology and molecular tests in total per day, so the increase in tests was completely unprecedented.

Then COVID Rapid Antigen Tests (RATs) arrived in the community, and things changed dramatically… For various reasons, the introduction of RATs into NZ for COVID diagnosis arrived relatively late and it also occurred very suddenly.  Our COVID-19 test volumes went from 3000 per day to 200 per day, literally overnight.

Once this happened, the staff could take a breather, catch up on other tasks & projects that had been put on the backburner, take some well-deserved downtime, take some leave, and recharge the batteries.

Despite the trials and tribulations, I have no doubt whatsoever that our molecular department has been left in a better place as a result of the COVID pandemic. The increased resourcing has allowed us to offer more molecular tests after hours and at weekends, thus improving our clinical service. It has also given us the staff resource to validate and implement new molecular assays, further extending our diagnostic menu. The increase in testing platforms within the department have also given us more testing options. The molecular staff, battle-hardened by COVID, are now a resilient bunch and well prepared for future challenges!

We continue to work hard to position ourselves as one of the leading molecular departments in the country. COVID has undoubtedly helped that process along.

How has COVID impacted on your molecular department?



4 thoughts on ““The impact of COVID on the molecular department of microbiology laboratories”

  1. Hallo Michael! Our lab’s changes were pretty mouch the same.. But unfortunately, when the pandemic wave weakened, other aspects predominated : employees were released, others became part-time.. Sadly, most of the times, managers are narrow-minded..

  2. Michael, excellent commentary. Covid is not over and RATs have enabled more person-centred management but PCRs are required to enable us to continue to monitor and undertake surveillance of emergent sub-variants. As the situation in China and the current surges in New Zealand and the Northern Hemisphere take effect I have no doubt that it is not a swarm we will be dealing with but a tsunami! We need microbiology to manage the sister impact of bacterial and multiidrug resistant organisms additionally swampting us the then the upcomine viral winter illnesses. Capacity and capability must continue to be supported and strengthened and networked/linked within our system to strengthen our ability to ‘weather’ the oncoming storms for the population’s health. Well done and keep positive.

    1. Thank you for your comments Sharon. Yes it is very important a subset of our diagnostic testing for COVID continues to be PCR based to permit whole genome sequencing and variant determination.

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