Tag Archives: COVID 19

“Avoiding Burnout in the COVID Marathon”

I have seen a lot of tired looking colleagues around. I have spoken to people that are tetchy who are not normally tetchy. I know of colleagues who have been working far in excess of their normal working hours…

Is this the new normal?

It has made me wonder about the sustainability of it all, and how many people are going to “fall over” next year when they come to realise that this pandemic is not going to go away anytime soon, even with the introduction of a vaccine.

It became obvious quite quickly that COVID-19 was going to be a marathon, not a sprint. Being a marathon runner myself, I am well used to pacing and knowing what happens if one sets off too quickly! There will be few people working in microbiology who have not been affected by the extra work pressures that this pandemic has recently caused. In my opinion 2021 will be more of a risk for burnout than 2020. Continued pressure leads to burnout…

Here are a few of my own personal tips for avoiding burnout, in the hope that I will be able to get through the next year relatively unscathed.

  1. Be very selective about voluntary work:- We may not realise it, but a lot of work we do is to a large extent “voluntary” in nature. Whether it is giving presentations, reviewing research papers, attending webinars, participating in advisory groups. In a pandemic situation all this type of work just adds to the stress, and eats away at our working hours. Please, be ruthless with this type of work, and just focus on your core work, even if some onlookers think you are being lazy…
  2. Don’t get caught up in the “work” hype:- In the pandemic situation, people lose perspective, and have a tendency to get caught up in the work frenzy, feeding off each other’s nervous tension, reading and responding to every work request. Don’t do this, keep perspective and be aware that you only have so many working hours each week to be as productive as possible.
  3. Take leave:- Mix this up between intermittent “treat” days off and the occasional period of longer leave (1 week plus). When you are on leave, you must be completely detached from work, no email contact, no texts, no Whatsapp groups, nothing. Switch off all your notifications. Ideally have a dedicated work phone and leave it there. I find that the people that adhere to these leave rules are the ones who have the best work-life balance.
  4. Don’t do backlogged work on return from leave:-  Taking leave is one thing. Returning from it is quite another! The last several times I have been on leave I have left an Out of Office message saying. I will be on leave between dates X and Y. Emails received during this period will not be read. If you have an important personal message for me then please resend it after date Y. I  then have an empty inbox within 1 minute of returning to work because all the emails received during leave get dumped immediately and unceremoniously into an archive folder without review. Trust me, the sky does not fall!, and I do not return from leave with an impending sense of doom. Rarely does anyone actually resend an email on my return, which goes to show how “impersonal” or trivial most email is…
  5. Don’t go to every meeting you are invited to:- I get invited to approximately 15 meetings a week. If I went to all of them, half my work hours would be gone in one fell swoop, just like that. I therefore am fairly ruthless about which meetings I go to. Are they meetings where I can influence the outcome, or where I need agreement from others for the agenda I am following? Otherwise it is just another hour down the drain.
  6. Be ignorant:- Nobody can be expected to be up to date with all the COVID research. Even if you are up to date, you will almost certainly be out of date within weeks, such is the pace of knowledge acquisition. Accept that you will be a bit ignorant! Pick a topic within COVID that particularly interests you and keep abreast of developments in that field. Then try and contribute in that area.
  7. Leave work at work:- Working out of hours should very much be the exception as opposed to the norm. When you finish work, go home to your family and the rest of your life and your other passions outside of work. You can start thinking about work again the next day.
  8. Connect and be kind:-. It is very easy to become short-tempered when you have a lot of work on your plate. However, before you have an argument, remember that you need to see and work with this person the next day, and the day after that. You can connect and be kind without having to be best friends.
  9. Share the blame:- I am a big believer in the philosphophy that a problem shared is a problem halved. There is nothing more stressful than trying to sort out a complex issue single handedly. 
  10. Build teams rather than being a linchpin:- From an individual point of view, it is nice to be seen as a linchpin, to be viewed as indispensable in your particular department or area of expertise. However from an institutional point of view and particularly during a simmering pandemic like this one, linchpins can be detrimental, because of an over-reliance on the linchpin. When the linchpin eventually falls over, because nobody can keep going forever, then the whole system runs into trouble. What you need is an effective team, where one person can go off on leave (or off sick) and there will be little difference to the productivity. This pandemic has made me realise how critical it is to function as a team, rather than putting all your efforts into being a linchpin.

I currently have 2 jobs and a family of 8 at home. If anyone is going to burn out, it will be me! I am very aware of the need to listen to my own advice and follow the rules above. Sometimes I lapse and then need to discipline myself in order to optimise work-life balance. 

Even with a vaccine on the horizon, the COVID-19 pandemic will keep us all occupied for at least the next year, and most likely a bit longer than that. We each need to have a personal plan of how to navigate through it from a work point of view.

Look after yourself, and look after each other.


“Between the devil and the deep blue pool…”

Pooling of COVID-19/SARS-CoV-2 samples has been an important and integral part of the NZ laboratory response to COVID-19.

Two weeks ago, following the appearance of COVID-19 cases in the community following a 100 day hiatus, test volumes surged  nationally from 4000 samples to 27000 samples a day, literally overnight…

It goes without saying that without widespread pooling of samples, we would have had testing backlogs of several days if not weeks, completely devaluing the usefulness of the results in terms of contact tracing and significantly increasing the risk of exponential growth in the outbreak.

Microbiologists, by nature, are purists. They understandably want their laboratory to produce the “perfect” result. Accreditation agencies may have similar views, with a narrow focus on the quality of the results produced. That’s their job after all…

But the world, and in particular the COVID world that we now live in, is far from perfect, and we need to keep looking at the big picture.

Pooling of clinical samples for a PCR assay has a small effect on sensitivity. Because we measure virus counts on a logarithmic scale this effect is almost, but not quite negligible, if a small number of samples are pooled. We have the potential to miss “positive” samples with very low viral loads, likely coming from patients who are almost certainly non-infectious. In my anecdotal experience, most of the results produced at the limit of detection are in patients who are recovering from infection, in the recent or not so recent past. Our experience shows that the loss of sensitivity by pooling samples is probably less than using a throat swab instead of a nasopharyngeal swab.

The other potential drawback of pooling is that if you get a positive pool, you then need to test all the samples in the pool individually. If positivity rates are high then pooling becomes self-defeating, creating even more work! However positivity rates in NZ have up until now been very low, so this has not been an issue for us.

As far as I am aware, NZ diagnostic laboratories that have utilised pooling (most of them) have validated the methodology over different platforms to the best of their ability, within the considerable time and resource constraints they have had to work within. In addition they have implemented IT solutions to facilitate the pooling of samples from a pre-analytical point of view.

Registration and molecular staff all over the world have been under the pump recently due to COVID-19 testing. Long, long hours, validation of new assays and platforms, pressure to get results out quickly… It is tough and I am in utmost admiration of our molecular team. Pooling is one of several ways to reduce this pressure on staff and try and prevent burnout. COVID-19 and the associated high testing volumes are not going to go away. This was always going to be a marathon effort, not a sprint, so testing processes need to be sustainable in the long term.

COVID-19 is a new disease but pooling of laboratory samples is not. The thing that has become very clear with regards to this infection, is that effective control depends to a large degree on testing large numbers of people and getting the results out quickly so that appropriate isolation and contact tracing can be performed. We should be embracing policies that allow us to achieve this goal.

Up until now at my own lab, our largest volume molecular test was Neisseria gonorrhoeae/Chlamydia trachomatis PCR, approximately 60,000 tests per annum. SARS-CoV-2 test numbers are going to completely and utterly dwarf this!

We need to adapt, in a pragmatic and realistic fashion, to the situation that we are currently faced with.


There are plenty of examples of SARS-CoV-2 pooling studies out there. Here is one for starters!

“Influenza in NZ 2020: Gone AWOL…”

We are currently heading towards the end of July, which is well through the winter respiratory virus season in the Southern Hemisphere. And still we have not seen any Influenza (or RSV for that matter) circulating in New Zealand. At first I thought it was the lockdown through March and April which was blocking viral transmission through social distancing. However we are now a couple of months post-lockdown… Social distancing has essentially all but disappeared and still there is no Influenza and RSV in New Zealand. This must be now due to the fact we have a closed border and the fact that nobody can currently enter New Zealand without staying in a quarantine facility for 2 weeks on arrival. This seems to be blocking any potential influenza and RSV introductions into NZ*

The winter respiratory virus season still has a couple of months to run here, but things are looking very promising. An average influenza season in NZ causes an average of 400-500 fatalities. There is little doubt that RSV will also cause significant mortality in those with advanced respiratory disease and in the frail elderly. I would suspect that respiratory viruses as a group would count for well over 1000 fatalities per annum in NZ, not to mention several thousand hospital admissions. In contrast the 22 COVID-19 fatalities, although tragic, seems a meagre toll…

Clearly we (NZ) cannot keep our international borders closed indefinitely, because human nature will simply not allow it. We do however have to be very smart about re-opening our borders, using all the risk mitigation tools we can lay our hands on. We have a nation of 5 million COVID-19 virgins to look after, but that is another story.

When the borders do re-open can we still control the winter influenza season? We may not be as successful as we have been this year but I think 2020 has shown that control of seasonal influenza is entirely possible by trying to minimise “introductions” and their subsequent effects.  I would suggest the following measures:

  • Having a low threshold for testing, treating(oseltamivir) and isolating  travellers coming back into New Zealand who have respiratory symptoms
  • Influenza & RSV in returning travellers should be notifiable to Public Health so that the appropriate measures can be taken.
  • Influenza vaccination should be strongly encouraged for travellers coming into New Zealand, particularly those coming from the Northern Hemisphere
  • Routinely vaccinate all children to further reduce the chances of transmission, should any introductions occur

Put quite simply, we set the bar too low for seasonal influenza control in NZ. We regard the winter influenza season as an inevitability. We shouldn’t. We are a small island nation, and our COVID-19 response has shown that we can be united and disciplined when we want to be!

“We set the bar too low for seasonal influenza control in New Zealand”

Let’s make the NZ winter influenza season the exception as opposed to the rule…


Interestingly rhinoviruses, although much suppressed during the lockdown period, survived and are now flourishing, and possibly filling a niche created by the influenza and RSV vacuum. See this interesting blog post from Australia