Category Archives: Confessions of a Microbiologist

“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


“The Remote Microbiologist”

I have been doing some work from home during the New Zealand COVID-19 lockdown period.

With 6 children, 4 cats and a dog at home, this is not always easy! I barricade myself in one of the bedrooms (no office), put a sign on the door (see above), put on some headphones to dull the screams and yells outside, and get down to work…

Clinical microbiologists can do a good proportion of their work remotely. Any work that involves sitting in front of a computer or attending meetings can be done at home with the right equipment. I would say this comprises about 80% of my total workload.

The other 20%, such as reviewing culture plates and Gram stains, familiarisation with new testing platforms, performing AMS ward rounds, infection control ward reviews, and giving educational presentations require me to be either in the lab or hospital. With the digitalisation of culture images (Kiestra TLA) and Gram stains, this percentage may well decrease even further. We do have the Kiestra TLA in our lab, I just need to organise remote viewing…

I think the 80/20 breakdown of remote/in-house work is realistic.

We convince ourselves that we always need to be “present” in the workplace. But for clinical microbiologists this is just not the case. Of course it is nice to talk to and meet people face to face but it is not absolutely necessary to be physically in the lab every day. And I have lost count of how many times I have driven 1 or 2 hours just to meet with people who I could have spoken to via teleconference/videoconference.

Being an introvert, I must admit I am not a huge fan of teleconferences and videoconferences. I need those non-verbal signals that one can only pick up from being face to face. But I must say I have started to get used to them. When you are doing 2 or 3 Zoom (or similar) meetings a day, you have no choice in the matter really.

So I think when the lockdown in NZ finishes, the new “normal” will likely not be as before. I will have a lower threshold for working from home when I don’t absolutely need to be at the workplace (also saving precious time on the commute), I will think twice about driving long distances for meetings and I will try and continue to embrace videoconferencing technologies.

And all the children will be back at school so I will get some peace!


What do other clinical microbiologists think?

“COVID-19 at the bottom of the world”

We have all become amateur epidemiologists… “Epidemic curves, flattening the curve, attack rates, etc.” We know all the lingo now, and we all have an opinion..

I am lucky enough to live in the beautiful country of New Zealand. With regards to COVID-19, New Zealand has some inherent advantages. It is an island, 3 hours flight from anywhere else in the world, not that anyone is flying these days. Auckland aside, it is also relatively sparsely populated. In addition to these natural advantages, it also has a very good Public Health system and tight border controls.  People coming into New Zealand are now required to self-isolate for 14 days. All these factors added together are probably why New Zealand has been fortunate enough to avoid widespread community transmission to date. As of today (17th March), there have only been 11 cases of COVID-19 in New Zealand and all the cases have been directly related to overseas travel.

So Kiwis are watching with some anxiety the skyrocketing COVID-19 numbers from Europe and elsewhere in the world, along with the “lockdowns”, the school closures and other drastic measures to try and “flatten the curve”. And we in New Zealand are left wondering just what is in store for us…

In my opinion, the most likely scenario is that we (NZ) will eventually get community transmission, but probably not at the same transmission rates as we have seen in mainland Europe, giving us a flatter but possibly more prolonged epidemic curve, i.e. a “slow burner” of an outbreak.

Next most likely is an outbreak with a fast rise in numbers, a high peak and a rapid decline induced by herd immunity, giving the classic bell-shaped epidemic curve. This scenario would stretch our Healthcare resources to the limits and beyond.

It is probably wishful thinking that New Zealand could completely avoid a COVID-19 outbreak, whilst the rest of the world suffers, although this is not completely implausible. The chances of this happening are reduced further by the fact that our nearest neighbours, Australia, have just had approximately 70 cases in the past 24 hours, so they are “off and running”, so to speak…

If we do manage to stay COVID-19 free in the community, the downside will be that we have a population in New Zealand with no immunity and which will therefore continue to remain vulnerable to a COVID-19 outbreak into the future. This scenario could potentially lead to prolonged travel restrictions both in and out of the country and may not be the ideal outcome that it first looks like on paper.

The worst thing is actually not knowing what is in store for us. We really know very little about this virus, so we are essentially in uncharted territory with regards to disease modelling and management. Public Health decisions globally are being made more on expert opinion as opposed to any strong evidence base, and during a pandemic, everybody becomes an expert, including the politicians!

So all we can do in New Zealand is wash our hands and wave at each other, watch the politicians look increasingly rattled day by day,  check our bank accounts as our pension savings fall through the floor, and wait and see what happens in this unfolding drama.

Due to their geographic isolation, Kiwis are a resilient people. Recent events such as the Christchurch earthquake, the Mosque shootings and the White Island volcano eruption has only hardened the national psyche further. NZ will cope with whatever scenario is played out, and we will recover quicker than most!


(These views are my own, and do not necessarily represent those of my employers or children.)