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Blinding you with science
Of course, as soon as I posted yesterday I remembered all the things I’d left out. If I put all of them in this would be novel-length, but I thought I’d mention the most important one and also give a glimpse of the really quite awesome science and procedures we’re using in New Zealand to chase this thing down.
The important thing I missed was the critical role of PPE, handwashing and social distancing. Although 95% of our transmissions have been through close contacts rather than casual contacts, that still leaves room for occasional casual transmission and so masks, handwashing and social distancing still are important. As an example: all of the cases in New Zealand’s new outbreak have now been linked to a single cluster – except one. That case was a maintenance worker working at the hotel being used as the Auckland quarantine facility.
Backing up a bit to explain the sitch:
During our original outbreak, New Zealand closed its borders completely until we got to zero cases. If we’d stayed that way we wouldn’t have had to worry about Covid ever again, but because that’s a bit impractical, at that point we opened our borders again only to returning New Zealanders. To make sure any Covid those people brought with them didn’t get into the community, we set up what we now know as MIQ: managed isolation/quarantine. All new arrivals stay for 14 days in managed isolation (in other words, a hotel with security around it), are tested on the third and twelfth day of their isolation, and if they are or become infected are transferred to the quarantine facility (another hotel).
Clearly under this system any workers at the managed isolation and quarantine facilities are potential vectors of transmission, so they receive regular tests. Recent testing turned up the case of an infected maintenance worker at the quarantine facility. He was immediately isolated, as were his close contacts, and testing showed he hadn’t passed on the infection to any of them. Phew. The question still remained, however, as to how the worker had become infected.
Because we’ve had such a small number of cases, we’ve been able to do genomic sequencing on most of them, including all the cases from the original outbreak. As well as being super awesome just by itself (right?), it’s also been really useful in seeing how all the clusters from the original outbreak fit together, and equally useful now at tracing infections. The maintenance worker’s case was sequenced and compared to the genomic sequences already held for the people who’d been in quarantine, and matched to one of those cases. The maintenance worker turned out to have never had any personal interaction with that person, so we then used CCTV footage and swipe card data to see where their paths had crossed.
It turned out that the two people had used the same lift [elevator], not together, but the maintenance worker closely in time after the infected person. It’s therefore hypothesised that the infection was passed via the lift button.
This is such a tricky virus. The lift button! Had the maintenance worker washed his hands just afterwards, the chances are that transmission would have been prevented. So we all need to keep doing that stuff even though infection chances through casual contact are low.
And this example also shows how much trouble we are able to go to in New Zealand, because of our small number of cases, to track them down, learning a lot about the virus as we go. Despite that, however, we can’t yet nail down how the current cluster started. But it’s certainly not for want of trying.
First of all, we sequenced the earliest cases in the cluster. Sequencing showed it was highly unlikely to have been somehow left over from our original outbreak: the sequence found was rare in New Zealand then but common overseas, meaning the overwhelming likelihood is that it’s related somehow to a returning New Zealander bringing it in over the border. We tested everyone with border jobs – frontline airport staff, drivers, airline crew – but couldn’t find a match. We compared the genomic sequences to those of all the quarantine cases – no match.
Then we turned our focus further outwards. One of the initial cases worked at Americold, and there was some concern that the virus had come in, preserved by the cold, on Americold’s freight, especially as there’s been an Americold-linked outbreak in Melbourne. So as well as testing the staff at Americold, we found all the contractors who had visited Americold and tested them, and also tested all the staff at the port where Americold’s containers come in. We even did tons of surfaces testing at Americold and compared the genomic sequences with the ones from the Melbourne outbreak. Nothing.
So although we've learned some things, like that surface transmission over more than a short period of time is unlikely to happen, we’re still stumped as to exactly where this outbreak has come from. See above re tricky virus. But is all this awesomely sciency or what?
I still haven’t got to why we’re going in this direction, but this is way too long as it is, so again, that’s for another post.
The important thing I missed was the critical role of PPE, handwashing and social distancing. Although 95% of our transmissions have been through close contacts rather than casual contacts, that still leaves room for occasional casual transmission and so masks, handwashing and social distancing still are important. As an example: all of the cases in New Zealand’s new outbreak have now been linked to a single cluster – except one. That case was a maintenance worker working at the hotel being used as the Auckland quarantine facility.
Backing up a bit to explain the sitch:
During our original outbreak, New Zealand closed its borders completely until we got to zero cases. If we’d stayed that way we wouldn’t have had to worry about Covid ever again, but because that’s a bit impractical, at that point we opened our borders again only to returning New Zealanders. To make sure any Covid those people brought with them didn’t get into the community, we set up what we now know as MIQ: managed isolation/quarantine. All new arrivals stay for 14 days in managed isolation (in other words, a hotel with security around it), are tested on the third and twelfth day of their isolation, and if they are or become infected are transferred to the quarantine facility (another hotel).
Clearly under this system any workers at the managed isolation and quarantine facilities are potential vectors of transmission, so they receive regular tests. Recent testing turned up the case of an infected maintenance worker at the quarantine facility. He was immediately isolated, as were his close contacts, and testing showed he hadn’t passed on the infection to any of them. Phew. The question still remained, however, as to how the worker had become infected.
Because we’ve had such a small number of cases, we’ve been able to do genomic sequencing on most of them, including all the cases from the original outbreak. As well as being super awesome just by itself (right?), it’s also been really useful in seeing how all the clusters from the original outbreak fit together, and equally useful now at tracing infections. The maintenance worker’s case was sequenced and compared to the genomic sequences already held for the people who’d been in quarantine, and matched to one of those cases. The maintenance worker turned out to have never had any personal interaction with that person, so we then used CCTV footage and swipe card data to see where their paths had crossed.
It turned out that the two people had used the same lift [elevator], not together, but the maintenance worker closely in time after the infected person. It’s therefore hypothesised that the infection was passed via the lift button.
This is such a tricky virus. The lift button! Had the maintenance worker washed his hands just afterwards, the chances are that transmission would have been prevented. So we all need to keep doing that stuff even though infection chances through casual contact are low.
And this example also shows how much trouble we are able to go to in New Zealand, because of our small number of cases, to track them down, learning a lot about the virus as we go. Despite that, however, we can’t yet nail down how the current cluster started. But it’s certainly not for want of trying.
First of all, we sequenced the earliest cases in the cluster. Sequencing showed it was highly unlikely to have been somehow left over from our original outbreak: the sequence found was rare in New Zealand then but common overseas, meaning the overwhelming likelihood is that it’s related somehow to a returning New Zealander bringing it in over the border. We tested everyone with border jobs – frontline airport staff, drivers, airline crew – but couldn’t find a match. We compared the genomic sequences to those of all the quarantine cases – no match.
Then we turned our focus further outwards. One of the initial cases worked at Americold, and there was some concern that the virus had come in, preserved by the cold, on Americold’s freight, especially as there’s been an Americold-linked outbreak in Melbourne. So as well as testing the staff at Americold, we found all the contractors who had visited Americold and tested them, and also tested all the staff at the port where Americold’s containers come in. We even did tons of surfaces testing at Americold and compared the genomic sequences with the ones from the Melbourne outbreak. Nothing.
So although we've learned some things, like that surface transmission over more than a short period of time is unlikely to happen, we’re still stumped as to exactly where this outbreak has come from. See above re tricky virus. But is all this awesomely sciency or what?
I still haven’t got to why we’re going in this direction, but this is way too long as it is, so again, that’s for another post.