It all comes down to adjacent hotel rooms and a domestic flight, new research suggests.

I know I’ve said this before, but one of the many benefits of New Zealand’s elimination strategy for Covid-19 is that our lack of community transmission, coupled with our testing and genomic sequencing capabilities, is helping us and the world better understand how the virus transmits between people. 

Remember the excellent study by Jemma Geoghegan and Tara Swadi and their collaborators which showed how the virus transmitted between passengers on a long-haul flight to New Zealand? Well Jemma and team are back with another cracker. This time they’ve got to the bottom of the “bin lid” case we had back in September last year, where it looked like someone got infected in managed isolation and quarantine (MIQ) from touching a bin lid. They’ve just published their findings in the CDC’s Emerging Infectious Diseases journal. 

After reading this piece, maybe you’ll understand why I’ve been so frustrated that Air New Zealand and other airlines are still serving refreshments on short haul flights while there’s a mask mandate.

A new mystery cluster

In late September 2020, the Ministry of Health announced that someone who had recently finished their 14-day stay in MIQ had developed symptoms of Covid-19 and tested positive. After testing that person’s close contacts and their close contacts we ended up with a cluster of nine cases: A, B, C, D, E, F, G, H, and I. 

G was that first case identified, the person who had been through MIQ. H and I are their family members, who hadn’t been overseas. So how did G get infected and where do all the others fit into the picture? This is where genome sequencing backed by the public health investigation helped the team figure it all out. The clear links between all the cases and use of the test-trace-isolate strategy also meant we avoided a move up the alert levels to get the cluster under control.

Genome sequencing to the rescue

As I’ve explained before, the SARS-CoV-2 virus responsible for Covid-19 is an RNA virus with a genome that’s about 30,000 nucleotides long. Those nucleotides – adenine, cytosine, guanine, and uracil – are more commonly known by their abbreviations, A, C, G, and U. Each time the virus enters a new cell and replicates, its RNA also needs to be copied. It’s here that errors can creep in, replacing the nucleotides that should be at a certain position. We can think of each of these errors as a mutation. Scientists call them single nucleotide polymorphisms or SNPs for short. Following how mutations or SNPs appear within the virus’s genome can help us to see who might have infected whom.

In all, the virus genomes of the nine people from the mystery cluster differed by just one to four mutations. The genomes from cases A and B were identical, though these people didn’t know each other. The genomes from cases C and D were identical to each other but differed from A and B by one SNP/mutation. The genomes from E, F, and G were identical to each other, but another SNP/mutation different to C and D (and so two away from A and B). Lastly, the genomes from H and I were identical and two SNPs/mutations different to E, F, and G (so four away from A and B). 

Transmission on a plane, and another plane, and in managed isolation …

Here’s what happened. Cases A, B, and C were all on the same 18-hour repatriation flight from India to Christchurch via Fiji. They didn’t know each other but B and C were both sat within 2 rows of A. It looks like A and/or B got infected in India, and then transmitted to C during the flight. Passengers were required to wear masks during the flight but would have presumably removed them to eat and drink. 

Case C tested positive in MIQ at their day-12 test. They had a room next door to D and D’s child, E. D is the person who was initially thought to have been infected by touching a bin lid that C had also touched some 20 hours before. Now we know that SARS-CoV-2 is airborne, a much more likely scenario is that case D was infected by exposure to airborne virus shed by case C. 

CCTV footage showed that C and D were never outside their MIQ rooms at the same time. But they both got their day 12 swabs taken on the same day. And these were taken from their doorways. C was tested first. Then there was a 50-second window between them closing their door and D opening theirs to be swabbed. It looks like having the hotel room doors open for as long as it took to be swabbed was enough to move airborne virus from C and their room into the enclosed and unventilated corridor and then on to D and into their room. From the genome sequencing, it looks like D then infected their child, E, and another household member, F. 

But what about G, the case that sparked it all? Well, D, E, and G all left MIQ on the same day. Remember, D had been exposed to the virus just a couple of days before but must have been infectious by this stage. They all took a chartered flight from Christchurch to Auckland and G sat in the seat in front of D and E. Again, masks were worn. But it looks like transmission happened on that short flight. I can’t tell you whether the airline served refreshments or if everyone had their masks on the whole time. Even if they did, we know that while surgical masks are better than nothing, they aren’t as effective as properly fitted N95’s masks for stopping the transmission of airborne virus particles. 

So, there you have it. Not only another documented case of transmission on a long-haul flight, but also likely on a short-haul flight within New Zealand, and from airborne virus particles travelling between adjacent hotel rooms.