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Positive cases were staying in adjacent rooms in the MIQ hotel. Photo: Getty
Positive cases were staying in adjacent rooms in the MIQ hotel. Photo: Getty

ScienceMarch 20, 2021

Siouxsie Wiles: The great Covid bin lid mystery – solved

Contributing writer
Positive cases were staying in adjacent rooms in the MIQ hotel. Photo: Getty
Positive cases were staying in adjacent rooms in the MIQ hotel. Photo: Getty

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. 

More Reading

    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. 

    Sequence of probable transmission events and associated relevant locations in-flight and MIQ, from the CDC’s Emerging Infectious Diseases journal

     

    Keep going!
    Lead researcher Jose Polo in front of magnified images of iBlastoids (Photo: Monash University/supplied)
    Lead researcher Jose Polo in front of magnified images of iBlastoids (Photo: Monash University/supplied)

    ScienceMarch 18, 2021

    NZ scientists set to lose out on major embryo research breakthrough

    Contributing writer
    Lead researcher Jose Polo in front of magnified images of iBlastoids (Photo: Monash University/supplied)
    Lead researcher Jose Polo in front of magnified images of iBlastoids (Photo: Monash University/supplied)

    A new embryo model could change the way scientists overseas research fertility and prenatal development, but the methods they use won’t fly here, reports Mirjam Guesgen.

    Australian, US and Singaporean scientists have created a human embryo model that they think could make huge headway in understanding infertility, developmental diseases and miscarriage. But it may be beyond the reach of New Zealand scientists.

    The embryo model, described today in the scientific journal Nature, was made by reprogramming skin cells into something similar to a blastocyst – a ball of cells that’s one of the earliest forms of an embryo.

    The model, called iBlastoid, will give researchers the ability to study early developmental diseases, find ways to screen for and treat them, and offers tremendous potential for understanding infertility and miscarriages. Miscarriages remain something that doctors know very little about, yet affects a fifth (probably more) of New Zealanders.

    “Because these iBlastoids are derived from skin cells generated in the laboratory many hundreds of them can be produced each day and used for meaningful experiments [that] would otherwise be impossible due to the limited availability and ethical issues around the use of human embryos for research,” said lead researcher Jose Polo from Monash University.

    iBlastoids (Photo: Monash University/supplied)

    But this potentially life-changing, and life-giving, embryo model probably won’t be available to New Zealand scientists. Since the government has never approved guidelines for research using human embryos, there is effectively a ban on such research, even though it’s not prohibited by law.

    The new model falls into a legal grey area, University of Otago medical ethicist Gareth Jones told The Spinoff, because the technology simply wasn’t conceivable when the laws governing embryo research were first made in the mid 1980s.

    iBlastoids are pretty similar to human embryos made during conception except for a few vital differences. Those differences mean they can be used for research in Australia.

    Unlike a human embryo that forms when an egg and a sperm combine, iBlastoids are made in the lab by reprogramming skin cells using a range of proteins and genes in a petri dish. Second, iBlastoids are missing a thick membrane around them that would normally help embryos implant themselves in the uterus.

    Perhaps most importantly, the scientists meticulously watched how the iBlastoids developed, and found a raft of evidence that the model would only go through the early stages of development. The ball of cells didn’t fold inwards on itself, which would be the next step to becoming a viable human.

    Limiting how much these embryo models can develop is crucial because under both international and Australian rules, embryos used for research can only develop up to 14 days after the egg and sperm combine, or up until the point when a structure called a primitive streak (which signals the very early beginnings of developing a nervous system) forms.

    “[The researchers are] simply wanting to investigate what happens in very early human development. Surely there’s no problem with that because you haven’t started from a normal embryo… You’ve gone from adult tissue to embryo-like tissue,” said Jones. Nonetheless, previous experience leads Jones to think that the model couldn’t be used here.

    The Human Assisted Reproductive Technologies Act regulates reproductive procedures in New Zealand, with the aim of protecting the wellbeing of people born through, or giving birth via, in-vitro fertilisation (IVF) or other procedures.

    The act doesn’t state an outright ban on embryo experiments but researchers need to get approval from the ministerial ethics committee. The ethics committee acts on advice from a panel of experts, after consultation with the general public, and, in the end, it’s up to the minister of health to enact that advice.

    In 2005 Jones was part of the committee that advised that embryo research should be allowed, within certain limits of course, but “that’s where everything has stalled,” he said. “Health ministers from both parties haven’t wanted to touch it. They think it’s a hot potato. It’s hanging in the air.”

    Without guidance there’s in effect a blanket ban, he said.

    Jones is among an influential group of New Zealand clinicians, biologists and social scientists who say that the ban is limiting improvements to reproductive technologies like IVF, which currently has a success rate of around 50% for a 30-year-old woman and closer to 10% for those over 40.

    A paper Jones co-wrote in 2018 states that many researchers don’t even bother trying to do research in this area because they know they’ll be rejected by the ethics committee.

    “It is apparent that New Zealand is missing out on opportunities in reproductive science and medicine with this current legislation in place,” the paper states.

    Other research methods, such as using mouse models, do exist but “in the end mice are not human… So you’ve always got that jump. You’ve always got that uncertainty,” said Jones.

    He and others in the reproductive biology sphere are calling for clarity from the ministry around the act. The iBlastoid model may renew those cries.

    In response to questions from The Spinoff, minister of health Andrew Little said in an email: “I am aware of the issue and the matter is under consideration.”