Coronavirus Covid 19: the three theories of the August outbreak in Auckland

Scientists have turned Auckland’s complex history of the Covid-19 August cluster into a fascinating interactive one, matching their cases with genomic data. Science reporter Jamie Morton Spoken to Dr. James Hadfield, a Wanaka-based phylogeneticist from Seattle’s Bedford Laboratory, on what we’ve learned and the three possible explanations for the mysterious outbreak.

Genomic sequencing helps scientists and public health officials identify the lineages of each positive case and connect them to other local cases, along with what is circulating in other countries. How did the genomic profile of the August Auckland group differ from that of earlier New Zealand groups?

Reviewing our first series of outbreaks, between February and June, we know that there were more than 250 separate introductions of Sars-CoV-2 in Aotearoa New Zealand, accounting for “almost all of the genomic diversity present in the global viral population.”

The Auckland August Cluster belongs to a lineage found on multiple continents around the world. We have seen this lineage only once before in New Zealand, in a couple of cases in mid-April that were in administered isolation in Auckland.

Given the timing, epidemiological data and worldwide prevalence of the lineage, we think it is highly likely that the Auckland August cluster is a new import from abroad.

How can we know that the recent Auckland outbreak came from a single viral source?

Sequencing the genomes of many different cases of the outbreak shows that they are all clustered, with no global isolates involved.

This is what we would expect from a group that has spread within New Zealand and originated from a single viral source. The exception to this was the case of the Rydges Hotel.

Can you tell me about Nextstrain, the global platform you are contributing to, and the interactive narrative you have created here? What does it show us?

Nextstrain has been around for about four years and is an academic project that uses genome sequencing of pathogens like Covid-19 to produce rapid analyzes.

These results are intended to be “actionable” or to be useful in informing public health responses.

We disseminate the results freely through nextstrain.org so that everyone can interact.

Understanding these analyzes can be difficult without prior training in phylogenetics, so I have been exploring ways we can better communicate the insights that genomics provides.

Narratives allow scientists to write reports where each section of the text is displayed alongside a specific visualization of the data.

In other words, the scientist can guide the viewer through the data and pass on the information he gets from it.

We wrote this particular narrative for Kiwis to read, with the goal of better communicating the data and what it tells us, and not what, about the current situation.

I hope people find this medium accessible.

Genomic analysis suggests three possible sources for the outbreak: a border incursion from abroad, namely from the UK or Ecuador; undetected community transmission; and the virus that arrives through foreign merchandise. Can you explain each of these and which one might be the most likely?

The first hypothesis, and the most likely, is a border incursion from abroad: that an international arrival brought the virus back and subsequently transmitted it to the community.

Finding a recent case in managed isolation and quarantine (MIQ) or anywhere else on the border that matches this cluster lineage would be strong evidence for the border incursion scenario.

We don’t have any such direct evidence, but this doesn’t mean it didn’t happen.
Although we have attempted to sequence all the positive cases identified at the border, about 40% contain genetic material (RNA) too little or too degraded to obtain a complete genome sequence.

Furthermore, the smear test for Covid-19 is known to miss a proportion of cases, so even the MIQ testing regimen, with testing on days three and 12, could miss about 4 percent of cases. true positive cases.

Due to how genetically similar the Auckland Cluster genome is to others around the world, it is difficult to use those international samples to identify specific geographic sources with certainty.

For example, the closest samples we have are from Ecuador, but there were no returnees from Ecuador to New Zealand from early June to late July, when the first Auckland cluster case developed symptoms, so it is unlikely that such be the route.

The second hypothesis is that the source was a case of undetected community transmission from our previous outbreaks.

An isolate from New Zealand is genetically similar to the current Auckland group, which came from a case known to be infected prior to its arrival in New Zealand and was immediately quarantined in Auckland in April.

Given the mutations between the April case and the August group, and the time period involved, our analysis estimates that there is a less than 1% chance that this case is the source of the outbreak.

Extensive testing and contact tracing determined that the first case found to date was an Americold refrigerated store worker who first showed symptoms on July 31, with the group’s initial spread focused on this refrigerated store, that imports frozen products.

Therefore, the third hypothesis is that the virus could have been imported in packaging material, where it could have survived in low temperature conditions, and then infected a worker in the refrigerated store.

This hypothesis is further credible because of the possible genomic link to Ecuador, as viral particles have been found in China in frozen shrimp packages from Ecuador.

However, the refrigerator in question did not receive shipments from Ecuador.

Our analysis shows that the estimated mutation rate in the branch leading to the bunch is not much lower than in other parts of the tree, which makes little importance of the possibility of the virus remaining inactive in the packaging material for a long period. of time.

Environmental testing of the August 15 refrigerated facility found a weak positive sample on the packaging, which was considered consistent with contamination.

Confirming or excluding fomite transmission is very difficult to test in uncontrolled or non-laboratory settings, but so far it appears that fomite transmission is not very common.

The narrative presents all of these in more detail along with interactive visualizations of the data.

Is it fair to assume that we will never know exactly what that source was?

We may never know, every situation is different.

We have seen examples since then, the Rydges case and the recent “Christchurch returnee cases”, where the data was more conclusive in identifying the source.

That Rydges Hotel case actually turned out to be an interesting outlier. What did this tell us about the value of rapid genome sequencing and also that random pop-ups like this can happen?

Two days after the positive test result, sequencing data showed that the case was not part of the larger group in Auckland, but was very similar to a returnee who had stayed in Rydges before testing positive.

This prevented contact trackers from spending valuable time searching for a non-existent link between this case and the ongoing Auckland group.

The analysis also indicates that our understanding of the genomic picture could change. Why is this?

Tracking outbreaks like these relies on comparing genomes from the Auckland group to everything else that’s available.

If we can get more genomes, for example, from the July MIQ cases, which we haven’t been able to sequence so far, then that data may give us more confidence in one of the hypotheses we present here.

A central idea behind nextstrain is that as we get more data, we can continue to update the analysis and our findings.