The Auckland outbreak is New Zealand's
largest and most complex cluster to date, with 159 people, including 85 who have tested positive and their household contacts.
Contact-tracing data show that before Auckland's move to level 3, the reproduction number was between 2 and 3.
This means that on average each new case passed the virus on to two or three other people.
We have seen transmission in workplaces, churches, public transport and shops, as well as within households. The fact that the infection was passed between strangers on bus journeys shows how stealthily this virus can spread. It also emphasizes how rapidly it can move around the city.
As Auckland prepares to relax restrictions on Monday, contact-tracing data show the rapid decision to place New Zealand's largest city under alert level 3 lockdown has undoubtedly prevented an explosive outbreak of COVID-19.
Restrictions on gatherings of more than 10 people and compulsory mask use on public transport will help. But the best way to prevent a resurgence of the virus at level 2 is if we all avoid the three Cs: closed spaces, crowded places and close contacts.
...genome sequencing results are now available overnight, and sometimes even on the same day. This allows health authorities to infer a connection between cases or pinpoint potential sources of infection much more promptly than before.So far, the technique has confirmed Auckland’s second wave of cases are all part of the same cluster, except for one case identified on Tuesday who contracted the virus via exposure to a returned traveller from the United States. There are now 87 confirmed cases in the new Auckland cluster. All are in quarantine, along with some of their close contacts.
First, it identified a new case without links to the current community cluster. A maintenance worker at the Rydges Hotel managed isolation facility tested positive on Sunday. By Tuesday, sequencing results showed this case was not part of the wider cluster, but rather that the genetic sequences matched those from a US returnee who had stayed at the Rydges before testing positive and being moved into quarantine.
Without rapid genome sequencing, contact tracers would have spent considerable effort looking for a link to the known cluster. Instead, their work is now focused on finding out how the worker got infected and whether there are any intermediate cases.
The virus can be transmitted in managed isolation facilities, as the recent Rydges hotel case underlines. Around 40% of cases found in managed facilities have no available genome sequence because the sample contains too little viral material. This usually indicates a low viral load (and low level of infectiousness), but it does not rule out transmission. The source may be among one of these cases.
Neither can we rule out the possibility that a case in managed isolation or elsewhere at the border was not detected. Even testing twice (currently on days three and 12 of quarantine) is expected to miss at least 4% of cases, based on a false negative rate that is at best 20%. This high false negative rate is one reason to insist on 14 days of isolation.
Second, genome sequencing has also shown that all other cases so far are part of a single cluster.
It indicates the current cluster comes from the so-called B.1.1.1 lineage, most frequently documented in the UK but more recently found in Europe, Australia and South Africa. This lineage has been seen once before in New Zealand, in a pair of cases in mid-April who were in managed isolation in Auckland.
Even trying to determine the country of origin is hard. Many lineages, including B.1.1.1, have a wide global spread. We can understand the extent of the spread using GISAID, the global database in which viral genomes are shared. But with different countries having radically different sequencing efforts (of the 81,000 genomes on GISAID, 35,000 are from the UK alone), finding a link to a country could merely indicate that country has done lots of sequencing.