Efforts to track down the origin of the new cases of COVID-19 in the community are ongoing.
Director-General of Health Dr Ashley Bloomfield said in this afternoon’s media conference that genomic sequencing had not yet revealed an exact link between the new cluster of cases and border quarantine cases. So far, the new community cases have most closely resembled genomic sequences identified in cases from Australia and the UK. Meanwhile, wider community testing is underway around the country.
The SMC asked experts to comment on the use of genome sequencing and pooled testing to trace the spread of the virus in New Zealand. Feel free to use these comments in your reporting or follow up with the contact details provided.
Dr Jemma Geoghegan, Virologist, Senior Lecturer, University of Otago, comments:
“As before, the samples are being referred to ESR for genomic sequencing. It is vital that genomics is part of this response to enable us to track where these cases may have arisen and to estimate the size and number of clusters present. By comparing the virus genomes from these cases to those from both the quarantine facilities and the global population, we can determine their likely origin and how long they have been circulating in the community.”
No conflict of interest
Dr David Welch, Centre for Computational Evolution and School of Computer Science, University of Auckland, comments:
“It is encouraging to see that genomic methods for finding the source of recent cases found in the community are being used. For genomic surveillance to be useful, all cases whether they are found in the community or at the border need to be sent for sequencing as soon as they are found.
“The turnaround time for sequencing is about a day, so useful information about which cases are genetically linked can be fed back to contact tracers within the day.
“Ideally, the Ministry of Health should make it part of the contract that diagnostic labs must send positive samples for sequencing immediately so that this important process is not left to goodwill.
“Comparing genetic sequences is a very powerful way to identify chains of transmission and locate the source of infection for a cases. For example, it can identify which quarantined case a new case is linked to, or whether there is more than one chain of transmission in the community.”
No conflict of interest.
Professor David Murdoch, Clinical Microbiologist and Infectious Diseases Physician, Dean and Head of Campus, University of Otago, Christchurch, and Co-Director, One Health Aotearoa, comments:
“There have been several recent references to ‘pooled testing’ for COVID-19, including by politicians. So what is pooled testing and why is it done?
“Instead of testing one sample at a time, with pooled testing samples from multiple people are mixed together and tested as one. These small groups of samples (typically less than 8) are called ‘pools.’
“If the test comes back negative, all samples in the pool are negative. If the test comes back positive, each sample in the pool needs to be tested individually to determine which ones are positive.
“Pooled testing enables a laboratory to test more samples, using fewer tests, at reduced cost. It is particularly useful when only a small proportion of the population to be tested is infected. Higher infection rates mean that more pools come back positive and, consequently, more samples need to be retested, with lower cost savings. Indeed, pooling is no longer worthwhile when the infection rate gets above about 15%.
“In theory, pooling may reduce the ability of the test to detect a positive sample (reduced sensitivity) because of the diluting effect of mixing samples. However, pooled testing for COVID-19 has been shown to have similar accuracy to testing individual samples, and several New Zealand laboratories have successfully developed the ability for pooled testing.”
No conflict of interest
Professor Shaun Hendy, Director of Te Pūnaha Matatini, comments:
“All cases to date are linked to the coldstore cluster. This is reassuring even though it will likely take a good deal of work by our public health officials to contain all the downstream cases that eventuate from this cluster. Nonetheless, we would be confident that they can do this, especially if Level 3 is extended for a period of time.
“We are particularly interested in the ‘upstream’ contact tracing. This is where contact tracing is used to find the source of infections, rather than the resulting cases, and it is a technique that was used widely in Japan to contain their outbreak (‘cluster-busting’).
“In this case, we still haven’t identified the source of the coldstore outbreak and this remains concerning. To date, the genomic information suggests this cluster is not linked to a managed isolation and quarantine facility. The business itself is linked to international freight, air and sea, which does suggest that this is a possible entry route, whether via packaging, or more likely, via person-to-person.
“People should be aware of the possibility that it has spread beyond Auckland. Obviously some members of the cluster travelled to Rotorua, so people there should be vigilant for symptoms, staying home and seeking a test if they become unwell. There is also a reasonable chance it has spread to other parts of the North Island, and a small but significant chance it is also present in the South Island.
“Aucklanders who have left the region in the last week or so should consider self-isolating for five days. Again, they should monitor themselves and their family members closely for symptoms.”
Conflict of interest statement: Te Pūnaha Matatini is funded by the TEC, but is also currently working under an MBIE contract to supply COVID-19 modelling to government.
Dr Virginia Hope, Medical Director, ESR, comments:
“ESR has undertaken genomic sequencing and analysis of the four positive COVID-19 samples reported on Tuesday.
“As discussed by Director-General of Health Dr Ashley Bloomfield at today’s 1pm media stand-up, we have some preliminary results, but investigations are still ongoing. No links have been found with the full sequences obtained from cases in managed isolation and quarantine facilities.
“Sequencing of samples from cases in these facilities continues, with more results available tomorrow. Genome sequences most similar to these cases are from the United Kingdom. Investigations and epidemiological analysis are continuing, including comparisons with Australian genomes.
“Genome sequencing is just one part of the puzzle. It is just one tool in the pandemic response to complement contact tracing and epidemiological investigation. It does not give us all the information we need to understand the origin of cases. The information is used to inform the investigation by public health units, epidemiologists and others working with the Government to trace the origin of these cases and manage their spread.
“ESR has been sequencing isolation and quarantine cases in New Zealand for months now, and we are growing our body of knowledge about this novel virus. In some cases in New Zealand, the genome of the virus gave us clues that have helped us understand how a person was infected. This process was simpler when cases were linked to clusters where we could have said it may be associated with a certain event and therefore know how the transmission events might have happened. We cannot be sure of what we will find when we look at these new samples, but we will use the data we have already collected to find clues on where the virus might have come from.
“We will also share the viral genomes, where appropriate, with international partners as part of the global response pandemic. No private patient info will be sent to third parties.
“We will continue to sequence positive cases as we receive them. We will continue to report to the Ministry of Health for them to share.
“The quicker we receive the specimens, the better the condition of the specimen and the more likely we can identify the genome. Results will be shared through the Ministry of Health and they will update the public.
“This work also feeds into a research project. This a collaboration between ESR and Otago University which was allocated $600,000 from the Ministry of Business, Innovation and Employment (MBIE) COVID-19 Innovation Acceleration Fund in May.
“The grant allows an international team of scientists to sequence the genomes of all of New Zealand’s positive COVID-19 cases and track how the virus spread across New Zealand.
“It is led by ESR lead bioinformatics researcher Dr Joep de Ligt and University of Otago Senior Lecturer and Associate Senior Scientist at ESR Dr Jemma Geoghegan. Collaborating scientists range from Te Pūnaha Matatini, Auckland, Otago, Massey and Victoria university, as well as Nextstrain, US and UK.”
No conflict of interest