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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

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