Covid-19 Coronavirus: New ‘Missing Match’ Cases Are Hugely Significant

One virologist says it is “hugely significant” that there is no genomic match between the new cases and none at MIQ, possibly pointing to a missing link in the community or a leak from another part of the border.

Genome sequencing creates a “genetic fingerprint” of a virus that has infected a person, allowing health officials to untangle or link different cases.

Sequencing was especially crucial in the August outbreak, and also in New Zealand’s more recent community forays, giving officials more confidence that the virus had been isolated and eliminated.

But in the latter case, there was no genomic match with any positive case detected in controlled isolation and quarantine (MIQ).

Virologist at the University of Otago and ESR, Dr. Jemma Geoghegan, said that fact was “very significant.”

“That is why the city was closed, because there is no physical or genomic link that we can immediately identify in a way that links this case to our border, and that is very concerning,” he said.

“It’s like going back to [the Auckland August cluster], where we’ve had this lineage at MIQ before, but it’s not a direct link.

“So, either we are losing people in this transmission chain or it is another source of leakage from the border, and not through MIQ.

“At this point, many pieces of the puzzle are still missing and we may not find an answer, as we did not in August.”

He added that it was positive that the tests so far had not revealed more hidden community cases.

ESR’s director of bioinformatics, Dr Joep de Ligt, agreed that a “middle step” may be missing.

“It’s another line of evidence that we have to be cautious and we have to take the precautions that are being taken now,” he said.

“We just have to do everything we can to find those missing links, and in the meantime also make sure they don’t spread any further.”

De Ligt said the scientists had tried to sequence almost all the positive cases that had been detected at the border.

Some of those samples had a low viral load of the virus, making it difficult to obtain a complete genome.

“But even in those where we have a partial genome, we look for the specific mutations that are present in these cases, and we haven’t found a link.”

Some other samples that were recently collected have yet to be sequenced.

“So if there are any leads we can find, we will find out as soon as possible.”

The latest cases come when ESR recently expanded its sequencing work to its Mount Albert Science Center in Auckland.

Since its opening late last month, the center has now sequenced multiple SARS-CoV-2 genomes in 12 sequencing runs.

The first sample was received on January 25, when urgent work was needed to sequence the cases involved in the Northland scare last month, and the latest included the cases from Sunday.

Until last month, sequencing in downtown Auckland was carried out for research and development of sequencing methods for forensic applications.

The Auckland team, working alongside scientists from ESR’s Kenepuru Science Center in Wellington, includes staff with experience profiling DNA and RNA from case samples.

ESR has also provisioned its Christchurch facility for any urgent samples needing sequencing from the South Island.