How Genome Testing Helps Uncover the Origin of Community Covid

Scientists involved in the genomic sequencing of current community-acquired cases say the analysis is ongoing and it is hoped that the results will determine if the quarantine facility was the source of the infection.

Dr. Jemma Geoghegan said Kathryn Ryan experts continue to compare the genomes of four positive Covid-19 cases at the heart of the current community outbreak with other cases globally and nationally, and He said he did not send a report.

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Dr. Ashley Bloomfield, Director of Health, said some of the key questions that the government would need within a day or two to identify how this sequencing started the outbreak and determine the next steps. Can be answered.

On Wednesday, the Auckland region entered a Level 3 blockade, other parts of the country entered into Level 2 regulations, and health officials fought to determine the extent of the infection. The limits will be fixed on Friday based on new information from testing and analysis.

Geoghegan, a senior lecturer on virus evolution at the University of Otago, said the test could identify which quarantine facilities or outposts the virus originated from for the Auckland family.

“We hope we can do that. Our aim is to compare the genomes generated from new cases and publish them to the managed isolation facility genomes and published. Is being compared with the genomes around the world.

“Then we can see what they are related to and hopefully where and when the leaks from managed isolation cases etc. have occurred.”

Geoghegan, who works on genome sequencing at the Institute of Environmental Science and Research (ESR), said that small mutations in the genome of a virus could provide scientific methods to infer the origin of infection in the entire chain of transmission. I am.

“The virus mutates slightly as it passes from person to person, so it looks much the same when comparing the genome of one Covid-19 patient to another, compared to the one captured from this genome. another.

“But comparing the viral genomes from more infected people, those differences between the viruses become more pronounced, it’s like building a family tree. Guessing the chain of transmission and where it originated I can do it.”

The slower rate of mutation compared to other viruses such as influenza means that it is difficult to determine which individual was infected with another virus.

However, it can narrow the transmission point to a managed isolation function or cluster. When this happens, use the contact traces to close the information gap by looking for close contacts with this cluster or facility and testing them.

There was speculation that the community had been infected for weeks. She says genomic testing procedures can reconstruct the chain of transmission and shed light on the matter.

“By comparing the genomes of new cases to isolation facilities, the global population and other cases in New Zealand, we began to understand how long the transmission chain could last, and when the virus emerged. We can estimate that, and first arrived in New Zealand.”

The genome sequencing procedure takes approximately 10 hours after receiving a Covid-positive sample at the ESR laboratories in Wellington or Auckland.

“The main thing after that is the analysis of the data. This is a very detailed process as it requires a lot of computational power to examine it and compare it to the rest of the available genomes.”

Experts, to her knowledge, said the ESR has not sent a report on a new case of genomic testing to the government because of the ongoing analysis and comparison of global and national Covid cases.