13 Aug 2020

How genome testing could help reveal the source of community Covid

From Nine To Noon, 9:20 am on 13 August 2020

A scientist involved in genome sequencing of current community-transmission cases says analysis is ongoing and that it is hoped results will determine if a quarantine facility was the source of infection.

Dr Jemma Geoghegan told Kathryn Ryan experts were continuing to compare genomes of the four positive Covid-19 cases at the centre of the current community outbreak to other cases globally and nationally, and were yet to send a report to the government.

COVID-19, Coronavirus, group of viruses that cause diseases in mammals and birds. In humans, the virus causes respiratory infections. 3D illustration.

Photo: 123rf.com

Director-General of Health Dr Ashley Bloomfield says the sequencing it will help identify how the outbreak started and possibly answer some critical questions the government needs within the next day or two to determine its next steps.

On Wednesday, the Auckland region went into level 3 lockdown, while the rest of the country entered level 2 restrictions as health officials scrambled to determine the extent of transmission. The restrictions will be revised on Friday, based on new information from testing and analysis.

Geoghegan, a senior lecturer in viral evolution at the University of Otago, says the testing would potentially identify which quarantine facility or border outpost the virus originated from in the Auckland family’s case.

“There is a hope that we will be able to do that. Our aim is to compare the genomes that we’re generating from the new cases and compare them to the ones from the managed-isolation facilities, as well as the genomes from around the world that have been generated and publicly shared.

“Then we will be able to see which ones these are related to and hopefully that will tell us where and when a leak potentially from a managed isolation case, or otherwise, came from.”

Geoghegan, who is working on genome sequencing with Institute of Environmental Science and Research (ESR), says slight mutations in the virus’ genome offer a scientific way to infer the origin of an infection in the overall chain of transmission.

“When the virus passes from human-to-human it mutates slightly and so when a genome from one Covid-19 patient is compared with another patient, when they compared it with the one they caught it from this genome will almost appear identical to one another.

“However, once you compare the virus genome from people that have transmitted it further, those differences between the viruses become more apparent and it’s like constructing a family tree. We can infer the chain of transmission and where it likely originated from.”

The slow rate of mutation compared with other viruses such as influenza means identifying which individual passed the virus to another is difficult.

However, there is a possibility of narrowing the transmission point to a managed isolation facility, or a cluster. Once this has happened, contact tracing will be used to fill in the information gaps by hunting down close contacts with this cluster or facility and testing them.

There has been speculation that community transmission has been happening for weeks. The genome testing procedure can restructure the chain of transmission events and shed light on that question too, she says.

“By comparing the genomes of the new cases to those from the isolation facilities as well as the global population and the other cases in New Zealand, we can begin to understand how long that chain of transmission potentially is, and likely estimate when that virus emerged and first arrived into New Zealand.”

The genome-sequencing procedure takes approximately 10 hours once the ESR laboratory in Wellington or Auckland received the Covid-positive sample.

“The major thing afterwards is analysing the data. It takes a lot of computational power to look at that data and compare them with the rest of the genomes available, so that’s quite an in-depth process.”

The specialist said, to her knowledge, ESR had not sent any reports on genome testing of the new cases to the government, as analysis and comparison to global and national Covid cases was ongoing.