COVID-19: Genome sequencing and how it can help fight New Zealand's community transmission

New Zealand has four new cases of community transmission, and as reiterated by Dr Ashley Bloomfield, health officials will be using all the tools in their toolbox to fight a potential resurgence of the virus. 

One of these tools is genome sequencing - a term Kiwis may have heard during recent press conferences - which plays a critical role in New Zealand's public health response to COVID-19, the disease caused by the SARS-CoV-2 coronavirus strain. 

What is genome sequencing?

In instances of community transmission - when a case is acquired locally from an unknown source - scientists can work to decode, or "sequence", the genetic puzzle of the virus' genome. A genome is an organism's complete set of DNA, including all of its genes. Each genome contains all of the information needed to build and maintain that organism.

Decoding or sequencing the genome can reveal to scientists where a specific case came from. It also allows scientists to differentiate a case from a horde of other infections. 

In New Zealand, scientists have been able to complete sequences in less than 24 hours. 

Addressing the media during a press conference on Wednesday morning, Prime Minister Jacinda Ardern noted that alongside testing, the results of genome sequencing will also play heavily into whether the country will move up an alert level. Auckland is currently at level 3 while the rest of the country is level 2. 

When questioned on the likelihood of Auckland being placed under alert level 4 lockdown, Ardern said the decision will depend on testing and "what genome sequencing tells us". 

"Genome sequencing can potentially provide us information as to whether or not the cases are connected to a particular MIQ [managed isolation and quarantine facility] or existing COVID case," Ardern explained.

"So that basically can tell us about different strains of COVID - there are different strains, some are more common than others. It may help us narrow down information, it may not."

Auckland has been placed under alert level 3 until midnight on Friday, while the rest of New Zealand must observe alert level 2 protocol.
Auckland has been placed under alert level 3 until midnight on Friday, while the rest of New Zealand must observe alert level 2 protocol. Photo credit: Getty

What has genome sequencing shown us so far?

In a preprint of a collaborative study, which has yet to be peer-reviewed, University of Otago and ESR evolutionary virologist Dr Jemma Geoghegan and her colleagues shared data from 649 SARS-CoV-2 genome sequences generated from New Zealand's infected patients, with samples collected between February 26 and May 22 - representing 56 percent of all confirmed cases in this time period.

Despite the small size of the New Zealand outbreak, there were 277 separate introductions of the virus out of the 649 cases considered.

The team found just 19 percent of virus introductions into New Zealand resulted in a "transmission lineage" of more than one additional case - meaning less than 5 percent of those who arrived in New Zealand with the virus actually transmitted COVID-19 to more than one person. 

The team estimated that 24 percent led to only one other secondary case, while the remaining 57 percent did not lead to transmission. 

The genome sequencing found that most of the cases that resulted in a transmission lineage originated from North America, rather than Asia - where the virus first emerged - or from across the ditch in Australia. 

"Genomic data helped link more infections to a major transmission cluster than through epidemiological data alone," says the study, providing "probable sources of infections" for cases in which the source was unclear. 

The result of genome sequencing found New Zealand's most significant clusters were primarily associated with social gatherings such as weddings, hospitality and conferences.

Genome sequencing found that New Zealand's largest cluster most likely originated in the United States. The "significant" cluster of community transmission was likely initiated by a "superspreading" event at a Southland wedding, according to the research. 

The team found no evidence the virus had been circulating before New Zealand's first case was reported on February 26.

Overall, genome sequencing is 'very helpful' to tracing sources of community transmission

When asked if health officials had prepared for the possibility that the source of the four new cases may never be pinpointed, Dr Bloomfield said that genome sequencing "will be very helpful" in identifying the origin of the community transmission.

Alongside genome sequencing and tracing and testing close and casual contacts of the four cases, environmental testing will also be performed in the workplace of the first confirmed case. Surfaces in the cool store where the man works will be tested for traces of the virus, as overseas studies have shown that COVID-19 is capable of surviving in "refrigerated environments for quite some time", Dr Bloomfield said.

"We are confident [that] we didn't have any community transmission for quite a long period... we're not ruling anything in or out at this point, we're very open-minded." 

The research, 'Genomic epidemiology reveals transmission patterns and dynamics of SARS-CoV-2 in Aotearoa New Zealand', was released on medRxiv on August 7.