Coronavirus Australia: Doubts cast on SA virus strain claim

The second virus wave threatening SA has been described as ‘particularly sneaky’ strain. But is it a new one?

South Australian Chief Public Health Officer Nicola Spurrier. Picture: Kelly Barnes/Getty Images

Doubts have been cast on the claim that a new virus strain is circulating in South Australia, with the state’s health department confirming it has not yet identified the genetic sequence of the strain.

In response to questions from The Australian about the virus strain’s genetic sequence, SA health said it was not yet known. “While it is too early to identify, the strain we are currently seeing in SA appears to have a very short incubation period compared to what we experienced in the first wave,” the health department said.

SA Premier Stephen Marshall has described the virus strain circulating in South Australia as “particularly sneaky”. with the state’s chief health officer Nicola Spurrier saying it appeared to be highly infectious. The apparent short incubation period of the virus strain was used to justify a six-day lockdown “circuit breaker”.

“This particularly strain has had certain characteristics,” Professor Spurrier said. “It has a very, very short incubation period, that means when somebody gets exposed it’s taking 24 hours or even less for that person to become infectious to others.

UNSW epidemiologist Mary-Louise McLaws. Picture: Supplied

“And the other characteristic of the cases we’ve seen so far is they’ve had minimal symptoms and sometimes no symptoms but have been able to pass it on to other people.”

A strain of COVID-19 that has as a characteristic a 24-hour incubation period has not been observed anywhere else in the world. The scientific literature establishes that the usual incubation period for SARS-CoV-2 is between one and 14 days.

“We have always known that 50% of people become infectious on day 4, but there is a large proportion that become infectious on day 3, and a small, tiny proportion, possibly one per cent, are infectious on day one and day two,” says UNSW epidemiologist Mary-Louise McLaws. “That’s been the known observation with SARS-CoV-2 since about April.”

‘Hoping it’s an aberration’

“South Australia may be thinking that a couple of cases that are infectious on day one or two is now a new version of the virus, that it’s changed its contagiousness,” Professor McLaws said. “But I’m hoping it’s an aberration, that it hasn’t changed its infectivity. Because if it really is different we are in for a really rough ride.”

University of Queensland Virologist Ian Mackay said it that the Parafield Gardens family cluster in Adelaide was likely to be a “superspreader” event, which occurs when many people get exposed to a high viral load, or the virus circulates readily in unventilated indoor areas where people may be speaking loudly or shouting.

“It may be that it has been difficult to accurately identify when one person was infected by another in a large family setting with many shared surfaces and airspaces providing lots of opportunities for transmission,” Professor Mackay said. “A superspreading event may also have occurred, with varying incubation periods among the infected, making the determination of the occurrence of infection harder to interpret. We are still early in this cluster and need to gather more evidence. In the meantime, we need to be careful not to be overly speculative.”

The SARS-CoV-2 virus is not known to mutate rapidly. However, it has adapted over time. The dominant strain throughout the world is now known as the D614G strain, which is more readily transmitted than the original SARS-CoV-2 strain.

“For now, SARS-CoV-2 and its variants can still be considered as a single ‘virus’,” Professor Mackay said. “As far as we know, all SARS-CoV-2 variants react to antibodies raised against any of them and their sequences don’t dramatically change the proteins they encode.

“Most of what we read about in terms of ‘new strains’ is mostly about small genetic and sometimes amino acid (affecting the protein) changes, the impact of which is either unknown or not obvious.”