Health authorities are urging caution after the emergence of a hybrid Omicron variant of Covid-19 in Australia.
The recombinant variant, known as XE, is a combination of BA.2 – “stealth Omicron” – and BA.1 – the original and highly transmissible Omicron variant of the virus.
The first confirmed case of XE in Australia was detected in an overseas traveller who tested positive to the subvariant on 9 April after touching down in New South Wales.
No further XE cases have been detected, however since Monday, mandatory negative Covid tests prior to arriving in Australia have been lifted, prompting concern subvariants of the virus popping up in Africa and Europe could spread undetected.
BA.2 is now the dominant strain of Covid worldwide, accounting for about 97% of cases in NSW. Omicron – both BA.1 and BA.2 – is now the only variant to have been identified circulating in the state in recent weeks.
Since XE was first identified in the United Kingdom on 19 January, more than 1,100 cases have been confirmed in England.
Early indications suggest the subvariant may be more transmissible than BA.2, which is 30 to 50% more infectious than BA.1, however more research is needed.
The UK Health Security Agency (UKHSA) is yet to have sounded the alarm on the recombinant variant – which emerges when someone becomes infected with two or more virus strains, forming a new single strain that combines genomes from both.
At this stage, there is no evidence the subvariant XE causes more severe illness than other strains or is more resistant to vaccines.
The chief medical adviser of UKHSA, Prof Susan Hopkins, said there was insufficient evidence about the growth rate or other properties of XE, however recombinant variants were not an “unusual occurrence”.
“Several have been identified over the course of the pandemic to date. As with other kinds of variant, most will die off relatively quickly,” she said.
“This particular recombinant … has shown a variable growth rate and we cannot yet confirm whether it has a true growth advantage.
“So far there is not enough evidence to draw conclusions about transmissibility, severity or vaccine effectiveness.”
The World Health Organization (WHO) is continuing to monitor XE but has not yet deemed it a variant of concern or interest.
Its early estimates suggested XE had a growth rate of 10% compared with BA.2, however the finding required “further confirmation”.
“XE belongs to the Omicron variant until significant differences in transmission and disease characteristics, including severity, may be reported,” WHO said in its latest report.
“WHO continues to closely monitor and assess the public health risk associated with recombinant variants, alongside other Sars-CoV-2 variants, and will provide updates as further evidence becomes available.”
Deakin University chair in epidemiology Prof Catherine Bennett said XE added “another layer” to the pandemic challenge but she was doubtful its emergence would change health authorities’ approach to living with the virus.
“The ancestral strains of XE are two variants we know and, as they themselves are quite closely related, it is less likely to lead to a step change in risk for us, or for the effectiveness of our existing acquired immunity from vaccination and infection,” she said.
“So far there is some evidence XE might be a bit more infectious again, but no change has been shown in relation to severity of illness which was also quite similar between B.A.1 and B.A.2.
“We are not genomically characterizing all infections in Australia now so it is possible this strain was already here before the NSW report, but if it is more infectious again then we can expect numbers to rise.”
A spokesperson from the Department of Health said only a small number of XE sequences had been reported internationally and it was too early to tell if the variant would become dominant and circulate widely.
But they said continued emergence of further Sars-CoV-2 lineages and recombinant variants was likely as the virus continued to mutate.
In Australia, states and territories use targeted genomic sequencing sampling to detect emerging Covid variants and how they are spreading.
Another recombinant of BA.2 and BA.1 has previously been detected in NSW however it was not of the XE lineage, while “Deltacron”, a combination of Delta and Omicron, was also previously reported in NSW.
The state recorded 16 Covid deaths on Friday and 15,367 new cases. There were 1,485 people being treated in hospital with the virus including 69 people requiring intensive care.
Victoria recorded seven deaths to Covid-19 and 9,664 new cases. Three hundred and seventy-four people were being treated in hospital with the virus and 14 people were in intensive care.
It comes as a new subvariant of Omicron has been detected in wastewater in Victoria’s Tullamarine catchment.
Health authorities said a small number of cases of the subvariant had been recently detected in South Africa, Botswana, Belgium, Denmark, the United Kingdom and Germany.
There were no known significant epidemiological differences between the new strain and the BA.2 strain.
Queensland recorded a further 7,673 Covid cases on Friday and two deaths.
