NSW health authorities have reported Australia’s first case of the XE coronavirus infection, however new sub-variants being detected in Africa and Europe may be a cause for greater concern when mandatory tests for international arrivals are scrapped next week.
The case of XE, which is a merging of Omicron’s BA.1 and BA.2 sub-variants known as a “recombinant”, was detected in a recently returned overseas traveller last week.
NSW has sequenced Australia’s first XE infection, in a recent international arrival.Credit:AP
While the World Health Organisation has said XE may be 10 per cent more transmissible than the BA.2 variant, there is no evidence abroad that it has led to more severe disease. However, virologists were concerned by the development of Omicron’s BA.4 and BA.5 sub-variants, which have been reported in growing numbers in France and South Africa.
The bulk of XE infections have been reported in the UK, particularly in the south-east of England. Other cases have been detected around the globe, usually in international travellers.
A recombinant infection occurs when two separate virus strains merge, forming a new, single strain.
Associate Professor Stuart Turville, a virologist at the Kirby Institute, said recombinant strains were to be expected when the timelines of different strains of a virus overlap, as has occurred with the Omicron BA.1 and BA.2 variants in NSW.
He said it seemed the Omicron recombinants were similar enough to BA.1 and BA.2 that they should induce comparable illness. Omicron antibodies should also help prevent reinfection against its recombinants.
“The spike proteins are intact, so it is not going to be a seismic shift, like when Omicron displaced Delta,” he said.
Professor William Rawlinson, a virologist with the University of NSW, said people who have been infected with recombinants overseas have so far not shown worse outcomes.
“We need to keep a close eye on the relationship between these cases and severity of disease,” he said. “The reality is that the natural evolution of the virus means is that it will likely become transmissible over time.”
With the first XE infections in the UK detected in January, Rawlinson said it was unlikely to significantly shift infection patterns in Australia.
“If it was going to spread at a rapid pace, I think we would have seen it,” he said.
Turville said there was growing concern among virologists about the development of Omicron’s BA.4 and BA.5 sub-variants, which are yet to be detected in Australian surveillance programs.
“They have a key change in [spike protein mutation] L452R which will make it harder for antibodies to bind to. It will make the virus fitter,” he said.
World Health Organisation authorities told reporters they were following the two sub-variants closely on Wednesday, although its director Tedros Adhanom Ghebreyesus said low sequencing and testing rates worldwide were making it difficult.
“Our ability to monitor trends is compromised as testing has significantly reduced,” he said.
While the vast majority of coronavirus infections in NSW are never genomically sequenced, those that are provide an insight into which COVID-19 strains are emerging or becoming dominant as community transmission continues.
Omicron’s newer BA.2 sub-variant has been the dominant infection in NSW for several weeks.
From Monday, international arrivals will no longer need to test negative to COVID-19 before leaving for Australia, meaning it is likely more variants will be detected locally.
NSW Health prioritises genomic sequencing for people hospitalised with COVID-19, as well as conducting surveillance on infections in international arrivals, pregnant women and other groups of interest, meaning the rates of different variants reported by the surveillance are not necessarily reflective of those in the general community.
NSW has previously reported two recombinant infections: one “Deltacron” infection, a combination of the Delta and Omicron variants, and another BA.1/BA.2 infection (which was not XE).
with Lucy Carroll
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