Viral soup: flu season kicks off with high levels of circulating viruses

“So [this winter] we have all these viruses in a virus soup, and they are competing with each other, and they are interacting with each other”

The flu season is getting underway at the same time as high levels of COVID-19, RSV and other respiratory illnesses in a virus soup. It is making for a complex winter, says ESR virologist Sue Huang. 

This time last year, influenza was the dominant respiratory virus detected by laboratories nationwide, particularly influenza A (H1N1) and influenza B. But this year, positive flu specimens started increasing in mid-May, joining already high case numbers of SARS-CoV-2 (which causes COVID-19), RSV (respiratory syncytial virus) and rhinovirus. 

The most common influenza strain to date is H3N2, the swine flu virus, which dominated the first post-pandemic flu season in 2022.  

“H3N2 is the virus we have to be careful about as it hits the elderly very hard and also very young children. So, we need to watch out for this virus,” Dr Huang says. 

Dr Huang, the ESR WHO National Influenza Centre director, pointed to the deaths from H3N2 in late January/early February at a Coromandel resthome. “Again, the message is that vaccination is the key for mitigating the risks.”

New Zealand Doctor Rata Aotearoa has approached Te Whatu Ora for an update on flu vaccination trends compared with the same time last year.

Last year’s flu season, with the return of H1N1 and Influenza B, had an initial early peak in April. It was a long season due to an immunity gap after the country had virtually no flu in 2020 and 2021, Dr Huang says.  

However, this year, it has taken until May for labs to detect a surge in influenza viruses and for the flu season to get underway. 

Dr Huang says another difference this year is that as the flu season starts, SARS-CoV-2 and RSV are also circulating. “COVID is still not settling in as a seasonal virus,” says Dr Huang. 

“So [this winter], we have all these viruses in a virus soup, and they are competing with each other, and they are interacting with each other.” 

She says this will result in a complex and busy respiratory-illness winter season. Three people were off sick in her own team working on the WellKiwi influenza studies, not necessarily with the flu but with other viruses. “It feels like we are already deep in the season when we are still not there yet in terms of flu.”

The ESR respiratory illness dashboard shows Auckland hospitalisations for severe acute respiratory illness (SARI) to date are stable but higher than the same time in 2023 and over the “baseline seasonal threshold”.

As of 19 May, most of the hospitalisations in children under five are due to RSV and rhinovirus. The SARI hospitalisations due to SARS-CoV-2 are like those in 2022 and 2023; the influenza hospitalisation was like that in 2023, slightly above the baseline seasonal level.

Last year, influenza hospitalisations peaked in April, late June/early July and September. Cumulatively, the peaks meant the season was considered moderately severe. Pre-pandemic, the flu season usually peaked in July/August.

Dr Huang says usually high flu activity lasts eight to 10 weeks in a normal flu season. She says with the 2024 season underway in May, we could see elevated flu levels in June, with maybe a peak in late June.

Influenza and RSV were also detected in the last two weeks of patient swabs carried out in the community by GPs and nurses under the ESR’s sentinel GP practice surveillance system. 

The ESR respiratory illness dashboard shows that in mid-May, rhinovirus was overtaken by flu and RSV as the most commonly detected virus from sentinel practices, along with a small spike in metapneumovirus. 

In an emailed response, ESR epidemiology team leader Andrea McNeill says, to date, the agency has 75 general practices participating in its network of respiratory surveillance sentinel sites nationwide. 

“We have fewer practices than we would like in the Counties Manukau region and are continuing to try to recruit additional practices,” Dr McNeill says.