When it comes to winter viruses, the patterns in Australia have changed.
Winter bugs are now not just confined to the colder months, but spread throughout the year.
New winter virus strains have emerged, while others have been left “extinct”.
And there have been major outbreaks of typically winter viruses oddly erupting in summer.
So what’s behind this phenomenon, and when will we and our families finally get a break from being holed up with stuffy noses, surrounded by tissues?
The landscape for winter viruses in Australia changed with the pandemic, says virologist Dr John-Sebastian Eden, from the University of Sydney Institute for Infectious Diseases.
“If we look back historically, most of the viruses we have had a very clear seasonality,” Dr Eden says.
“But when we saw the lockdowns and other restrictions put in place, basically flu and RSV, which were on their way up around April and May of 2020, just flatlined.
“We didn’t really see any cases.”
Dr Eden said different winter viruses returned at different stages, as public health measures were relaxed and international borders reopened in February.
RSV, or respiratory syncytial virus, is one of the regular winter viruses in Australia.
The common virus generally causes mild, cold-like symptoms but infection can be serious, particularly for infants and the elderly.
But incidences of RSV underwent a huge change, thanks to Covid.
Dr Eden was the lead researcher in a University of Sydney-led study released in May which looked into how the pandemic changed the normal patterns of winter viruses in Australia.
During 2020, the winter RSV epidemic was absent for the first time on record, because of Covid travel restrictions and infection control measures.
But as pandemic rules eased, the virus was one of the first of the key respiratory viruses to pop up.
There were “unprecedented” outbreaks of RSV occurring out of season, during the 2020-21 summer across the country.
Surprisingly, most of the previous RSV strains known before Covid went “extinct”.
Genetic studies showed new strains had emerged, the study published in the Nature Communications journal found.
These new strains dominated each outbreak in Western Australia, NSW and the ACT.
The virus then made its way into Victoria, where there was another major outbreak.
“Around October and November of 2020, when things opened up for a few weeks, RSV took off and we saw these big summer outbreaks, which were unprecedented,” Dr Eden said.
RSV was not the only major winter virus to turn up in summer in a major way.
Last year, Western Australia also had off-season outbreaks of human metapneumovirus (HMPV) in summer.
The common respiratory virus causes an upper respiratory infection, like a cold, and usually occurs in the winter and early spring, similar to RSV and the flu.
“The RSV and HMPV, like most of these viruses, tend to impact the elderly, the young, the immunocompromised,” Dr Eden said.
“The impacts are probably underappreciated.
“You can have nursing homes, where someone gets HMPV and ultimately they just succumb to their infection.
“If you’re a healthy adult, you have a rough couple of days but severe disease is probably unlikely.”
The one winter virus that powered through the pandemic, though, and never really disappeared was the common cold.
“The main reason for that is it’s just everywhere,” Dr Eden explained.
“Adults and kids carry it with often no sign of disease.
“But also, people just have mild colds and they don’t really think much of it.”
The closure of international borders worked well to keep Australians protected from the dreaded flu as the threat from Covid emerged as Australia’s biggest concern over the last two years.
But it returned this year with a vengeance – and much earlier than usual.
As of June 5, Australia’s national disease surveillance system reported almost 88,000 flu cases – with more than half of them diagnosed in the two weeks prior.
Since mid-April, the number of influenza cases confirmed by a laboratory had soared above the five-year average, the Australian Influenza Surveillance Report revealed.
“We controlled the flu locally with all the lockdowns,” Dr Eden said.
“That’s why the flu really came back a lot later, because obviously the international borders weren’t opened up until much later.
“The flu, to really sustain itself, needs that international swapping of viruses.”
Sanjaya Senanayake, associate professor of infectious diseases at Australian National University, described the flu’s absence during the pandemic as “just extraordinary”.
“The last two years, particularly last year, were remarkable in the sense that we almost had zero flu,” he said.
Dr Senanayake said Covid safe measures, in addition to a strong flu vaccine take-up in 2020, helped keep it at bay.
“We therefore worried that as we withdrew the restrictions for Covid and we hadn’t seen flu for a couple of years and people’s immunity was waning, we’d see a resurgence.
“And we certainly have.”
Despite the high notifications, it’s not the worst flu season Australia has seen.
“Even in terms of hospitalisations, and deaths, if you compare it to the figures for 2019 at this stage, it’s not up there yet,” Dr Senanayake said.
“But you have to remember it’s still a bad flu year, and we‘ve got Covid and all the other viruses that we see during winter.”
Australia is in the grip of its third Omicron wave, which chief medical officer Paul Kelly has described as “very significant”.
In the seven days to Tuesday, about 300,000 Covid cases were reported across the country.
However, authorities believe it’s likely that case numbers are at least double that.
Omicron was first reported last November, but the new Covid variant had multiple mutations, helping it spread faster than the original Wuhan virus and Delta variant.
The Omicron BA.4 and BA.5 sub variants are now dominant across Australia, and expected to continue driving up case numbers, reinfections and hospital admissions.
All indications suggested cases would continue rising in Australia over the coming month, given the new BA.5 sub variant is much more infectious than previous strains, Dr Kelly told a press conference last week.
Dr Senanayake hoped by the end of August the notifications and hospital admissions for both Covid and the flu would begin to go down.
“Covid-19 is very much showing that it can act like a typical respiratory virus with surges in winter,” he said.
“That’s not to say there won’t be cases throughout the year, but for various reasons, it looks like the most activity is going to be in winter and we know that’s definitely the case with influenza and a lot of other respiratory viruses, too.
“Hopefully, some other horrible sub variant that can evade the immune system won’t suddenly appear and reset everything.”
Pre-Covid, it was not unusual for the flu to peak earlier than usual or after winter.
“Flu can do all sorts of funny things,” Dr Senanayake said.
“Sometimes you don’t see much activity during the cold winter months, but a few years ago we suddenly had a peak in September.
“We’ve clearly seen a lot of flu activity now, so I’d hope by the end of winter, that will taper off.”
After two years of lockdowns and pandemic life, there is no doubt Australians are sick of being sick – or at the very least, tired of being worried about getting sick.
We are battle fatigued from stretches in isolation, working from home and homeschooling our children.
It should be noted though, that the return of children to school has elevated the risks of viruses spreading.
“For most respiratory viruses, the major reservoir or transmitters of these are children, particularly with flu,” Dr Senanayake said.
“That’s another reason we think we haven’t had much flu in the last couple of years – because of all the school closures.
“Children weren’t mixing with each other and spreading flu.
“Now children are back at preschool and school and kindergarten, and it’s winter, we’re going to see a lot more activity in those areas.”
So will spring and summer finally bring some respite from these winter viruses?
“It should definitely improve, by what degree I’m not sure,” Dr Senanayake said.
“The only light at the end of the tunnel for me is that BA4 and BA5 are so infectious that it would be hard to find a new sub variant that’s even more infectious to take over from them.
“I’m hoping that’s very unlikely, at least in the short term.
“If we get a BA4 and BA5 specific vaccine the next few months, it should rein everything in.
“I’m just hoping we’ll have a few months’ respite.”
While Covid fatigue was real, we had to think about Omicron as a new pandemic until the current wave was over.
The current crop of vaccines helped against severe disease but weren’t developed specifically for the highly infectious Omicron BA 4 and BA 5 strains, Dr Senanayake said.
Therefore, being Covid safe, working from home, wearing a mask and social distancing all played a role in keeping the virus at bay.
The University of Sydney’s Dr Eden said there was no doubt the emergence of Covid had changed the genetic landscape of virus strains and created new uncertainty.
“Before, the priority was mostly around flu and there was more appreciation for RSV, but given Covid has entered the picture, it’s really all three now,” he said.
“A few weeks ago, we had Covid cases, flu and RSV, all up at the same time, and they’re the three big viruses in terms of hospitalisations.
“It’s quite a large health burden on the system, generally.”
Dr Eden predicted it may be a couple of years before winter viruses settled into their normal seasonal patterns as people resumed mixing locally and internationally.
“The dynamic is all thrown in the air a little bit,” he said.
“But these are all predominantly winter viruses and the conditions for infection around winter are still favourable.
“Relative to that summer outbreak we saw over a year or so ago, RSV has actually returned in winter. And the flu obviously did as well.
“Most of the peaks would try to get back into sync around winter.
“It’s not really normal that we’re going to see summer outbreaks and everything’s just out of sync.
“But to return to that same rhythm we saw before still could take a couple of years.”
Originally published as How Covid has changed seasonal patterns of winter viruses
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