Influenza in Australia before, during and after the COVID-19 pandemic

The COVID-19 pandemic and the control measures that were put in place to ameliorate the effects of the pandemic, had a profound impact on influenza circulation as well as most other respiratory viruses – almost stopping their circulation completely.^1,2 In 2020 in Australia, there were only 21,343 laboratory-confirmed influenza (LCI) cases reported to the National Notifiable Disease Surveillance System (NNDSS, see https://nindss.health.gov.au/pbi-dashboard/) mostly during January–March 2020 before COVID-19 restrictions were introduced and these numbers dropped dramatically later in the year and in the following year of 2021, when only 749 LCI cases were reported. Following Australia’s opening of international borders for COVID-19 vaccinated people on 21 February 2022 and the relaxation of COVID-19 restrictions on domestic movement, influenza cases rose quickly in March and April reaching a peak by week 24 of 2022 (mid-June). This was much earlier than the usual pre-pandemic years where the peak of the season was traditionally mid-August, except for the 2019 season, which also peaked early at week 26, during a prolonged and severe influenza season.³

The 2023 influenza season again began early, peaking at week 26 similar to the following year of 2024, where the peak was reached at week 27 with both years peaking much earlier than in most pre-pandemic years (Fig. 1).³ Whether this ‘early season’ trend in the past 3 years of the post-pandemic period will persist in future years or if we will return to later seasons remains to be seen, but interestingly this earlier trend has also been seen globally since the pandemic. One aspect of influenza seasons that does appear to be normalising in 2023–2024 is the length of the seasons. In 2022, the season was short and sharp and only lasted for ~15 weeks but had 233,446 LCI cases over the year; however, the 2023 influenza season lasted for ~29 weeks with 289,129 cases and the 2024 season is of similar length with some 343,501 LCI cases (NNDSS database up to 28 September 2024, see https://nindss.health.gov.au/pbi-dashboard/; Table 1 and Fig. 1), the highest number of LCI cases per year recorded in the history of the NNDSS (see https://nindss.health.gov.au/pbi-dashboard/). The longer influenza seasons in 2023 and 2024 were more like the pre-pandemic years such as 2019, where the season lasted for ~24 weeks. An interesting aspect of the 2023 season was the higher number of cases in the last 3 months of the year when 43,526 LCI cases were recorded on the NNDSS (compared to 8149 NNDSS cases in 2022 and 16,317 cases in 2019 over the same period, see https://nindss.health.gov.au/pbi-dashboard/). Most of these cases (80%) were recorded from the eastern Australian states and may have been responsible for the above-average LCI cases seen in the first 3 months of 2024 (Fig. 1). One factor that is hard to gauge when comparing LCI cases pre- and post-COVID-19 is the level of increased testing for influenza due to the increased usage of multiplex PCR-based testing, during and since the pandemic (targets usually include: influenza, COVID-19, respiratory syncytial virus, RSV, and possibly other respiratory pathogens). However, this factor is likely to have stabilised over the past 3 years making LCI cases post-COVID-19 comparisons, more comparable. To date, rapid antigen tests (RATs, also known as point of care tests, POCs) have become more popular following COVID-19, but these results are not recorded on the NNDSS, even though their sensitivity has improved and a single device can now be purchased for a reasonably low cost and can detect influenza, A or B, SARS-CoV-2 and RSV.⁴

Fig. 1.

Laboratory-confirmed cases of influenza notified to the NNDSS (2017–2022 September 2024). The years 2020 and 2021 are excluded when comparing the current season to historical periods when influenza virus has circulated without public health restrictions. As such, the 5-year mean includes the years 2017–2019 and 2022–2023. Figure reproduced from the Australian Respiratory Surveillance Report (ARSR) 13, 2024,¹⁶ Australian Government Department of Health and Aged Care, Australian Centre for Disease Control.

Apart from looking at just laboratory-confirmed cases it is also important to assess the severity of the influenza seasons post-pandemic. The measures used for this in Australia are hospitalisations with influenza, as recorded by the FluCAN⁵ (the Influenza Complications Alert Network) and deaths due to influenza. FluCAN is a series of sentinel Australian hospitals that record hospital admissions and intensive care unit (ICU) admissions of patients with LCI during the main influenza season from 1 April to 31 October each year. FluCAN also covers COVID-19 hospitalisations and ICU admissions year-round and has also recorded RSV hospitalisations in 2023–2034. FluCAN influenza hospitalisations in 2024 were similar to 2023, which were higher than 2022, but fewer than 2019 (Table 1).³ The other measure used is deaths associated with influenza, which are reported to the NNDSS.³ Both hospitalisations and deaths recorded on the NNDSS are certain to be underestimates of the annual burden of influenza due to their limited catchments and operational periods (FluCAN) or under reporting and lack of association with influenza in subsequent deaths (NNDSS). Other developed countries such as the USA through their Centers for Disease Control and Prevention (CDC) have much more-sophisticated measures of the severity of influenza seasons including a near-real time national reporting system for paediatric (<18 years of age) deaths due to or associated with influenza.⁶

The number of deaths reported to the NNDSS during recent years was in line with level of circulation levels of influenza and the major type or subtype of influenza circulating in that year. In 2019, the combination of high case numbers and a mostly A(H3N2) season resulted in a severe season with 902 NNDSS deaths recorded (Table 1). The following pandemic years 2020–2021 saw very few influenza-related deaths but from 2022 onwards, influenza-related deaths returned to moderate levels (2022, 308 deaths; 2023, 376 deaths) and then rose again in 2024 (409 deaths, up to 28 September) (Table 1). These trends were also reflected in the numbers of hospitalisations recorded for these years. In 2023, there was extensive circulation of A(H1N1)pdm and influenza B in most Australian States and Territories and these viruses predominantly affect children, especially school-aged children, more so than the elderly. In 2024, there has been co-dominance of circulation of A(H1N1)pdm09 and A(H3N2) viruses with little influenza B (Fig. 2). Although a higher number of deaths may have been expected in 2022 because of the wide-spread circulation of A(H3N2), other factors may have had an effect on the severity of this season, such as reduced movement of elderly, COVID-19 fears or the increased use of mask wearing, or an increase in the vaccination rates that was seen in 2022.⁷

Fig. 2.

Type and subtype breakdown of influenza viruses circulating in Australia 2022–2024 by state and territory (from samples submitted to the WHO Centre in Melbourne).

Since the emergence of SARS-CoV-2, it was anticipated that the virus would eventually adopt a largely winter seasonality along with the other seasonal coronaviruses (OC43, HKU-1, 229E and NL63); however, to date this has failed to materialise with waves of COVID-19 cases occurring throughout the year.³ Interestingly for the last few years, dips in COVID-19 cases during autumn have coincided with an uptick in influenza cases and the start of the influenza season. Whether this is a coincidence or there is a true interplay with the circulation of these two respiratory viruses remains to be seen. Other respiratory viruses such as RSV have exhibited this ‘hierarchy of circulation’ in Australia, with RSV cases generally beginning and peaking before the main influenza season.⁸ Viral interference has been shown experimentally to exist albeit for only short periods of time,⁹ blocking infections with another respiratory virus, but in some situations having a COVID-19 infection may make individuals more susceptible to subsequent infections with influenza, once this short period of interference expires. These interactions will need to be studied over future years to determine if there is an order of circulation and if SARS-CoV-2 indeed settles into a strictly winter pattern and if it affects influenza severity. If both viruses do occur mainly during autumn–winter periods, this will simplify the timing and administration of vaccines for both pathogens and encourage the manufacturers to combine vaccines to COVID-19 and influenza into a single dose, as some are already doing.^10,11

Although individual vaccines are available for both COVID-19 periodically and influenza annually, their uptake is variable and both vaccines have limitations in terms of their effectiveness and length of protection. Nevertheless, both vaccines have clear merits with COVID-19 being effective at preventing serious consequences, such as hospitalisation and death following infection, as does the influenza vaccine. A recent influenza vaccine effectiveness (VE) study performed in Queensland in 2022, reported an adjusted VE (aVE) against influenza-associated hospitalisation that had an overall aVE of 54% (95% CI: 48–59) and a VE of 67% (95% CI: 49–61) in children <9 years of age.¹² Unfortunately, vaccination rates for both vaccines have been dropping or have plateaued in recent years with only 672,600 (35.6%) of individuals aged 75 years and over and 573,300 (23.6%) of individuals aged 65–74 years receiving a COVID-19 vaccination up to 24 July 2024.¹³ For influenza vaccinations, only 8,727,446 (32%) of Australians have been vaccinated in 2024 (up to 22 September).¹⁴ For those aged 65 years and over, only 60.5% have been vaccinated (up to 31 August 2024) even though this age group is the highest risk group and where the influenza vaccine is free through the National Immunisation Program (NIP), as is the COVID-19 vaccine. Coverage rates remain in the 60% range for this group since 2020, well down from the levels achieved in 2022 (69.2%).¹⁴ Influenza, unlike COVID-19, can also have serious outcomes in young children and, for this reason, the influenza vaccine for the age group 6 months to <5 years old is also free under the NIP. Vaccination rates in this age group have, however, been disappointingly low, with rates generally in the 20–30% range, with the exception of 2020, when 47.3% coverage was achieved. Low influenza-vaccination rates were seen in other age groups in 2024 (up to 31 August: 5–<15 years old, 14.0%; 15–<50 years old, 20.4%; 50–<65 years old, 32.7%).¹⁴ Fortunately, rates of influenza antiviral resistance to date to licensed neuraminidase inhibitors, such as oseltamivir (Tamiflu) and zanamivir (Relenza), have been extremely low (<0.1%).

In conclusion, influenza and other respiratory viruses, such as RSV, have re-emerged in Australia after the COVID-19 pandemic and have largely resumed their winter seasonality patterns. However, in the 3 years since the pandemic (2022–2024), there appears to have been subtle changes in the timing of the influenza season with an earlier start and earlier peaks than in most pre-pandemic seasons. The severity of influenza seasons has generally been moderate in the years following the pandemic, even though the number of LCI cases has been high (230,000 plus cases per year) with little change in the influenza vaccination rates. One factor that may have contributed to the moderate severity seen in 2023 and 2024 was the high circulation of A(H1N1)pdm09 influenza viruses along with high influenza B rates in 2023. This is because both of these viruses generally affect children and young adults more than the elderly, who are more susceptible to A(H3N2). One other change to the circulating influenza viruses since the COVID-19 pandemic has been the disappearance of B/Yamagata/16/88 lineage viruses, which have not been detected after March 2020¹⁵ and appear to now be extinct after circulating in Australia since 2002. Vaccination rates continue to be worryingly low for both COVID-19 and, in most age groups, for influenza. Novel ideas and strong support from Australian government and medical bodies will be needed in order to improve these vaccination rates in the future, to help protect people from the moderate–severe consequences of infection as well as preventing increased levels of frailty that these diseases can cause, especially on the elderly and those with co-morbidities.