Where has all the influenza gone? The impact of COVID-19 on the circulation of influenza and other respiratory viruses, Australia, March to September 2020.

The coronavirus disease pandemic was declared in March 2020, as the southern hemisphere's winter approached. Australia expected co-circulation of severe acute respiratory syndrome coronavirus 2, influenza and other seasonal respiratory viruses. However, influenza notifications were 7,029 (March-September) compared with an average 149,832 for the same period in 2015-2019 [corrected], despite substantial testing. Restrictions on movement within and into Australia may have temporarily eliminated influenza. Other respiratory pathogens also showed remarkably changed activity in 2020.

Influenza-like illness in Australia: A comparison of general practice surveillance system with electronic medical records.

Surveillance systems are fundamental to detect infectious disease outbreaks and guide public health responses. We compared influenza-like illness (ILI) rates for 2015-2017 using data from the Australian Sentinel Practice Research Network (ASPREN) and electronic medical records from 550 general practices across Australia (MedicineInsight). There was a high correlation between both sources (r = .84-.95) and a consistent higher ILI rate in 2017. Both sources also showed higher ILI rates among women and patients aged 20-49 years. The use of routinely collected electronic medical records like those in MedicineInsight could be used to complement active influenza surveillance systems in Australia.

Diagnostic accuracy of an app-guided, self-administered test for influenza among individuals presenting to general practice with influenza-like illness: study protocol.

INTRODUCTION: Diagnostic tests for influenza in Australia are currently only authorised for use in clinical settings. At-home diagnostic testing for influenza could reduce the need for patient contact with healthcare services, which potentially could contribute to symptomatic improvement and reduced spread of influenza. We aim to determine the accuracy of an app-guided nasal self-swab combined with a lateral flow immunoassay for influenza conducted by individuals with influenza-like illness (ILI). METHODS AND ANALYSIS: Adults (≥18 years) presenting with ILI will be recruited by general practitioners (GP) participating in Australian Sentinel Practices Research Network. Eligible participants will have a nasal swab obtained by their GP for verification of influenza A/B status using reverse transcription polymerase chain reaction (RT-PCR) test at an accredited laboratory. Participants will receive an influenza test kit and will download an app that collects self-reported symptoms and influenza risk factors, then instructs them in obtaining a low-nasal self-swab, running a QuickVue influenza A+B lateral flow immunoassay (Quidel Corporation) and interpreting the results. Participants will also interpret an enhanced image of the test strip in the app. The primary outcome will be the accuracy of participants' test interpretation compared with the laboratory RT-PCR reference standard. Secondary analyses will include accuracy of the enhanced test strip image, accuracy of an automatic test strip reader algorithm and validation of prediction rules for influenza based on self-reported symptoms. A post-test survey will be used to obtain participant feedback on self-test procedures. ETHICS AND DISSEMINATION: The study was approved by the Human Research and Ethic Committee (HREC) at the University of Adelaide (H-2019-116). Protocol details and any amendments will be reported to https://www.tga.gov.au/. Results will be published in the peer-reviewed literature, and shared with stakeholders in the primary care and diagnostics communities. TRIAL REGISTRATION NUMBER: Australia New Zealand Clinical Trial Registry (U1111-1237-0688).

Heterogeneity in influenza seasonality and vaccine effectiveness in Australia, Chile, New Zealand and South Africa: early estimates of the 2019 influenza season.

We compared 2019 influenza seasonality and vaccine effectiveness (VE) in four southern hemisphere countries: Australia, Chile, New Zealand and South Africa. Influenza seasons differed in timing, duration, intensity and predominant circulating viruses. VE estimates were also heterogeneous, with all-ages point estimates ranging from 7-70% (I2: 33%) for A(H1N1)pdm09, 4-57% (I2: 49%) for A(H3N2) and 29-66% (I2: 0%) for B. Caution should be applied when attempting to use southern hemisphere data to predict the northern hemisphere influenza season.

Influenza immunisation coverage from 2015 to 2017: A national study of adult patients from Australian general practice.

OBJECTIVES: To assess influenza immunisation rates and coverage in adult patients from Australian general practice and identify whether practice or patients' characteristics are associated with vaccination uptake. DESIGN: Open cohort study. SETTING: 550 Australian general practices included in the MedicineInsight database. PARTICIPANTS: Patients aged 18+ years who had at least one consultation during influenza season between 2015 and 2017. Two samples were considered: (1) 'active' patients (at least three consultations in any two consecutive years) and (2) 'every year' patients (at least one consultation per year). MAIN OUTCOME MEASURES: Influenza vaccination rates per 1,000 consultations and coverage (% vaccinated among those who consulted) from 2015 to 2017. RESULTS: Between 2015 and 2017 the influenza vaccine rate changed from 57.4 to 51.7 and 67.0 per 1,000 consultations, while correspondent values for coverage were 29.3%, 25.2% and 27.6% (in 'active' patients). Vaccine coverage was at least 30% higher in inner regional areas, among patients aged 65+ years or those with comorbidities. Similar associations were found among 'every year' patients, but average coverage across the three years was higher (41% vs 27%). Aboriginal and Torres Strait Islander people, either with or without comorbidity, showed a vaccine coverage 10-30% higher than non-Indigenous people for those aged less than 65 years (p-value for interaction < 0.001). CONCLUSION: MedicineInsight data is a useful and low-cost method to monitor influenza immunisation coverage. Independent of the sample used, vaccination coverage among Indigenous people or patients with comorbidities could be improved. Targeted strategies for high-risk groups need to be developed.

Intraseason decline in influenza vaccine effectiveness during the 2016 southern hemisphere influenza season: A test-negative design study and phylogenetic assessment.

BACKGROUND: We estimated the effectiveness of seasonal inactivated influenza vaccine and the potential influence of timing of immunization on vaccine effectiveness (VE) using data from the 2016 southern hemisphere influenza season. METHODS: Data were pooled from three routine syndromic sentinel surveillance systems in general practices in Australia. Each system routinely collected specimens for influenza testing from patients presenting with influenza-like illness. Next generation sequencing was used to characterize viruses. Using a test-negative design, VE was estimated based on the odds of vaccination among influenza-positive cases as compared to influenza-negative controls. Subgroup analyses were used to estimate VE by type, subtype and lineage, as well as age group and time between vaccination and symptom onset. RESULTS: A total of 1085 patients tested for influenza in 2016 were included in the analysis, of whom 447 (41%) tested positive for influenza. The majority of detections were influenza A/H3N2 (74%). One-third (31%) of patients received the 2016 southern hemisphere formulation influenza vaccine. Overall, VE was estimated at 40% (95% CI: 18-56%). VE estimates were highest for patients immunized within two months prior to symptom onset (VE: 60%; 95% CI: 26-78%) and lowest for patients immunized >4 months prior to symptom onset (VE: 19%; 95% CI: -73-62%). DISCUSSION: Overall, the 2016 influenza vaccine showed good protection against laboratory-confirmed infection among general practice patients. Results by duration of vaccination suggest a significant decline in effectiveness during the 2016 influenza season, indicating immunization close to influenza season offered optimal protection.

Characterising seasonal influenza epidemiology using primary care surveillance data.

Understanding the epidemiology of seasonal influenza is critical for healthcare resource allocation and early detection of anomalous seasons. It can be challenging to obtain high-quality data of influenza cases specifically, as clinical presentations with influenza-like symptoms may instead be cases of one of a number of alternate respiratory viruses. We use a new dataset of confirmed influenza virological data from 2011-2016, along with high-quality denominators informing a hierarchical observation process, to model seasonal influenza dynamics in New South Wales, Australia. We use approximate Bayesian computation to estimate parameters in a climate-driven stochastic epidemic model, including the basic reproduction number R0, the proportion of the population susceptible to the circulating strain at the beginning of the season, and the probability an infected individual seeks treatment. We conclude that R0 and initial population susceptibility were strongly related, emphasising the challenges of identifying these parameters. Relatively high R0 values alongside low initial population susceptibility were among the results most consistent with these data. Our results reinforce the importance of distinguishing between R0 and the effective reproduction number (Re) in modelling studies.

Low interim influenza vaccine effectiveness, Australia, 1 May to 24 September 2017.

In 2017, influenza seasonal activity was high in the southern hemisphere. We present interim influenza vaccine effectiveness (VE) estimates from Australia. Adjusted VE was low overall at 33% (95% confidence interval (CI): 17 to 46), 50% (95% CI: 8 to 74) for A(H1)pdm09, 10% (95% CI: -16 to 31) for A(H3) and 57% (95% CI: 41 to 69) for influenza B. For A(H3), VE was poorer for those vaccinated in the current and prior seasons.

The Australian Sentinel Practices Research Network, 1 January to 31 March 2017.

The Australian Sentinel Practices Research Network was established in 1991 to provide a rapid, national, monitoring scheme for infectious diseases that can alert public health officials of epidemics before they arise. The network consists of general practitioners, throughout all 8 states and territories in Australia, who report presentations on a number of defined medical conditions each week. This report presents data from the 1st quarter of 2017 (1 January to 31 March) and includes the syndromic surveillance of influenza-like-illness, gastroenteritis, chicken pox, and shingles, and the virological surveillance of respiratory viruses including influenza A, influenza B, RSV and rhinovirus.

Effectiveness of seasonal influenza vaccine in Australia, 2015: An epidemiological, antigenic and phylogenetic assessment.

BACKGROUND: A record number of laboratory-confirmed influenza cases were notified in Australia in 2015, during which type A(H3) and type B Victoria and Yamagata lineages co-circulated. We estimated effectiveness of the 2015 inactivated seasonal influenza vaccine against specific virus lineages and clades. METHODS: Three sentinel general practitioner networks conduct surveillance for laboratory-confirmed influenza amongst patients presenting with influenza-like illness in Australia. Data from the networks were pooled to estimate vaccine effectiveness (VE) for seasonal trivalent influenza vaccine in Australia in 2015 using the case test-negative study design. RESULTS: There were 2443 eligible patients included in the study, of which 857 (35%) were influenza-positive. Thirty-three and 19% of controls and cases respectively were reported as vaccinated. Adjusted VE against all influenza was 54% (95% CI: 42, 63). Antigenic characterisation data suggested good match between vaccine and circulating strains of A(H3); however VE for A(H3) was low at 44% (95% CI: 21, 60). Phylogenetic analysis indicated most circulating viruses were from clade 3C.2a, rather than the clade included in the vaccine (3C.3a). VE point estimates were higher against B/Yamagata lineage influenza (71%; 95% CI: 57, 80) than B/Victoria (42%, 95% CI: 13, 61), and in younger people. CONCLUSIONS: Overall seasonal vaccine was protective against influenza infection in Australia in 2015. Higher VE against the B/Yamagata lineage included in the trivalent vaccine suggests that more widespread use of quadrivalent vaccine could have improved overall effectiveness of influenza vaccine. Genetic characterisation suggested lower VE against A(H3) influenza was due to clade mismatch of vaccine and circulating viruses.