Establishing thresholds and parameters for pandemic influenza severity assessment, Australia

Objective: To implement the World Health Organization's pandemic influenza severity assessment tool in Australia, using multiple sources of data to establish thresholds and measure influenza severity indicators. Methods: We used data from four reliable sources: sentinel general practitioner surveillance, hospital surveillance, a public health hotline and an influenza-like illness survey system. We measured three influenza severity indicators (transmissibility, impact and disease seriousness) defined using pandemic influenza severity assessment guidelines. We used the moving epidemic method and a seriousness indicator-specific method to set thresholds for indicator parameters using 2012-2016 data. We then applied the thresholds to data from the 2017 influenza season. Findings: We were able to measure and produce thresholds for each severity indicator. At least one laboratory-confirmed influenza parameter was used to measure each indicator. When thresholds were applied to the 2017 season, there was good agreement across all data sources in measuring activity for each indicator. The season was characterized as having high transmissibility and extraordinary impact. Seriousness was characterized as moderate overall and in all age groups except those aged ≥ 65 years for whom it was high. This matched the description of the season produced by the Australian national influenza surveillance committee, based on expert opinion and historical ranges. Conclusion: The pandemic influenza severity assessment and moving epidemic method provide a robust and flexible method to enable an evidence-based assessment of seasonal influenza severity across diverse data sources. This is useful for national assessment and will contribute to global monitoring and response to circulating influenza with pandemic potential.Flutracking, the influenza complications alert network and the Australian sentinel practices research network are supported by the Australian Department of Health. Healthdirect Australia is supported by the Australian and state and territory governments. This research was supported by scholarship funding for the Master of Philosophy (Applied Epidemiology) at the Australian National Universit

An Infectious Interest: Epidemiology of Communicable Diseases in Australia

While placed in the Communicable Disease Epidemiology and Surveillance Section in the Office of Health Protection at the Australian Government Department of Health, I focused on five projects. Using the World Health Organization's (WHO) Pandemic Influenza Severity Assessment (PISA), I established parameters and thresholds to measure the transmissibility, seriousness and impact of circulating influenza in Australia. I found that when these measures were applied to the 2017 influenza season, they aligned with the characterisation of the season by the National Influenza Surveillance Committee based on expert opinion and historical ranges. My implementation of PISA is now being used nationally to make evidence-based, reproducible assessments of the influenza season in real-time. To gain international experience with PISA, I am interning with WHO's Global Influenza Programme following thesis submission. I conducted an evaluation of the Australian Paediatric Surveillance Unit's surveillance of acute flaccid paralysis using the United States Centers for Disease Control and Prevention's Guidelines for Evaluating Public Health Surveillance Systems. I found the surveillance system to have high stability, acceptability, representativeness and predictive value positive. To increase the usefulness of the system, I recommended that timeliness should be enhanced by reducing the complexity of the system, and that facilitation of increased stool sampling to exclude poliovirus infection should be improved. I used data from the National Enhanced Listeriosis Surveillance System to describe and analyse predisposing risk factors and outcomes amongst nationally notified listeriosis cases in Australia from 2010-17. When compared to the population without each risk factor, I found the risk of listeriosis was 658 times higher in organ transplant recipients, 174 times higher in those with non-haematological cancers, and a range of 1.5-38 times higher in those with other chronic conditions, cases >45 years, pregnant women and those with international backgrounds. The study also highlighted a higher rate of meningitis and death amongst cases without identified susceptibility risk factors compared to cases with any risk factors. In 2017-18, an unusual Salmonella Typhimurium (STm) multiple-locus variable-number tandem repeats analysis (MLVA) profile (3-25-13-12-523) appeared in the Australian Capital Territory. I undertook a retrospective case-case analysis to generate a hypothesis about the infectious source. As part of this I compared two case-control selection methods; one using MLVA-differentiated STm case-controls, and the other using case-controls selected from other Salmonella serovars. When cases were compared to STm case-controls, significantly higher egg consumption was detected in cases through multivariate analysis. No significant exposures were found when cases were compared to non-STm case-controls. This study provided a hypothesis for the source of infections and demonstrated that MLVA may be useful in expanding case- control selection to include those from the same Salmonella serovar. I was also involved in communicable disease surveillance and response for the Gold Coast Commonwealth Games. I established a system of international disease surveillance and reporting, and participated in local monitoring and response through placement at the Gold Coast Public Health Unit. Each of these projects has informed disease surveillance, prevention and control in Australia and has contributed to the understanding of the diseases' epidemiology

SEROLOGICAL TESTING OF BLOOD DONORS TO CHARACTERISE THE IMPACT OF COVID-19 IN MELBOURNE, AUSTRALIA, 2020

Rapidly identifying and isolating people with acute SARS-CoV-2 infection has been a core strategy to contain COVID-19 in Australia, but a proportion of infections go undetected. We estimated SARS-CoV-2 specific antibody prevalence (seroprevalence) among blood donors in metropolitan Melbourne following a COVID-19 outbreak in the city between June and September 2020. The aim was to determine the extent of infection spread and whether seroprevalence varied demographically in proportion to reported cases of infection. The design involved stratified sampling of residual specimens from blood donors (aged 20-69 years) in three postcode groups defined by low (7 cases/1,000 population) COVID-19 incidence based on case notification data. All specimens were tested using the Wantai SARS-CoV-2 total antibody assay. Seroprevalence was estimated with adjustment for test sensitivity and specificity for the Melbourne metropolitan blood donor and residential populations, using multilevel regression and poststratification. Overall, 4,799 specimens were collected between 23 November and 17 December 2020. Seroprevalence for blood donors was 0.87% (90% credible interval: 0.25-1.49%). The highest estimates, of 1.13% (0.25-2.15%) and 1.11% (0.28-1.95%), respectively, were observed among donors living in the lowest socioeconomic areas (Quintiles 1 and 2) and lowest at 0.69% (0.14-1.39%) among donors living in the highest socioeconomic areas (Quintile 5). When extrapolated to the Melbourne residential population, overall seroprevalence was 0.90% (0.26-1.51%), with estimates by demography groups similar to those for the blood donors. The results suggest a lack of extensive community transmission and good COVID-19 case ascertainment based on routine testing during Victoria's second epidemic wave. Residual blood donor samples provide a practical epidemiological tool for estimating seroprevalence and information on population patterns of infection, against which the effectiveness of ongoing responses to the pandemic can be assessed

Serological testing of blood donors to characterise the impact of COVID-19 in Melbourne, Australia, 2020.

Rapidly identifying and isolating people with acute SARS-CoV-2 infection has been a core strategy to contain COVID-19 in Australia, but a proportion of infections go undetected. We estimated SARS-CoV-2 specific antibody prevalence (seroprevalence) among blood donors in metropolitan Melbourne following a COVID-19 outbreak in the city between June and September 2020. The aim was to determine the extent of infection spread and whether seroprevalence varied demographically in proportion to reported cases of infection. The design involved stratified sampling of residual specimens from blood donors (aged 20-69 years) in three postcode groups defined by low (7 cases/1,000 population) COVID-19 incidence based on case notification data. All specimens were tested using the Wantai SARS-CoV-2 total antibody assay. Seroprevalence was estimated with adjustment for test sensitivity and specificity for the Melbourne metropolitan blood donor and residential populations, using multilevel regression and poststratification. Overall, 4,799 specimens were collected between 23 November and 17 December 2020. Seroprevalence for blood donors was 0.87% (90% credible interval: 0.25-1.49%). The highest estimates, of 1.13% (0.25-2.15%) and 1.11% (0.28-1.95%), respectively, were observed among donors living in the lowest socioeconomic areas (Quintiles 1 and 2) and lowest at 0.69% (0.14-1.39%) among donors living in the highest socioeconomic areas (Quintile 5). When extrapolated to the Melbourne residential population, overall seroprevalence was 0.90% (0.26-1.51%), with estimates by demography groups similar to those for the blood donors. The results suggest a lack of extensive community transmission and good COVID-19 case ascertainment based on routine testing during Victoria's second epidemic wave. Residual blood donor samples provide a practical epidemiological tool for estimating seroprevalence and information on population patterns of infection, against which the effectiveness of ongoing responses to the pandemic can be assessed

Seroprevalence of SARS-CoV-2-specific antibodies in Sydney after the first epidemic wave of 2020

Objectives: To estimate SARS-CoV-2-specific antibody seroprevalence after the first epidemic wave of coronavirus disease 2019 (COVID-19) in Sydney. Setting, participants: People of any age who had provided blood for testing at selected diagnostic pathology services (general pathology); pregnant women aged 20–39 years who had received routine antenatal screening; and Australian Red Cross Lifeblood plasmapheresis donors aged 20–69 years. Design: Cross-sectional study; testing of de-identified residual blood specimens collected during 20 April – 2 June 2020. Main outcome measure: Estimated proportions of people seropositive for anti-SARS-CoV-2-specific IgG, adjusted for test sensitivity and specificity. Results: Thirty-eight of 5339 specimens were IgG-positive (general pathology, 19 of 3231; antenatal screening, 7 of 560; plasmapheresis donors, 12 of 1548); there were no clear patterns by age group, sex, or location of residence. Adjusted estimated seroprevalence among people who had had general pathology blood tests (all ages) was 0.15% (95% credible interval [CrI], 0.04–0.41%), and 0.29% (95% CrI, 0.04–0.75%) for plasmapheresis donors (20–69 years). Among 20–39-year-old people, the age group common to all three collection groups, adjusted estimated seroprevalence was 0.24% (95% CrI, 0.04–0.80%) for the general pathology group, 0.79% (95% CrI, 0.04–1.88%) for the antenatal screening group, and 0.69% (95% CrI, 0.04–1.59%) for plasmapheresis donors. Conclusions: Estimated SARS-CoV-2 seroprevalence was below 1%, indicating that community transmission was low during the first COVID-19 epidemic wave in Sydney. These findings suggest that early control of the spread of COVID-19 was successful, but efforts to reduce further transmission remain important

Seroprevalence of Severe Acute Respiratory Syndrome Coronavirus 2-Specific Antibodies in Australia After the First Epidemic Wave in 2020: A National Survey

Background: As of mid-2021, Australia's only nationwide coronavirus disease 2019 (COVID-19) epidemic occurred in the first 6 months of the pandemic. Subsequently, there has been limited transmission in most states and territories. Understanding community spread during the first wave was hampered by initial limitations on testing and surveillance. To characterize the prevalence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-specific antibody seroprevalence generated during this time, we undertook Australia's largest national SARS-CoV-2 serosurvey. Methods: Between June 19 and August 6, 2020, residual specimens were sampled from people undergoing general pathology testing (all ages), women attending antenatal screening (20-39 years), and blood donors (20-69 years) based on the Australian population's age and geographic distributions. Specimens were tested by Wantai total SARS-CoV-2-antibody assay. Seroprevalence estimates adjusted for test performance were produced. The SARS-CoV-2 antibody-positive specimens were characterized with microneutralization assays. Results: Of 11,317 specimens (5132 general pathology; 2972 antenatal; 3213 blood-donors), 71 were positive for SARS-CoV-2-specific antibodies. Seroprevalence estimates were 0.47% (95% credible interval [CrI], 0.04%-0.89%), 0.25% (CrI, 0.03%-0.54%), and 0.23% (CrI, 0.04%-0.54%), respectively. No seropositive specimens had neutralizing antibodies. Conclusions: Australia's seroprevalence was extremely low (<0.5%) after the only national COVID-19 wave thus far. These data and the subsequent limited community transmission highlight the population's naivety to SARS-CoV-2 and the urgency of increasing vaccine-derived protection

High rate of persistent symptoms up to 4 months after community and hospital-managed SARS-CoV-2 infection

Recovery after severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection remains uncertain. A considerable proportion of patients experience persistent symptoms after SARS-CoV-2 infection which impacts health-related quality of life and physical function