Investigating vaccine preventable diseases and the COVID-19 pandemic

Abstract

Vaccination is widely regarded to be one of the greatest public health achievements of the 20th century. While 2020 was the Year of COVID-19, 2021 is being regarded as the Year of the Vaccine, with vaccinations in the public spotlight, serving as a cornerstone of global pandemic management. This thesis contains work undertaken for the Master of Philosophy in Applied Epidemiology (MAE) while on placement at the National Centre for Immunisation Research and Surveillance (NCIRS) in 2020 and 2021. The MAE core requirements presented in this thesis cover four pillars of epidemiology: investigation of an acute public health problem or threat (outbreak investigation), public health data analysis, epidemiological study, and the establishment or evaluation of a surveillance system. The outbreak investigation competency is fulfilled by my participation in the COVID-19 Schools Study, which ran across both 2020 and 2021. This was an active surveillance project carried out in all NSW schools and early childhood education and care (ECEC) services to quantify and characterise the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in these settings. I present some of the findings in Chapter 2, showing that while spread in educational settings was limited, a small number of outbreaks did occur and transmission within these outbreaks may have been facilitated by delayed outbreak recognition, very close or prolonged contact with a case, and specific high-risk transmission events. The risk of school and ECEC outbreaks may be mitigated by stay-at-home-if-sick messaging, school-based mitigation measures aimed at improving infection control, and restricting high-risk activities to times with low community incidence of disease. In Chapter 3, I present a detailed analysis of national measles notifications, hospitalisations, and deaths from 2012 to 2019 which fulfilled the competency for conducting an epidemiological study. Australia was verified as having eliminated measles in 2014, but incidence almost doubled in the 2012 to 2019 period compared with 2000 to 2011. While the data presented in Chapter 3 support Australia's continuing elimination status, global progress towards elimination has stalled, and a global resurgence is expected as a result of increased immunity gaps due to the COVID-19 pandemic. Australia will need to remain vigilant, maintaining robust surveillance and high coverage of measles vaccination. The MAE requirement of carrying out a public health data analysis project is demonstrated in Chapter 4, in which I report my analysis of two decades of national diphtheria notification, hospitalisation, and mortality data (1999-2019). Although still exceedingly rare, Australia has seen an increase in notified cases of diphtheria in the last decade, likely driven by a combination of a series of case definition changes occurring over the period and improvements in case ascertainment. It remains important to maintain high levels of vaccination coverage. In particular, pre-travel booster vaccination should continue to be encouraged. A surveillance system evaluation project is presented in Chapter 5, in which I evaluated the COVID-19 and Paediatric Multisystem Inflammatory Syndrome-Temporally Associated with SARS-CoV-2 (PIMS-TS) components of the Paediatric Active Enhanced Disease Surveillance (PAEDS) system. The evaluation followed the Centers for Disease Control and Prevention's Updated Guidelines for the Evaluation of Public Health Surveillance Systems using a mixed methods approach, and provided recommendations for ensuring PAEDS can continue to continue to support Australia's national surveillance goals into the future. Chapter 6 outlines teaching activities undertaken during my MAE and lessons learnt through such activities. The work presented in this thesis represents my MAE activities at NCIRS, and a contribution to public health in Australia.