Abstract
Pandemic preparedness must account not only for emerging and re-emerging infectious diseases but also for seasonal respiratory viruses that circulate continuously in human and animal populations. Viral transmission is sustained through uninterrupted chains of infection, fuelled by global travel, demographic change and climate pressures, while viral evolution enables ongoing immune evasion. Although only three influenza virus pandemics occurred during the 20th century, the first quarter of the 21st century has already seen eight viral pandemics, four caused by respiratory pathogens, including three novel coronaviruses. This underscores the urgent need to understand viral evolution and transmission dynamics, particularly for respiratory viruses that pose the greatest and most frequent threats to human health.
This thesis presents a comprehensive investigation of three major respiratory viruses circulating in Aotearoa New Zealand. The COVID-19 pandemic caused unprecedented disruption to global respiratory virus ecology, and New Zealand’s stringent border restrictions created a natural experiment for studying introductions, reintroductions and nationwide transmission. Using clinical samples, whole-genome sequencing and detailed epidemiological metadata, I reconstructed viral dynamics across time and space and quantified how border measures shaped pathogen flow.
Across SARS-CoV-2, RSV and seasonal influenza viruses, introductions into New Zealand were rare and strongly dependent on overseas circulation and travel patterns. COVID-19 restrictions successfully blocked most incursions during 2020 and 2021, yet a single introduction of the SARS-CoV-2 Delta variant seeded widespread community transmission. Similarly, only a small number of RSV and influenza virus A(H3N2) introductions occurred post-2020, with onward spread dominated by superspreading events. RSV re-entered New Zealand in 2021 following quarantine-free travel with Australia during an atypical outbreak there, while influenza virus did not re-establish until 2022 when border restrictions eased and Northern Hemisphere activity increased. Transmission intensity was consistently higher in densely populated North Island regions.
Phylogeographic analyses revealed strong source-sink dynamics for influenza virus A(H3N2), with the North Island acting as the primary source of transmission before spread southwards. Genomic diversity of both RSV and influenza virus was markedly reduced following the pandemic interruption, demonstrating that sustained circulation is required to maintain evolutionary diversity. In contrast, extensive replication of the SARS-CoV-2 Delta variant in 2021 drove substantial genomic change, including the emergence of a notable 10-nt deletion. Post-pandemic seasonality of RSV and influenza virus shifted, with both viruses causing unusually early outbreaks driven by heightened susceptibility and altered global circulation.
These studies were enabled by systematic whole-genome sequencing, highlighting the transformative value of genomic epidemiology compared with traditional qualitative PCR based surveillance. Together, this work demonstrates how integrating genomic data into routine respiratory virus surveillance can enhance pandemic preparedness, refine public health responses and deepen understanding of viral evolution and transmission.