Human respiratory syncytial virus (RSV) is a major cause of acute respiratory infection. In 2020, RSV was effectively eliminated from the community in New Zealand due to non-pharmaceutical interventions (NPI) used to control the spread of COVID-19. However, in April 2021, following a brief quarantine-free travel agreement with Australia, there was a large-scale nationwide outbreak of RSV that led to reported cases more than five times higher, and hospitalisations more than three times higher, than the typical seasonal pattern. In this study, we generated 1,471 viral genomes of both RSV-A and RSV-B sampled between 2015 and 2022 from across New Zealand. Using a phylodynamics approach, we used these data to better understand RSV transmission patterns in New Zealand prior to 2020, and how RSV became re-established in the community following the relaxation of COVID-19 restrictions. We found that in 2021, there was a large epidemic of RSV in New Zealand that affected a broader age group range compared to the usual pattern of RSV infections. This epidemic was due to an increase in RSV importations, leading to several large genomic clusters of both RSV-A ON1 and RSV-B BA9 genotypes in New Zealand. However, while a number of importations were detected, there was also a major reduction in RSV genetic diversity compared to pre-pandemic seasonal outbreaks. These genomic clusters were temporally associated with the increase of migration in 2021 due to quarantine-free travel from Australia at the time. The closest genetic relatives to the New Zealand RSV genomes, when sampled, were viral genomes sampled in Australia during a large, off-season summer outbreak several months prior, rather than cryptic lineages that were sustained but not detected in New Zealand. These data reveal the impact of NPI used during the COVID-19 pandemic on other respiratory infections and highlight the important insights that can be gained from viral genomes.

The authors have declared no competing interest.

LJ is funded by a University of Otago Doctoral Scholarship. JLG is funded by a New Zealand Royal Society Rutherford Discovery Fellowship (RDF-20-UOO-007). This study was supported by a New Zealand Health Research Council Grant (22/138) awarded to JLG, JdL, DW, SH, LJ, NF and DW. Our grateful thanks to FluLab for funding the SHIVERS-V team to undertake research encompassed by the project called Influenza in a post-COVID world which has allowed researchers in Aotearoa New Zealand to collect crucial data on influenza virus and produce local innovations and international impact with a Southern Hemisphere population laboratory. The SHIVERS/WellKiwis cohort is funded by the US National Institute of Allergy and Infectious Diseases (NIAID): SHIVERS-III infant funded by the US-NIAID (U01 AI 144616); SHIVERS-IV household funded by the US-NIAID (CEIRR contract: 75N93021C00016).

I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained.

Yes

The details of the IRB/oversight body that provided approval or exemption for the research described are given below:

The New Zealand Northern A Health and Disability Ethics Committee approved this study (reference number: NTX/11/11/102).

I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals.

Yes

I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance).

Yes

I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable.

Yes

The genomes generated are available on GISAID under two blocks of consecutive accession numbers (EPI_ISL_16959469 - EPI_ISL_16960152 and EPI_ISL_19206151 - EPI_ISL_19207488).

https://www.gisaid.org