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Abstract
Human respiratory syncytial virus (RSV) is a major cause of acute respiratory infection. In 2020, RSV was eliminated from New Zealand due to non-pharmaceutical interventions (NPI) used to control the spread of SARS-CoV-2. However, in 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 than typical seasonal patterns. We generated 1470 viral genomes of both RSV-A and RSV-B sampled between 2015–2022 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 due to an increase in importations, leading to several large genomic clusters of both RSV-A ON1 and RSV-B BA9 genotypes. However, while a number of viral importations were detected, there was also a major reduction in RSV genetic diversity compared to pre-pandemic years. 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.
Non-pharmaceutical interventions for COVID-19 control impacted transmission of other pathogens including respiratory syncytial virus (RSV). Here, the authors perform phylodynamic analyses of RSV genomes from New Zealand to explore dynamics before, during, and after the COVID-19 pandemic.
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1 Institute of Environmental Science and Research, Wellington, New Zealand (GRID:grid.419706.d) (ISNI:0000 0001 2234 622X); University of Otago, Department of Microbiology and Immunology, Dunedin, New Zealand (GRID:grid.29980.3a) (ISNI:0000 0004 1936 7830)
2 University of Auckland, Centre for Computational Evolution, Auckland, New Zealand (GRID:grid.9654.e) (ISNI:0000 0004 0372 3343); University of Auckland, Department of Physics, Auckland, New Zealand (GRID:grid.9654.e) (ISNI:0000 0004 0372 3343)
3 Institute of Environmental Science and Research, Wellington, New Zealand (GRID:grid.419706.d) (ISNI:0000 0001 2234 622X)
4 Coast and Hutt Valley, Regional Public Health, Te Whatu Ora – Health New Zealand Capital, Wellington, New Zealand (GRID:grid.419706.d)
5 University of Auckland, Centre for Computational Evolution, Auckland, New Zealand (GRID:grid.9654.e) (ISNI:0000 0004 0372 3343); University of Auckland, School of Computer Science, Auckland, New Zealand (GRID:grid.9654.e) (ISNI:0000 0004 0372 3343)
6 University of Auckland, Department of General Practice and Primary Care, Auckland, New Zealand (GRID:grid.9654.e) (ISNI:0000 0004 0372 3343)
7 University of Otago, Department of Primary Health Care and General Practice, Dunedin, New Zealand (GRID:grid.29980.3a) (ISNI:0000 0004 1936 7830)
8 Te Whatu Ora—Health New Zealand Counties Manukau, Auckland, New Zealand (GRID:grid.29980.3a)
9 St Jude Children’s Research Hospital, Department of Host-Microbe Interactions, Memphis, USA (GRID:grid.240871.8) (ISNI:0000 0001 0224 711X)
10 Massey University, Tāwharau Ora/School of Veterinary Science, Palmerston North, New Zealand (GRID:grid.148374.d) (ISNI:0000 0001 0696 9806)