Spatial and temporal transmission dynamics of respiratory syncytial virus in New Zealand before and after the COVID-19 pandemic

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.

Fig. 1. Temporal, special, and demographic factors associated with RSV genomes generated.

a Number of RSV-A (orange) and RSV-B (green) genomes generated over time based on sample collection date. The reflected grey bars below show the number of reported RSV-positive cases in New Zealand over the same timeframe. b, c Map of New Zealand, coloured by the number of positive RSV-A and -B cases in each District Health Board. d The number of RSV genomes generated from cases reported in the community, hospital, intensive care unit (ICU), and those from unknown sources. e The number of RSV genomes generated from female and male patients. f The age distribution of patients from which RSV genomes were generated. A box plot indicates the mean (red), lower and upper quartiles (black), and whiskers (black lines), and the scatter points show the raw data. Source data are provided as a Source Data file.

Fig. 2. Evolutionary history of RSV-A in New Zealand.

a Map of New Zealand (where regions are categorised by District Health Board (DHB)), Australia (dark grey), and the rest of the world (light grey). b Number of RSV-A genomes sampled per region, where colours correspond to those in (a). c Root-to-tip regression analysis of RSV-A genomes versus sampling time. d Maximum likelihood time-scaled phylogenetic tree showing 755 RSV-A genomes sampled from New Zealand (coloured circles based on DHB region), 662 RSV-A genomes sampled from Australia (dark grey), and 2913 RSV-A genomes sampled from the rest of the world (light grey). A yellow vertical bar highlights the year 2021 and a dotted box shows the major New Zealand clades sampled. e, f Maximum likelihood time-scaled phylogenetic trees showing the major clades sampled in New Zealand during 2021 and their closest sampled genetic relatives, showing percentage bootstrap support from 1000 replicates for the nodes of the New Zealand clusters. Source data are provided as a Source Data file.

Fig. 3. Evolutionary history of RSV-B in New Zealand.

a Map of New Zealand (where regions are categorised by District Health Board (DHB)), Australia (dark grey), and the rest of the world (light grey). b Number of RSV-B genomes sampled per region, where colours correspond to those in a. c Root-to-tip regression analysis of RSV-B genomes versus sampling time. d Maximum likelihood time-scaled phylogenetic tree showing 715 RSV-B genomes sampled from New Zealand (coloured circles based on DHB region), 518 RSV-B genomes sampled from Australia (dark grey), and 2577 RSV-B genomes sampled from the rest of the world (light grey). A yellow vertical bar highlights the year 2021 and a dotted box shows the major New Zealand clade sampled. e Maximum likelihood time-scaled phylogenetic tree showing the major clades sampled in New Zealand during 2021 and their closest sampled genetic relatives, showing percentage bootstrap support from 1000 replicates for the nodes of the New Zealand clusters. Source data are provided as a Source Data file.

Fig. 4. RSV importations into New Zealand over time.

a Number of people arriving ino New Zealand (blue), number of people departing New Zealand (green), and the overall net migration of people into New Zealand (red). b, c Estimated migration rates of RSV-A and-B into New Zealand over time (mean estimates are shown in white, and 95% credible intervals are coloured). A grey-shaded area shows the period in which New Zealand underwent border restrictions during the COVID-19 pandemic. A purple-shaded area shows the quarantine-free travel period with Australia. Source data are provided as a Source Data file.