Jelley Lauren, Douglas Jordan, O'Neill Meaghan, Berquist Klarysse, Claasen Ana, Wang Jing, Utekar Srushti, Johnston Helen, Bocacao Judy, Allais Margot, de Ligt Joep, Ee Tan Chor, Seeds Ruth, Wood Tim, Aminisani Nayyereh, Jennings Tineke, Welch David, Turner Nikki, McIntyre Peter, Dowell Tony, Trenholme Adrian, Byrnes Cass, Webby Richard, French Nigel, Winter David, Huang Q Sue, Geoghegan Jemma L
Institute of Environmental Science and Research, Wellington, New Zealand.
Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand.
medRxiv. 2024 Jul 16:2024.07.15.24310412. doi: 10.1101/2024.07.15.24310412.
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.
人呼吸道合胞病毒（RSV）是急性呼吸道感染的主要病因。2020年，由于用于控制COVID-19传播的非药物干预措施（NPI），RSV在新西兰社区中被有效消除。然而，2021年4月，在与澳大利亚达成一项简短的免检疫旅行协议后，RSV在全国范围内大规模爆发，报告病例数比典型季节性模式高出五倍多，住院人数高出三倍多。在本研究中，我们从2015年至2022年期间在新西兰各地采集了1471个RSV-A和RSV-B病毒基因组。使用系统动力学方法，我们利用这些数据更好地了解2020年之前新西兰的RSV传播模式，以及在COVID-19限制措施放宽后RSV如何在社区中重新出现。我们发现，2021年新西兰发生了大规模的RSV疫情，与通常的RSV感染模式相比，受影响的年龄组范围更广。这次疫情是由于RSV输入增加，导致新西兰出现了几个RSV-A ON1和RSV-B BA9基因型的大型基因组簇。然而，虽然检测到了一些输入病例，但与大流行前的季节性疫情相比，RSV的遗传多样性也大幅降低。这些基因组簇在时间上与2021年因当时从澳大利亚的免检疫旅行导致的移民增加有关。在采样时，与新西兰RSV基因组亲缘关系最近的是几个月前在澳大利亚一次大型非季节性夏季疫情期间采样的病毒基因组，而不是在新西兰持续存在但未被检测到的隐匿谱系。这些数据揭示了COVID-19大流行期间使用的NPI对其他呼吸道感染的影响，并突出了从病毒基因组中可以获得的重要见解。
