Journal Articles

Permanent URI for this collectionhttps://mro.massey.ac.nz/handle/10179/7915

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Author: search.filters.author.de Ligt JSubject: search.filters.subject.genomic epidemiology

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    Spatial and temporal transmission dynamics of respiratory syncytial virus in New Zealand before and after the COVID-19 pandemic.
    (Cold Spring Harbor Laboratory, 2024-07-17) Jelley L; Douglas J; O'Neill M; Berquist K; Claasen A; Wang J; Utekar S; Johnston H; Bocacao J; Allais M; de Ligt J; Ee Tan C; Seeds R; Wood T; Aminisani N; Jennings T; Welch D; Turner N; McIntyre P; Dowell T; Trenholme A; Byrnes C; SHIVERS investigation team; Webby R; French N; Winter D; Huang QS; Geoghegan JL
    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.
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    Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2 with grinch
    (F1000 Research Limited, 2021-09-17) O'Toole Á; Hill V; Pybus OG; Watts A; Bogoch II; Khan K; Messina JP; COVID-19 Genomics UK (COG-UK) consortium; Network for Genomic Surveillance in South Africa (NGS-SA); Brazil-UK CADDE Genomic Network; Tegally H; Lessells RR; Giandhari J; Pillay S; Tumedi KA; Nyepetsi G; Kebabonye M; Matsheka M; Mine M; Tokajian S; Hassan H; Salloum T; Merhi G; Koweyes J; Geoghegan JL; de Ligt J; Ren X; Storey M; Freed NE; Pattabiraman C; Prasad P; Desai AS; Vasanthapuram R; Schulz TF; Steinbrück L; Stadler T; Swiss Viollier Sequencing Consortium; Parisi A; Bianco A; García de Viedma D; Buenestado-Serrano S; Borges V; Isidro J; Duarte S; Gomes JP; Zuckerman NS; Mandelboim M; Mor O; Seemann T; Arnott A; Draper J; Gall M; Rawlinson W; Deveson I; Schlebusch S; McMahon J; Leong L; Lim CK; Chironna M; Loconsole D; Bal A; Josset L; Holmes E; St George K; Lasek-Nesselquist E; Sikkema RS; Oude Munnink B; Koopmans M; Brytting M; Sudha Rani V; Pavani S; Smura T; Heim A; Kurkela S; Umair M; Salman M; Bartolini B; Rueca M; Drosten C; Wolff T; Silander O; Eggink D; Reusken C; Vennema H; Park A; Carrington C; Sahadeo N; Carr M; Gonzalez G; SEARCH Alliance San Diego; National Virus Reference Laboratory; SeqCOVID-Spain; Danish Covid-19 Genome Consortium (DCGC); Communicable Diseases Genomic Network (CDGN); Dutch National SARS-CoV-2 surveillance program; Division of Emerging Infectious Diseases (KDCA); de Oliveira T; Faria N; Rambaut A; Kraemer MUG
    Late in 2020, two genetically-distinct clusters of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with mutations of biological concern were reported, one in the United Kingdom and one in South Africa. Using a combination of data from routine surveillance, genomic sequencing and international travel we track the international dispersal of lineages B.1.1.7 and B.1.351 (variant 501Y-V2). We account for potential biases in genomic surveillance efforts by including passenger volumes from location of where the lineage was first reported, London and South Africa respectively. Using the software tool grinch (global report investigating novel coronavirus haplotypes), we track the international spread of lineages of concern with automated daily reports, Further, we have built a custom tracking website (cov-lineages.org/global_report.html) which hosts this daily report and will continue to include novel SARS-CoV-2 lineages of concern as they are detected.