Genomic epidemiology of Delta SARS-CoV-2 during transition from elimination to suppression in Aotearoa New Zealand

Simple item page
dc.citation.issue1
dc.citation.volume13
dc.contributor.authorJelley L
dc.contributor.authorDouglas J
dc.contributor.authorRen X
dc.contributor.authorWinter D
dc.contributor.authorMcNeill A
dc.contributor.authorHuang S
dc.contributor.authorFrench N
dc.contributor.authorWelch D
dc.contributor.authorHadfield J
dc.contributor.authorde Ligt J
dc.contributor.authorGeoghegan JL
dc.coverage.spatialEngland
dc.date.accessioned2024-01-23T01:31:27Z
dc.date.accessioned2024-07-25T06:43:42Z
dc.date.available2022-07-12
dc.date.available2024-01-23T01:31:27Z
dc.date.available2024-07-25T06:43:42Z
dc.date.issued2022-07-12
dc.description.abstractNew Zealand's COVID-19 elimination strategy heavily relied on the use of genomics to inform contact tracing, linking cases to the border and to clusters during community outbreaks. In August 2021, New Zealand entered its second nationwide lockdown after the detection of a single community case with no immediately apparent epidemiological link to the border. This incursion resulted in the largest outbreak seen in New Zealand caused by the Delta Variant of Concern. Here we generated 3806 high quality SARS-CoV-2 genomes from cases reported in New Zealand between 17 August and 1 December 2021, representing 43% of reported cases. We detected wide geographical spread coupled with undetected community transmission, characterised by the apparent extinction and reappearance of genomically linked clusters. We also identified the emergence, and near replacement, of genomes possessing a 10-nucleotide frameshift deletion that caused the likely truncation of accessory protein ORF7a. By early October, New Zealand moved from an elimination strategy to a suppression strategy and the role of genomics changed markedly from being used to track and trace, towards population-level surveillance.
dc.description.confidentialfalse
dc.format.pagination4035-
dc.identifier.author-urlhttps://www.ncbi.nlm.nih.gov/pubmed/35821124
dc.identifier.citationJelley L, Douglas J, Ren X, Winter D, McNeill A, Huang S, French N, Welch D, Hadfield J, de Ligt J, Geoghegan JL. (2022). Genomic epidemiology of Delta SARS-CoV-2 during transition from elimination to suppression in Aotearoa New Zealand.. Nat Commun. 13. 1. (pp. 4035-).
dc.identifier.doi10.1038/s41467-022-31784-5
dc.identifier.eissn2041-1723
dc.identifier.elements-typejournal-article
dc.identifier.issn2041-1723
dc.identifier.number4035
dc.identifier.pii10.1038/s41467-022-31784-5
dc.identifier.urihttps://mro.massey.ac.nz/handle/10179/70755
dc.languageeng
dc.publisherSpringer Nature Limited
dc.publisher.urihttps://www.nature.com/articles/s41467-022-31784-5
dc.relation.isPartOfNat Commun
dc.rights(c) The author/sen
dc.rights.licenseCC BY 4.0en
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/en
dc.subjectCOVID-19
dc.subjectCommunicable Disease Control
dc.subjectGenomics
dc.subjectHumans
dc.subjectNew Zealand
dc.subjectSARS-CoV-2
dc.titleGenomic epidemiology of Delta SARS-CoV-2 during transition from elimination to suppression in Aotearoa New Zealand
dc.typeJournal article
pubs.elements-id454824
pubs.organisational-groupOther
Files
Original bundle
Now showing 1 - 5 of 6
Thumbnail Image
Name:
Published
Size:
2.19 MB
Format:
Adobe Portable Document Format
Description:
Download
Thumbnail Image
Name:
Evidence 1
Size:
329.93 KB
Format:
Adobe Portable Document Format
Description:
Download
Thumbnail Image
Name:
Evidence 2
Size:
329.93 KB
Format:
Adobe Portable Document Format
Description:
Download
Thumbnail Image
Name:
Evidence 3
Size:
329.93 KB
Format:
Adobe Portable Document Format
Description:
Download
Thumbnail Image
Name:
Evidence 4
Size:
329.99 KB
Format:
Microsoft Excel XML
Description:
Download
Collections
Journal Articles