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Volume 27, Number 9—September 2021
Research

Real-Time Genomics for Tracking Severe Acute Respiratory Syndrome Coronavirus 2 Border Incursions after Virus Elimination, New Zealand

Jordan DouglasComments to Author , Jemma L. Geoghegan, James Hadfield, Remco Bouckaert, Matthew Storey, Xiaoyun Ren, Joep de Ligt, Nigel French, and David Welch
Author affiliations: University of Auckland, Auckland, New Zealand (J. Douglas, R. Bouckaert, D. Welch); University of Otago, Dunedin, New Zealand (J.L. Geoghegan); Institute of Environmental Science and Research Limited, Porirua, New Zealand (J.L. Geoghegan, M. Storey, X. Ren, J. de Ligt); Fred Hutchinson Cancer Research Center, Seattle, Washington, USA (J. Hadfield); Massey University, Palmerston North, New Zealand (N. French); Te Pūnaha Matatini: The Centre for Complex Systems and Networks, New Zealand (D. Welch)

Main Article

Table

Summary of all coronavirus disease community cases in New Zealand since elimination was first achieved*

Outbreak First case report date Last case report date Genomes Community Lineage(s) No. unique genomes No. segregating sites Origin
Compassionate
Exemption
 2020 Jun 16
 2020 Jun 16
 2/2
 2
 A.11
 1
 0
 MIQ
Auckland August 2020 Lockdown
 2020 Aug 11
 2020 Oct 20
 155/179
 179
 C.12
 40
 44
 Unknown
Rydges MIQ
 2020 Aug 1
 2020 Aug 16
 2/2
 1
 B.1.509
 1
 0
 MIQ
Crowne Plaza MIQ
 2020 Aug 30
 2020 Sep 22
 9/9
 6
 B.1.36.18
 4
 4
 MIQ
Sudima MIQ
 2020 Oct 10
 2020 Nov 3
 24/33
 2
 B.1.1, B.1.1.397
 1, 2, 7
 0, 1, 14
 MIQ
Sofrana Surville
 2020 Oct 17
 2020 Oct 22
 3/4
 4
 B.1
 1
 0
 Cargo vessel
Defence Force
 2020 Nov 6
 2020 Nov 18
 5/8
 6
 B.1.36
 1
 0
 MIQ
Airline Crew 1
 2020 Dec 12
 2020 Dec 12
 1/1
 1
 B.1.1.7
 1
 0
 Airline/ abroad
Pullman MIQ
 2021 Jan 13
 2021 Feb 4
 3/5
 4
 B.1.351
 2
 1
 MIQ
Auckland February 2021 Lockdown
 2021 Feb 13
 2021 Feb 28
 14/15
 15
 B.1.1.7
 4
 3
 Unknown
Airline Crew 2
 2021 Mar 7
 2021 Mar 7
 1/1
 1
 B.1.1.317
 1
 0
 Airline/ abroad
Grand Millennium MIQ
 2021 Mar 13
 2021 Apr 11
 4/4
 3
 B.1.1.7
 1
 0
 MIQ
Auckland Airport
 2021 Apr 15
 2021 Apr 20
 2/2
 1
 B.1.1.7
 1
 0
 Airport
Total
 NA
 NA
 225/265
 225
 NA
 NA
 NA
 NA
*Pangolin lineages are specified (version 2.3.9) (3) as well as the number of complete genomes/no. confirmed cases and no. community cases. No. unique genomes and no. segregating sites (i.e., no. genome positions that differ) within each cluster are counted, or within the 3 subclusters of the Sudima outbreak. All dates are the dates of report for the laboratory test. MIQ, managed isolation and quarantine; NA, not applicable.

Main Article

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