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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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Page created: July 08, 2021
Page updated: August 17, 2021
Page reviewed: August 17, 2021
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