Use of Genomics to Track Coronavirus Disease Outbreaks, New Zealand

Geoghegan, Jemma L.; Douglas, Jordan; Ren, Xiaoyun; Storey, Matthew; Hadfield, James; Silander, Olin K.; Freed, Nikki E.; Jelley, Lauren; Jefferies, Sarah; Sherwood, Jillian; Paine, Shevaun; Huang, Sue; Sporle, Andrew; Baker, Michael G; Murdoch, David R.; Drummond, Alexei J.; Welch, David; Simpson, Colin R; French, Nigel P.; Holmes, Edward C.; Ligt, Joep de

doi:10.3201/eid2705.204579

Cited by 32 publications

(32 citation statements)

References 20 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…[36]. Other variants have been introduced, such as B.1.1.1 (the now extinct C.12 lineage) associated with the second SARS-CoV-2 outbreak that occurred in August 2020 [37], while viruses from other lineages have been imported but restricted to the quarantine facilities over the course of the pandemic, e.g., B.1.509 [18]. Nevertheless, the worldwide cumulative prevalence of the SARS-CoV-2 lineages described in this study, from early March 2020 (B.55 and B.31), has diminished considerably, to less than 0.5%, since April 2020 (https://cov-lineages.org, accessed on 31 August 2021).…”

Section: Discussionmentioning

confidence: 99%

Rapid Response to SARS-CoV-2 in Aotearoa New Zealand: Implementation of a Diagnostic Test and Characterization of the First COVID-19 Cases in the South Island

Lawley

Grant

Harfoot

et al. 2021

Viruses

View full text Add to dashboard Cite

It has been 20 months since we first heard of SARS-CoV-2, the novel coronavirus detected in the Hubei province, China, in December 2019, responsible for the ongoing COVID-19 pandemic. Since then, a myriad of studies aimed at understanding and controlling SARS-CoV-2 have been published at a pace that has outshined the original effort to combat HIV during the beginning of the AIDS epidemic. This massive response started by developing strategies to not only diagnose individual SARS-CoV-2 infections but to monitor the transmission, evolution, and global spread of this new virus. We currently have hundreds of commercial diagnostic tests; however, that was not the case in early 2020, when just a handful of protocols were available, and few whole-genome SARS-CoV-2 sequences had been described. It was mid-January 2020 when several District Health Boards across New Zealand started planning the implementation of diagnostic testing for this emerging virus. Here, we describe our experience implementing a molecular test to detect SARS-CoV-2 infection, adapting the RT-qPCR assay to be used in a random-access platform (Hologic Panther Fusion® System) in a clinical laboratory, and characterizing the first whole-genome SARS-CoV-2 sequences obtained in the South Island, right at the beginning of the SARS-CoV-2 outbreak in New Zealand. We expect that this work will help us and others prepare for the unequivocal risk of similar viral outbreaks in the future.

show abstract

Section: Discussionmentioning

confidence: 99%

Rapid Response to SARS-CoV-2 in Aotearoa New Zealand: Implementation of a Diagnostic Test and Characterization of the First COVID-19 Cases in the South Island

Lawley

Grant

Harfoot

et al. 2021

Viruses

View full text Add to dashboard Cite

show abstract

“…All nasopharyngeal swabs underwent routine rRT-PCR diagnostic testing by using the Cepheid Xpert Xpress SARS-CoV-2 assay (Cepheid, https://www.cepheid.com ) or an E gene rRT-PCR laboratory-developed test on the Panther Fusion platform (Hologic, https://www.hologic.com ) ( 10 , 11 ). WGS and phylogenetic analysis was undertaken as previously described ( 12 , 13 ). In brief, we assigned SARS-CoV-2 genomes from persons A, B, C, D, and E as lineage B.1.617.2 (Delta variant) by using Pangolin ( 14 ).…”

Section: Methodsmentioning

confidence: 99%

Airborne Transmission of SARS-CoV-2 Delta Variant within Tightly Monitored Isolation Facility, New Zealand (Aotearoa)

Fox‐Lewis¹,

Williamson²,

Harrower³

et al. 2022

Emerg. Infect. Dis.

Self Cite

View full text Add to dashboard Cite

In New Zealand, international arrivals are quarantined and undergo severe acute respiratory syndrome coronavirus 2 screening; those who test positive are transferred to a managed isolation facility (MIF). Solo traveler A and person E from a 5-person travel group (BCDEF) tested positive. After transfer to the MIF, person A and group BCDEF occupied rooms >2 meters apart across a corridor. Persons B, C, and D subsequently tested positive; viral sequences matched A and were distinct from E. The MIF was the only shared location of persons A and B, C, and D, and they had no direct contact. Security camera footage revealed 4 brief episodes of simultaneous door opening during person A’s infectious period. This public health investigation demonstrates transmission from A to B, C, and D while in the MIF, with airborne transmission the most plausible explanation. These findings are of global importance for coronavirus disease public health interventions and infection control practices.

show abstract

“…The cluster included a healthcare worker who was infected during work at an MIQ facility where community case-patients were sent to quarantine (18). Although the index case-patients worked at a cold chain supply facility linked to the border, the source of the outbreak was never established (19). Complete genomes were available for 87% of cases in this outbreak, which we believe makes it one of the most comprehensively sampled large COVID-19 outbreaks.…”

Section: Auckland August 2020 Lockdownmentioning

confidence: 99%

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

Douglas¹,

Geoghegan²,

Hadfield³

et al. 2021

Emerg. Infect. Dis.

Self Cite

View full text Add to dashboard Cite

show abstract

Use of Genomics to Track Coronavirus Disease Outbreaks, New Zealand

Cited by 32 publications

References 20 publications

Rapid Response to SARS-CoV-2 in Aotearoa New Zealand: Implementation of a Diagnostic Test and Characterization of the First COVID-19 Cases in the South Island

Rapid Response to SARS-CoV-2 in Aotearoa New Zealand: Implementation of a Diagnostic Test and Characterization of the First COVID-19 Cases in the South Island

Airborne Transmission of SARS-CoV-2 Delta Variant within Tightly Monitored Isolation Facility, New Zealand (Aotearoa)

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

Contact Info

Product

Resources

About