Genomic epidemiology reveals transmission patterns and dynamics of SARS-CoV-2 in Aotearoa New Zealand

Geoghegan, Jemma L.; Ren, Xiaoyun; Storey, Matthew; Hadfield, James; Jelley, Lauren; Jefferies, Sarah; Sherwood, Jill; Paine, Shevaun; Huang, Q. Sue; Douglas, Jordan; Mendes, Fábio K.; Sporle, Andrew; Baker, Michael G; Murdoch, David R.; French, Nigel P.; Simpson, Colin R; Welch, David; Drummond, Alexei J.; Holmes, Edward C.; Duchêne, Sebastián; Ligt, Joep de

doi:10.1038/s41467-020-20235-8

Cited by 109 publications

(95 citation statements)

References 44 publications

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“…We obtained 212 complete genomes (Fig 1B), mostly from samples with higher viral loads (Fig 1B). Consensus genomes had a median of 7 substitutions relative to the Wuhan-Hu-1/2019 reference sequence (range [4][5][6][7][8][9][10][11][12]. Phylogenetic analysis of whole consensus genomes identified 10 unique evolutionary lineages in our cohort (lineages determined by the PANGOLIN system, see Methods; Fig 1C).…”

Section: Resultsmentioning

confidence: 99%

“…Over the course of the SARS-CoV-2 pandemic, whole genome sequencing has been widely used to characterize patterns of broad geographic spread, transmission in local clusters, and the spread of specific viral variants [1][2][3][4][5][6]. Early reports demonstrated that SARS-CoV-2 exhibits genetic diversity within infected hosts, but this has been less studied than consensus-level genomic diversity [7].…”

Section: Introductionmentioning

confidence: 99%

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Temporal dynamics of SARS-CoV-2 mutation accumulation within and across infected hosts

et al. 2021

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Analysis of SARS-CoV-2 genetic diversity within infected hosts can provide insight into the generation and spread of new viral variants and may enable high resolution inference of transmission chains. However, little is known about temporal aspects of SARS-CoV-2 intrahost diversity and the extent to which shared diversity reflects convergent evolution as opposed to transmission linkage. Here we use high depth of coverage sequencing to identify within-host genetic variants in 325 specimens from hospitalized COVID-19 patients and infected employees at a single medical center. We validated our variant calling by sequencing defined RNA mixtures and identified viral load as a critical factor in variant identification. By leveraging clinical metadata, we found that intrahost diversity is low and does not vary by time from symptom onset. This suggests that variants will only rarely rise to appreciable frequency prior to transmission. Although there was generally little shared variation across the sequenced cohort, we identified intrahost variants shared across individuals who were unlikely to be related by transmission. These variants did not precede a rise in frequency in global consensus genomes, suggesting that intrahost variants may have limited utility for predicting future lineages. These results provide important context for sequence-based inference in SARS-CoV-2 evolution and epidemiology.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Temporal dynamics of SARS-CoV-2 mutation accumulation within and across infected hosts

et al. 2021

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“…Genomes of the first 649 viral isolates collected in New Zealand show that only 19% of introductions were estimated to infect more than one other person. 9 Therefore, counts of border failures are sensitive to how they are identified and defined. Indeed, with increased testing (eg, testing of people after leaving quarantine on day 16 as is now common in Australia), we may be detecting breaches that previously went undetected.…”

Section: Discussionmentioning

confidence: 99%

Estimating the Failure Risk of Quarantine Systems for Preventing COVID-19 Outbreaks in Australia and New Zealand

Grout

Katar

Ouakrim

et al. 2021

Preprint

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Aim: With increasing global use of hotel-based quarantine as part of COVID-19 border control efforts, we aimed to assess its risk of failure. Methods: We searched official websites in both Australia and New Zealand (NZ) to identify outbreaks and border control failures associated with hotel quarantine (searches conducted up to 12 February 2021). We used two denominators: a) the estimated number of travelers who went through these facilities during the 2020 year up to 31 January 2021; and b) the equivalent number of SARS-CoV-2 positive people who went through these facilities. Results: Up to 31 January 2021, Australia had seven failures with one causing over 800 deaths and six resulting in lockdowns. In NZ there were nine failures, with one causing an outbreak with three deaths, and also a lockdown. The overall failure risk for those transiting quarantine was estimated at one failure per 20,702 travelers and one failure per 252 SARS-CoV-2 positive cases (both countries combined). At the country level, there were 15.5 failures per 1000 SARS-CoV-2 positive cases transiting quarantine in NZ (95%CI: 5.4 to 25.7), compared to 2.0 per 1000 SARS-CoV-2 positive cases in Australia (0.5 to 3.5), a greater than seven-fold difference in risk. Approaches to infection control and surveillance in hotel quarantine were found to vary widely by country and by state/territory. Conclusions: There appears to be a notable risk of failure with the use of hotel quarantine in these two countries. The large variation in infection control practices suggests opportunity for risk reduction.

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“…During 2020, laboratories and institutes around the world produced and shared over 300000 whole SARS-CoV-2 genome sequences in the GISAID repository ( 1 ), providing an unparalleled data set that permits detailed analyses of virus transmission and dissemination. These achievements have provided insights into the sources of SARS-CoV-2 importation and early transmission dynamics in individual countries and geographical regions ( 2 – 5 ), and have enabled the exploration of viral transmission history at a global scale ( 6 ). Phylogenetic methods, including molecular clock models and phylogeographic and phylodynamic methods, are now used routinely to analyse such genomic data from emerging outbreaks ( 7 ).…”

Section: Introductionmentioning

confidence: 99%

Genomic epidemiology of SARS-CoV-2 transmission lineages in Ecuador

Gutierrez

Márquez

Prado-Vivar

et al. 2021

Preprint

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Characterisation of SARS-CoV-2 genetic diversity through space and time can reveal trends in virus importation and domestic circulation, and permit the exploration of questions regarding the early transmission dynamics. Here we present a detailed description of SARS-CoV-2 genomic epidemiology in Ecuador, one of the hardest hit countries during the early stages of the COVID-19 pandemic. We generate and analyse 160 whole genome sequences sampled from all provinces of Ecuador in 2020. Molecular clock and phylgeographic analysis of these sequences in the context of global SARS-CoV-2 diversity enable us to identify and characterise individual transmission lineages within Ecuador, explore their spatiotemporal distributions, and consider their introduction and domestic circulation. Our results reveal a pattern of multiple international importations across the country, with apparent differences between key provinces. Transmission lineages were mostly introduced before the implementation of non-pharmaceutical interventions (NPIs), with differential degrees of persistence and national dissemination.

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Genomic epidemiology reveals transmission patterns and dynamics of SARS-CoV-2 in Aotearoa New Zealand

Cited by 109 publications

References 44 publications

Temporal dynamics of SARS-CoV-2 mutation accumulation within and across infected hosts

Temporal dynamics of SARS-CoV-2 mutation accumulation within and across infected hosts

Estimating the Failure Risk of Quarantine Systems for Preventing COVID-19 Outbreaks in Australia and New Zealand

Genomic epidemiology of SARS-CoV-2 transmission lineages in Ecuador

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