Tracing the international arrivals of SARS-CoV-2 Omicron variants after Aotearoa New Zealand reopened its border

Douglas, Jordan; Winter, David J.; McNeill, Andrea; Carr, Sam; Bunce, Michael; French, Nigel P.; Hadfield, James; Ligt, Joep de; Welch, David; Geoghegan, Jemma L.

doi:10.1038/s41467-022-34186-9

Cited by 21 publications

(22 citation statements)

References 51 publications

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“…The B.1.1.529 (Omicron) variant of SARS-CoV-2 was designated a variant of concern by the World Health Organization on 26 November 2021 [1] subsequent to a rapid growth in cases of COVID-19 in southern Africa [2]. Following transmission from cases in managed isolation facilities into the community in January 2022 [3], New Zealand experienced a large Omicron wave with a cumulative attack rate of around 220 confirmed cases per 1000 people between 1 February and 31 May 2022. This wave was dominated by the BA.2 subvariant, which accounted for an estimated 84% of cases, with BA.1 accounting for the remaining 16%.…”

Section: Introductionmentioning

confidence: 99%

Modelling the impact of the Omicron BA.5 subvariant in New Zealand

Lustig¹,

Vattiato

Maclaren

et al. 2023

J. R. Soc. Interface.

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New Zealand experienced a wave of the Omicron variant of SARS-CoV-2 in early 2022, which occurred against a backdrop of high two-dose vaccination rates, ongoing roll-out of boosters and paediatric doses, and negligible levels of prior infection. New Omicron subvariants have subsequently emerged with a significant growth advantage over the previously dominant BA.2. We investigated a mathematical model that included waning of vaccine-derived and infection-derived immunity, as well as the impact of the BA.5 subvariant which began spreading in New Zealand in May 2022. The model was used to provide scenarios to the New Zealand Government with differing levels of BA.5 growth advantage, helping to inform policy response and healthcare system preparedness during the winter period. In all scenarios investigated, the projected peak in new infections during the BA.5 wave was smaller than in the first Omicron wave in March 2022. However, results indicated that the peak hospital occupancy was likely to be higher than in March 2022, primarily due to a shift in the age distribution of infections to older groups. We compare model results with subsequent epidemiological data and show that the model provided a good projection of cases, hospitalizations and deaths during the BA.5 wave.

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Section: Introductionmentioning

confidence: 99%

Modelling the impact of the Omicron BA.5 subvariant in New Zealand

Lustig¹,

Vattiato

Maclaren

et al. 2023

J. R. Soc. Interface.

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“…Prior to removal, border screening programmes provided rich data on the importation of SARS-CoV-2 (Williams et al, 2021), and helped to map the international prevalence of new variants (Douglas et al, 2022). With the reduction in large-scale screening of inbound passengers, many countries have begun to adopt monitoring of aircraft wastewater as a potentially non-intrusive alternative for monitoring pathogens entering a country or region (Ahmed et al, 2022; Le Targa et al, 2022; Farkas et al, 2023).…”

Section: Introductionmentioning

confidence: 99%

Evaluating the theoretical performance of aircraft wastewater monitoring as a tool for SARS-CoV-2 surveillance

Shingleton¹,

Lilley²,

Wade³

2023

Preprint

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Background Air travel plays an import role in the cross-border spread of infectious diseases. During the SARS-CoV-2 pandemic many countries introduced strict border testing protocols to monitor the incursion of the virus. However, the high implementation cost and significant inconvenience to passengers has led public health authorities to consider alternative methods of disease surveillance at borders. Aircraft wastewater monitoring has been proposed as one such alternative. In this paper we assess the theoretical limits of aircraft wastewater monitoring and compare its performance to post-arrival border screening approaches. Methods We use an infectious disease model to simulate an unmitigated SARS-CoV-2 epidemic in a seed country. Seeding of the epidemic into the United Kingdom (UK) is simulated through daily flights between the two countries. We use a probabilistic approach to estimate the time of first detection of the disease in the UK in both aircraft wastewater and respiratory swab screening at the border. Results For simulations across a broad range of model parameters, our analysis indicates that the median time between the first incursion of a pathogen and its detection in wastewater would be approximately 17 days (IQR: 7 - 28 days), resulting in a median of 25 cumulative cases (IQR: 6 - 84 cases) in the UK at the point of detection. Comparisons to respiratory swab screening suggest that aircraft wastewater monitoring is as effective as screening of 20% of passengers at the border, using a test with 95% sensitivity. For testing regimes with sensitivity of 85% or less, the required coverage to outperform wastewater monitoring increases to 30%. These results demonstrate the potential use cases of aircraft wastewater monitoring and its utility in a wider system of public health surveillance.

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“…Genomic and real-time surveillance played a pivotal role in sustaining this state of elimination and also realized which new variants might gain a foothold and trigger new waves of infection. 12,13 To date, whole genome sequencing (WGS) has served as the gold standard for distinguishing Omicron subvariants including BA.2, BA.4, and BA.5. [14][15][16] Due to the similar spike proteins in these three subvariants, less known polymerase chain reaction (PCR)-based molecular typing has been discussed to compare with previously reported VOCs.…”

Section: Introductionmentioning

confidence: 99%

“…An urgent need for variant phenotyping of circulating sublineage is necessary for epidemiological surveillance during Omicron surges. Genomic and real‐time surveillance played a pivotal role in sustaining this state of elimination and also realized which new variants might gain a foothold and trigger new waves of infection 12,13 . To date, whole genome sequencing (WGS) has served as the gold standard for distinguishing Omicron subvariants including BA.2, BA.4, and BA.5 14–16 .…”

Section: Introductionmentioning

confidence: 99%

Accelerating pandemic response with the emergency Omicron RT‐PCR test: A comprehensive solution for COVID‐19 diagnosis and tracking

Chung

Jian

Chang

et al. 2023

Journal of Medical Virology

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The Omicron variant of concern (VOC) has surged in many countries and replaced the previously reported VOC. To identify different Omicron strains/sublineages on a rapid, convenient, and precise platform, we report a novel multiplex real‐time reverse transcriptase polymerase chain reaction (RT‐PCR) method in one tube based on the Omicron lineage sequence variants' information. Severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) subvariants were used in a PCR‐based assay for rapid identification of Omicron sublineage genotyping in 1000 clinical samples. Several characteristic mutations were analyzed using specific primers and probes for the spike gene, del69–70, and F486V. To distinguish Omicron sublineages (BA.2, BA.4, and BA.5), the NSP1:141–143del in the ORF1a region and D3N mutation in membrane protein occurring outside the spike protein region were analyzed. Results from the real‐time PCR assay for one‐tube accuracy were compared to those of whole genome sequencing. The developed PCR assay was used to analyze 400 SARS‐CoV‐2 positive samples. Ten samples determined as BA.4 were positive for NSP1:141–143del, del69–70, and F486V mutations; 160 BA.5 samples were positive for D3N, del69–70, and F486V mutations, and 230 BA.2 samples were without del69–70. Screening these samples allowed the identification of epidemic trends at different time intervals. Our novel one‐tube multiplex PCR assay was effective in identifying Omicron sublineages.

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Tracing the international arrivals of SARS-CoV-2 Omicron variants after Aotearoa New Zealand reopened its border

Cited by 21 publications

References 51 publications

Modelling the impact of the Omicron BA.5 subvariant in New Zealand

Modelling the impact of the Omicron BA.5 subvariant in New Zealand

Evaluating the theoretical performance of aircraft wastewater monitoring as a tool for SARS-CoV-2 surveillance

Accelerating pandemic response with the emergency Omicron RT‐PCR test: A comprehensive solution for COVID‐19 diagnosis and tracking

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