Detection of the Omicron (B.1.1.529) variant of SARS-CoV-2 in aircraft wastewater

Abstract

On the 26th of November 2021 the World Health Organization (WHO) designated the newly detected B.1.1.529 lineage of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) the Omicron Variant of Concern (VOC). The genome of the Omicron VOC contains more than 50 mutations, many of which have been associated with increased transmissibility, differing disease severity, and potential to evade immune responses developed for previous VOCs such as Alpha and Delta. In the days since the designation of B.1.1.529 as a VOC, infections with the lineage have been reported in countries around the globe and many countries have implemented travel restrictions and increased border controls in response. We putatively detected the Omicron variant in an aircraft wastewater sample from a flight arriving to Darwin, Australia from Johannesburg, South Africa on the 25th of November 2021 via positive results on the CDC N1, CDC N2, and del(69–70) RT-qPCR assays per guidance from the WHO. The Australian Northern Territory Health Department detected one passenger onboard the flight who was infected with SARS-CoV-2, which was determined to be the Omicron VOC by sequencing of a nasopharyngeal swab sample. Subsequent sequencing of the aircraft wastewater sample using the ARTIC V3 protocol with Nanopore and ATOPlex confirmed the presence of the Omicron variant with a consensus genome that clustered with the B.1.1.529 BA.1 sub-lineage. Our detection and confirmation of a single onboard Omicron infection via aircraft wastewater further bolsters the important role that aircraft wastewater can play as an independent and unintrusive surveillance point for infectious diseases, particularly coronavirus disease 2019.

Emergence of SARS-CoV-2 Omicron (B.1.1.529) variant, salient features, high global health concerns and strategies to counter it amid ongoing COVID-19 pandemic

“…Additionally, the SNP analysis enabled the assay to distinguish between the other VOCs and Omicron and the assay may be further modified as per the requirements to detect new mutations if required ( Sexton et al, 2022 ). Omicron has been detected in an aircraft wastewater sample using the CDC N1, CDC N2, and del (69–70) RT-qPCR assays per guidance from the WHO and sequencing further confirmed the presence of Omicron belonging to BA.1 sub-lineage ( Ahmed et al, 2022 ).…”

Monitoring of SARS-CoV-2 variant dynamics in wastewater by digital RT-PCR : from Alpha to Omicron BA.2 VOC

“…These approaches have been developed and applied to the emergence of Alpha and Delta VOC. To our knowledge, few data are available regarding the emergence and the dynamics of the Omicron BA.1 and BA.2 VOC (Agrawal et al, 2022b; Ahmed et al, 2022; Chassalevris et al, 2022; Kirby et al, 2022; Smyth et al, 2022).…”

An Update on Protective Effectiveness of Immune Responses After Recovery From COVID-19

“…About two years after the first identified coronavirus disease 2019 (COVID-19) outbreak, it is still hard to precisely anticipate when the pandemic will finally end, and the protective immunity status in patients after severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is a global concern ( 1 , 2 ). Investigating whether cellular immune response and humoral immunity against SARS-CoV-2 are associated with a decreased risk of reinfection could be a vital issue.…”